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Genes
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Genomic Diagnosis of Human Cancers
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Genomic Diagnosis of Human Cancers

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Genetic Diagnosis".

Deadline for manuscript submissions: closed (10 December 2024) | Viewed by 5705

Special Issue Editor

Dr. Yael Goldberg

E-Mail Website
Guest Editor
The Raphael Recanati Genetics Institute, Rabin Medical Center–Beilinson Hospital, Petach Tikva, Israel Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
Interests: human genetics; medical genetics; genotype-phenotype; cancer predisposition genes; inherited colorectal cancer and polyposis; Lynch syndrome
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The genomic diagnosis of human cancer represents a revolutionary approach to understanding the genetic underpinnings of cancer at a molecular level. It involves the comprehensive analysis of an individual’s genetic information, specifically their DNA, to uncover the genetic mutations and alterations that may drive the development and progression of cancer. This diagnostic approach has significantly advanced our understanding of cancer, leading to more precise and personalized treatments and the potential for early detection and prevention.

Key aspects of the genomic diagnosis of human cancer include genetic profiling, the identification of driver mutation, personalized treatment strategies, prognostic insights, therapeutic resistance, early detection and prevention, research and drug development, and ethical and privacy considerations.

Overall, genomic diagnosis has revolutionized our approach to cancer by providing a deeper understanding of the molecular mechanisms that drive the disease. It has paved the way for more personalized and effective cancer treatment, giving hope to patients and researchers alike in the ongoing battle against cancer.

Dr. Yael Goldberg
Guest Editor

Manuscript Submission Information

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Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Genes is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • biomarker
  • cancer
  • DNA methylation
  • gene expression
  • protein
  • NGS
  • tumor germline
  • hereditary cancer syndromes

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Published Papers (4 papers)

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Research

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15 pages, 1428 KiB  
Article
Upregulation of ABLIM1 Differentiates Intrahepatic Cholangiocarcinoma from Hepatocellular Carcinoma and Both Colorectal and Pancreatic Adenocarcinoma Liver Metastases
by Tina Draškovič, Branislava Ranković, Nina Zidar and Nina Hauptman
Genes 2024, 15(12), 1545; https://doi.org/10.3390/genes15121545 - 28 Nov 2024
Viewed by 544
Abstract
Background: Altered gene expression in cancers holds great potential to improve the diagnostics and differentiation of primary and metastatic liver cancers. In this study, the expression of the protein-coding genes ring finger protein 135 (RNF135), ephrin-B2 (EFNB2), ring finger [...] Read more.
Background: Altered gene expression in cancers holds great potential to improve the diagnostics and differentiation of primary and metastatic liver cancers. In this study, the expression of the protein-coding genes ring finger protein 135 (RNF135), ephrin-B2 (EFNB2), ring finger protein 125 (RNF125), homeobox-C 4 (HOXC4), actin-binding LIM protein 1 (ABLIM1) and oncostatin M receptor (OSMR) and the long non-coding RNAs (lncRNA) prospero homeobox 1 antisense RNA 1 (PROX1-AS1) and leukemia inhibitory factor receptor antisense RNA 1 (LIFR-AS1) was investigated in hepatocellular carcinoma, cholangiocarcinoma, colorectal liver metastases and pancreatic ductal adenocarcinoma liver metastases. Methods: This study included 149 formalin-fixed, paraffin-embedded samples from 80 patients. After RNA isolation, quantification, reverse transcription and preamplification, real-time qPCR was performed. The gene expression between different groups was calculated relative to the expression of the reference genes using the ∆∆Cq method and statistically analyzed. The expression of the genes was additionally analyzed using the AmiCA and UCSC Xena platforms. Results: In primary cancers, our results showed differential expression between primary tumors and healthy tissues for all the genes and lncRNA examined. Moreover, we found downregulation of RNF135 in hepatocellular carcinoma, downregulation of OSMR in colorectal liver metastases and upregulation of HOXC4 in cholangiocarcinoma compared to primary liver cancers and metastatic cancers. The major finding is the upregulation of ABLIM1 in cholangiocarcinoma compared to hepatocellular carcinoma, colorectal liver metastases, pancreatic ductal adenocarcinoma liver metastases and healthy liver tissue. We propose ABLIM1 as a potential biomarker that differentiates cholangiocarcinoma from other cancers and healthy liver tissue. Conclusions: This study emphasizes the importance of understanding the differences in gene expression between healthy tissues and primary and metastatic cancers and highlights the potential use of altered gene expression as a diagnostic biomarker in these malignancies. Full article
(This article belongs to the Special Issue Genomic Diagnosis of Human Cancers)
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10 pages, 570 KiB  
Article
Distribution of BCR::ABL1 Transcripts in the Different Clinical Phases of Chronic Myeloid Leukemia: Effect on Hematological Parameters and Patient Survival
by Pablo Romero-Morelos, Ana Lilia González-Yebra, Anaid Herrerías-García, Francisco Arath Ruíz-Velázquez, Luis Jonathan Bueno-Rosario and Beatríz González-Yebra
Genes 2024, 15(5), 567; https://doi.org/10.3390/genes15050567 - 28 Apr 2024
Viewed by 1611
Abstract
Chronic myeloid leukemia (CML) is a hematopoietic stem cell disorder characterized by the presence of the Philadelphia chromosome, a product of the reciprocal translocation t(9;22)(q34;q11), in the BCR and ABL genes. These rearrangements in both genes lead to the formation of various fusion [...] Read more.
Chronic myeloid leukemia (CML) is a hematopoietic stem cell disorder characterized by the presence of the Philadelphia chromosome, a product of the reciprocal translocation t(9;22)(q34;q11), in the BCR and ABL genes. These rearrangements in both genes lead to the formation of various fusion mRNA products, with preferential expression of b2a2, b3a2, and other BCR::ABL1 mRNA variants, combined with additional chromosomal abnormalities. Notably, the distribution and frequency of different mRNA variants vary in different populations. However, studies concerning this in Mexico are limited, and the results have been inconclusive. This study therefore aimed to determine the distribution of BCR::ABL1 mRNA variants in different clinical phases of CML and their effect on hematological parameters and patient survival. This study included 33 patients, whose demographic, clinical, and molecular data on BCR::ABL1 mRNA variants and hematological parameters were collected to identify potential associations. A total of 84.8% (n = 28) of patients had BCR::ABL1 translocation and increased platelet and basophil counts. The most frequent mRNA variant was b3a2 (64.3%), followed by b2a2 (28.6%) and e1a2 (3.6%). Concerning the clinical phases of CML, 75.8% (n = 25), 21.2% (n = 7), and 3% (n = 1) of patients were in the chronic, blast, and accelerated phases, respectively. Moreover, the b3a2 mRNA variant was more commonly identified in patients in the chronic phase. No correlation was observed between mRNA variant expression and patient survival. However, b2a2 was indicative of patients with longer survival as well as those treated with imatinib or nilotinib. Additionally, platelet count could be a marker of BCR::ABL1 translocation. Full article
(This article belongs to the Special Issue Genomic Diagnosis of Human Cancers)
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13 pages, 963 KiB  
Article
Frequencies of BCR::ABL1 Transcripts in Patients with Chronic Myeloid Leukemia: A Meta-Analysis
by Pablo Romero-Morelos, Ana Lilia González-Yebra, Daniela Muñoz-López, Elia Lara-Lona and Beatriz González-Yebra
Genes 2024, 15(2), 232; https://doi.org/10.3390/genes15020232 - 12 Feb 2024
Cited by 3 | Viewed by 2153
Abstract
Chronic myeloid leukemia (CML) is associated with the Philadelphia chromosome and distinct BCR::ABL1 gene transcripts. We assessed the frequencies of these transcripts in Mexico, Latin America, and worldwide. We determined the prevalence of BCR::ABL1 transcripts in CML patients and intercontinental or regional variations [...] Read more.
Chronic myeloid leukemia (CML) is associated with the Philadelphia chromosome and distinct BCR::ABL1 gene transcripts. We assessed the frequencies of these transcripts in Mexico, Latin America, and worldwide. We determined the prevalence of BCR::ABL1 transcripts in CML patients and intercontinental or regional variations using specialized databases and keywords. We analyzed 34 studies from 20 countries, encompassing 5795 patients. Keyword-based searches in specialized databases guided data collection. ANOVA was employed for transcript distribution analysis. The b3a2 transcript was most prevalent globally, followed by b2a2, with e1a2 being the least frequent. Interestingly, Mexico City exhibited a higher incidence of b2a2, while b3a2 predominated in the remaining country. Overall, no significant intercontinental or regional variations were observed. b3a2 was the most common BCR::ABL1 transcript worldwide, with b2a2 following closely; e1a2 was infrequent. Notably, this trend remained consistent in Mexico. Evaluating transcript frequencies holds clinical relevance for CML management. Understanding the frequency of transcript informs personalized CML treatments. Full article
(This article belongs to the Special Issue Genomic Diagnosis of Human Cancers)
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8 pages, 547 KiB  
Brief Report
Preservation of 5-Hydroxymethylcytosine Levels in LRIG1 across Genomic DNA and Cell-Free DNA in Glioma Patients
by Daša Jevšinek Skok, Luka Bolha and Nina Hauptman
Genes 2024, 15(5), 535; https://doi.org/10.3390/genes15050535 - 24 Apr 2024
Viewed by 1136
Abstract
Cell-free DNA (cfDNA) has recently emerged as a promising minimally invasive diagnostic biomarker for various cancers. In this study, our aim was to identify cfDNA biomarkers by investigating genes that displayed significant differences between glioma patients and their corresponding controls. To accomplish this, [...] Read more.
Cell-free DNA (cfDNA) has recently emerged as a promising minimally invasive diagnostic biomarker for various cancers. In this study, our aim was to identify cfDNA biomarkers by investigating genes that displayed significant differences between glioma patients and their corresponding controls. To accomplish this, we utilized publicly available data from the Gene Expression Omnibus, focusing on 5-hydroxymethylcytosine (5hmC) profiles in both cfDNA and genomic DNA (gDNA) from glioma patients and healthy individuals. The intersection of gene lists derived from these comparative analyses unveiled LRIG1 and ZNF703 as the two genes with elevated 5hmC levels in both the cfDNA of glioma patients and gDNA of glioma tissue compared to their respective controls. The gene expression data revealed both genes were upregulated in glioma tissue compared to normal brain tissue. Integration of 5hmC data revealed a strong positive correlation in the glioma tissue group between 5hmC and the gene expression of the LRIG1 gene. Furthermore, exploration using the AmiCa web tool indicated that LRIG1 gene expression was elevated compared to 17 other cancers included in the database, emphasizing its potential as a distinctive biomarker across multiple cancer types. Full article
(This article belongs to the Special Issue Genomic Diagnosis of Human Cancers)
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