2024

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13 pages, 478 KiB

Open AccessArticle

Comparative Analysis of Vascular Calcification Risk Factors in Pre-Hemodialysis and Prevalent Hemodialysis Adult Patients: Insights into Calcification Biomarker Associations and Implications for Intervention Strategies in Chronic Kidney Disease

by Marko Petrović, Voin Brković, Marko Baralić, Ivko Marić, Nenad Petković, Sanja Stanković, Nataša Lalić, Dejana Stanisavljević, Ljubica Đukanović and Višnja Ležaić

Diagnostics 2024, 14(8), 824; https://doi.org/10.3390/diagnostics14080824 - 17 Apr 2024

Viewed by 188

Abstract

This retrospective study aimed to compare risk factors for vascular calcification (VC) between pre-hemodialysis (HD) and prevalent HD adult patients while investigating associations with calcification biomarkers. Baseline data from 30 pre-HD and 85 HD patients were analyzed, including iPTH, vitamin D, FGF 23, [...] Read more.

This retrospective study aimed to compare risk factors for vascular calcification (VC) between pre-hemodialysis (HD) and prevalent HD adult patients while investigating associations with calcification biomarkers. Baseline data from 30 pre-HD and 85 HD patients were analyzed, including iPTH, vitamin D, FGF 23, fetuin-A, sclerostin, and VC scores (Adragao method). Prevalence of VC was similar in both groups, but HD patients had more frequent VC scores ≥ 6. Pre-HD patients were older, with higher prevalence of hypertension and less frequent use of calcium phosphate binders. Both groups showed similar patterns of hyperphosphatemia, low vitamin D, and iPTH. Fetuin-A and sclerostin levels were higher in pre-HD, while FGF 23 was elevated in HD patients. Higher VC risk in pre-HD patients was associated with male gender, older age, lower fetuin-A and higher sclerostin, lower ferritin, and no vitamin D treatment, while in HD patients with higher sclerostin, FGF 23 and urea, and lower iPTH. Conclusion: Biomarkers could be measurable indicators of biological processes underlying VC in CKD patients that may serve as a potential guide for considering personalized therapeutic approaches. Further studies are needed to elucidate the underlying pathways. Full article

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2023

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18 pages, 911 KiB

Open AccessReview

IgG N-glycan Signatures as Potential Diagnostic and Prognostic Biomarkers

by Benjamin S. Haslund-Gourley, Brian Wigdahl and Mary Ann Comunale

Diagnostics 2023, 13(6), 1016; https://doi.org/10.3390/diagnostics13061016 - 07 Mar 2023

Cited by 5 | Viewed by 3119

Abstract

IgG N-glycans are an emerging source of disease-specific biomarkers. Over the last decade, the continued development of glycomic databases and the evolution of glyco-analytic methods have resulted in increased throughput, resolution, and sensitivity. IgG N-glycans promote adaptive immune responses through antibody-dependent cellular cytotoxicity [...] Read more.

IgG N-glycans are an emerging source of disease-specific biomarkers. Over the last decade, the continued development of glycomic databases and the evolution of glyco-analytic methods have resulted in increased throughput, resolution, and sensitivity. IgG N-glycans promote adaptive immune responses through antibody-dependent cellular cytotoxicity (ADCC) and complement activation to combat infection or cancer and promote autoimmunity. In addition to the functional assays, researchers are examining the ability of protein-specific glycosylation to serve as biomarkers of disease. This literature review demonstrates that IgG N-glycans can discriminate between healthy controls, autoimmune disease, infectious disease, and cancer with high sensitivity. The literature also indicates that the IgG glycosylation patterns vary across disease state, thereby supporting their role as specific biomarkers. In addition, IgG N-glycans can be collected longitudinally from patients to track treatment responses or predict disease reoccurrence. This review focuses on IgG N-glycan profiles applied as diagnostics, cohort discriminators, and prognostics. Recent successes, remaining challenges, and upcoming approaches are critically discussed. Full article

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2022

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11 pages, 1224 KiB

Open AccessArticle

Serum Periostin May Help to Identify Patients with Poor Collaterals in the Hyperacute Phase of Ischemic Stroke

by Dora Spantler, Peter Csecsei, Katalin Borocz, Timea Berki, Laszlo Zavori, Attila Schwarcz, Gabor Lenzser and Tihamer Molnar

Diagnostics 2022, 12(8), 1942; https://doi.org/10.3390/diagnostics12081942 - 11 Aug 2022

Viewed by 1180

Abstract

Background: Periostin is a glycoprotein that mediates cell functions in the extracellular matrix and appears to be a promising biomarker in neurological damage, such as ischemic stroke (IS). We aimed to measure serum periostin levels in the hyperacute phase of ischemic stroke to [...] Read more.

Background: Periostin is a glycoprotein that mediates cell functions in the extracellular matrix and appears to be a promising biomarker in neurological damage, such as ischemic stroke (IS). We aimed to measure serum periostin levels in the hyperacute phase of ischemic stroke to explore its predictive power in identification of patients with poor collaterals (ASPECT < 6). Methods: We prospectively enrolled 122 patients with acute ischemic stroke within the first 6 h after onset. The early ischemic changes were evaluated by calculating ASPECT score on admission using a native CT scan. An unfavorable outcome was defined as the modified Rankin Scale (mRS) > 2 at 90 days follow-up. Blood samples were collected on admission immediately after CT scan and periostin serum concentrations were determined by ELISA. Results: The admission concentration of serum periostin was significantly higher in patients with unfavorable outcome than in patients with favorable outcome (615 ng/L, IQR: 443–1070 vs. 390 ng/L, 260–563, p < 0.001). In a binary logistic regression model, serum periostin level was a significant predictor for ASPECT < 6 status on admission, within 6 h after stroke onset (OR, 5.911; CI, 0.990–0.999; p = 0.015). Conclusion: Admission periostin levels can help to identify patients who are not suitable for neurointervention, especially if advanced neuroimaging is not available. Full article

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20 pages, 1607 KiB

Open AccessArticle

Quantitation of a Urinary Profile of Biomarkers in Gaucher Disease Type 1 Patients Using Tandem Mass Spectrometry

by Iskren Menkovic, Michel Boutin, Abdulfatah Alayoubi, Filipa Curado, Peter Bauer, François E. Mercier and Christiane Auray-Blais

Diagnostics 2022, 12(6), 1414; https://doi.org/10.3390/diagnostics12061414 - 08 Jun 2022

Cited by 3 | Viewed by 1557

Abstract

Gaucher disease is a rare inherited disorder caused by a deficiency of the lysosomal acid beta-glucocerebrosidase enzyme. Metabolomic studies by our group targeted several new potential urinary biomarkers. Apart from lyso-Gb₁, these studies highlighted lyso-Gb₁ analogs −28, −26, −12 (A/B), [...] Read more.

Gaucher disease is a rare inherited disorder caused by a deficiency of the lysosomal acid beta-glucocerebrosidase enzyme. Metabolomic studies by our group targeted several new potential urinary biomarkers. Apart from lyso-Gb₁, these studies highlighted lyso-Gb₁ analogs −28, −26, −12 (A/B), +2, +14, +16 (A/B), +30, and +32 Da, and polycyclic lyso-Gb₁ analogs 362, 366, 390, and 394 Da. The main objective of the current study was to develop and validate a robust UPLC-MS/MS method to study the urine distribution of these biomarkers in patients. Method: Urine samples were purified using solid-phase extraction. A 12 min UPLC-MS/MS method was developed. Results: Validation assays revealed high precision and accuracy for creatinine and lyso-Gb₁. Most lyso-Gb₁ analogs had good recovery rates and high intra- and interday precision assays. Biomarker-estimated LOD and LOQ levels ranged from 56–109 pM to 186–354 pM, respectively. Comparison between GD patients and healthy controls showed significant differences in most biomarker levels. Typically, treated GD patients presented lower biomarker levels compared to untreated patients. Conclusions: These data suggest that the metabolites investigated might be interesting GD biomarkers. More studies with a larger cohort of patients will be needed to better understand the clinical significance of these GD biomarkers. Full article

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16 pages, 2391 KiB

Open AccessArticle

First Characterization of ADAMTS-4 in Kidney Tissue and Plasma of Patients with Chronic Kidney Disease—A Potential Novel Diagnostic Indicator

by Ivana Kovacevic Vojtusek, Mario Laganovic, Marija Burek Kamenaric, Stela Bulimbasic, Stela Hrkac, Grgur Salai, Vanja Ivkovic, Marijana Coric, Rudjer Novak and Lovorka Grgurevic

Diagnostics 2022, 12(3), 648; https://doi.org/10.3390/diagnostics12030648 - 07 Mar 2022

Cited by 7 | Viewed by 2502

Abstract

Background: We have previously shown that metzincin protease ADAMTS-4 accompanies renal fibrogenesis, as it appears in the blood of hemodialysis patients. Methods: Native kidney (NKB) and kidney transplant (TXCI) biopsy samples as well as plasma from patients with various stages of CKD were [...] Read more.

Background: We have previously shown that metzincin protease ADAMTS-4 accompanies renal fibrogenesis, as it appears in the blood of hemodialysis patients. Methods: Native kidney (NKB) and kidney transplant (TXCI) biopsy samples as well as plasma from patients with various stages of CKD were compared to controls. In paired analysis, 15 TXCI samples were compared with their zero-time biopsies (TX0). Tissues were evaluated and scored (interstitial fibrosis and tubular atrophy (IFTA) for NKB and Banff ci for TXCI). Immunohistochemical (IHC) staining for ADAMTS-4 and BMP-1 was performed. Plasma ADAMTS-4 was detected using ELISA. Results: ADAMTS-4 IHC expression was significantly higher in interstitial compartment (INT) of NKB and TXCI group in peritubular capillaries (PTC) and interstitial stroma (INT). Patients with higher stages of interstitial fibrosis (ci > 1 and IFTA > 1) expressed ADAMTS-4 in INT more frequently in both groups (p = 0.005; p = 0.013; respectively). In paired comparison, TXCI samples expressed ADAMTS-4 in INT and PTC more often than TX0. ADAMTS-4 plasma concentration varied significantly across CKD stages, being highest in CKD 2 and 3 compared to other groups (p = 0.0064). Hemodialysis patients had higher concentrations of ADAMTS-4 compared to peritoneal dialysis (p < 0.00001). Conclusion: ADAMTS-4 might have a significant role in CKD as a potential novel diagnostic indicator. Full article

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13 pages, 1683 KiB

Open AccessArticle

The Diagnostic Role of Uric Acid to Creatinine Ratio for the Identification of Patients with Adverse Pulmonary Embolism Outcomes

by Konstantinos Bartziokas, Christos Kyriakopoulos, Dimitrios Potonos, Konstantinos Exarchos, Athena Gogali and Konstantinos Kostikas

Diagnostics 2022, 12(1), 193; https://doi.org/10.3390/diagnostics12010193 - 14 Jan 2022

Cited by 2 | Viewed by 1855

Abstract

Background: Uric acid (UA) is the final product of purine metabolism and a marker of oxidative stress that may be involved in the pathophysiology of cardiovascular and thromboembolic disease. The aim of the current study is to investigate the potential value of UA [...] Read more.

Background: Uric acid (UA) is the final product of purine metabolism and a marker of oxidative stress that may be involved in the pathophysiology of cardiovascular and thromboembolic disease. The aim of the current study is to investigate the potential value of UA to creatinine ratio (UA/Cr) as a diagnostic tool for the outcome of patients admitted with acute pulmonary embolism (PE) and the correlations with other parameters. Methods: We evaluated 116 patients who were admitted for PE in a respiratory medicine department. PE was confirmed with computed tomography pulmonary angiography. Outcomes evaluated were hospitalization duration, mortality or thrombolysis and a composite endpoint (defined as mortality or thrombolysis). Patients were assessed for PE severity with the PE Severity Index (PESI) and the European Society of Cardiology (ESC) 2019 risk stratification. Results: The median (interquartile range) UA/Cr level was 7.59 (6.3–9.3). UA/Cr was significantly associated with PESI (p < 0.001), simplified PESI (p = 0.019), and ESC 2019 risk stratification (p < 0.001). The area under the curve (AUC) for prediction of 30-day mortality by UA/Cr was 0.793 (95% CI: 0.667–0.918). UA/Cr levels ≥7.64 showed 87% specificity and 94% negative predictive value for mortality. In multivariable analysis UA/Cr was an independent predictor of mortality (HR (95% CI): 1.620 (1.245–2.108), p < 0.001) and composite outcome (HR (95% CI): 1.521 (1.211–1.908), p < 0.001). Patients with elevated UA/Cr levels (≥7.64) had longer hospitalization (median (IQR) 7 (5–11) vs. 6 (5–8) days, p = 0.006)), higher mortality (27.3% vs. 3.2%, p = 0.001) and worse composite endpoint (32.7% vs. 3.4%, p < 0.001). Conclusion: Serum UA/Cr ratio levels at the time of PE diagnosis are associated with disease severity and risk stratification, and may be a useful biomarker for the identification of patients at risk of adverse outcomes. Full article

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2021

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10 pages, 1170 KiB

Open AccessArticle

Loss of DUSP4 Expression as a Prognostic Biomarker in Clear Cell Renal Cell Carcinoma

by Seongsik Bang, Seungyun Jee, Hwangkyu Son, Young Chan Wi, Hyunsung Kim, Hosub Park, Jaekyung Myung, Su-Jin Shin and Seung Sam Paik

Diagnostics 2021, 11(10), 1939; https://doi.org/10.3390/diagnostics11101939 - 19 Oct 2021

Cited by 3 | Viewed by 1828

Abstract

Dual-specificity protein phosphatase 4 (DUSP4) is a negative regulator of mitogen-activated protein kinases. The prognostic impact of DUSP4 expression in renal cell carcinoma is not well studied. Therefore, we evaluated the clinicopathological implications of DUSP4 expression in clear cell renal cell carcinoma by [...] Read more.

Dual-specificity protein phosphatase 4 (DUSP4) is a negative regulator of mitogen-activated protein kinases. The prognostic impact of DUSP4 expression in renal cell carcinoma is not well studied. Therefore, we evaluated the clinicopathological implications of DUSP4 expression in clear cell renal cell carcinoma by performing immunohistochemistry (IHC). The clinical outcome according to DUSP4 expression was evaluated through survival analyses, and the association between mRNA expression and prognosis was confirmed by online analysis (Kaplan–Meier plotter). Loss of DUSP4 expression was noted in most histological subtypes of renal cell carcinoma. Loss of DUSP4 expression in clear cell renal cell carcinoma was significantly correlated with old age (p = 0.033), high histologic grade (p < 0.001), tumor necrosis (p < 0.001), and high pT category (p < 0.001). In survival analysis, loss of DUSP4 expression was associated with poor clinical outcomes in cancer-specific survival and recurrence-free survival (p = 0.010 and p = 0.007, respectively). Upon TCGA data analysis, patients with low DUSP4 mRNA expression showed a shorter overall survival (p = 0.023). These results suggest that loss of DUSP4 expression can be used as a potential biomarker for predicting clinical outcomes in clear cell renal cell carcinoma patients. Full article

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18 pages, 342 KiB

Open AccessArticle

Association of Adiponectin, Leptin and Resistin Plasma Concentrations with Echocardiographic Parameters in Patients with Coronary Artery Disease

by Kamila Puchałowicz, Karolina Kłoda, Violetta Dziedziejko, Monika Rać, Andrzej Wojtarowicz, Dariusz Chlubek and Krzysztof Safranow

Diagnostics 2021, 11(10), 1774; https://doi.org/10.3390/diagnostics11101774 - 26 Sep 2021

Cited by 6 | Viewed by 2111

Abstract

The imbalanced network of adipokines may contribute to the development of systemic low-grade inflammation, metabolic diseases and coronary artery disease (CAD). In the last decade, three classic adipokines—adiponectin, leptin and resistin—have been of particular interest in studies of patients with CAD due to [...] Read more.

The imbalanced network of adipokines may contribute to the development of systemic low-grade inflammation, metabolic diseases and coronary artery disease (CAD). In the last decade, three classic adipokines—adiponectin, leptin and resistin—have been of particular interest in studies of patients with CAD due to their numerous properties in relation to the cardiovascular system. This has directed our attention to the association of adipokines with cardiac structure and function and the development of heart failure (HF), a common end effect of CAD. Thus, the purpose of this study was to analyse the associations of plasma concentrations of adiponectin, leptin and resistin with parameters assessed in the echocardiographic examinations of CAD patients. The presented study enrolled 167 Caucasian patients (133 male; 34 female) with CAD. Anthropometric, echocardiographic and basic biochemical measurements, together with plasma concentrations of adiponectin, leptin and resistin assays, were performed in each patient. Adiponectin concentrations were negatively associated with left ventricular ejection fraction (LVEF) and shortening fraction (LVSF), and positively associated with mitral valve E/A ratio (E/A), left ventricular end-diastolic volume (LVEDV), left ventricular end-diastolic diameter (LVEDD), left ventricular end-systolic diameter LVESD, and left atrium diameter (LAD). Resistin concentrations were negatively associated with E/A. Leptin concentrations, although correlated with HF severity assessed by the New York Heart Association (NYHA) Functional Classification, were not independently associated with the echocardiographic parameters of cardiac structure or function. In conclusion, adiponectin and resistin, but not leptin, are associated with the echocardiographic parameters of cardiac remodelling and dysfunction. These associations suggest that adiponectin and resistin might be involved in mechanisms of cardiac remodelling or compensative response. We also suggest the possible benefits of adiponectin and resistin level measurements in the monitoring of patients with CAD. Full article

22 pages, 2782 KiB

Open AccessArticle

Design of InnoPrimers-Duplex Real-Time PCR for Detection and Treatment Response Prediction of EBV-Associated Nasopharyngeal Carcinoma Circulating Genetic Biomarker

by Mai Abdel Haleem Abusalah, Siti Asma Binti Hassan, Norhafiza Mat Lazim, Baharudin Abdullah, Wan Fatihah Binti Wan Sohaimi, Azlan Husin, Kueh Yee Cheng and Chan Yean Yean

Diagnostics 2021, 11(10), 1761; https://doi.org/10.3390/diagnostics11101761 - 25 Sep 2021

Cited by 4 | Viewed by 2046

Abstract

Nasopharyngeal carcinoma (NPC) is an epithelial tumor with high prevalence in southern China and Southeast Asia. NPC is well associated with the Epstein-Barr virus (EBV) latent membrane protein 1 (LMP1) 30 bp deletion by having its vital role in increased tumorigenicity and decreased [...] Read more.

Nasopharyngeal carcinoma (NPC) is an epithelial tumor with high prevalence in southern China and Southeast Asia. NPC is well associated with the Epstein-Barr virus (EBV) latent membrane protein 1 (LMP1) 30 bp deletion by having its vital role in increased tumorigenicity and decreased immune recognition of EBV-related tumors. This study developed an InnoPrimers-duplex qPCR for detection of NPC blood circulating LMP1 30 bp deletion genetic biomarker for early diagnosis and treatment response prediction of NPC patients. The analytical and diagnostic evaluation and treatment response prediction were conducted using NPC patients’ whole blood (WB) and tissue samples and non-NPC cancer patients and healthy individuals’ WB samples. The assay was able to detect as low as 20 ag DNA per reaction (equivalent to 173 copies) with high specificity against broad reference microorganisms and archive NPC biopsy tissue and FNA samples. The diagnostic sensitivity and specificity were 83.3% and 100%, respectively. The 30 bp deletion genetic biomarker was found to be a good prognostic biomarker associated with overall clinical outcome of NPC WHO type III patients. This sensitive and specific assay can help clinicians in early diagnosis and treatment response prediction of NPC patients, which will enhance treatment outcome and lead to better life-saving. Full article

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13 pages, 2989 KiB

Open AccessArticle

Molecular RNA Correlates of the SOFA Score in Patients with Sepsis

by Agnes S. Meidert, Dominik Buschmann, Florian Brandes, Kristiyan Kanev, Jean-Noël Billaud, Melanie Borrmann, Matthias Witte, Benedikt Kirchner, Marlene Reithmair, Michael W. Pfaffl and Gustav Schelling

Diagnostics 2021, 11(9), 1649; https://doi.org/10.3390/diagnostics11091649 - 09 Sep 2021

Cited by 4 | Viewed by 2051

Abstract

The most common scoring system for critically ill patients is the Sequential Organ Failure Assessment (SOFA) score. Little is known about specific molecular signaling networks underlying the SOFA criteria. We characterized these networks and identified specific key regulatory molecules. We prospectively studied seven [...] Read more.

The most common scoring system for critically ill patients is the Sequential Organ Failure Assessment (SOFA) score. Little is known about specific molecular signaling networks underlying the SOFA criteria. We characterized these networks and identified specific key regulatory molecules. We prospectively studied seven patients with sepsis and six controls with high-throughput RNA sequencing (RNAseq). Quantitative reverse transcription PCR (RT-qPCR) confirmation was performed in a second independent cohort. Differentially and significantly expressed miRNAs and their target mRNA transcripts were filtered for admission SOFA criteria and marker RNAs for the respective criteria identified. We bioinformatically constructed molecular signaling networks specifically reflecting these criteria followed by RT-qPCR confirmation of RNAs with important regulatory functions in the networks in the second cohort. RNAseq identified 82 miRNAs (45% upregulated) and 3254 mRNAs (50% upregulated) differentially expressed between sepsis patients and controls. Bioinformatic analysis characterized 6 miRNAs and 76 mRNA target transcripts specific for the SOFA criteria. RT-qPCR validated miRNA and mRNAs included IGFBP2 (respiratory system); MMP9 and PDE4B (nervous system); PPARG (cardiovascular system); AKR1B1, ANXA1, and LNC2/NGAL (acute kidney injury); GFER/ALR (liver); and miR-30c-3p (coagulopathy). There are specific canonical networks underlying the SOFA score. Key regulatory miRNA and mRNA transcripts support its biologic validity. Full article

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3 pages, 565 KiB

Open AccessCorrection

Correction: Visani et al. miR-196B-5P and miR-200B-3P Are Differentially Expressed in Medulloblastomas of Adults and Children. Diagnostics 2020, 10, 265

by Michela Visani, Gianluca Marucci, Dario de Biase, Felice Giangaspero, Francesca Romana Buttarelli, Alba Ariela Brandes, Enrico Franceschi, Giorgia Acquaviva, Alessia Ciarrocchi, Kerry Jane Rhoden, Giovanni Tallini and Annalisa Pession

Diagnostics 2021, 11(9), 1633; https://doi.org/10.3390/diagnostics11091633 - 07 Sep 2021

Viewed by 1130

Abstract

The authors wish to make the following corrections to this paper [...] Full article

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14 pages, 2403 KiB

Open AccessArticle

Urinary mRNA Expression of Glomerular Podocyte Markers in Glomerular Disease and Renal Transplant

by Silvia Armelloni, Deborah Mattinzoli, Masami Ikehata, Carlo Alfieri, Mirco Belingheri, Gabrilella Moroni, Donata Cresseri, Patrizia Passerini, Roberta Cerutti and Piergiorgio Messa

Diagnostics 2021, 11(8), 1499; https://doi.org/10.3390/diagnostics11081499 - 20 Aug 2021

Cited by 2 | Viewed by 2061

Abstract

The research of novel markers in urinary samples, for the description of renal damage, is of high interest, and several works demonstrated the value of urinary mRNA quantification for the search of events related to renal disease or affecting the outcome of transplant [...] Read more.

The research of novel markers in urinary samples, for the description of renal damage, is of high interest, and several works demonstrated the value of urinary mRNA quantification for the search of events related to renal disease or affecting the outcome of transplant kidneys. In the present pilot study, a comparison of the urine mRNA expression of specific podocyte markers among patients who had undergone clinical indication to renal transplanted (RTx, n = 20) and native (N, n = 18) renal biopsy was performed. The aim of this work was to identify genes involved in podocytes signaling and cytoskeletal regulation (NPHS1, NPHS2, SYNPO, WT1, TRPC6, GRM1, and NEUROD) in respect to glomerular pathology. We considered some genes relevant for podocytes signaling and for the function of the glomerular filter applying an alternative normalization approach. Our results demonstrate the WT1 urinary mRNA increases in both groups and it is helpful for podocyte normalization. Furthermore, an increase in the expression of TRPC6 after all kinds of normalizations was observed. According to our data, WT1 normalization might be considered an alternative approach to correct the expression of urinary mRNA. In addition, our study underlines the importance of slit diaphragm proteins involved in calcium disequilibrium, such as TRPC6. Full article

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14 pages, 2846 KiB

Open AccessArticle

Overexpressed Proteins in HCC Cell-Derived Exosomes, CCT8, and Cofilin-1 Are Potential Biomarkers for Patients with HCC

by Hyo Jung Cho, Geum Ok Baek, Moon Gyeong Yoon, Hye Ri Ahn, Ju A Son, Soon Sun Kim, Jae Youn Cheong and Jung Woo Eun

Diagnostics 2021, 11(7), 1221; https://doi.org/10.3390/diagnostics11071221 - 06 Jul 2021

Cited by 6 | Viewed by 2560

Abstract

Protein markers of hepatocellular carcinoma (HCC)-derived exosomes (HEX) have not yet been fully evaluated. Here, we identified novel protein contents of HEX and their clinical significance as biomarkers. Exosomes were isolated from human HCC cell lines and an immortalized normal hepatocyte cell line. [...] Read more.

Protein markers of hepatocellular carcinoma (HCC)-derived exosomes (HEX) have not yet been fully evaluated. Here, we identified novel protein contents of HEX and their clinical significance as biomarkers. Exosomes were isolated from human HCC cell lines and an immortalized normal hepatocyte cell line. Proteomic analyses revealed 15 markedly overexpressed proteins in HEX. The clinical relevance of the 15 proteins was analyzed in public RNA-sequencing datasets, and 6 proteins were selected as candidate of potential biomarkers. Serum CCT8 and CFL1 were markedly overexpressed in test cohort (n = 8). In the validation cohort (n = 224), the area under the curve (AUC) of serum CCT8 and CFL1 for HCC diagnosis was calculated as 0.698 and 0.677, respectively, whereas that of serum alpha-fetoprotein (AFP) was 0.628. The combination of three serum markers (CCT8, CFL1, and AFP) demonstrated the highest AUC for HCC diagnosis. (AUC = 0.838, 95% confidence interval = 0.773–0.876) Furthermore, higher serum CCT8 and CFL1 concentrations were significantly associated with the presence of vascular invasion, advanced tumor stage, poor disease-free survival, and poor overall survival. Cofilin-1 and CCT8, enriched proteins in HEX, were identified as potential diagnostic and prognostic serum biomarkers for HCC patients. Full article

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13 pages, 291 KiB

Open AccessReview

Cytogenetic and Biochemical Genetic Techniques for Personalized Drug Therapy in Europe

by Tatjana Huebner, Catharina Scholl and Michael Steffens

Diagnostics 2021, 11(7), 1169; https://doi.org/10.3390/diagnostics11071169 - 26 Jun 2021

Cited by 1 | Viewed by 2318

Abstract

For many authorized drugs, accumulating scientific evidence supports testing for predictive biomarkers to apply personalized therapy and support preventive measures regarding adverse drug reactions and treatment failure. Here, we review cytogenetic and biochemical genetic testing methods that are available to guide therapy with [...] Read more.

For many authorized drugs, accumulating scientific evidence supports testing for predictive biomarkers to apply personalized therapy and support preventive measures regarding adverse drug reactions and treatment failure. Here, we review cytogenetic and biochemical genetic testing methods that are available to guide therapy with drugs centrally approved in the European Union (EU). We identified several methods and combinations of techniques registered in the Genetic Testing Registry (GTR), which can be used to guide therapy with drugs for which pharmacogenomic-related information is provided in the European public assessment reports. Although this registry provides information on genetic tests offered worldwide, we identified limitations regarding standard techniques applied in clinical practice and the information on test validity rarely provided in the according sections. Full article

16 pages, 2096 KiB

Open AccessArticle

Importance of Potential New Biomarkers in Patient with Serouse Ovarian Cancer

by Aneta Cymbaluk-Płoska, Karolina Chudecka, Anita Chudecka-Głaz, Katarzyna Piotrowska, Sebastian Kwiatkowski and Maciej Tarnowski

Diagnostics 2021, 11(6), 1026; https://doi.org/10.3390/diagnostics11061026 - 03 Jun 2021

Cited by 2 | Viewed by 1876

Abstract

Ovarian cancer remains the gynecological cancer with the highest mortality rate. In our study, we compare a number of proteins from different effector pathways to assess their usefulness in the diagnosis of ovarian cancer. The tissue expression of the tested proteins was assessed [...] Read more.

Ovarian cancer remains the gynecological cancer with the highest mortality rate. In our study, we compare a number of proteins from different effector pathways to assess their usefulness in the diagnosis of ovarian cancer. The tissue expression of the tested proteins was assessed by two methods: qRT-PCR and an immunohistochemical analysis. A significantly higher level of mRNA expression was found in the ovarian cancer group for YAP and TEAD4 (p = 0.004 and p = 0.003, respectively). There was no statistical significance in the expression of mRNA for SMAD3, and there was borderline statistical significance for SMAD2 between the groups of ovarian cancer patients and other subgroups of patients with simple cysts and healthy ovarian tissue (p = 0.726 and p = 0.046, respectively). Significantly higher levels of transferrin receptor (CD71), H2A.X, and ADH1A gene expression were found in the ovarian cancer group compared to the control group for YAP, and TEAD4 showed strong nuclear and cytoplasmic staining in ovarian carcinoma and weak staining in non-carcinoma ovarian samples, ADH1A1 showed strong staining in the cytoplasm of carcinoma sections and a weak positive reaction in the non-carcinoma section, H2A.X showed strong positive nuclear staining in carcinoma sections and moderate positive staining in non-carcinoma samples, and CD71 showed moderate positive staining in carcinoma and non-carcinoma samples. YAP, TEAD4, and ADH1A proteins appear to be promising biomarkers in the diagnosis of ovarian cancer. Full article

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19 pages, 3125 KiB

Open AccessArticle

Diagnostic and Prognostic Value of Circulating Cell-Free DNA for Cholangiocarcinoma

by Preawwalee Wintachai, Jing Quan Lim, Anchalee Techasen, Worachart Lert-itthiporn, Sarinya Kongpetch, Watcharin Loilome, Jarin Chindaprasirt, Attapol Titapun, Nisana Namwat, Narong Khuntikeo and Apinya Jusakul

Diagnostics 2021, 11(6), 999; https://doi.org/10.3390/diagnostics11060999 - 30 May 2021

Cited by 9 | Viewed by 3526

Abstract

The analysis of cfDNA has been applied as a liquid biopsy in several malignancies. However, its value in the diagnosis and prognosis of cholangiocarcinoma (CCA) have not been well defined. We aimed to investigate the diagnostic and prognostic values of cfDNA level and [...] Read more.

The analysis of cfDNA has been applied as a liquid biopsy in several malignancies. However, its value in the diagnosis and prognosis of cholangiocarcinoma (CCA) have not been well defined. We aimed to investigate the diagnostic and prognostic values of cfDNA level and tumor-specific mutation in circulating DNA (ctDNA) in CCA. The plasma cfDNA levels from 62 CCA patients, 33 benign biliary disease (BBD) patients and 30 normal controls were quantified by fluorescent assay. Targeted probe-based sequencing of 60 genes was applied for mutation profiling in 10 ctDNA samples and their corresponding treatment-naïve tissues. cfDNA levels in CCA were significantly higher than those in BBD and normal controls. We found that cfDNA levels at 0.2175 and 0.3388 ng/µL significantly discriminated CCA from healthy controls and BBD with 88.7 and 82.3% sensitivity and 96.7 and 57.6% specificity, respectively. cfDNA levels showed superior diagnostic efficacy in detecting CCA compared to CEA and CA19-9. ARID1A (30%), PBRM1 (30%), MTOR (30%), and FGFR3 (30%) mutations were the most common. Using nine frequently mutated genes in the ctDNA samples, the diagnostic accuracy of cfDNA sequencing was 90.8%, with 96.7% average sensitivity and 72.4% specificity. This study supports the use of cfDNA as a diagnosis and prognostic biomarker for CCA. Full article

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15 pages, 1818 KiB

Open AccessArticle

Multi-Solvent Extraction Procedure for the Pioneer Fecal Metabolomic Analysis—Identification of Potential Biomarkers in Stable Kidney Transplant Patients

by Soumaya Kouidhi, Nessrine Souai, Muhanad Alhujaily, Oumaima Zidi, Ameni Kochbati, Alaeddine Redissi, Tareg M. Belali, Imene El Kossai, Jamelddine El Manaa, Ameur Cherif, Wissem Mnif and Amor Mosbah

Diagnostics 2021, 11(6), 962; https://doi.org/10.3390/diagnostics11060962 - 26 May 2021

Cited by 1 | Viewed by 2137

Abstract

Metabolic alteration plays a functional role in kidney allograft complications. Metabolomics is a promising high-throughput approach in nephrology but is still limited by the lack of overlap in metabolite coverage. We performed an untargeted fecal metabolomic analysis of forty stable kidney allograft recipients [...] Read more.

Metabolic alteration plays a functional role in kidney allograft complications. Metabolomics is a promising high-throughput approach in nephrology but is still limited by the lack of overlap in metabolite coverage. We performed an untargeted fecal metabolomic analysis of forty stable kidney allograft recipients and twenty non-transplant controls. First, we applied the ultra-high performance liquid chromatography (UHPLC) analysis coupled with the Diod Array detector. The potential biomarkers were then collected and identified by gas chromatography-mass spectrometry (GCMS). In order to allow for complete coverage of the fecal polar and non-polar metabolites, the performance of five organic solvents with increasing polarity was investigated successively. UHPLC analysis revealed that the fecal metabolite profiles following the five extractions were significantly different between controls and kidney allografts. GC-MS analysis showed that the best predictors’ metabolites belonged mainly to long-chain fatty acids, phenolic compounds, and amino acids. Collectively, our results showed the efficiency of our pioneer method to successfully discriminate stable kidney-transplant recipients from controls. These findings suggest that distinct metabolic profiles mainly affect fatty acid biosynthesis and amino acid metabolism. In such a context, the novel insights into metabolomic investigation may be a valuable tool that could provide useful new relevant biomarkers for preventing kidney transplant complications. Full article

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20 pages, 2756 KiB

Open AccessArticle

Fecal Metabolomics Reveals Distinct Profiles of Kidney Transplant Recipients and Healthy Controls

by Soumaya Kouidhi, Oumaima Zidi, Muhanad Alhujaily, Nessrine Souai, Amor Mosbah, Tareg M. Belali, Kais Ghedira, Imene El Kossai, Jamelddine El Manaa, Wissem Mnif and Ameur Cherif

Diagnostics 2021, 11(5), 807; https://doi.org/10.3390/diagnostics11050807 - 29 Apr 2021

Cited by 6 | Viewed by 2440

Abstract

Monitoring graft recipients remains dependent on traditional biomarkers and old technologies lacking specificity, sensitivity, or accuracy. Recently, metabolomics is becoming a promising approach that may offer to kidney transplants a more effective and specific monitoring. Furthermore, emerging evidence suggested a fundamental role of [...] Read more.

Monitoring graft recipients remains dependent on traditional biomarkers and old technologies lacking specificity, sensitivity, or accuracy. Recently, metabolomics is becoming a promising approach that may offer to kidney transplants a more effective and specific monitoring. Furthermore, emerging evidence suggested a fundamental role of gut microbiota as an important determinant of patients’ metabolomes. In the current study, we enrolled forty stable renal allografts recipients compared to twenty healthy individuals. Samples were taken at different time points from patient to patient following transplantation surgery, which varied from 3 months to 22 years post-graft. All patients started the immunosuppression therapy immediately following kidney graft (Day 0). Gas chromatography–mass spectrometry (GC–MS) was employed to perform untargeted analysis of fecal metabolites. Globally, the fecal metabolic signature was significantly different between kidney transplants and the control group. Fecal metabolome was dominated by lipids (sterols and fatty acids) in the stable transplant group compared to the controls (p < 0.05). Overall, 18 metabolites were significantly altered within kidney transplant recipients. Furthermore, the most notable altered metabolic pathways in kidney transplants include ubiquinone and other terpenoid-quinone biosynthesis, tyrosine metabolism, tryptophan biosynthesis, and primary bile acid biosynthesis. Fecal metabolites could effectively distinguish stable transplant recipients from controls, supporting the potential utility of metabolomics in rapid and non-invasive diagnosis to produce relevant biomarkers and to help clinicians in monitoring kidney transplants. Further investigations are needed to clarify the physiological relevance of fecal metabolome and to assess the impact of microbiota modulation. Full article

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13 pages, 2610 KiB

Open AccessArticle

Clinicopathological Association of Autophagy Related 5 Protein with Prognosis of Colorectal Cancer

by Wan-Hsiang Hu, Wen-Chi Yang, Pei-Feng Liu, Ting-Ting Liu, Paul Morgan, Wei-Lun Tsai, Hung-Wei Pan, Cheng-Hsin Lee and Chih-Wen Shu

Diagnostics 2021, 11(5), 782; https://doi.org/10.3390/diagnostics11050782 - 26 Apr 2021

Cited by 7 | Viewed by 1802

Abstract

Gene mutation and pathogenesis bacteria are highly associated with colorectal cancer (CRC) development and progression. Autophagy is a self-clearance pathway to degrade abnormal proteins and infected bacteria in cells. Autophagy plays a dual role in cancer development. Among the autophagy-related (ATG) proteins, ATG5 [...] Read more.

Gene mutation and pathogenesis bacteria are highly associated with colorectal cancer (CRC) development and progression. Autophagy is a self-clearance pathway to degrade abnormal proteins and infected bacteria in cells. Autophagy plays a dual role in cancer development. Among the autophagy-related (ATG) proteins, ATG5 is the key component required for the core machinery of autophagy. However, the role of ATG5 in CRC malignancy remains unclear. Herein, we found that a high ATG5 protein level was correlated with poor overall survival (OS) and disease-free survival (DFS) of 118 patients with CRC. After stratification with demographic and clinicopathologic factors, a high ATG5 protein level was significantly correlated with unfavorable overall survival in female and elder (>60 year) CRC patients and tumor tissues with poor differentiation, late T stages (III + IV), whereas the ATG5 protein level was positively associated with the overall survival in CRC patients without lymph node invasion and radiation therapy. In contrast, a high ATG5 protein level was significantly associated with worse DFS in CRC patients with early stage of AJCC and no radiation therapy. In addition, colorectal cancer cells stably harboring small interfering RNA (siRNA) against ATG5 diminished the tumorsphere formation and sensitized cancer cells to chemotherapeutic agents. Taken together, our results suggest that ATG5 might be a prognostic biomarker for CRC and a potential therapeutic target for CRC patients. Full article

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20 pages, 3347 KiB

Open AccessArticle

Monitoring of B Cell in Kidney Transplantation: Development of a Novel Clusters Analysis and Role of Transitional B Cells in Transplant Outcome

by Rafael Alfaro, Isabel Legaz, Gema González-Martínez, Víctor Jimenez-Coll, Helios Martínez-Banaclocha, José Antonio Galián, Carmen Botella, Jesús de la Peña-Moral, María Rosa Moya-Quiles, José Antonio Campillo, Alfredo Minguela, Santiago Llorente and Manuel Muro

Diagnostics 2021, 11(4), 641; https://doi.org/10.3390/diagnostics11040641 - 01 Apr 2021

Cited by 13 | Viewed by 2170

Abstract

Background: B lymphocytes (BL) seem to play an important role in transplantation, although the and role of different subpopulations in monitoring and outcome is not clear. Our aim was to monitoring immunological profiles based on BL subpopulations in kidney recipients (KR) with the [...] Read more.

Background: B lymphocytes (BL) seem to play an important role in transplantation, although the and role of different subpopulations in monitoring and outcome is not clear. Our aim was to monitoring immunological profiles based on BL subpopulations in kidney recipients (KR) with the risk of acute rejection (AR). Methods: Monitoring of BL subpopulations was performed by flow cytometry in PBLs before transplantation and three and six months after transplantation (PTX). We used two methodological approaches, a traditional analysis, and a novel cluster analysis, to determine the association between BL subpopulations, AR incidence, and graft function. Results: After three months of PTX, KRs with a B phenotype enriched in transitional BL and plasmablasts had better kidney function and lower AR incidence. KRs with decreased transitional BL and plasmablasts were associated with lower kidney function and higher AR PTX. KRs that had an increase in transitional BL PTX had a better clinical outcome. The increase in transitory BL during PTX was also associated with an increase in Tregs. Indeed, KRs receiving thymoglobulin as induction therapy showed a slight decrease in the relative frequency of naive BLs after three months of PTX. Conclusion: The monitoring of BL subpopulations may serve as a non-invasive tool to improve immunological follow-up of patients after kidney transplantation. However, further studies are needed to confirm the obtained results, define cut-off values, and standardize more optimal and even custom/customized protocols. Full article

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14 pages, 2728 KiB

Open AccessArticle

Can the Determination of HE4 and CA125 Markers Affect the Treatment of Patients with Endometrial Cancer?

by Aneta Cymbaluk-Płoska, Paula Gargulińska, Michał Bulsa, Sebastian Kwiatkowski, Anita Chudecka-Głaz and Kaja Michalczyk

Diagnostics 2021, 11(4), 626; https://doi.org/10.3390/diagnostics11040626 - 31 Mar 2021

Cited by 11 | Viewed by 2015

Abstract

The aim of our research was to determine the use of CA125 and HE4 as prognostic factors in patients with different clinical staging of endometrial cancer. Sixty-two patients with advanced endometrial cancer and 287 patients with early stage endometrial cancer participated in the [...] Read more.

The aim of our research was to determine the use of CA125 and HE4 as prognostic factors in patients with different clinical staging of endometrial cancer. Sixty-two patients with advanced endometrial cancer and 287 patients with early stage endometrial cancer participated in the study. Based on the results obtained in the study, the cut-off value for HE4 was established at 186 pmol/l and correlated with the possibility of cytoreductive surgery in patients with recurrent endometrial cancer. Univariate logistic regression revealed that serum concentrations for the median CA125 correlated with DFS (HR = 1.76, p = 0.033) and OS (HR = 1.42, p = 0.025), while the median of HE4 marker correlated with DFS (HR = 1.96, p = 0.015) and OS (HR = 1.83, p = 0.004). In the multivariate analysis, a decrease in CA125 level below normal range correlated positively with DFS and OS (HR = 1.45, p = 0.026; HR = 1.38, p = 0.037). HE4 levels correlated with DFS as follows: values below the normal range (HR = 2.31, p = 0.01), and with OS (HR = 1.89, p = 0.004). Based on the results obtained in the study, we found that HE4 is a sensitive tool for predicting the risk of recurrence and overall survival in patients with endometrial cancer. Full article

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12 pages, 520 KiB

Open AccessArticle

High Expression of PD-L1 Is Associated with Better Survival in Pancreatic/Periampullary Cancers and Correlates with Epithelial to Mesenchymal Transition

by Nishant Thakur, Kwang Yeol Paik, Gyoyeon Hwang and Yosep Chong

Diagnostics 2021, 11(4), 597; https://doi.org/10.3390/diagnostics11040597 - 26 Mar 2021

Cited by 5 | Viewed by 1750

Abstract

Periampullary cancers (PACs) are characterized by tumor-infiltrating lymphocytes (TILs), severe fibrosis, and epithelial to mesenchymal transition (EMT). The immune checkpoint marker programmed death-1 (PD-1) and its ligands 1 and 2 have gained popularity in cancers with TILs. Evidence suggests a strong relationship between [...] Read more.

Periampullary cancers (PACs) are characterized by tumor-infiltrating lymphocytes (TILs), severe fibrosis, and epithelial to mesenchymal transition (EMT). The immune checkpoint marker programmed death-1 (PD-1) and its ligands 1 and 2 have gained popularity in cancers with TILs. Evidence suggests a strong relationship between immune checkpoint markers and EMT in cancers. Here, we evaluated the expression and prognostic significance of immune checkpoint and EMT markers in PAC using an automated image analyzer. Formalin-fixed, paraffin-embedded surgically excised PAC tissues from laboratory archives (1998–2014) were evaluated by immunohistochemical staining for PD-1, PD-L1, and PD-L2 in a tissue microarray. In total, 115 PAC patients (70 males and 45 females) with an average age of 63 years were analyzed. Location, gross type, size, radial resection margin, N-M stage, lymphatic invasion, vascular invasion, perineural invasion, histologically well-differentiated severe inflammation, and high PD-L1 expression were significantly associated with recurrence. Higher PD-L1 expression, but not PD-1 and PD-L2, was significantly related to better overall survival (OS) and disease-free survival (DFS). PD-L1 and PD-L2 were significantly related to EMT markers. Aside from other clinicopathologic parameters, high PD-L1 expression was significantly related to better OS and DFS of PAC patients. Moreover, immune checkpoint markers were significantly associated with EMT markers. Therefore, PD-L1 expression can be a good prognostic marker to guide future immune target-based therapies in PAC patients. Full article

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15 pages, 1288 KiB

Open AccessArticle

CEA, EpCAM, αvβ6 and uPAR Expression in Rectal Cancer Patients with a Pathological Complete Response after Neoadjuvant Therapy

by Daan Linders, Marion Deken, Maxime van der Valk, Willemieke Tummers, Shadhvi Bhairosingh, Dennis Schaap, Gesina van Lijnschoten, Elham Zonoobi, Peter Kuppen, Cornelis van de Velde, Alexander Vahrmeijer, Arantza Farina Sarasqueta, Cornelis Sier and Denise Hilling

Diagnostics 2021, 11(3), 516; https://doi.org/10.3390/diagnostics11030516 - 14 Mar 2021

Cited by 6 | Viewed by 3209

Abstract

Rectal cancer patients with a complete response after neoadjuvant therapy can be monitored with a watch-and-wait strategy. However, regrowth rates indicate that identification of patients with a pathological complete response (pCR) remains challenging. Targeted near-infrared fluorescence endoscopy is a potential tool to improve [...] Read more.

Rectal cancer patients with a complete response after neoadjuvant therapy can be monitored with a watch-and-wait strategy. However, regrowth rates indicate that identification of patients with a pathological complete response (pCR) remains challenging. Targeted near-infrared fluorescence endoscopy is a potential tool to improve response evaluation. Promising tumor targets include carcinoembryonic antigen (CEA), epithelial cell adhesion molecule (EpCAM), integrin αvβ6, and urokinase-type plasminogen activator receptor (uPAR). To investigate the applicability of these targets, we analyzed protein expression by immunohistochemistry and quantified these by a total immunostaining score (TIS) in tissue of rectal cancer patients with a pCR. CEA, EpCAM, αvβ6, and uPAR expression in the diagnostic biopsy was high (TIS > 6) in, respectively, 100%, 100%, 33%, and 46% of cases. CEA and EpCAM expressions were significantly higher in the diagnostic biopsy compared with the corresponding tumor bed (p < 0.01). CEA, EpCAM, αvβ6, and uPAR expressions were low (TIS < 6) in the tumor bed in, respectively, 93%, 95%, 85%, and 62.5% of cases. Immunohistochemical evaluation shows that CEA and EpCAM could be suitable targets for response evaluation after neoadjuvant treatment, since expression of these targets in the primary tumor bed is low compared with the diagnostic biopsy and adjacent pre-existent rectal mucosa in more than 90% of patients with a pCR. Full article

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12 pages, 2312 KiB

Open AccessArticle

Comparison of Ki-67 Labeling Index Patterns of Diffuse Large B-Cell Lymphomas and Burkitt Lymphomas Using Image Analysis: A Multicenter Study

by Yosep Chong, Tae Eun Kim, Uiju Cho, Min-Sun Jin, Kwangil Yim, Nishant Thakur, Jong Ok Kim, Inju Cho and Gyeongsin Park

Diagnostics 2021, 11(2), 343; https://doi.org/10.3390/diagnostics11020343 - 19 Feb 2021

Viewed by 2556

Abstract

Diffuse large B-cell lymphoma (DLBCL) is the most common high-grade B-cell lymphoma found in Korea; it manifests with a variety of cellular morphologies and a high proliferation index. It is difficult to differentiate between DLBCL and Burkitt lymphoma (BL) based on immunohistochemistry, histology, [...] Read more.

Diffuse large B-cell lymphoma (DLBCL) is the most common high-grade B-cell lymphoma found in Korea; it manifests with a variety of cellular morphologies and a high proliferation index. It is difficult to differentiate between DLBCL and Burkitt lymphoma (BL) based on immunohistochemistry, histology, and Epstein-Barr virus infection status owing to the overlap in findings. In this study, we performed comparative morphometric analysis to understand the proportional difference in Ki-67 staining between DLBCL and BL. We analyzed Ki-67-stained slides of 103 DLBCLs and 29 BLs that were pathologically confirmed using a three-tier classification system (negative, 1+, 2+, and 3+) to compare Ki-67 expression between BL and activated B-cell and germinal center B-cell subtypes of DLBCL and DLBCL with high proliferation indices (>90% of 2+ and 3+ cells). Patients with DLBCL were older than those with BL (62.1 versus 51.0 years). The number and proportion of negative cells (passenger and true negative cells) were significantly lower in BLs than those in DLBCLs (337.4, 5.9% versus 690.3, 12.4%). The number and proportion of 3+ cells were significantly higher in BLs than those in DLBCLs (5213.6, 96.3% versus 3132.4, 62.0%). BLs and DLBCLs with a high proliferation index showed similar results as those between BLs and overall DLBCLs. We were able to differentiate BLs and DLBCLs with 98.1% sensitivity and 100.0% specificity using an optimal cut-off of 97.9% of 2+/3+ Ki-67-positive cells. Thus, the Ki-67 labeling index may be a good differential biomarker for DLBCLs and BLs. Full article

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10 pages, 6178 KiB

Open AccessArticle

Targeted Next-Generation Sequencing of Liquid Biopsy Samples from Patients with NSCLC

by Hestia Mellert, Jordan Reese, Leisa Jackson, Victoria Maxwell, Chérie Tschida and Gary A. Pestano

Diagnostics 2021, 11(2), 155; https://doi.org/10.3390/diagnostics11020155 - 21 Jan 2021

Cited by 5 | Viewed by 4519

Abstract

Liquid biopsy tests have become an integral part of the molecular diagnosis of patients with non-small cell lung cancer (NSCLC). We describe a new test panel that uses very low input (20 ng) of cell-free nucleic acids extracted from human plasma, which is [...] Read more.

Liquid biopsy tests have become an integral part of the molecular diagnosis of patients with non-small cell lung cancer (NSCLC). We describe a new test panel that uses very low input (20 ng) of cell-free nucleic acids extracted from human plasma, which is designed to yield results in less than 72 h. In this study, we performed novel amplicon-based targeted next-generation sequencing with a semiconductor-based system, the Ion GeneStudio S5 Prime. The analytic performance of the assay was evaluated using contrived and retrospectively collected clinical specimens. The cumulative percent coefficient of variation for the new test process was very precise at 8.4% for inter-day, 4.0% for inter-operator and 3.4% for inter-instrument. We also observed significant agreement (95.7–100%) with an orthogonal, high-sensitivity droplet digital™ Polymerase Chain Reaction (ddPCR) test. This method offers a valuable supplement to assessing targeted mutations from blood while conserving specimens and maintaining sensitivity, with rapid turn-around times to actionable results. Full article

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2020

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19 pages, 926 KiB

Open AccessReview

Biomarkers for Inner Ear Disorders: Scoping Review on the Role of Biomarkers in Hearing and Balance Disorders

by Nahla A. Gomaa, Zaharadeen Jimoh, Sandra Campbell, Julianna K. Zenke and Agnieszka J. Szczepek

Diagnostics 2021, 11(1), 42; https://doi.org/10.3390/diagnostics11010042 - 29 Dec 2020

Cited by 13 | Viewed by 4163

Abstract

The diagnostics of inner ear diseases are primarily functional, but there is a growing interest in inner ear biomarkers. The present scoping review aimed to elucidate gaps in the literature regarding the definition, classification system, and an overview of the potential uses of [...] Read more.

The diagnostics of inner ear diseases are primarily functional, but there is a growing interest in inner ear biomarkers. The present scoping review aimed to elucidate gaps in the literature regarding the definition, classification system, and an overview of the potential uses of inner ear biomarkers. Relevant biomarkers were categorized, and their possible benefits were evaluated. The databases OVID Medline, EMBASE, EBSCO COINAHL, CA PLUS, WOS BIOSIS, WOS Core Collection, Proquest Dissertations, Theses Global, PROSPERO, Cochrane Library, and BASE were searched using the keywords “biomarker” and “inner ear”. Of the initially identified 1502 studies, 34 met the inclusion criteria. The identified biomarkers were classified into diagnostic, prognostic, therapeutic, and pathognomonic; many were detected only in the inner ear or temporal bone. The inner-ear-specific biomarkers detected in peripheral blood included otolin-1, prestin, and matrilin-1. Various serum antibodies correlated with inner ear diseases (e.g., anti-type II collagen, antinuclear antibodies, antibodies against cytomegalovirus). Further studies are advised to elucidate the clinical significance and diagnostic or prognostic usage of peripheral biomarkers for inner ear disorders, filling in the literature gaps with biomarkers pertinent to the otology clinical practice and integrating functional and molecular biomarkers. These may be the building blocks toward a well-structured guideline for diagnosing and managing some audio-vestibular disorders. Full article

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11 pages, 1479 KiB

Open AccessArticle

Nuclear Expression Loss of SSBP2 Is Associated with Poor Prognostic Factors in Colorectal Adenocarcinoma

by Yumin Chung, Hyunsung Kim, Seongsik Bang, Kiseok Jang, Seung Sam Paik and Su-Jin Shin

Diagnostics 2020, 10(12), 1097; https://doi.org/10.3390/diagnostics10121097 - 16 Dec 2020

Cited by 6 | Viewed by 1851

Abstract

Single-stranded DNA binding protein 2 (SSBP2) is involved in DNA damage response and may induce growth arrest in cancer cells, having a potent tumor suppressor role. SSBP2 is ubiquitously expressed and the loss of its expression has been reported in various tumor types. [...] Read more.

Single-stranded DNA binding protein 2 (SSBP2) is involved in DNA damage response and may induce growth arrest in cancer cells, having a potent tumor suppressor role. SSBP2 is ubiquitously expressed and the loss of its expression has been reported in various tumor types. However, the correlation between SSBP2 expression and colorectal cancer (CRC) prognosis remains unclear. SSBP2 nuclear expression was evaluated immunohistochemically in 48 normal colonic mucosae, 47 adenomas, 391 primary adenocarcinomas, and 131 metastatic carcinoma tissue samples. The clinicopathological factors, overall survival (OS), and recurrence-free survival were evaluated, and associations with the clinicopathological parameters were analyzed in 391 colorectal adenocarcinoma patients. A diffuse nuclear SSBP2 expression was detected in all normal colonic mucosa and adenoma samples. SSBP2 expression loss was observed in 131 (34.3%) primary adenocarcinoma and 100 (76.3%) metastatic carcinoma samples. SSBP2 expression was significantly associated with poor prognostic factors, such as vascular invasion (p = 0.005), high pT category (p = 0.045), and shorter OS (p = 0.038), using univariate survival analysis. Nuclear SSBP2 expression loss was significantly observed in colorectal carcinoma and metastatic carcinoma tissues, being associated with poor prognostic factors. SSBP2 acts as a tumor suppressor and may be used as a CRC prognostic biomarker. Full article

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26 pages, 1742 KiB

Open AccessReview

MicroRNA in Gastric Cancer Development: Mechanisms and Biomarkers

by Fatimat Kipkeeva, Tatyana Muzaffarova, Alexandra Korotaeva, Maxim Nikulin, Kristina Grishina, Danzan Mansorunov, Pavel Apanovich and Alexander Karpukhin

Diagnostics 2020, 10(11), 891; https://doi.org/10.3390/diagnostics10110891 - 31 Oct 2020

Cited by 22 | Viewed by 3261

Abstract

Gastric cancer (GC) is one of the most common and difficult diseases to treat. The study of signaling pathway regulation by microRNA provides information on the mechanisms of GC development and is the basis for biomarker creation. In this study, a circuit of [...] Read more.

Gastric cancer (GC) is one of the most common and difficult diseases to treat. The study of signaling pathway regulation by microRNA provides information on the mechanisms of GC development and is the basis for biomarker creation. In this study, a circuit of microRNA interactions with signaling pathways was constructed. The microRNAs, associated with metastasis and chemoresistance, are described. In most cases, microRNAs in GC regulate the Wnt/β-catenin, PI3K/AKT/mTOR, RAS/RAF/ERK/MAPK, NF-kB, TGF-β, and JAK/STAT pathways. Part of the microRNA acts on several target genes that function in different pathways. This often leads to an intensification of the induced processes. MicroRNAs have also been described that have the opposite effect on different pathways, causing different functional consequences. By acting on several target genes, or genes associated with several pathways, microRNAs can function in a signaling network. MicroRNAs associated with metastasis most often interact with the Wnt/β-catenin pathway. MicroRNAs affecting chemoresistance, in most cases, affect the regulators of apoptosis and are associated with the PI3K/AKT/mTOR pathway. The characteristics of microRNAs proposed as candidates for GC biomarkers were analyzed. The currently developed diagnostic and prognostic panels of microRNAs are also considered. Full article

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9 pages, 847 KiB

Open AccessArticle

The Association between Plasma Levels of Intact and Cleaved uPAR Levels and the Risk of Biochemical Recurrence after Radical Prostatectomy for Prostate Cancer

by Hein Vincent Stroomberg, Gitte Kristensen, Kasper Drimer Berg, Solvej Lippert, Klaus Brasso and Martin Andreas Røder

Diagnostics 2020, 10(11), 877; https://doi.org/10.3390/diagnostics10110877 - 28 Oct 2020

Cited by 2 | Viewed by 1516

Abstract

Radical prostatectomy (RP) is a curatively intended treatment option for clinically localized non-metastatic prostate cancer (PCa). Novel biomarkers could refine treatment choice based on a better identification of men at risk of biochemical recurrence (BCR) following therapy. The urokinase plasminogen activator receptor (uPAR) [...] Read more.

Radical prostatectomy (RP) is a curatively intended treatment option for clinically localized non-metastatic prostate cancer (PCa). Novel biomarkers could refine treatment choice based on a better identification of men at risk of biochemical recurrence (BCR) following therapy. The urokinase plasminogen activator receptor (uPAR) system is a promising biomarker of aggressiveness in many cancers. The predictive value of uPAR after curatively intended treatment for PCa remains to be elucidated. This was a prospective evaluation of uPAR analysis in men with prostate cancer (Copenhagen uPAR prostate cancer (CuPCA) database). Risk of BCR following RP was analyzed using cumulative incidences with competing risk and tested with Gray’s test. Associations between quartile groups of uPAR levels and BCR were assessed with uni- and multivariate Cox proportional hazards. In total, 532 men were included. With more advanced tumor stage, Gleason score (GS), and prostate-specific antigen (PSA) the uPAR I–III + II–III plasma levels increased. Quartile levels of plasma uPAR I–III, I–III + II–III showed no significant association between the risk of BCR and the plasma uPAR levels in uni- and multivariate analysis. Despite increased levels of uPAR I–III + II–III in advanced tumor stage, intact and cleaved uPAR levels were not associated with BCR and are not predictive biomarkers for BCR following curatively intended treatment of PCa. It is unlikely that further studies of uPAR in RP treated patients is needed. Full article

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10 pages, 8219 KiB

Open AccessArticle

Effect of Baseline Characteristics and Tumor Burden on Vaspin Expression and Progressive Disease in Operable Colorectal Cancer

by Jung-Yu Kan, Yi-Chen Lee, Yu-Da Lin, Wan-Yi Ho and Sin-Hua Moi

Diagnostics 2020, 10(10), 801; https://doi.org/10.3390/diagnostics10100801 - 09 Oct 2020

Cited by 6 | Viewed by 1866

Abstract

Colorectal cancer is a highly heterogeneous malignancy in the Asian population, and it is considered an important prognostic factor for baseline characteristics, tumor burden, and tumor markers. This study investigated the effect of baseline characteristics and tumor burden on tumor marker expression and [...] Read more.

Colorectal cancer is a highly heterogeneous malignancy in the Asian population, and it is considered an important prognostic factor for baseline characteristics, tumor burden, and tumor markers. This study investigated the effect of baseline characteristics and tumor burden on tumor marker expression and progressive disease in colorectal cancer by using partial least squares variance-based path modeling (PLS-PM). PLS-PM can be used to evaluate the complex relationship between prognostic variables and progressive disease status with a small sample of measurements and structural models. A total of 89 tissue samples of colorectal cancer were analyzed. Our results suggested that the expression of visceral adipose tissue-derived serpin (vaspin) is a potential indicator of colorectal cancer progression and may be affected by baseline characteristics such as age, sex, body mass index, and diabetes mellitus. Moreover, according to the characteristics of tumor burden, the expression of vaspin was generally higher in each progressive disease patient. The overall findings suggest that vaspin is a potential indicator of the progressive disease and may be affected by the baseline characteristics of patients. Full article

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10 pages, 233 KiB

Open AccessArticle

Association of Bone Mineral Density and Coronary Artery Calcification in Patients with Osteopenia and Osteoporosis

by Tzyy-Ling Chuang, Malcolm Koo and Yuh-Feng Wang

Diagnostics 2020, 10(9), 699; https://doi.org/10.3390/diagnostics10090699 - 16 Sep 2020

Cited by 6 | Viewed by 1986

Abstract

The aim of this study was to investigate the association between bone mineral density (BMD) and coronary artery calcification (CAC) in adults with osteopenia or osteoporosis. A retrospective medical review study was conducted in a regional hospital in southern Taiwan. Medical records of [...] Read more.

The aim of this study was to investigate the association between bone mineral density (BMD) and coronary artery calcification (CAC) in adults with osteopenia or osteoporosis. A retrospective medical review study was conducted in a regional hospital in southern Taiwan. Medical records of patients who underwent both a coronary computed tomography scan and a BMD measurement were identified. Multinomial logistic regression analyses were used to assess the association between BMD and CAC levels in patients with osteopenia or osteoporosis. Of the 246 patients, 119 were female and 42.3% had CAC. For patients with osteopenia, after adjusting for the significant factors of CAC, no significant association was observed between BMD with either moderate CAC (0 < CAC score ≤ 100) or high CAC (CAC score > 100). However, in patients with osteoporosis, after adjusting for the significant factors of CAC, BMD in the lumbar spine was inversely associated with moderate CAC (odds ratio = 0.38, p = 0.035). In conclusion, a lower BMD in the lumbar spine was associated with an increased risk of moderate CAC in patients with osteoporosis. It is crucial to take action to maintain bone health, particularly in those who already have osteoporosis, to reduce the risk of developing CAC and its associated morbidity and mortality. Full article

13 pages, 1297 KiB

Open AccessArticle

Quantitative Multiplex Real-Time Reverse Transcriptase–Polymerase Chain Reaction with Fluorescent Probe Detection of Killer Immunoglobulin-Like Receptors, KIR2DL4/3DL3

by Wipaporn Wongfieng, Rungtiwa Nutalai, Amonrat Jumnainsong and Chanvit Leelayuwat

Diagnostics 2020, 10(8), 588; https://doi.org/10.3390/diagnostics10080588 - 13 Aug 2020

Cited by 1 | Viewed by 2173

Abstract

(1) Background: KIR2DL4/KIR3DL3 are the framework genes present in all KIR haplotypes, with unique expression patterns being present only in women and CD56bright NK cells. KIR genes have a high degree of DNA sequence identity. Consequently, they are one of the most challenging [...] Read more.

(1) Background: KIR2DL4/KIR3DL3 are the framework genes present in all KIR haplotypes, with unique expression patterns being present only in women and CD56bright NK cells. KIR genes have a high degree of DNA sequence identity. Consequently, they are one of the most challenging genes for molecular detection—especially regarding expressions; (2) Methods: We developed an effective method to determine KIR3DL3/KIR2DL4 expressions based on a multiplex quantitative real-time Reverse transcription polymerase chain reaction (qRT-PCR )with fluorescent probes using NK92; (3) Results: Standardizations of the singleplex KIR2DL4 and KIR3DL3 were performed to evaluate the sensitivity and specificity for further development of the multiplex assay. The limit of detection was at 500 copies each. There was cross-amplification with the presence of related KIR genes at a level of 5 × 10⁷ copies. This is not biologically significant because this high level of KIR expression has not been found in clinical samples. The multiplex assay was reproducible equivalent to its singleplex (KIR2DL4; R² = 0.995, KIR3DL3; R² = 0.996, but lower sensitivity of 10³ copies). Furthermore, the validation of the developed method on samples of blood donors showed high sensitivity (100%) and specificity (99.9%); (4) Conclusions: The developed method is reliable and highly specific suitable for evaluation of the KIR2DL4/3DL3 mRNA expressions in further applications. Full article

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14 pages, 2991 KiB

Open AccessArticle

Predictive Biomarkers and Patient Outcome in Platinum-Resistant (PLD-Treated) Ovarian Cancer

by Isabel J. Dionísio de Sousa, Durval S. Marques, Catarina Príncipe, Raquel V. Portugal, Sule Canberk, Hugo Prazeres, José M. Lopes, Etel R. P. Gimba, Raquel T. Lima and Paula Soares

Diagnostics 2020, 10(8), 525; https://doi.org/10.3390/diagnostics10080525 - 28 Jul 2020

Cited by 5 | Viewed by 3025

Abstract

Identification of predictive biomarkers for ovarian cancer (OC) treatment, particularly in the platinum-resistant/refractory setting, is highly relevant for clinical management. E-cadherin, vimentin, and osteopontin (OPN) are proteins associated with tumor microenvironment (TME) remodelling that play key roles in cancer. This study aimed to [...] Read more.

Identification of predictive biomarkers for ovarian cancer (OC) treatment, particularly in the platinum-resistant/refractory setting, is highly relevant for clinical management. E-cadherin, vimentin, and osteopontin (OPN) are proteins associated with tumor microenvironment (TME) remodelling that play key roles in cancer. This study aimed to evaluate the association between the staining patterns of these proteins with survival outcomes in a series of OC patients, namely in patients with platinum-resistant/refractory disease. Low E-cadherin expression and high vimentin expression in all patient groups (as well as for E-cadherin in the platinum-resistant arm) were significantly associated with longer overall survival (OS). Low cytoplasmic OPN expression (and cytoplasmic and membrane OPN in the platinum-resistant arm) were significantly associated with longer OS. In patients that responded to treatment (pegylated liposomal doxorubicin (PLD) or other), low cytoplasmic OPN expression was also associated with longer progression-free survival (PFS). In the other hand, high nuclear OPN-c expression in patients that respond to treatment was associated with longer OS and longer PFS. Longer PFS was also associated with high expression of both nuclear and cytoplasm OPN-c, in platinum-resistant patients and in those that responded to PLD. Our study indicates that the expression of E-cadherin, vimentin, and OPN may have prognostic implications. Nuclear OPN-c and cytoplasm OPN expression are putative predictive markers in platinum-resistant (PLD treated) ovarian cancer patients. Full article

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19 pages, 1401 KiB

Open AccessArticle

L1CAM, CA9, KLK6, HPN, and ALDH1A1 as Potential Serum Markers in Primary and Metastatic Colorectal Cancer Screening

by Francis Yew Fu Tieng, Nadiah Abu, Surani Sukor, Zairul Azwan Mohd Azman, Norshahidah Mahamad Nadzir, Learn-Han Lee and Nurul Syakima Ab Mutalib

Diagnostics 2020, 10(7), 444; https://doi.org/10.3390/diagnostics10070444 - 30 Jun 2020

Cited by 15 | Viewed by 3585

Abstract

Background: Colorectal cancer (CRC) screening at the earlier stages could effectively decrease CRC-related mortality and incidence; however, accurate screening strategies are still lacking. Considerable interest has been generated in the detection of less invasive tests requiring a small sample volume with the potential [...] Read more.

Background: Colorectal cancer (CRC) screening at the earlier stages could effectively decrease CRC-related mortality and incidence; however, accurate screening strategies are still lacking. Considerable interest has been generated in the detection of less invasive tests requiring a small sample volume with the potential to detect several cancer biomarkers simultaneously. Due to this, the ELISA-based method was undertaken in this study. Methods: Concentrations of neural cell adhesion molecule L1 (L1CAM), carbonic anhydrase IX (CA9), mesothelin (MSLN), midkine (MDK), hepsin (HPN), kallikrein 6 (KLK6), transglutaminase 2 (TGM2) aldehyde dehydrogenase 1 family, member A1 (ALDH1A1), epithelial cell adhesion molecule (EpCAM), and cluster of differentiation 44 (CD44) from blood serum of 36 primary CRC and 24 metastatic CRC (mCRC) were calculated via MAGPIX^® System (Luminex Corporation, USA). Results: Significantly increased concentration (p < 0.05) of three serum biomarkers (L1CAM, CA9, and HPN) were shown in mCRC when compared with primary CRC. HPN and KLK6 showed significant differences (p < 0.05) in concentration among different stages of CRC. In contrast, levels of HPN and ALDH1A1 were significantly elevated (p < 0.05) in chemotherapy-treated CRC patients as compared with nontreated ones. Conclusion: Serum biomarkers could act as a potential early CRC diagnostics test, but further additional testings are needed. Full article

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11 pages, 1890 KiB

Open AccessArticle

KCTD15 Protein Expression in Peripheral Blood and Acute Myeloid Leukemia

by Giovanni Smaldone, Luigi Coppola, Mariarosaria Incoronato, Rosanna Parasole, Mimmo Ripaldi, Luigi Vitagliano, Peppino Mirabelli and Marco Salvatore

Diagnostics 2020, 10(6), 371; https://doi.org/10.3390/diagnostics10060371 - 04 Jun 2020

Cited by 4 | Viewed by 3441

Abstract

Leukocytes are major cellular components of the inflammatory and immune response systems. After their generation in the bone marrow from hematopoietic stem cells, they maturate as granulocytes (neutrophils, eosinophils, and basophils), monocytes, and lymphocytes. The abnormal accumulation and proliferation of immature blood cells [...] Read more.

Leukocytes are major cellular components of the inflammatory and immune response systems. After their generation in the bone marrow from hematopoietic stem cells, they maturate as granulocytes (neutrophils, eosinophils, and basophils), monocytes, and lymphocytes. The abnormal accumulation and proliferation of immature blood cells (blasts) lead to severe and widespread diseases such as leukemia. We have recently shown that KCTD15, a member of the potassium channel tetramerization domain containing protein family (KCTD), is remarkably upregulated in leukemic B-cells. Here, we extend our investigation by monitoring the KCTD15 expression levels in circulating lymphocytes, monocytes, and granulocytes, as well as in leukemia cells. Significant differences in the expression level of KCTD15 were detected in normal lymphocytes, monocytes, and granulocytes. Interestingly, we also found overexpression of the protein following leukemic transformation in the case of myeloid cell lineage. Indeed, KCTD15 was found to be upregulated in K562 and NB4 cells, as well as in HL-60 cell lines. This in vitro finding was corroborated by the analysis of KCTD15 mRNA of acute myeloid leukemia (AML) patients reported in the Microarray Innovations in Leukemia (MILE) dataset. Collectively, the present data open interesting perspectives for understanding the maturation process of leukocytes and for the diagnosis/therapy of acute leukemias. Full article

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14 pages, 1792 KiB

Open AccessArticle

Biomarkers of Muscle Metabolism in Peripheral Artery Disease: A Dynamic NIRS-Assisted Study to Detect Adaptations Following Revascularization and Exercise Training

by Fabio Manfredini, Nicola Lamberti, Valentina Ficarra, Elpiniki Tsolaki, Sofia Straudi, Paolo Zamboni, Nino Basaglia and Vincenzo Gasbarro

Diagnostics 2020, 10(5), 312; https://doi.org/10.3390/diagnostics10050312 - 16 May 2020

Cited by 14 | Viewed by 3214

Abstract

We assessed whether muscle metabolism biomarkers (MMb) identified by near-infrared spectroscopy (NIRS) are valid for determining adaptations following revascularization or exercise training in peripheral artery disease (PAD). Eighteen patients (males n = 13; 69 ± 7 years) were randomized to receive revascularization (Rev [...] Read more.

We assessed whether muscle metabolism biomarkers (MMb) identified by near-infrared spectroscopy (NIRS) are valid for determining adaptations following revascularization or exercise training in peripheral artery disease (PAD). Eighteen patients (males n = 13; 69 ± 7 years) were randomized to receive revascularization (Rev = 6) or pain-free home-based exercise (Ex = 12). MMb were safely collected via a NIRS-assisted treadmill test as area-under-curve for the spectra of oxygenated (-oxy), deoxygenated (-deoxy), differential (-diff) and total (-tot) hemoglobin traces. MMb, ankle–brachial index (ABI), pain-free (PFWD) and 6-min (6MWD) walking distances were assessed at baseline and after four months. MMb were correlated at baseline with ABI (MMb-oxy r = 0.46) and 6MWD (MMb-tot r = 0.51). After treatments, MMb-oxy showed an expected increase, which was more relevant for Rev group than the Ex (56% vs. 20%), with trends towards normalization for the other MMb. These changes were significantly correlated with variations in ABI (MMb-oxy r = 0.71; p = 0.002) and 6MWD (MMb-tot r = 0.58; p = 0.003). The MMb-diff in Rev group and MMb-deoxy in Ex group at baseline predicted clinical outcomes being correlated with PFWD improvements after 4-month (r = −0.94; p = 0.005 and r = −0.57; p = 0.05, respectively). A noninvasive NIRS-based test, feasible in a clinical setting, identified muscle metabolism biomarkers in PAD. The novel MMb were associated with validated outcome measures, selectively modified after different interventions and able to predict long-term functional improvements after surgery or exercise training. Full article

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14 pages, 1787 KiB

Open AccessReview

CCNE1 Amplification as a Predictive Biomarker of Chemotherapy Resistance in Epithelial Ovarian Cancer

by Justin W. Gorski, Frederick R. Ueland and Jill M. Kolesar

Diagnostics 2020, 10(5), 279; https://doi.org/10.3390/diagnostics10050279 - 05 May 2020

Cited by 58 | Viewed by 7628

Abstract

Ovarian cancer is the most-deadly gynecologic malignancy, with greater than 14,000 women expected to succumb to the disease this year in the United States alone. In the front-line setting, patients are treated with a platinum and taxane doublet. Although 40–60% of patients achieve [...] Read more.

Ovarian cancer is the most-deadly gynecologic malignancy, with greater than 14,000 women expected to succumb to the disease this year in the United States alone. In the front-line setting, patients are treated with a platinum and taxane doublet. Although 40–60% of patients achieve complete clinical response to first-line chemotherapy, 25% are inherently platinum-resistant or refractory with a median overall survival of about one year. More than 80% of women afflicted with ovarian cancer will recur. Many attempts have been made to understand the mechanism of platinum and taxane based chemotherapy resistance. However, despite decades of research, few predictive markers of chemotherapy resistance have been identified. Here, we review the current understanding of one of the most common genetic alterations in epithelial ovarian cancer, CCNE1 (cyclin E1) amplification, and its role as a potential predictive marker of cytotoxic chemotherapy resistance. CCNE1 amplification has been identified as a primary oncogenic driver in a subset of high grade serous ovarian cancer that have an unmet clinical need. Understanding the interplay between cyclin E1 amplification and other common ovarian cancer genetic alterations provides the basis for chemotherapeutic resistance in CCNE1 amplified disease. Exploration of the effect of cyclin E1 amplification on the cellular machinery that causes dysregulated proliferation in cancer cells has allowed investigators to explore promising targeted therapies that provide the basis for emerging clinical trials. Full article

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16 pages, 1658 KiB

Open AccessArticle

Single Nucleotide and Copy-Number Variants in IL4 and IL13 Are Not Associated with Asthma Susceptibility or Inflammatory Markers: A Case-Control Study in a Mexican-Mestizo Population

by Enrique Ambrocio-Ortiz, Gustavo Galicia-Negrete, Gloria Pérez-Rubio, Areli J. Escobar-Morales, Edgar Abarca-Rojano, Alma D. Del Angel-Pablo, Manuel D. J. Castillejos-López and Ramcés Falfán-Valencia

Diagnostics 2020, 10(5), 273; https://doi.org/10.3390/diagnostics10050273 - 30 Apr 2020

Cited by 2 | Viewed by 3176

Abstract

Background: Asthma is a complex and chronic inflammatory airway disease. Asthma’s etiology is unknown; however, genetic and environmental factors could affect disease susceptibility. We designed a case-control study aimed to evaluate the role of single-nucleotide polymorphisms (SNP), and copy-number variants (CNV) in the [...] Read more.

Background: Asthma is a complex and chronic inflammatory airway disease. Asthma’s etiology is unknown; however, genetic and environmental factors could affect disease susceptibility. We designed a case-control study aimed to evaluate the role of single-nucleotide polymorphisms (SNP), and copy-number variants (CNV) in the IL4 and IL13 genes in asthma susceptibility and their participation in plasma cytokine levels depending on genotypes Methods: We include 486 subjects, divided into asthma patients (AP, n = 141) and clinically healthy subjects (CHS, n = 345). We genotyped three SNP, two in the IL4 and two in the IL13 gene; also, two CNVs in IL4. The IL-4, IL-13 and IgE plasma levels were quantified. Results: Biomass-burning smoke exposure was higher in the AP group compared to CHS (47.5% vs. 20.9%; p < 0.01, OR = 3.4). No statistical differences were found in the genetic association analysis. In both CNV, we only found the common allele. For the analysis of IL-4, IL-13, and IgE measures stratified by genotypes, no significant association or correlation was found. Conclusion: In the Mexican-mestizo population, SNPs neither CNVs in IL4 nor IL13 are associated with asthma susceptibility or involved serum cytokine levels. Biomass-burning smoke is a risk factor in asthma susceptibility. Full article

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28 pages, 4438 KiB

Open AccessArticle

miR-196B-5P and miR-200B-3P Are Differentially Expressed in Medulloblastomas of Adults and Children

by Michela Visani, Gianluca Marucci, Dario de Biase, Felice Giangaspero, Francesca Romana Buttarelli, Alba Ariela Brandes, Enrico Franceschi, Giorgia Acquaviva, Alessia Ciarrocchi, Kerry Jane Rhoden, Giovanni Tallini and Annalisa Pession

Diagnostics 2020, 10(5), 265; https://doi.org/10.3390/diagnostics10050265 - 29 Apr 2020

Cited by 6 | Viewed by 3033 | Correction

Abstract

Medulloblastoma is a highly aggressive brain tumor that typically affects children, while in adults it represents ~1% of all brain tumors. Little is known about microRNA expression profile of the rare adult medulloblastoma. The main aim of this study was to identify peculiar [...] Read more.

Medulloblastoma is a highly aggressive brain tumor that typically affects children, while in adults it represents ~1% of all brain tumors. Little is known about microRNA expression profile of the rare adult medulloblastoma. The main aim of this study was to identify peculiar differences in microRNA expression between childhood and adult medulloblastoma. Medulloblastomas were profiled for microRNA expression using the Exiqon Human miRNome panel (I + II) analyzing 752 microRNAs in a training set of six adult and six childhood cases. Then, the most differentially expressed microRNAs were validated in a total of 21 adult and 19 childhood cases. Eight microRNAs (miR-196b-5p, miR-183-5p, miR-200b-3p, miR-196a-5p, miR-193a-3p, miR-29c-3p, miR-33b-5p, and miR-200a-3p) were differentially expressed in medulloblastoma of adults and children. Analysis of the validation set confirmed that miR-196b-5p and miR-200b-3p were significantly overexpressed in medulloblastoma of adults as compared with those of children. We followed an in silico approach to investigate direct targets and the pathways involved for the two microRNAs (miR-196b and miR-200b) differently expressed between adult and childhood medulloblastoma. Adult and childhood medulloblastoma have different miRNA expression profiles. In particular, the differential dysregulation of miR-196b-5p and miR-200b-3p characterizes the miRNA profile of adult medulloblastoma and suggests potential targets for novel diagnostic, prognostic, or therapeutic strategies. Full article

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12 pages, 1916 KiB

Open AccessArticle

Circulating Tumor Cells Enumerated by a Centrifugal Microfluidic Device as a Predictive Marker for Monitoring Ovarian Cancer Treatment: A Pilot Study

by Hyera Kim, Minji Lim, Jin Young Kim, So-Jin Shin, Yoon-Kyoung Cho and Chi Heum Cho

Diagnostics 2020, 10(4), 249; https://doi.org/10.3390/diagnostics10040249 - 23 Apr 2020

Cited by 14 | Viewed by 4429

Abstract

We investigated the size-based isolation and enumeration of circulating tumor cells (CTCs) using a centrifugal microfluidic device equipped with a fluid-assisted separation technology (FAST) disc. We further assessed the correlations among CTCs, cancer antigen-125 (CA125) levels, and clinical course of the disease in [...] Read more.

We investigated the size-based isolation and enumeration of circulating tumor cells (CTCs) using a centrifugal microfluidic device equipped with a fluid-assisted separation technology (FAST) disc. We further assessed the correlations among CTCs, cancer antigen-125 (CA125) levels, and clinical course of the disease in a prospective analysis of 47 serial blood samples collected at multiple time-points from 13 ovarian cancer patients. CTCs were isolated from whole blood using the FAST disc and were classified as epithelial cell adhesion molecule (EpCAM)/cytokeratin+, CD45−, and 4′,6-diamidino-2-phenylindole (DAPI)+. Mean CTC count at baseline was 20.2; 84.62% of patients had more than one CTC at baseline and had decreased CTCs counts after surgery and chemotherapy. The CTC counts in eight patients with complete responses were <3. CTC counts were correlated with CA125 levels in three patients without recurrence; they were elevated in three patients with recurrence and normal CA125 concentrations. CTC counts and CA125 levels showed high concordance with directional changes (increasing 71.4%; non-increasing 75.0%). CTC counts showed higher associations with clinical status, sensitivity (100.0% vs. 60.0%), positive predictive value (55.6% vs. 42.9%), and negative predictive value (100.0% vs. 87.5%) than CA125 levels. CTC counts were better associated with treatment response and recurrence than CA125 levels. Full article

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13 pages, 1621 KiB

Open AccessArticle

Serum Has Higher Proportion of Janus Kinase 2 V617F Mutation Compared to Paired EDTA-Whole Blood Sample: A Model for Somatic Mutation Quantification Using qPCR and the 2^-∆∆Cq Method

by Gustavo Barcelos Barra, Ticiane Henriques Santa Rita, Ana Luisa Santa Cruz Almeida, Rafael Henriques Jácomo and Lídia Freire Abdalla Nery

Diagnostics 2020, 10(3), 153; https://doi.org/10.3390/diagnostics10030153 - 12 Mar 2020

Cited by 9 | Viewed by 2926

Abstract

Detection of the Janus Kinase-2 (JAK2) V617F mutation is a diagnostic criterion for myeloproliferative neoplasms, and high levels of mutant alleles are associated with worse outcomes. This mutation is usually tested on blood DNA by allele-specific qPCR (AS-qPCR) and measured using absolute quantification. [...] Read more.

Detection of the Janus Kinase-2 (JAK2) V617F mutation is a diagnostic criterion for myeloproliferative neoplasms, and high levels of mutant alleles are associated with worse outcomes. This mutation is usually tested on blood DNA by allele-specific qPCR (AS-qPCR) and measured using absolute quantification. However, some automated DNA extractions co-extracts of PCR inhibitors from blood and qPCR absolute quantification need increased efforts in order to maintain standard curves. JAK2 V617F can also be detected in serum using droplet digital PCR (ddPCR), a specimen with less inhibitors and favorable to automated extractions, but ddPCR instruments are not wide available as qPCR thermocyclers. Here, we evaluate whether JAK2 V617F could be accurately quantified by AS-qPCR using the 2^-∆∆Cq method on blood DNA and validate the assay using gold-standard molecular diagnostic protocols. Next, we apply the validated method to assess if the mutation could be reliably detected/quantified in serum. JAK2 V617F could be quantified by AS-qPCR using the 2^-∆∆Cq method—the assay was highly accurate (bias of 1.91%) compared to a commercial kit, highly precise (total CV% of 0.40%, 1.92%, 11.12% for samples with 93%, 54%, and 2.5% of mutant allele), highly sensitive (limit of detection of 0.15%), and demonstrated a linear detection response from 1.1% to 99.9%. Serum presented a higher mutant allele burden compared to the paired whole blood (mean of 4%), which allows for an increased JAK2 mutant detection rate and favors increased JAK2 V617F high-throughput analysis. Full article

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12 pages, 1397 KiB

Open AccessArticle

BRCAness as an Important Prognostic Marker in Patients with Triple-Negative Breast Cancer Treated with Neoadjuvant Chemotherapy: A Multicenter Retrospective Study

by Yoshimasa Kosaka, Yutaka Yamamoto, Hirokazu Tanino, Hiroshi Nishimiya, Mutsuko Yamamoto-Ibusuki, Yuko Hirota, Hirotaka Iwase, Seigo Nakamura and Sadako Akashi-Tanaka

Diagnostics 2020, 10(2), 119; https://doi.org/10.3390/diagnostics10020119 - 21 Feb 2020

Cited by 6 | Viewed by 3434

Abstract

Triple-negative breast cancer (TNBC) has several subtypes. The identification of markers associated with recurrence and poor prognosis in patients with TNBC is urgently needed. BRCAness is a set of traits in which BRCA1 dysfunction, arising from gene mutation, methylation, or deletion, results in [...] Read more.

Triple-negative breast cancer (TNBC) has several subtypes. The identification of markers associated with recurrence and poor prognosis in patients with TNBC is urgently needed. BRCAness is a set of traits in which BRCA1 dysfunction, arising from gene mutation, methylation, or deletion, results in DNA repair deficiency. In the current study, we evaluated the clinical significance and prognosis of BRCAness in a multicenter retrospective study. Ninety-four patients with TNBC treated with neoadjuvant chemotherapy were enrolled from three university hospitals for this retrospective study. BRCAness was evaluated in 94 core needle biopsy (CNB) specimens prior to neoadjuvant chemotherapy and 49 surgical specimens without pathological complete response (pCR). The samples were assessed using multiplex ligation-dependent probe amplification, and the amplicons were scored. Of the 94 patients, 51 had BRCAness in CNB specimens. There were no significant differences in pCR rates or recurrence between the BRCAness and non-BRCAness groups. Among surgical specimens, the BRCAness group had a significantly shorter recurrence-free survival and overall survival compared with the non-BRCAness group. The BRCAness of surgical specimens was found to be an important marker to predict prognosis in patients with TNBC after neoadjuvant chemotherapy. A clinical trial to assess the clinical impact of carboplatin with BRCAness is planned. Full article

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14 pages, 806 KiB

Open AccessReview

Diagnostic, Prognostic, and Therapeutic Value of Non-Coding RNA Expression Profiles in Renal Transplantation

by Adriana Franco-Acevedo, Zesergio Melo and Raquel Echavarria

Diagnostics 2020, 10(2), 60; https://doi.org/10.3390/diagnostics10020060 - 22 Jan 2020

Cited by 7 | Viewed by 3190

Abstract

End-stage renal disease is a public health problem responsible for millions of deaths worldwide each year. Although transplantation is the preferred treatment for patients in need of renal replacement therapy, long-term allograft survival remains challenging. Advances in high-throughput methods for large-scale molecular data [...] Read more.

End-stage renal disease is a public health problem responsible for millions of deaths worldwide each year. Although transplantation is the preferred treatment for patients in need of renal replacement therapy, long-term allograft survival remains challenging. Advances in high-throughput methods for large-scale molecular data generation and computational analysis are promising to overcome the current limitations posed by conventional diagnostic and disease classifications post-transplantation. Non-coding RNAs (ncRNAs) are RNA molecules that, despite lacking protein-coding potential, are essential in the regulation of epigenetic, transcriptional, and post-translational mechanisms involved in both health and disease. A large body of evidence suggests that ncRNAs can act as biomarkers of renal injury and graft loss after transplantation. Hence, the focus of this review is to discuss the existing molecular signatures of non-coding transcripts and their value to improve diagnosis, predict the risk of rejection, and guide therapeutic choices post-transplantation. Full article

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2019

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14 pages, 1247 KiB

Open AccessArticle

Phospholipids are A Potentially Important Source of Tissue Biomarkers for Hepatocellular Carcinoma: Results of a Pilot Study Involving Targeted Metabolomics

by Erin B. Evangelista, Sandi A. Kwee, Miles M. Sato, Lu Wang, Christoph Rettenmeier, Guoxiang Xie, Wei Jia and Linda L. Wong

Diagnostics 2019, 9(4), 167; https://doi.org/10.3390/diagnostics9040167 - 29 Oct 2019

Cited by 10 | Viewed by 3596

Abstract

Background: Hepatocellular carcinoma (HCC) pathogenesis involves the alteration of multiple liver-specific metabolic pathways. We systematically profiled cancer- and liver-related classes of metabolites in HCC and adjacent liver tissues and applied supervised machine learning to compare their potential yield for HCC biomarkers. Methods: Tumor [...] Read more.

Background: Hepatocellular carcinoma (HCC) pathogenesis involves the alteration of multiple liver-specific metabolic pathways. We systematically profiled cancer- and liver-related classes of metabolites in HCC and adjacent liver tissues and applied supervised machine learning to compare their potential yield for HCC biomarkers. Methods: Tumor and corresponding liver tissue samples were profiled as follows: Bile acids by ultra-performance liquid chromatography (LC) coupled to tandem mass spectrometry (MS), phospholipids by LC-MS/MS, and other small molecules including free fatty acids by gas chromatography—time of flight MS. The overall classification performance of metabolomic signatures derived by support vector machine (SVM) and random forests machine learning algorithms was then compared across classes of metabolite. Results: For each metabolite class, there was a plateau in classification performance with signatures of 10 metabolites. Phospholipid signatures consistently showed the highest discrimination for HCC followed by signatures derived from small molecules, free fatty acids, and bile acids with area under the receiver operating characteristic curve (AUC) values of 0.963, 0.934, 0.895, 0.695, respectively, for SVM-generated signatures comprised of 10 metabolites. Similar classification performance patterns were observed with signatures derived by random forests. Conclusion: Membrane phospholipids are a promising source of tissue biomarkers for discriminating between HCC tumor and liver tissue. Full article

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14 pages, 3483 KiB

Open AccessArticle

The Effects of Low-Dose Irradiation on Human Saliva: A Surface-Enhanced Raman Spectroscopy Study

by Ioana Maria Colceriu-Șimon, Mihaela Hedeșiu, Valentin Toma, Gabriel Armencea, Alin Moldovan, Gabriela Știufiuc, Bogdan Culic, Viorica Țărmure, Cristian Dinu, Ioana Berindan-Neagoe, Rareș Ionuț Știufiuc and Mihaela Băciuț

Diagnostics 2019, 9(3), 101; https://doi.org/10.3390/diagnostics9030101 - 22 Aug 2019

Cited by 18 | Viewed by 3818

Abstract

Biological effects of low-dose ionizing radiation (IR) have been unclear until now. Saliva, because of the ease of collection, could be valuable in studying low-dose IR effects by means of surface-enhanced Raman spectroscopy (SERS). The objective of our study was to compare the [...] Read more.

Biological effects of low-dose ionizing radiation (IR) have been unclear until now. Saliva, because of the ease of collection, could be valuable in studying low-dose IR effects by means of surface-enhanced Raman spectroscopy (SERS). The objective of our study was to compare the salivary SER spectra recorded before and after low-dose IR exposure in the case of pediatric patients (PP). Unstimulated saliva was collected from ten PP before and after irradiation with a cone beam computed tomography (CBCT) machine used for diagnostic purposes. The SERS measurements have been recorded on dried saliva samples using a solid nanosilver plasmonic substrate synthesized using an original method developed in our laboratory. The experimental results showed that salivary SER spectra are dominated by three vibrational bands (441,735 and 2107 cm⁻¹) that can be assigned to bending and stretching vibrations of salivary thiocyanate (SCN-). After exposure, an immediate increase of vibrational bands assigned to SCN- has been recorded in the case of all samples, probably as a result of IR interaction with oral cavity. This finding suggests that SCN- could be used as a valuable biomarker for the detection and identification of low-dose radiation effects. Full article

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2018

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11 pages, 223 KiB

Open AccessArticle

Utility of Two-Dimensional Difference Gel Electrophoresis in Diagnosis of Multiple Sclerosis

by Michael Auer, Harald Hegen, Dagmar Rudzki, Georg Golderer and Florian Deisenhammer

Diagnostics 2018, 8(3), 44; https://doi.org/10.3390/diagnostics8030044 - 05 Jul 2018

Cited by 2 | Viewed by 5082

Abstract

Two-dimensional difference gel electrophoresis (2D-DIGE) has been used for identification of possible biomarkers in the cerebrospinal fluid (CSF) of multiple sclerosis (MS) patients. However, in different studies inconsistent results have been obtained. We wanted to analyze the diagnostic value of 2D-DIGE in early [...] Read more.

Two-dimensional difference gel electrophoresis (2D-DIGE) has been used for identification of possible biomarkers in the cerebrospinal fluid (CSF) of multiple sclerosis (MS) patients. However, in different studies inconsistent results have been obtained. We wanted to analyze the diagnostic value of 2D-DIGE in early MS patients by comparing protein patterns between single and pooled samples of MS patients and controls. CSF samples of 20 MS patients and 10 control subjects were processed with 2D-DIGE. The so obtained protein patterns were analyzed with DeCyder 6.5 software, whereby we described variation of patterns presented in one gel as well as between different gels. Even when running single samples of patients of the same group in one gel, variation of protein patterns was high. The number of identified spots with different protein level varied between 4 and 30, depending on which sample batches were compared. We did not find a consistent pattern throughout all possible batch combinations. The inter-individual variation of protein expression as well as the susceptibility of 2D-DIGE for methodological variations makes use of 2D-DIGE as a diagnostic tool for MS and for detection of possible candidate biomarkers difficult, since detected proteins vary depending on which samples are compared. Full article

2017

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1111 KiB

Open AccessReview

Single Domain Antibodies as New Biomarker Detectors

by Chiuan Herng Leow, Katja Fischer, Chiuan Yee Leow, Qin Cheng, Candy Chuah and James McCarthy

Diagnostics 2017, 7(4), 52; https://doi.org/10.3390/diagnostics7040052 - 17 Oct 2017

Cited by 26 | Viewed by 11699

Abstract

Biomarkers are defined as indicators of biological processes, pathogenic processes, or pharmacological responses to a therapeutic intervention. Biomarkers have been widely used for early detection, prediction of response after treatment, and for monitoring the progression of diseases. Antibodies represent promising tools for recognition [...] Read more.

Biomarkers are defined as indicators of biological processes, pathogenic processes, or pharmacological responses to a therapeutic intervention. Biomarkers have been widely used for early detection, prediction of response after treatment, and for monitoring the progression of diseases. Antibodies represent promising tools for recognition of biomarkers, and are widely deployed as analytical tools in clinical settings. For immunodiagnostics, antibodies are now exploited as binders for antigens of interest across a range of platforms. More recently, the discovery of antibody surface display and combinatorial chemistry techniques has allowed the exploration of new binders from a range of animals, for instance variable domains of new antigen receptors (V_NAR) from shark and variable heavy chain domains (V_HH) or nanobodies from camelids. These single domain antibodies (sdAbs) have some advantages over conventional murine immunoglobulin owing to the lack of a light chain, making them the smallest natural biomarker binders thus far identified. In this review, we will discuss several biomarkers used as a means to validate diseases progress. The potential functionality of modern singe domain antigen binders derived from phylogenetically early animals as new biomarker detectors for current diagnostic and research platforms development will be described. Full article

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581 KiB

Open AccessArticle

Comparison of Direct Sequencing, Real-Time PCR-High Resolution Melt (PCR-HRM) and PCR-Restriction Fragment Length Polymorphism (PCR-RFLP) Analysis for Genotyping of Common Thiopurine Intolerant Variant Alleles NUDT15 c.415C>T and TPMT c.719A>G (TPMT*3C)

by Wai-Ying Fong, Chi-Chun Ho and Wing-Tat Poon

Diagnostics 2017, 7(2), 27; https://doi.org/10.3390/diagnostics7020027 - 12 May 2017

Cited by 14 | Viewed by 11587

Abstract

Thiopurine intolerance and treatment-related toxicity, such as fatal myelosuppression, is related to non-function genetic variants encoding thiopurine S-methyltransferase (TPMT) and Nudix hydrolase 15 (NUDT15). Genetic testing of the common variants NUDT15:NM_018283.2:c.415C>T (Arg139Cys, dbSNP rs116855232 T allele) and TPMT: NM_000367.4:c.719A>G (TPMT*3C, dbSNP rs1142345 G [...] Read more.

Thiopurine intolerance and treatment-related toxicity, such as fatal myelosuppression, is related to non-function genetic variants encoding thiopurine S-methyltransferase (TPMT) and Nudix hydrolase 15 (NUDT15). Genetic testing of the common variants NUDT15:NM_018283.2:c.415C>T (Arg139Cys, dbSNP rs116855232 T allele) and TPMT: NM_000367.4:c.719A>G (TPMT*3C, dbSNP rs1142345 G allele) in East Asians including Chinese can potentially prevent treatment-related complications. Two complementary genotyping approaches, real-time PCR-high resolution melt (PCR-HRM) and PCR-restriction fragment length morphism (PCR-RFLP) analysis were evaluated using conventional PCR and Sanger sequencing genotyping as the gold standard. Sixty patient samples were tested, revealing seven patients (11.7%) heterozygous for NUDT15 c.415C>T, one patient homozygous for the variant and one patient heterozygous for the TPMT*3C non-function allele. No patient was found to harbor both variants. In total, nine out of 60 (15%) patients tested had genotypic evidence of thiopurine intolerance, which may require dosage adjustment or alternative medication should they be started on azathioprine, mercaptopurine or thioguanine. The two newly developed assays were more efficient and showed complete concordance (60/60, 100%) compared to the Sanger sequencing results. Accurate and cost-effective genotyping assays by real-time PCR-HRM and PCR-RFLP for NUDT15 c.415C>T and TPMT*3C were successfully developed. Further studies may establish their roles in genotype-informed clinical decision-making in the prevention of morbidity and mortality due to thiopurine intolerance. Full article

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