Cells

13 pages, 847 KiB

Open AccessArticle

Excess Weight Impairs Oocyte Quality, as Reflected by mtDNA and BMP-15

by Emiliya Sigal, Maya Shavit, Yuval Atzmon, Nardin Aslih, Asaf Bilgory, Daniella Estrada, Mediea Michaeli, Nechama Rotfarb, Yasmin Shibli Abu-Raya, Shilhav Meisel-Sharon and Einat Shalom-Paz

Cells 2024, 13(22), 1872; https://doi.org/10.3390/cells13221872 - 12 Nov 2024

Abstract

This prospective, case-control study evaluated the impact of obesity on oocyte quality based on mtDNA expression in cumulus cells (CC), and on bone morphogenetic protein 15 (BMP-15) and heparan sulfate proteoglycan 2 (HSPG2) in follicular fluid (FF). It included women 18 to <40 [...] Read more.

This prospective, case-control study evaluated the impact of obesity on oocyte quality based on mtDNA expression in cumulus cells (CC), and on bone morphogenetic protein 15 (BMP-15) and heparan sulfate proteoglycan 2 (HSPG2) in follicular fluid (FF). It included women 18 to <40 years of age, divided according to BMI < 24.9 (Group 1, n = 28) and BMI > 25 (Group 2, n = 22). Demographics, treatment, and pregnancy outcomes were compared. The mtDNA in CC, BMP-15, HSPG2, the lipid profile, the hormonal profile, and C-reactive protein were evaluated in FF and in blood samples. The BMP-15 levels in FF and the mitochondrial DNA in CC were higher in Group 1 (38.8 ± 32.5 vs. 14.3 ± 10.8 ng/mL; p = 0.001 and 1.10 ± 0.3 vs. 0.87 ± 0.18-fold change; p = 0.016, respectively) than in Group 2. High-density lipoprotein levels in blood and FF were higher in Group 1 (62 ± 18 vs. 50 ± 12 mg/dL; p = 0.015 and 34 ± 26 vs. 20.9 ± 7.2 mg/dL; p = 0.05, respectively). Group 2 had higher blood C-reactive protein (7.1 ± 5.4 vs. 3.4 ± 4.3 mg/L; p = 0.015), FF (5.2 ± 3.8 vs. 1.5 ± 1.6 mg/L; p = 0.002) and low-density lipoprotein levels (91 ± 27 vs. 71 ± 22 mg/dL; p = 0.008) vs. Group 1. Group 1 demonstrated a trend toward a better clinical pregnancy rate (47.8% vs. 28.6%: p = 0.31) and frozen embryo transfer rate (69.2% vs. 53.8; p = 0.69). Higher BMI resulted in lower BMP-15 levels and reduced mtDNA expression, which reflect decreased oocyte quality in overweight women. Full article

(This article belongs to the Special Issue Cellular and Molecular Mechanisms in Reproductive System Diseases)

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5 pages, 189 KiB

Open AccessEditorial

Oxidative Stress and Antioxidant Strategies: Relationships and Cellular Pathways for Human Health

by Alessia Remigante and Rossana Morabito

Cells 2024, 13(22), 1871; https://doi.org/10.3390/cells13221871 - 11 Nov 2024

Abstract

Chronic diseases and aging have increased significantly in recent decades [...] Full article

(This article belongs to the Special Issue Oxidative Stress and Antioxidant Strategies: Relationships and Cellular Pathways for Human Health)

22 pages, 2206 KiB

Open AccessReview

Structural and Functional Insights into Dishevelled-Mediated Wnt Signaling

by Lei Wang, Rui Zhu, Zehua Wen, Hua-Jun Shawn Fan, Teresa Norwood-Jackson, Danielle Jathan and Ho-Jin Lee

Cells 2024, 13(22), 1870; https://doi.org/10.3390/cells13221870 - 11 Nov 2024

Abstract

Dishevelled (DVL) proteins precisely control Wnt signaling pathways with many effectors. While substantial research has advanced our understanding of DVL’s role in Wnt pathways, key questions regarding its regulatory mechanisms and interactions remain unresolved. Herein, we present the recent advances and perspectives on [...] Read more.

Dishevelled (DVL) proteins precisely control Wnt signaling pathways with many effectors. While substantial research has advanced our understanding of DVL’s role in Wnt pathways, key questions regarding its regulatory mechanisms and interactions remain unresolved. Herein, we present the recent advances and perspectives on how DVL regulates signaling. The experimentally determined conserved domain structures of DVL in conjunction with AlphaFold-predicted structures are used to understand the DVL’s role in Wnt signaling regulation. We also summarize the role of DVL in various diseases and provide insights into further directions for research on the DVL-mediated signaling mechanisms. These findings underscore the importance of DVL as a pharmaceutical target or biological marker in diseases, offering exciting potential for future biomedical applications. Full article

(This article belongs to the Special Issue From Mechanisms to Therapeutics: Wnt Signaling in Cancer—Second Edition)

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20 pages, 1558 KiB

Open AccessReview

Clinical Applications of Antisense Oligonucleotides in Cancer: A Focus on Glioblastoma

by Alexandre Khuu, Maïté Verreault, Philippe Colin, Helene Tran and Ahmed Idbaih

Cells 2024, 13(22), 1869; https://doi.org/10.3390/cells13221869 - 11 Nov 2024

Abstract

Antisense oligonucleotides (ASOs) are promising drugs capable of modulating the protein expression of virtually any target with high specificity and high affinity through complementary base pairing. However, this requires a deep understanding of the target sequence and significant effort in designing the correct [...] Read more.

Antisense oligonucleotides (ASOs) are promising drugs capable of modulating the protein expression of virtually any target with high specificity and high affinity through complementary base pairing. However, this requires a deep understanding of the target sequence and significant effort in designing the correct complementary drug. In addition, ASOs have been demonstrated to be well tolerated during their clinical use. Indeed, they are already used in many diseases due to pathogenic RNAs of known sequences and in several neurodegenerative diseases and metabolic diseases, for which they were given marketing authorizations (MAs) in Europe and the United States. Their use in oncology is gaining momentum with several identified targets, promising preclinical and clinical results, and recent market authorizations in the US. However, many challenges remain for their clinical use in cancer. It seems necessary to take a step back and review our knowledge of ASOs and their therapeutic uses in oncology. The objectives of this review are (i) to summarize the current state of the art of ASOs; (ii) to discuss the therapeutic use of ASOs in cancer; and (iii) to focus on ASO usage in glioblastoma, the challenges, and the perspective ahead. Full article

(This article belongs to the Special Issue Nucleic Acid Therapeutics (NATs): Advances and Perspectives)

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13 pages, 1415 KiB

Open AccessReview

The Hippo Signaling Pathway, Reactive Oxygen Species Production, and Oxidative Stress: A Two-Way Traffic Regulation

by Bella Amanda, Rangga Pragasta, Haris Cakrasana, Arifa Mustika, Zakiyatul Faizah and Delvac Oceandy

Cells 2024, 13(22), 1868; https://doi.org/10.3390/cells13221868 - 11 Nov 2024

Abstract

The Hippo signaling pathway is recognized for its significant role in cell differentiation, proliferation, survival, and tissue regeneration. Recently, the Hippo signaling pathway was also found to be associated with oxidative stress and reactive oxygen species (ROS) regulation, which are important in the [...] Read more.

The Hippo signaling pathway is recognized for its significant role in cell differentiation, proliferation, survival, and tissue regeneration. Recently, the Hippo signaling pathway was also found to be associated with oxidative stress and reactive oxygen species (ROS) regulation, which are important in the regulation of cell survival. Studies indicate a correlation between components of the Hippo signaling pathway, including MST1, YAP, and TAZ, and the generation of ROS. On the other hand, ROS and oxidative stress can activate key components of the Hippo signaling pathway. For example, ROS production activates MST1, which subsequently phosphorylates FOXO3, leading to apoptotic cell death. ROS was also found to regulate YAP, in addition to MST1/2. Oxidative stress and ROS formation can impair lipids, proteins, and DNA, leading to many disorders, including aging, neurodegeneration, atherosclerosis, and diabetes. Consequently, understanding the interplay between the Hippo signaling pathway, ROS, and oxidative stress is crucial for developing future disease management strategies. This paper aimed to review the association between the Hippo signaling pathway, regulation of ROS production, and oxidative stress to provide beneficial information in understanding cell function and pathological processes. Full article

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23 pages, 19767 KiB

Open AccessArticle

Small and Long Non-Coding RNA Analysis for Human Trophoblast-Derived Extracellular Vesicles and Their Effect on the Transcriptome Profile of Human Neural Progenitor Cells

by Jessica A. Kinkade, Pallav Singh, Mohit Verma, Teka Khan, Toshihiko Ezashi, Nathan J. Bivens, R. Michael Roberts, Trupti Joshi and Cheryl S. Rosenfeld

Cells 2024, 13(22), 1867; https://doi.org/10.3390/cells13221867 - 11 Nov 2024

Abstract

In mice, the fetal brain is dependent upon the placenta for factors that guide its early development. This linkage between the two organs has given rise to the term, the placenta–brain axis. A similar interrelationship between the two organs may exist in humans. [...] Read more.

In mice, the fetal brain is dependent upon the placenta for factors that guide its early development. This linkage between the two organs has given rise to the term, the placenta–brain axis. A similar interrelationship between the two organs may exist in humans. We hypothesize that extracellular vesicles (EVs) released from placental trophoblast (TB) cells transport small RNA and other informational biomolecules from the placenta to the brain where their contents have pleiotropic effects. Here, EVs were isolated from the medium in which human trophoblasts (TBs) had been differentiated in vitro from induced pluripotent stem cells (iPSC) and from cultured iPSC themselves, and their small RNA content analyzed by bulk RNA-seq. EVs derived from human TB cells possess unique profiles of miRs, including hsa-miR-0149-3p, hsa-302a-5p, and many long non-coding RNAs (lncRNAs) relative to EVs isolated from parental iPSC. These miRs and their mRNA targets are enriched in neural tissue. Human neural progenitor cells (NPCs), generated from the same iPSC, were exposed to EVs from either TB or iPSC controls. Both sets of EVs were readily internalized. EVs from TB cells upregulate several transcripts in NPCs associated with forebrain formation and neurogenesis; those from control iPSC upregulated a transcriptional phenotype that resembled glial cells more closely than neurons. These results shed light on the possible workings of the placenta–brain axis. Understanding how the contents of small RNA within TB-derived EVs affect NPCs might yield new insights, possible biomarkers, and potential treatment strategies for neurobehavioral disorders that originate in utero, such as autism spectrum disorders (ASDs). Full article

(This article belongs to the Special Issue Human Placenta and Trophoblast Cells in Pregnancy Development)

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16 pages, 581 KiB

Open AccessReview

Pathophysiology of Congenital Anomalies of the Kidney and Urinary Tract: A Comprehensive Review

by Maximilian Brockwell, Sean Hergenrother, Matthew Satariano, Raghav Shah and Rupesh Raina

Cells 2024, 13(22), 1866; https://doi.org/10.3390/cells13221866 - 11 Nov 2024

Abstract

Congenital anomalies of the kidney and urinary tract (CAKUT) represent a broad range of diseases with differing mechanisms, clinical presentations, and prognoses. With an estimated prevalence of between 4 and 60 per 10,000 births, CAKUT represents a sizable number of patients for pediatric [...] Read more.

Congenital anomalies of the kidney and urinary tract (CAKUT) represent a broad range of diseases with differing mechanisms, clinical presentations, and prognoses. With an estimated prevalence of between 4 and 60 per 10,000 births, CAKUT represents a sizable number of patients for pediatric and adult nephrologists as therapies have progressed, allowing longer life spans. Many CAKUT disorders are associated with genetic mutations, and with advances in genomic sequencing, these genes are being identified at an increasing rate. Understanding these mutations provides insight into these conditions’ molecular mechanisms and pathophysiology. In this article, we discuss the epidemiology, presentation, and outcomes of CAKUT in addition to our current understanding of genetic and molecular mechanisms in these diseases. Full article

(This article belongs to the Section Cellular Pathology)

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5 pages, 6841 KiB

Open AccessCorrection

Correction: Huynh et al. Spike Protein Impairs Mitochondrial Function in Human Cardiomyocytes: Mechanisms Underlying Cardiac Injury in COVID-19. Cells 2023, 12, 877

by Tin Van Huynh, Lekha Rethi, Ting-Wei Lee, Satoshi Higa, Yu-Hsun Kao and Yi-Jen Chen

Cells 2024, 13(22), 1865; https://doi.org/10.3390/cells13221865 - 11 Nov 2024

Abstract

There was an error in the original publication [...] Full article

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26 pages, 1516 KiB

Open AccessReview

In Vitro Models of Diabetes: Focus on Diabetic Retinopathy

by Giulia Galgani, Giorgia Bray, Alma Martelli, Vincenzo Calderone and Valentina Citi

Cells 2024, 13(22), 1864; https://doi.org/10.3390/cells13221864 - 11 Nov 2024

Abstract

Diabetic retinopathy is a major eye complication in patients with diabetes mellitus, and it is the leading cause of blindness and visual impairment in the world. Chronic hyperglycemia induces endothelial damage with consequent vascular lesions, resulting in global vasculitis, which affects the small [...] Read more.

Diabetic retinopathy is a major eye complication in patients with diabetes mellitus, and it is the leading cause of blindness and visual impairment in the world. Chronic hyperglycemia induces endothelial damage with consequent vascular lesions, resulting in global vasculitis, which affects the small vessels of the retina. These vascular lesions cause ischemic conditions in certain areas of the retina, with a consequent increase in the release of pro-angiogenic mediators. In addition to pharmacological interventions for controlling the blood glycaemic level, the main strategies for treating diabetic retinopathy are the intravitreal injections of drugs, surgical treatments, and vitrectomies. The complexity of diabetic retinopathy is due to its close interactions with different cell types (endothelial cells, astrocytes, and Müller cells). The evaluation of the efficacy of novel pharmacological strategies is mainly performed through in vivo models. However, the use of different animal species leads to heterogenic results and ethical concerns. For these reasons, the development of new and reliable in vitro models, such as cell co-cultures and eye organoids, represents an urgent need in this area of research. This review features an overview of the in vitro models used to date and highlights the advances in technology used to study this pathology. Full article

(This article belongs to the Special Issue State-of-the-Art of Cell Cultures in Drug Validation and Toxicity Assessment)

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14 pages, 11443 KiB

Open AccessFeature PaperArticle

Immunohistochemical Characterization of Spermatogenesis in the Ascidian Ciona robusta

by Haruka Sakurai, Kogiku Shiba, Katsumi Takamura and Kazuo Inaba

Cells 2024, 13(22), 1863; https://doi.org/10.3390/cells13221863 - 11 Nov 2024

Abstract

Animals show diverse processes of gametogenesis in the evolutionary pathway. Here, we characterized the spermatogenic cells in the testis of the marine invertebrate Ciona robusta. Ciona sperm differentiate in a non-cystic type of testis, comprising many follicles with various sizes and stages of [...] Read more.

Animals show diverse processes of gametogenesis in the evolutionary pathway. Here, we characterized the spermatogenic cells in the testis of the marine invertebrate Ciona robusta. Ciona sperm differentiate in a non-cystic type of testis, comprising many follicles with various sizes and stages of spermatogenic cells. In the space among follicles, we observed free cells that were recognized by antibody against Müllerian inhibiting substance, a marker for vertebrate Sertoli cells. We further categorized the spermatogenic cells into four round stages (RI to RIV) and three elongated stages (EI to EIII) by morphological and immunohistochemical criteria. An antibody against a vertebrate Vasa homolog recognized a few large spermatogonium-like cells (RI) near the basal wall of a follicle. Consistent with the period of meiosis, a synaptonemal complex protein SYCP3 was recognized from early spermatocytes (RII) to early spermatids (E1). Acetylated tubulins were detected in spermatids before flagellar elongation at the RIV stage and became distributed along the flagella. Electron microscopy showed that the free cells outside the testicular follicle possessed a characteristic of vertebrate Sertoli cells. These results would provide a basis for basic and comparative studies on the mechanism of spermatogenesis. Full article

(This article belongs to the Special Issue The Cell Biology of Fertilization)

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12 pages, 2735 KiB

Open AccessArticle

CD47 in Osteosarcoma: Correlation with Metastasis and Macrophage-Mediated Phagocytosis

by Yunmi Ko, Seog-Yun Park, Jong Woong Park, June Hyuk Kim, Hyun Guy Kang and Jun Ah Lee

Cells 2024, 13(22), 1862; https://doi.org/10.3390/cells13221862 - 10 Nov 2024

Abstract

CD47 is expressed on cell surfaces and acts as a “don’t eat me” signal by interacting with signal-regulatory protein-α on the macrophage surface. Some cancer cells express CD47 protein and can evade macrophage phagocytosis. Herein, we evaluated the feasibility of targeting CD47 for [...] Read more.

CD47 is expressed on cell surfaces and acts as a “don’t eat me” signal by interacting with signal-regulatory protein-α on the macrophage surface. Some cancer cells express CD47 protein and can evade macrophage phagocytosis. Herein, we evaluated the feasibility of targeting CD47 for osteosarcoma by analyzing its expression patterns, clinicopathological correlations, and immunotherapeutic potential. We performed a retrospective analysis on 24 biopsy samples from patients with osteosarcoma to investigate correlations between CD47 protein positivity and clinicopathological characteristics. CD47 protein expression was detected in 20.8% of the biopsy samples. CD47 positivity correlated with metastasis at diagnosis. Patients with CD47-positive tumors were older than those with CD47-negative tumors. However, CD47 protein expression was not associated with sex, tumor size, or histologic response to preoperative chemotherapy. In vitro, CD47 antibody (B6H12) did not affect osteosarcoma cell viability or apoptosis. In a wound-healing assay, CD47 inhibited the migration of osteosarcoma cells. Differentiated macrophages exhibited higher phagocytic activity against osteosarcoma cells when pretreated with B6H12 compared with the isotype control. Our preliminary data suggest a possible interaction between CD47 protein and macrophage phagocytosis in osteosarcoma metastasis. A better understanding of the role of CD47 is necessary to develop an innovative immunotherapeutic approach against osteosarcoma. Full article

(This article belongs to the Special Issue Cell–Cell Interactome-Based Therapies for Osteosarcoma)

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21 pages, 9955 KiB

Open AccessOpinion

Unlocking Potential: A Comprehensive Overview of Cell Culture Banks and Their Impact on Biomedical Research

by Sabine Weiskirchen, Antonio M. Monteiro, Radovan Borojevic and Ralf Weiskirchen

Cells 2024, 13(22), 1861; https://doi.org/10.3390/cells13221861 - 10 Nov 2024

Abstract

Cell culture banks play a crucial role in advancing biomedical research by providing standardized, reproducible biological materials essential for various applications, from drug development to regenerative medicine. This opinion article presents a comprehensive overview of cell culture banks, exploring their establishment, maintenance, and [...] Read more.

Cell culture banks play a crucial role in advancing biomedical research by providing standardized, reproducible biological materials essential for various applications, from drug development to regenerative medicine. This opinion article presents a comprehensive overview of cell culture banks, exploring their establishment, maintenance, and characterization processes. The significance of ethical considerations and regulatory frameworks governing the use of cell lines is discussed, emphasizing the importance of quality control and validation in ensuring the integrity of research outcomes. Additionally, the diverse types of cell culture banks—primary cells, immortalized cell lines, and stem cells—and their specific contributions to different fields such as cancer research, virology, and tissue engineering are examined. The impact of technological advancements on cell banking practices is also highlighted, including automation and biobanking software that enhance efficiency and data management. Furthermore, challenges faced by researchers in accessing high-quality cell lines are addressed, along with proposed strategies for improving collaboration between academic institutions and commercial entities. By unlocking the potential of cell culture banks through these discussions, this article aims to underline their indispensable role in driving innovation within biomedical research and fostering future discoveries that could lead to significant therapeutic breakthroughs. Full article

(This article belongs to the Special Issue Primary and Continued Cell Cultures)

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24 pages, 4683 KiB

Open AccessArticle

Polyphenolic Compounds Activate SERCA1a and Attenuate Methylglyoxal- and Palmitate-Induced Impairment in Pancreatic INS-1E Beta Cells

by Vladimir Heger, Barbora Benesova, Magdalena Majekova, Petronela Rezbarikova, Attila Hunyadi, Lubica Horakova and Jana Viskupicova

Cells 2024, 13(22), 1860; https://doi.org/10.3390/cells13221860 - 9 Nov 2024

Abstract

Sarco/endoplasmic reticulum Ca²⁺-ATPase (SERCA) is an important regulatory protein responsible for maintaining calcium homeostasis within cells. Impairment of SERCA associated with activity/expression decrease has been implicated in multiple chronic conditions, including cardiovascular diseases, diabetes, cancer, neurodegenerative diseases, and skeletal muscle pathologies. [...] Read more.

Sarco/endoplasmic reticulum Ca²⁺-ATPase (SERCA) is an important regulatory protein responsible for maintaining calcium homeostasis within cells. Impairment of SERCA associated with activity/expression decrease has been implicated in multiple chronic conditions, including cardiovascular diseases, diabetes, cancer, neurodegenerative diseases, and skeletal muscle pathologies. Natural polyphenols have been recognized to interact with several target proteins involving SERCA. To date, only a limited number of polyphenolic compounds or their derivatives have been described either to increase SERCA activity/expression directly or to affect Ca²⁺ signaling pathways. In this study, we tested polyphenols for their ability to activate SERCA1a in the absence or presence of methylglyoxal or palmitate and to impact insulin release in pancreatic beta cells. The protective effects of these compounds against methylglyoxal- or palmitate-induced injury were evaluated. Results indicate that 6-gingerol, resveratrol, and ellagic acid activate SERCA1a and protect against activity decrease induced by methylglyoxal and palmitate. Molecular docking analysis revealed the binding of these polyphenols to Glu439 in the SERCA1a P-domain, suggesting a critical role in the stimulation of enzyme activity. Ellagic acid was found to directly stimulate the activity of SERCA1a, marking the first instance of such an observation. Full article

(This article belongs to the Special Issue Recent Advances in Metabolism and Oxidative Stress in Human Diseases 2.0)

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22 pages, 3326 KiB

Open AccessArticle

Bioengineering the Human Intestinal Mucosa and the Importance of Stromal Support for Pharmacological Evaluation In Vitro

by Matthew Freer, Jim Cooper, Kirsty Goncalves and Stefan Przyborski

Cells 2024, 13(22), 1859; https://doi.org/10.3390/cells13221859 - 8 Nov 2024

Abstract

Drug discovery is associated with high levels of compound elimination in all stages of development. The current practices for the pharmacokinetic testing of intestinal absorption combine Transwell^® inserts with the Caco-2 cell line and are associated with a wide range of limitations. [...] Read more.

Drug discovery is associated with high levels of compound elimination in all stages of development. The current practices for the pharmacokinetic testing of intestinal absorption combine Transwell^® inserts with the Caco-2 cell line and are associated with a wide range of limitations. The improvement of pharmacokinetic research relies on the development of more advanced in vitro intestinal constructs that better represent human native tissue and its response to drugs, providing greater predictive accuracy. Here, we present a humanized, bioengineered intestinal construct that recapitulates aspects of intestinal microanatomy. We present improved histotypic characteristics reminiscent of the human intestine, such as a reduction in transepithelial electrical resistance (TEER) and the formation of a robust basement membrane, which are contributed to in-part by a strong stromal foundation. We explore the link between stromal–epithelial crosstalk, paracrine communication, and the role of the keratinocyte growth factor (KGF) as a soluble mediator, underpinning the tissue-specific role of fibroblast subpopulations. Permeability studies adapted to a 96-well format allow for high throughput screening and demonstrate the role of the stromal compartment and tissue architecture on permeability and functionality, which is thought to be one of many factors responsible for unexpected drug outcomes using current approaches for pharmacokinetic testing. Full article

(This article belongs to the Special Issue State-of-the-Art of Cell Cultures in Drug Validation and Toxicity Assessment)

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20 pages, 2258 KiB

Open AccessArticle

Förster Resonance Energy Transfer Measurements in Living Bacteria for Interaction Studies of BamA with BamD and Inhibitor Identification

by Sebastian Schreiber and Joachim Jose

Cells 2024, 13(22), 1858; https://doi.org/10.3390/cells13221858 - 8 Nov 2024

Abstract

The β-barrel assembly machinery (BAM) is a multimeric protein complex responsible for the folding of outer membrane proteins in gram-negative bacteria. It is essential for cell survival and outer membrane integrity. Therefore, it is of impact in the context of antibiotic resistance and [...] Read more.

The β-barrel assembly machinery (BAM) is a multimeric protein complex responsible for the folding of outer membrane proteins in gram-negative bacteria. It is essential for cell survival and outer membrane integrity. Therefore, it is of impact in the context of antibiotic resistance and can serve as a target for the development of new antibiotics. The interaction between two of its subunits, BamA and BamD, is essential for its function. Here, a FRET-based assay to quantify the affinity between these two proteins in living bacterial cells is presented. The method was applied to identify two interaction hotspots at the binding interface. BamD^Y184 was identified to significantly contribute to the binding between both proteins through hydrophobic interactions and hydrogen bonding. Additionally, two salt bridges formed between BamD^R94, BamD^R97, and BamA^E127 contributed substantially to the binding of BamA to BamD as well. Two peptides (RFIRLN and VAEYYTER) that mimic the amino acid sequence of BamD around the identified hotspots were shown to inhibit the interaction between BamA and BamD in a dose-dependent manner in the upper micromolar range. These two peptides can potentially act as antibiotic enhancers. This shows that the BamA–BamD interaction site can be addressed for the design of protein–protein interaction inhibitors. Additionally, the method, as presented in this study, can be used for further functional studies on interactions within the BAM complex. Full article

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18 pages, 4849 KiB

Open AccessArticle

Semaglutide Ameliorates Diabetic Neuropathic Pain by Inhibiting Neuroinflammation in the Spinal Cord

by Sing-Ong Lee, Yaswanth Kuthati, Wei-Hsiu Huang and Chih-Shung Wong

Cells 2024, 13(22), 1857; https://doi.org/10.3390/cells13221857 - 8 Nov 2024

Abstract

Glucagon-like peptide 1 (GLP-1) receptor agonists are frequently used to treat type 2 diabetes and obesity. Despite the development of several drugs for neuropathic pain management, their poor efficacy, tolerance, addiction potential, and side effects limit their usage. Teneligliptin, a DPP-4 inhibitor, has [...] Read more.

Glucagon-like peptide 1 (GLP-1) receptor agonists are frequently used to treat type 2 diabetes and obesity. Despite the development of several drugs for neuropathic pain management, their poor efficacy, tolerance, addiction potential, and side effects limit their usage. Teneligliptin, a DPP-4 inhibitor, has been shown to reduce spinal astrocyte activation and neuropathic pain caused by partial sciatic nerve transection. Additionally, we showed its capacity to improve the analgesic effects of morphine and reduce analgesic tolerance. Recent studies indicate that GLP-1 synthesized in the brain activates GLP-1 receptor signaling pathways, essential for neuroprotection and anti-inflammatory effects. Multiple in vitro and in vivo studies using preclinical models of neurodegenerative disorders have shown the anti-inflammatory properties associated with glucagon-like peptide-1 receptor (GLP-1R) activation. This study aimed to investigate the mechanism of antinociception and the effects of the GLP-1 agonist semaglutide (SEMA) on diabetic neuropathic pain in diabetic rats. Methods: Male Wistar rats, each weighing between 300 and 350 g, were categorized into four groups: one non-diabetic sham group and three diabetic groups. The diabetic group received a single intraperitoneal injection of streptozotocin (STZ) at a dosage of 60 mg/kg to induce diabetic neuropathy. After 4 weeks of STZ injection, one diabetic group was given saline (vehicle), and the other two were treated with either 1× SEMA (1.44 mg/kg, orally) or 2× SEMA (2.88 mg/kg, orally). Following a 4-week course of oral drug treatment, behavioral, biochemical, and immunohistochemical analyses were carried out. The mechanical allodynia, thermal hyperalgesia, blood glucose, advanced glycation end products (AGEs), plasma HbA1C, and spinal inflammatory markers were evaluated. Results: SEMA treatment significantly reduced both allodynia and hyperalgesia in the diabetic group. SEMA therapy had a limited impact on body weight restoration and blood glucose reduction. In diabetic rats, SEMA lowered the amounts of pro-inflammatory cytokines in the spinal cord and dorsal horn. It also lowered the activation of microglia and astrocytes in the dorsal horn. SEMA significantly reduced HbA1c and AGE levels in diabetic rats compared to the sham control group. Conclusions: These results indicate SEMA’s neuroprotective benefits against diabetic neuropathic pain, most likely by reducing inflammation and oxidative stress by inhibiting astrocyte and microglial activity. Our findings suggest that we can repurpose GLP-1 agonists as potent anti-hyperalgesic and anti-inflammatory drugs to treat neuropathic pain without serious side effects. Full article

(This article belongs to the Special Issue New Advances in Neuroinflammation)

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18 pages, 1180 KiB

Open AccessReview

Regulation of the Intestinal Stem Cell Pool and Proliferation in Drosophila

by Simona Trubin, Dhruv B. Patel and Aiguo Tian

Cells 2024, 13(22), 1856; https://doi.org/10.3390/cells13221856 - 8 Nov 2024

Abstract

Understanding the regulation of somatic stem cells, both during homeostasis and in response to environmental challenges like injury, infection, chemical exposure, and nutritional changes, is critical because their dysregulation can result in tissue degeneration or tumorigenesis. The use of models such as the [...] Read more.

Understanding the regulation of somatic stem cells, both during homeostasis and in response to environmental challenges like injury, infection, chemical exposure, and nutritional changes, is critical because their dysregulation can result in tissue degeneration or tumorigenesis. The use of models such as the Drosophila and mammalian adult intestines offers valuable insights into tissue homeostasis and regeneration, advancing our knowledge of stem cell biology and cancer development. This review highlights significant findings from recent studies, unveiling the molecular mechanisms that govern self-renewal, proliferation, differentiation, and regeneration of intestinal stem cells (ISCs). These insights not only enhance our understanding of normal tissue maintenance but also provide critical perspectives on how ISC dysfunction can lead to pathological conditions such as colorectal cancer (CRC). Full article

(This article belongs to the Special Issue Advances in Intestinal Epithelial Plasticity and Regeneration)

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24 pages, 3934 KiB

Open AccessArticle

Nuclear–Cytoplasmic Shuttling of the Usher Syndrome 1G Protein SANS Differs from Its Paralog ANKS4B

by Jacques S. Fritze, Felizitas F. Stiehler and Uwe Wolfrum

Cells 2024, 13(22), 1855; https://doi.org/10.3390/cells13221855 - 8 Nov 2024

Abstract

The USH1G protein SANS is a small multifunctional scaffold protein. It is involved in several different cellular processes, such as intracellular transport, in the cytoplasm, or splicing of pre-mRNA, in the cell nucleus. Here, we aimed to gain insight into the regulation of [...] Read more.

The USH1G protein SANS is a small multifunctional scaffold protein. It is involved in several different cellular processes, such as intracellular transport, in the cytoplasm, or splicing of pre-mRNA, in the cell nucleus. Here, we aimed to gain insight into the regulation of the subcellular localization and the nuclear–cytoplasmic shuttling of SANS and its paralog ANKS4B, not yet reported in the nucleus. We identified karyopherins mediating the nuclear import and export by screening the nuclear interactome of SANS. Sequence analyses predicted in silico evolutionarily conserved nuclear localization sequences (NLSs) and nuclear export sequences (NESs) in SANS, but only NESs in ANKS4B, which are suitable for karyopherin binding. Quantifying the nuclear–cytoplasmic localization of wild-type SANS and NLS/NES mutants, we experimentally confirmed in silico predicted NLS and NES functioning in the nuclear–cytoplasmic shuttling in situ in cells. The comparison of SANS and its paralog ANKS4B revealed substantial differences in the interaction with the nuclear splicing protein PRPF31 and in their nuclear localization. Finally, our results on pathogenic USH1G/SANS mutants suggest that the loss of NLSs and NESs and thereby the ability to control nuclear–cytoplasmic shuttling is disease-relevant. Full article

(This article belongs to the Section Cell Nuclei: Function, Transport and Receptors)

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19 pages, 6031 KiB

Open AccessArticle

GPS-pPLM: A Language Model for Prediction of Prokaryotic Phosphorylation Sites

by Chi Zhang, Dachao Tang, Cheng Han, Yujie Gou, Miaomiao Chen, Xinhe Huang, Dan Liu, Miaoying Zhao, Leming Xiao, Qiang Xiao, Di Peng and Yu Xue

Cells 2024, 13(22), 1854; https://doi.org/10.3390/cells13221854 - 8 Nov 2024

Abstract

In the prokaryotic kingdom, protein phosphorylation serves as one of the most important posttranslational modifications (PTMs) and is involved in orchestrating a broad spectrum of biological processes. Here, we report an updated online server named the group-based prediction system for prokaryotic phosphorylation language [...] Read more.

In the prokaryotic kingdom, protein phosphorylation serves as one of the most important posttranslational modifications (PTMs) and is involved in orchestrating a broad spectrum of biological processes. Here, we report an updated online server named the group-based prediction system for prokaryotic phosphorylation language model (GPS-pPLM), used for predicting phosphorylation sites (p-sites) in prokaryotes. For model training, two deep learning methods, a transformer and a deep neural network, were employed, and a total of 10 sequence features and contextual features were integrated. Using 44,839 nonredundant p-sites in 16,041 proteins from 95 prokaryotes, two general models for the prediction of O-phosphorylation and N-phosphorylation were first pretrained and then fine-tuned to construct 6 predictors specific for each phosphorylatable residue type as well as 134 species-specific predictors. Compared with other existing tools, the GPS-pPLM exhibits higher accuracy in predicting prokaryotic O-phosphorylation p-sites. Protein sequences in FASTA format or UniProt accession numbers can be submitted by users, and the predicted results are displayed in tabular form. In addition, we annotate the predicted p-sites with knowledge from 22 public resources, including experimental evidence, 3D structures, and disorder tendencies. The online service of the GPS-pPLM is freely accessible for academic research. Full article

(This article belongs to the Section Cell Methods)

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