1
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He W, Zhang J, Wen S, Li Y, Shen L, Zhou T, Wen Q, Fan Y. Epigenetic identification of LTBP4 as a putative tumor suppressor in breast cancer. Epigenomics 2024:1-14. [PMID: 39193795 DOI: 10.1080/17501911.2024.2388017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2024] [Accepted: 07/31/2024] [Indexed: 08/29/2024] Open
Abstract
Aim: To explore the LTBP4's expression, prognostic significance and molecular mechanism of action in breast cancer (BC).Methods: On the basis of omics datasets and experiments, we conducted a synthetical analysis of LTBP4 in BC.Results & conclusion: LTBP4 was downregulated in BC with high promoter methylation and low genetic alteration. DNA methylation was negatively associated with LTBP4 mRNA expression. Higher LTBP4 associated with better survival. LTBP4 was enrichment in extracellular matrix receptor interactions, cell adhesion molecules, cell cycle and MAPK pathway. LTBP4 expression and methylation were positively and negatively associated with tumor infiltrating immune cells, respectively. In conclusion, LTBP4 is a putative tumor suppressor in BC, which expression is regulated by DNA methylation and relates with prognosis.
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Affiliation(s)
- Wenfeng He
- Department of Oncology, The Affiliated Hospital of Southwest Medical University, 646000, Luzhou, PR China
| | - Jingheng Zhang
- Department of Oncology, The People's Hospital of Luzhou, 646000, Luzhou, PR China
| | - Siyuan Wen
- Faculty of Clinical Medicine, Southwest Medical University, 646000, Luzhou, PR China
| | - Ying Li
- Faculty of Clinical Medicine, Southwest Medical University, 646000, Luzhou, PR China
| | - Lin Shen
- Faculty of Clinical Medicine, Southwest Medical University, 646000, Luzhou, PR China
| | - Tiejun Zhou
- Department of Pathology, The Affiliated Hospital of Southwest Medical University, 646000, Luzhou, PR China
| | - Qinglian Wen
- Department of Oncology, The Affiliated Hospital of Southwest Medical University, 646000, Luzhou, PR China
| | - Yu Fan
- Department of Oncology, The Affiliated Hospital of Southwest Medical University, 646000, Luzhou, PR China
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2
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Xiong W, Zheng B, Liu D, Pu M, Zhou S, Deng Y. Quercetin inhibits endothelial & hepatocellular carcinoma cell crosstalk via reducing extracellular vesicle-mediated VEGFR2 mRNA transfer. Mol Carcinog 2024. [PMID: 39171838 DOI: 10.1002/mc.23807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 06/26/2024] [Accepted: 07/30/2024] [Indexed: 08/23/2024]
Abstract
This study aims to investigate the regulatory effects of quercetin extracellular vesicles (EVs)-mediated expression of vascular endothelial growth factor receptor 2 (VEGFR2) in hepatocellular carcinoma (HCC)-derived circulating tumor cells (CTCs) and the underlying mechanisms. CTCs were isolated from patients with pathologically diagnosed HCC, with VEGFR2 expression visualized by fluorescence in situ hybridization (FISH). The human HCC cell line Huh-7 and SK-HEP-1 were used for in vitro studies to assess EVs uptake, VEGFR2 mRNA transfer, invasion, migration, cancer stem cell (CSC) properties, and VEGF secretion. Results showed that VEGFR2 mRNA was commonly expressed in HCC-CTCs, with a higher incidence in biphenotypic CTCs. Its expression was limited in HCC cell lines, but present in certain liver cells. In vitro experiments confirmed that VEGFR2 mRNA could be transferred to HCC cells via EVs from primary tumor endothelial cells (PTECs), which was impaired by quercetin treatment. Quercetin significantly reduced VEGFR2 mRNA and protein expression in HCC cells, weakened their invasive and metastatic capacities, and diminished VEGFR2-mediated CSC properties. In vivo, quercetin reduced VEGF secretion, impaired angiogenesis, slowed tumor growth, and decreased the number and proportion of VEGFR2-positive CTCs. In summary, VEGFR2 mRNA is present in HCC-CTCs, potentially sourced from PTECs-derived EVs. Quercetin effectively inhibits VEGFR2 expression, impacting HCC cell invasion, metastasis, and CSC characteristics. Besides, it reduces VEGFR2-positive CTCs in vivo. These effects support its therapeutic potential in HCC treatment by targeting the angiogenesis and tumor dissemination pathway.
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Affiliation(s)
- Wei Xiong
- Department of Hepatobiliary Surgery, Sichuan Academy of Medical Science & Sichuan Provincial People's Hospital, Chengdu, Sichuan, China
| | - Bo Zheng
- Department of Hepatobiliary Surgery, Sichuan Academy of Medical Science & Sichuan Provincial People's Hospital, Chengdu, Sichuan, China
| | - Di Liu
- Cancer Center, Sichuan Academy of Medical Science & Sichuan Provincial People's Hospital, Chengdu, Sichuan, China
| | - Mo Pu
- Department of Hepatobiliary Surgery, Sichuan Academy of Medical Science & Sichuan Provincial People's Hospital, Chengdu, Sichuan, China
| | - Shijie Zhou
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Ying Deng
- Cancer Center, Sichuan Academy of Medical Science & Sichuan Provincial People's Hospital, Chengdu, Sichuan, China
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3
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Gatasheh MK. Identifying key genes against rutin on human colorectal cancer cells via ROS pathway by integrated bioinformatic analysis and experimental validation. Comput Biol Chem 2024; 112:108178. [PMID: 39191167 DOI: 10.1016/j.compbiolchem.2024.108178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 08/04/2024] [Accepted: 08/16/2024] [Indexed: 08/29/2024]
Abstract
Colorectal cancer (CRC) poses a significant global health challenge, characterized by substantial prevalence variations across regions. This study delves into the therapeutic potential of rutin, a polyphenol abundant in fruits, for treating CRC. The primary objectives encompass identifying molecular targets and pathways influenced by rutin through an integrated approach combining bioinformatic analysis and experimental validation. Employing Gene Set Enrichment Analysis (GSEA), the study focused on identifying potential differentially expressed genes (DEGs) associated with CRC, specifically those involved in regulating reactive oxygen species, metabolic reprogramming, cell cycle regulation, and apoptosis. Utilizing diverse databases such as GEO2R, CTD, and Gene Cards, the investigation revealed a set of 16 targets. A pharmacological network analysis was subsequently conducted using STITCH and Cytoscape, pinpointing six highly upregulated genes within the rutin network, including TP53, PCNA, CDK4, CCNEB1, CDKN1A, and LDHA. Gene Ontology (GO) analysis predicted functional categories, shedding light on rutin's potential impact on antioxidant properties. KEGG pathway analysis enriched crucial pathways like metabolic and ROS signaling pathways, HIF1a, and mTOR signaling. Diagnostic assessments were performed using UALCAN and GEPIA databases, evaluating mRNA expression levels and overall survival for the identified targets. Molecular docking studies confirmed robust binding associations between rutin and biomolecules such as TP53, PCNA, CDK4, CCNEB1, CDKN1A, and LDHA. Experimental validation included inhibiting colorectal cell HT-29 growth and promoting cell growth with NAC through MTT assay. Flow cytometric analysis also observed rutin-induced G1 phase arrest and cell death in HT-29 cells. RT-PCR demonstrated reduced expression levels of target biomolecules in HT-29 cells treated with rutin. This comprehensive study underscores rutin's potential as a promising therapeutic avenue for CRC, combining computational insights with robust experimental evidence to provide a holistic understanding of its efficacy.
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Affiliation(s)
- Mansour K Gatasheh
- Department of Biochemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia.
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4
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Wang S, Wang J, Liu C, Yang L, Tan X, Chen S, Xue Y, Ji H, Ge G, Chen J. Neoplastic ICAM-1 protects lung carcinoma from apoptosis through ligation of fibrinogen. Cell Death Dis 2024; 15:605. [PMID: 39168965 PMCID: PMC11339363 DOI: 10.1038/s41419-024-06989-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 08/05/2024] [Accepted: 08/08/2024] [Indexed: 08/23/2024]
Abstract
Intercellular cell adhesion molecule-1 (ICAM-1) is frequently overexpressed in non-small cell lung cancer (NSCLC) and associated with poor prognosis. However, the mechanism underlying the negative effects of neoplastic ICAM-1 remains obscure. Herein, we demonstrate that the survival of NSCLC cells but not normal human bronchial epithelial cells requires an anti-apoptosis signal triggered by fibrinogen γ chain (FGG)-ICAM-1 interaction. ICAM-1-FGG ligation preserves the tyrosine phosphorylation of ICAM-1 cytoplasmic domain and its association with SHP-2, and subsequently promotes Akt and ERK1/2 activation but suppresses JNK and p38 activation. Abolishing ICAM-1-FGG interaction induces NSCLC cell death by activating caspase-9/3 and significantly inhibits tumor development in a mouse xenograft model. Finally, we developed a monoclonal antibody against ICAM-1-FGG binding motif, which blocks ICAM-1‒FGG interaction and effectively suppresses NSCLC cell survival in vitro and tumor growth in vivo. Thus, suppressing ICAM-1-FGG axis provides a potential strategy for NSCLC targeted therapy.
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Affiliation(s)
- ShiHui Wang
- State Key Laboratory of Multi-Cell Systems, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China
| | - JunLei Wang
- State Key Laboratory of Multi-Cell Systems, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China
| | - Cui Liu
- State Key Laboratory of Multi-Cell Systems, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China
| | - Lei Yang
- State Key Laboratory of Multi-Cell Systems, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China
| | - XuanQian Tan
- State Key Laboratory of Multi-Cell Systems, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China
| | - ShiYang Chen
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China
| | - Yun Xue
- State Key Laboratory of Multi-Cell Systems, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China
| | - HongBin Ji
- State Key Laboratory of Multi-Cell Systems, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China
| | - GaoXiang Ge
- State Key Laboratory of Multi-Cell Systems, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China.
| | - JianFeng Chen
- State Key Laboratory of Multi-Cell Systems, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China.
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China.
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5
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Ward B, Pyr Dit Ruys S, Balligand JL, Belkhir L, Cani PD, Collet JF, De Greef J, Dewulf JP, Gatto L, Haufroid V, Jodogne S, Kabamba B, Lingurski M, Yombi JC, Vertommen D, Elens L. Deep Plasma Proteomics with Data-Independent Acquisition: Clinical Study Protocol Optimization with a COVID-19 Cohort. J Proteome Res 2024. [PMID: 39159935 DOI: 10.1021/acs.jproteome.4c00104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/21/2024]
Abstract
Plasma proteomics is a precious tool in human disease research but requires extensive sample preparation in order to perform in-depth analysis and biomarker discovery using traditional data-dependent acquisition (DDA). Here, we highlight the efficacy of combining moderate plasma prefractionation and data-independent acquisition (DIA) to significantly improve proteome coverage and depth while remaining cost-efficient. Using human plasma collected from a 20-patient COVID-19 cohort, our method utilizes commonly available solutions for depletion, sample preparation, and fractionation, followed by 3 liquid chromatography-mass spectrometry/MS (LC-MS/MS) injections for a 360 min total DIA run time. We detect 1321 proteins on average per patient and 2031 unique proteins across the cohort. Differential analysis further demonstrates the applicability of this method for plasma proteomic research and clinical biomarker identification, identifying hundreds of differentially abundant proteins at biological concentrations as low as 47 ng/L in human plasma. Data are available via ProteomeXchange with the identifier PXD047901. In summary, this study introduces a streamlined, cost-effective approach to deep plasma proteome analysis, expanding its utility beyond classical research environments and enabling larger-scale multiomics investigations in clinical settings. Our comparative analysis revealed that fractionation, whether the samples were pooled or separate postfractionation, significantly improved the number of proteins quantified. This underscores the value of fractionation in enhancing the depth of plasma proteome analysis, thereby offering a more comprehensive landscape for biomarker discovery in diseases such as COVID-19.
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Affiliation(s)
- Bradley Ward
- Integrated Pharmacometrics, Pharmacogenomics and Pharmacokinetics Group (PMGK), Louvain Drug Research Institute (LDRI), UCLouvain, Université Catholique de Louvain, 1200 Brussels, Belgium
| | - Sébastien Pyr Dit Ruys
- Integrated Pharmacometrics, Pharmacogenomics and Pharmacokinetics Group (PMGK), Louvain Drug Research Institute (LDRI), UCLouvain, Université Catholique de Louvain, 1200 Brussels, Belgium
| | - Jean-Luc Balligand
- Integrated Pharmacometrics, Pharmacogenomics and Pharmacokinetics Group (PMGK), Louvain Drug Research Institute (LDRI), UCLouvain, Université Catholique de Louvain, 1200 Brussels, Belgium
| | - Leïla Belkhir
- Integrated Pharmacometrics, Pharmacogenomics and Pharmacokinetics Group (PMGK), Louvain Drug Research Institute (LDRI), UCLouvain, Université Catholique de Louvain, 1200 Brussels, Belgium
| | - Patrice D Cani
- Integrated Pharmacometrics, Pharmacogenomics and Pharmacokinetics Group (PMGK), Louvain Drug Research Institute (LDRI), UCLouvain, Université Catholique de Louvain, 1200 Brussels, Belgium
| | - Jean-François Collet
- Integrated Pharmacometrics, Pharmacogenomics and Pharmacokinetics Group (PMGK), Louvain Drug Research Institute (LDRI), UCLouvain, Université Catholique de Louvain, 1200 Brussels, Belgium
| | - Julien De Greef
- Integrated Pharmacometrics, Pharmacogenomics and Pharmacokinetics Group (PMGK), Louvain Drug Research Institute (LDRI), UCLouvain, Université Catholique de Louvain, 1200 Brussels, Belgium
| | - Joseph P Dewulf
- Integrated Pharmacometrics, Pharmacogenomics and Pharmacokinetics Group (PMGK), Louvain Drug Research Institute (LDRI), UCLouvain, Université Catholique de Louvain, 1200 Brussels, Belgium
| | - Laurent Gatto
- Integrated Pharmacometrics, Pharmacogenomics and Pharmacokinetics Group (PMGK), Louvain Drug Research Institute (LDRI), UCLouvain, Université Catholique de Louvain, 1200 Brussels, Belgium
| | - Vincent Haufroid
- Integrated Pharmacometrics, Pharmacogenomics and Pharmacokinetics Group (PMGK), Louvain Drug Research Institute (LDRI), UCLouvain, Université Catholique de Louvain, 1200 Brussels, Belgium
| | - Sébastien Jodogne
- Integrated Pharmacometrics, Pharmacogenomics and Pharmacokinetics Group (PMGK), Louvain Drug Research Institute (LDRI), UCLouvain, Université Catholique de Louvain, 1200 Brussels, Belgium
| | - Benoît Kabamba
- Integrated Pharmacometrics, Pharmacogenomics and Pharmacokinetics Group (PMGK), Louvain Drug Research Institute (LDRI), UCLouvain, Université Catholique de Louvain, 1200 Brussels, Belgium
| | - Maxime Lingurski
- Integrated Pharmacometrics, Pharmacogenomics and Pharmacokinetics Group (PMGK), Louvain Drug Research Institute (LDRI), UCLouvain, Université Catholique de Louvain, 1200 Brussels, Belgium
| | - Jean Cyr Yombi
- Integrated Pharmacometrics, Pharmacogenomics and Pharmacokinetics Group (PMGK), Louvain Drug Research Institute (LDRI), UCLouvain, Université Catholique de Louvain, 1200 Brussels, Belgium
| | - Didier Vertommen
- Integrated Pharmacometrics, Pharmacogenomics and Pharmacokinetics Group (PMGK), Louvain Drug Research Institute (LDRI), UCLouvain, Université Catholique de Louvain, 1200 Brussels, Belgium
| | - Laure Elens
- Integrated Pharmacometrics, Pharmacogenomics and Pharmacokinetics Group (PMGK), Louvain Drug Research Institute (LDRI), UCLouvain, Université Catholique de Louvain, 1200 Brussels, Belgium
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6
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Acton S, O'Donnell MM, Periyasamy K, Dixit B, Eishingdrelo H, Hill C, Paul Ross R, Chesnel L. LPA3 agonist-producing Bacillus velezensis ADS024 is efficacious in multiple neuroinflammatory disease models. Brain Behav Immun 2024; 121:384-402. [PMID: 39147172 DOI: 10.1016/j.bbi.2024.08.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 08/08/2024] [Accepted: 08/10/2024] [Indexed: 08/17/2024] Open
Abstract
Neuroinflammation is a common component of neurological disorders. In the gut-brain-immune axis, bacteria and their metabolites are now thought to play a role in the modulation of the nervous and immune systems which may impact neuroinflammation. In this respect, commensal bacteria of humans have recently been shown to produce metabolites that mimic endogenous G-protein coupled receptor (GPCR) ligands. To date, it has not been established whether plant commensal bacteria, which may be ingested by animals including humans, can impact the gut-brain-immune axis via GPCR agonism. We screened an isopropanol (IPA) extract of the plant commensal Bacillus velezensis ADS024, a non-engrafting live biotherapeutic product (LBP) with anti-inflammatory properties isolated from human feces, against a panel of 168 GPCRs and identified strong agonism of the lysophosphatidic acid (LPA) receptor LPA3. The ADS024 IPA extracted material (ADS024-IPA) did not agonize LPA2, and only very weakly agonized LPA1. The agonism of LPA3 was inhibited by the reversible LPA1/3 antagonist Ki16425. ADS024-IPA signaled downstream of LPA3 through G-protein-induced calcium release, recruitment of β-arrestin, and recruitment of the neurodegeneration-associated proteins 14-3-3γ, ε and ζ but did not recruit the β isoform. Since LPA3 agonism was previously indirectly implicated in the reduction of pathology in models of Parkinson's disease (PD) and multiple sclerosis (MS) by use of the nonselective antagonist Ki16425, and since we identified an LPA3-specific agonist within ADS024, we sought to examine whether LPA3 might indeed be part of a broad underlying mechanism to control neuroinflammation. We tested oral treatment of ADS024 in multiple models of neuroinflammatory diseases using three models of PD, two models of MS, and a model each of amyotrophic lateral sclerosis (ALS), Huntington's disease (HD), and chemo-induced peripheral neuropathy (CIPN). ADS024 treatment improved model-specific functional effects including improvements in motor movement, breathing and swallowing, and allodynia suggesting that ADS024 treatment impacted a universal underlying neuroinflammatory mechanism regardless of the initiating cause of disease. We used the MOG-EAE mouse model to examine early events after disease initiation and found that ADS024 attenuated the increase in circulating lymphocytes and changes in neutrophil subtypes, and ADS024 attenuated the early loss of cell-surface LPA3 receptor expression on circulating white blood cells. ADS024 efficacy was partially inhibited by Ki16425 in vivo suggesting LPA3 may be part of its mechanism. Altogether, these data suggest that ADS024 and its LPA3 agonism activity should be investigated further as a possible treatment for diseases with a neuroinflammatory component.
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Affiliation(s)
| | | | | | | | | | - Colin Hill
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - R Paul Ross
- APC Microbiome Ireland, University College Cork, Cork, Ireland
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7
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Pir MS, Begar E, Yenisert F, Demirci HC, Korkmaz ME, Karaman A, Tsiropoulou S, Firat-Karalar EN, Blacque OE, Oner SS, Doluca O, Cevik S, Kaplan OI. CilioGenics: an integrated method and database for predicting novel ciliary genes. Nucleic Acids Res 2024; 52:8127-8145. [PMID: 38989623 DOI: 10.1093/nar/gkae554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 05/21/2024] [Accepted: 07/09/2024] [Indexed: 07/12/2024] Open
Abstract
Uncovering the full list of human ciliary genes holds enormous promise for the diagnosis of cilia-related human diseases, collectively known as ciliopathies. Currently, genetic diagnoses of many ciliopathies remain incomplete (1-3). While various independent approaches theoretically have the potential to reveal the entire list of ciliary genes, approximately 30% of the genes on the ciliary gene list still stand as ciliary candidates (4,5). These methods, however, have mainly relied on a single strategy to uncover ciliary candidate genes, making the categorization challenging due to variations in quality and distinct capabilities demonstrated by different methodologies. Here, we develop a method called CilioGenics that combines several methodologies (single-cell RNA sequencing, protein-protein interactions (PPIs), comparative genomics, transcription factor (TF) network analysis, and text mining) to predict the ciliary capacity of each human gene. Our combined approach provides a CilioGenics score for every human gene that represents the probability that it will become a ciliary gene. Compared to methods that rely on a single method, CilioGenics performs better in its capacity to predict ciliary genes. Our top 500 gene list includes 258 new ciliary candidates, with 31 validated experimentally by us and others. Users may explore the whole list of human genes and CilioGenics scores on the CilioGenics database (https://ciliogenics.com/).
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Affiliation(s)
- Mustafa S Pir
- Rare Disease Laboratory, School of Life and Natural Sciences, Abdullah Gul University, Kayseri, Turkiye
| | - Efe Begar
- Department of Molecular Biology and Genetics, Koc University, Istanbul 34450, Turkiye
| | - Ferhan Yenisert
- Rare Disease Laboratory, School of Life and Natural Sciences, Abdullah Gul University, Kayseri, Turkiye
| | - Hasan C Demirci
- Rare Disease Laboratory, School of Life and Natural Sciences, Abdullah Gul University, Kayseri, Turkiye
| | - Mustafa E Korkmaz
- Rare Disease Laboratory, School of Life and Natural Sciences, Abdullah Gul University, Kayseri, Turkiye
| | - Asli Karaman
- Istanbul Medeniyet University, Science and Advanced Technologies Research Center (BILTAM), 34700 Istanbul, Turkiye
| | - Sofia Tsiropoulou
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Elif Nur Firat-Karalar
- Department of Molecular Biology and Genetics, Koc University, Istanbul 34450, Turkiye
- School of Medicine, Koç University, Istanbul 34450, Turkiye
| | - Oliver E Blacque
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Sukru S Oner
- Istanbul Medeniyet University, Science and Advanced Technologies Research Center (BILTAM), 34700 Istanbul, Turkiye
- Goztepe Prof. Dr. Suleyman Yalcin City Hospital, Istanbul, Turkiye
| | - Osman Doluca
- Izmir University of Economics, Faculty of Engineering, Department of Biomedical Engineering, Izmir, Turkiye
| | - Sebiha Cevik
- Rare Disease Laboratory, School of Life and Natural Sciences, Abdullah Gul University, Kayseri, Turkiye
| | - Oktay I Kaplan
- Rare Disease Laboratory, School of Life and Natural Sciences, Abdullah Gul University, Kayseri, Turkiye
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8
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Ruixin S, Yifan L, Yansha S, Min Z, Yiwei D, Xiaoli H, Bizhi S, Hua J, Zonghai L. Dual targeting chimeric antigen receptor cells enhance antitumour activity by overcoming T cell exhaustion in pancreatic cancer. Br J Pharmacol 2024. [PMID: 39129178 DOI: 10.1111/bph.16505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 05/15/2024] [Accepted: 05/29/2024] [Indexed: 08/13/2024] Open
Abstract
BACKGROUND AND PURPOSE Although our previous data indicated that claudin 18 isoform 2 (CLDN18.2)-targeted chimeric antigen receptor (CAR) T cells displayed remarkable clinical efficacy in CLDN18.2-positive gastric cancer, their efficacy is limited in pancreatic ductal adenocarcinoma (PDAC). The tumour microenvironment (TME) is one of the main obstacles to the efficacy of CAR-T and remodelling the TME may be a possible way to overcome this obstacle. The TME of PDAC is characterized by abundant cancer-related fibroblasts (CAFs), which hinder the infiltration and function of CLDN18.2-targeted CAR-T cells. The expression of fibroblast activation protein alpha (FAP) is an important feature of active CAFs, providing potential targets for eliminating CAFs. EXPERIMENTAL APPROACH In this study, we generated 10 FAP/CLDN 18.2 dual-targeted CAR-T cells and evaluated their anti-tumour ability in vitro and in vivo. KEY RESULTS Compared with conventional CAR-T cells, some dual-targeted CAR-T cells showed improved therapeutic effects in mouse pancreatic cancers. Further, dual-targeted CAR-T cells with better anti-tumour effect could suppress the recruitment of myeloid-derived suppressor cells (MDSCs) to improve the immunosuppressive TME, which contributes to the survival of CD8+ T cells. Moreover, dual-targeted CAR-T cells reduced the exhaustion of T cells in transforming TGF-β dependent manner. CONCLUSION AND IMPLICATIONS The dual-targeted CAR-T cells obtained enhancement of T effector function, inhibition of T cell exhaustion, and improvement of tumour microenvironment. Our findings provide a theoretical rationale for dual-targeted FAP/CLDN 18.2 CAR-T cells therapy in PDAC.
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Affiliation(s)
- Sun Ruixin
- State Key Laboratory of Systems Medicine for Cancer, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
- Department of Laboratory Medicine, Shanghai Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Liu Yifan
- State Key Laboratory of Systems Medicine for Cancer, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Sun Yansha
- State Key Laboratory of Systems Medicine for Cancer, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Zhou Min
- State Key Laboratory of Systems Medicine for Cancer, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Dong Yiwei
- State Key Laboratory of Systems Medicine for Cancer, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Hu Xiaoli
- CARsgen Therapeutics, Shanghai, China
| | - Shi Bizhi
- State Key Laboratory of Systems Medicine for Cancer, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
- CARsgen Therapeutics, Shanghai, China
| | - Jiang Hua
- State Key Laboratory of Systems Medicine for Cancer, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
- CARsgen Therapeutics, Shanghai, China
| | - Li Zonghai
- State Key Laboratory of Systems Medicine for Cancer, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
- CARsgen Therapeutics, Shanghai, China
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9
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Zhang D, Liang P, Xia B, Wu J, Hu X. Comprehensive pan-cancer analysis of ZNF337 as a potential diagnostic, immunological, and prognostic biomarker. BMC Cancer 2024; 24:987. [PMID: 39123194 PMCID: PMC11313096 DOI: 10.1186/s12885-024-12703-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 07/25/2024] [Indexed: 08/12/2024] Open
Abstract
BACKGROUND Zinc Finger Protein 337 (ZNF337) is a novel Zinc Finger (ZNF) protein family member. However, the roles of ZNF337 in human cancers have not yet been investigated. METHODS In this study, with the aid of TCGA databases, GTEx databases, and online websites, we determined the expression levels of ZNF337 in pan-cancer and its potential value as a diagnostic and prognostic marker for pan-cancer and analyzed the relationship between ZNF337 expression and immune cell infiltration and immune checkpoint genes. We then focused our research on the potential of ZNF337 as a biomarker for diagnostic and prognostic in KIRC (kidney renal clear cell carcinoma) and validated in the E-MTAB-1980 database. Moreover, the expression of ZNF337 was detected through qRT-PCR and Western blotting (WB). CCK-8 experiment, colony formation experiment, and EDU experiment were performed to evaluate cell proliferation ability. Wound healing assay and transwell assay were used to analyze its migration ability. The qRT-PCR and WB were used to detect the expression of ZNF337 in tumor tissues and paracancerous tissues of KIRC patients. RESULTS The pan-cancer analysis revealed that abnormal ZNF337 expression was found in multiple human cancer types. ZNF337 had a high diagnostic value in pan-cancer and a significant association with the prognosis of certain cancers, indicating that ZNF337 may be a valuable prognostic biomarker for multiple cancers. Further analysis demonstrated that the expression level of ZNF337 displayed significant correlations with cancer-associated fibroblasts, immune cell infiltration, and immune checkpoint genes in many tumors. Additionally, ZNF337 was observed to have a high expression in KIRC. Its expression was significantly associated with poor prognosis [overall survival (OS), disease-specific survival (DSS)], age, TNM stage, histologic grade, and pathologic stage. The high ZNF337 expression was associated with poor prognosis in the E-MTAB-1980 validation cohort. The in vitro experiments suggested that the expression of ZNF337 in KIRC tumor tissues was higher than in adjacent tissues, and ZNF337 knockdown inhibited the proliferation and migration of KIRC cells, whereas overexpression of ZNF337 had the opposite effects. CONCLUSIONS ZNF337 might be an important prognostic and immunotherapeutic biomarker for pan-cancer, especially in KIRC.
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Affiliation(s)
- Dongxu Zhang
- Department of Urology, Beijing Chaoyang Hospital, Capital Medical University, NO. 8 Gongti South Road, Beijing, China
- Institute of Urology, Capital Medical University, Beijing, China
| | - Pu Liang
- Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, 100015, China
- Beijing Institute of Infectious Diseases, Beijing, 100015, China
- National Center for Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, 100015, China
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Beijing, 100015, China
| | - Bowen Xia
- Department of Urology, Beijing Chaoyang Hospital, Capital Medical University, NO. 8 Gongti South Road, Beijing, China
- Institute of Urology, Capital Medical University, Beijing, China
| | - Jitao Wu
- Department of Urology, Yantai Yuhuangding Hospital, Qingdao University, Yantai, Shandong, China
| | - Xiaopeng Hu
- Department of Urology, Beijing Chaoyang Hospital, Capital Medical University, NO. 8 Gongti South Road, Beijing, China.
- Institute of Urology, Capital Medical University, Beijing, China.
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10
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Üffing A, Weiergräber OH, Schwarten M, Hoffmann S, Willbold D. GABARAP interacts with EGFR - supporting the unique role of this hAtg8 protein during receptor trafficking. FEBS Lett 2024. [PMID: 39160442 DOI: 10.1002/1873-3468.14997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Revised: 07/02/2024] [Accepted: 07/24/2024] [Indexed: 08/21/2024]
Abstract
The human Atg8 family member GABARAP is involved in numerous autophagy-related and -unrelated processes. We recently observed that specifically the deficiency of GABARAP enhances epidermal growth factor receptor (EGFR) degradation upon ligand stimulation. Here, we report on two putative LC3-interacting regions (LIRs) within EGFR, the first of which (LIR1) is selected as a GABARAP binding site in silico. Indeed, in vitro interaction studies reveal preferential binding of LIR1 to GABARAP and GABARAPL1. Our X-ray data demonstrate interaction of core LIR1 residues FLPV with both hydrophobic pockets of GABARAP suggesting canonical binding. Although LIR1 occupies the LIR docking site, GABARAP Y49 and L50 appear dispensable in this case. Our data support the hypothesis that GABARAP affects the fate of EGFR at least in part through direct binding.
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Affiliation(s)
- Alina Üffing
- Heinrich-Heine-Universität Düsseldorf, Mathematisch-Naturwissenschaftliche Fakultät, Institut für Physikalische Biologie, Düsseldorf, Germany
- Forschungszentrum Jülich, Institut für Biologische Informationsprozesse: Strukturbiochemie (IBI-7), Jülich, Germany
| | - Oliver H Weiergräber
- Heinrich-Heine-Universität Düsseldorf, Mathematisch-Naturwissenschaftliche Fakultät, Institut für Physikalische Biologie, Düsseldorf, Germany
- Forschungszentrum Jülich, Institut für Biologische Informationsprozesse: Strukturbiochemie (IBI-7), Jülich, Germany
| | - Melanie Schwarten
- Forschungszentrum Jülich, Institut für Biologische Informationsprozesse: Strukturbiochemie (IBI-7), Jülich, Germany
| | - Silke Hoffmann
- Forschungszentrum Jülich, Institut für Biologische Informationsprozesse: Strukturbiochemie (IBI-7), Jülich, Germany
| | - Dieter Willbold
- Heinrich-Heine-Universität Düsseldorf, Mathematisch-Naturwissenschaftliche Fakultät, Institut für Physikalische Biologie, Düsseldorf, Germany
- Forschungszentrum Jülich, Institut für Biologische Informationsprozesse: Strukturbiochemie (IBI-7), Jülich, Germany
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11
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Rao P, Keyes MJ, Mi MY, Barber JL, Tahir UA, Deng S, Clish CB, Shen D, Farrell LA, Wilson JG, Gao Y, Yimer WK, Ekunwe L, Hall ME, Muntner PM, Guo X, Taylor KD, Tracy RP, Rich SS, Rotter JI, Xanthakis V, Vasan RS, Bouchard C, Sarzynski MA, Gerszten RE, Robbins JM. Plasma Proteomics of Exercise Blood Pressure and Incident Hypertension. JAMA Cardiol 2024; 9:713-722. [PMID: 38865108 PMCID: PMC11170454 DOI: 10.1001/jamacardio.2024.1397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 04/10/2024] [Indexed: 06/13/2024]
Abstract
Importance Blood pressure response during acute exercise (exercise blood pressure [EBP]) is associated with the future risk of hypertension and cardiovascular disease (CVD). Biochemical characterization of EBP could inform disease biology and identify novel biomarkers of future hypertension. Objective To identify protein markers associated with EBP and test their association with incident hypertension. Design, Setting, and Participants This study assayed 4977 plasma proteins in 681 healthy participants (from 763 assessed) of the Health, Risk Factors, Exercise Training and Genetics (HERITAGE; data collection from January 1993 to December 1997 and plasma proteomics from January 2019 to January 2020) Family Study at rest who underwent 2 cardiopulmonary exercise tests. Individuals were free of CVD at the time of recruitment. Individuals with resting SBP ≥160 mm Hg or DBP ≥100 mm Hg or taking antihypertensive drug therapy were excluded from the study. The association between resting plasma protein levels to both resting BP and EBP was evaluated. Proteins associated with EBP were analyzed for their association with incident hypertension in the Framingham Heart Study (FHS; n = 1177) and validated in the Jackson Heart Study (JHS; n = 772) and Multi-Ethnic Study of Atherosclerosis (MESA; n = 1367). Proteins associated with incident hypertension were tested for putative causal links in approximately 700 000 individuals using cis-protein quantitative loci mendelian randomization (cis-MR). Data were analyzed from January 2023 to January 2024. Exposures Plasma proteins. Main Outcomes and Measures EBP was defined as the BP response during a fixed workload (50 W) on a cycle ergometer. Hypertension was defined as BP ≥140/90 mm Hg or taking antihypertensive medication. Results Among the 681 participants in the HERITAGE Family Study, the mean (SD) age was 34 (13) years; 366 participants (54%) were female; 238 (35%) were self-reported Black and 443 (65%) were self-reported White. Proteomic profiling of EBP revealed 34 proteins that would not have otherwise been identified through profiling of resting BP alone. Transforming growth factor β receptor 3 (TGFBR3) and prostaglandin D2 synthase (PTGDS) had the strongest association with exercise systolic BP (SBP) and diastolic BP (DBP), respectively (TGFBR3: exercise SBP, β estimate, -3.39; 95% CI, -4.79 to -2.00; P = 2.33 × 10-6; PTGDS: exercise DBP β estimate, -2.50; 95% CI, -3.29 to -1.70; P = 1.18 × 10-9). In fully adjusted models, TGFBR3 was inversely associated with incident hypertension in FHS, JHS, and MESA (hazard ratio [HR]: FHS, 0.86; 95% CI, 0.75-0.97; P = .01; JHS, 0.87; 95% CI, 0.77-0.97; P = .02; MESA, 0.84; 95% CI, 0.71-0.98; P = .03; pooled cohort, 0.86; 95% CI, 0.79-0.92; P = 6 × 10-5). Using cis-MR, genetically predicted levels of TGFBR3 were associated with SBP, hypertension, and CVD events (SBP: β, -0.38; 95% CI, -0.64 to -0.11; P = .006; hypertension: odds ratio [OR], 0.99; 95% CI, 0.98-0.99; P < .001; heart failure with hypertension: OR, 0.86; 95% CI, 0.77-0.97; P = .01; CVD: OR, 0.84; 95% CI, 0.77-0.92; P = 8 × 10-5; cerebrovascular events: OR, 0.77; 95% CI, 0.70-0.85; P = 5 × 10-7). Conclusions and Relevance Plasma proteomic profiling of EBP identified a novel protein, TGFBR3, which may protect against elevated BP and long-term CVD outcomes.
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Affiliation(s)
- Prashant Rao
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts
- CardioVascular Institute, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | - Michelle. J. Keyes
- CardioVascular Institute, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | - Michael Y. Mi
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts
- CardioVascular Institute, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | - Jacob L. Barber
- CardioVascular Institute, Beth Israel Deaconess Medical Center, Boston, Massachusetts
- Department of Exercise Science, Arnold School of Public Health, University of South Carolina, Columbia
| | - Usman A. Tahir
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts
- CardioVascular Institute, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | - Shuliang Deng
- CardioVascular Institute, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | - Clary B. Clish
- Broad Institute of the Massachusetts Institute of Technology and Harvard, Cambridge
| | - Dongxiao Shen
- CardioVascular Institute, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | - Laurie. A. Farrell
- CardioVascular Institute, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | - James G. Wilson
- CardioVascular Institute, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | - Yan Gao
- Department of Data Sciences, University of Mississippi Medical Center, Jackson
| | - Wondwosen K. Yimer
- Department of Data Sciences, University of Mississippi Medical Center, Jackson
| | - Lynette Ekunwe
- Jackson Heart Study Field Center, University of Mississippi Medical Center, Jackson
| | - Michael E. Hall
- Department of Medicine, Division of Cardiology, University of Mississippi Medical Center, Jackson
| | - Paul M. Muntner
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham
| | - Xiuqing Guo
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, the Lundquist Institute for Biomedical Innovation at Harbor–University of California, Los Angeles Medical Center, Torrance
| | - Kent D. Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, the Lundquist Institute for Biomedical Innovation at Harbor–University of California, Los Angeles Medical Center, Torrance
| | - Russell P. Tracy
- Department of Pathology Laboratory Medicine, Larner College of Medicine, University of Vermont, Burlington
| | - Stephen S. Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville
| | - Jerome I. Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, the Lundquist Institute for Biomedical Innovation at Harbor–University of California, Los Angeles Medical Center, Torrance
| | - Vanessa Xanthakis
- Boston University’s and National Heart, Lung, and Blood Institute’s Framingham Heart Study, Framingham, Massachusetts
- Department of Medicine, Boston University School of Medicine, Boston, Massachusetts
| | - Ramachandran S. Vasan
- Boston University’s and National Heart, Lung, and Blood Institute’s Framingham Heart Study, Framingham, Massachusetts
- Department of Medicine, Boston University School of Medicine, Boston, Massachusetts
| | - Claude Bouchard
- Human Genomics Laboratory, Pennington Biomedical Research Center, Baton Rouge, Louisiana
| | - Mark A. Sarzynski
- Department of Exercise Science, Arnold School of Public Health, University of South Carolina, Columbia
| | - Robert E. Gerszten
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts
- CardioVascular Institute, Beth Israel Deaconess Medical Center, Boston, Massachusetts
- Broad Institute of the Massachusetts Institute of Technology and Harvard, Cambridge
| | - Jeremy M. Robbins
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts
- CardioVascular Institute, Beth Israel Deaconess Medical Center, Boston, Massachusetts
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12
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Cesnik A, Schaffer LV, Gaur I, Jain M, Ideker T, Lundberg E. Mapping the Multiscale Proteomic Organization of Cellular and Disease Phenotypes. Annu Rev Biomed Data Sci 2024; 7:369-389. [PMID: 38748859 PMCID: PMC11343683 DOI: 10.1146/annurev-biodatasci-102423-113534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/23/2024]
Abstract
While the primary sequences of human proteins have been cataloged for over a decade, determining how these are organized into a dynamic collection of multiprotein assemblies, with structures and functions spanning biological scales, is an ongoing venture. Systematic and data-driven analyses of these higher-order structures are emerging, facilitating the discovery and understanding of cellular phenotypes. At present, knowledge of protein localization and function has been primarily derived from manual annotation and curation in resources such as the Gene Ontology, which are biased toward richly annotated genes in the literature. Here, we envision a future powered by data-driven mapping of protein assemblies. These maps can capture and decode cellular functions through the integration of protein expression, localization, and interaction data across length scales and timescales. In this review, we focus on progress toward constructing integrated cell maps that accelerate the life sciences and translational research.
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Affiliation(s)
- Anthony Cesnik
- Department of Bioengineering, Stanford University, Stanford, California, USA;
| | - Leah V Schaffer
- Department of Medicine, University of California San Diego, La Jolla, California, USA;
| | - Ishan Gaur
- Department of Bioengineering, Stanford University, Stanford, California, USA;
| | - Mayank Jain
- Department of Medicine, University of California San Diego, La Jolla, California, USA;
| | - Trey Ideker
- Departments of Computer Science and Engineering and Bioengineering, University of California San Diego, La Jolla, California, USA
- Department of Medicine, University of California San Diego, La Jolla, California, USA;
| | - Emma Lundberg
- Chan Zuckerberg Biohub, San Francisco, California, USA
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
- Department of Pathology, Stanford University, Palo Alto, California, USA
- Department of Bioengineering, Stanford University, Stanford, California, USA;
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13
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Uribe C, Nery MF, Zavala K, Mardones GA, Riadi G, Opazo JC. Evolution of ion channels in cetaceans: a natural experiment in the tree of life. Sci Rep 2024; 14:17024. [PMID: 39043711 PMCID: PMC11266680 DOI: 10.1038/s41598-024-66082-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Accepted: 06/26/2024] [Indexed: 07/25/2024] Open
Abstract
Cetaceans represent a natural experiment within the tree of life in which a lineage changed from terrestrial to aquatic habitats. This shift involved phenotypic modifications, representing an opportunity to explore the genetic bases of phenotypic diversity. Among the different molecular systems that maintain cellular homeostasis, ion channels are crucial for the proper physiological functioning of all living species. This study aims to explore the evolution of ion channels during the evolutionary history of cetaceans. To do so, we created a bioinformatic pipeline to annotate the repertoire of ion channels in the genome of the species included in our sampling. Our main results show that cetaceans have, on average, fewer protein-coding genes and a higher percentage of annotated ion channels than non-cetacean mammals. Signals of positive selection were detected in ion channels related to the heart, locomotion, visual and neurological phenotypes. Interestingly, we predict that the NaV1.5 ion channel of most toothed whales (odontocetes) is sensitive to tetrodotoxin, similar to NaV1.7, given the presence of tyrosine instead of cysteine, in a specific position of the ion channel. Finally, the gene turnover rate of the cetacean crown group is more than three times faster than that of non-cetacean mammals.
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Affiliation(s)
- Cristóbal Uribe
- Department of Bioinformatics, Program in Sciences Mention Modeling of Chemical and Biological Systems, School of Bioinformatics Engineering, Center for Bioinformatics, Simulation and Modeling, CBSM, Faculty of Engineering, University of Talca, Campus Talca, Talca, Chile
| | - Mariana F Nery
- Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas-UNICAMP, Cidade Universitária, Campinas, Brazil
| | - Kattina Zavala
- Facultad de Medicina y Ciencia, Universidad San Sebastián, Valdivia, Chile
| | - Gonzalo A Mardones
- Facultad de Medicina y Ciencia, Universidad San Sebastián, Valdivia, Chile
- Integrative Biology Group, Valdivia, Chile
| | - Gonzalo Riadi
- Department of Bioinformatics, Center for Bioinformatics, Simulation and Modeling, Faculty of Engineering, CBSM, University of Talca, Talca, Chile.
- Millennium Nucleus of Ion Channel-Associated Diseases (MiNICAD), Valdivia, Chile.
| | - Juan C Opazo
- Facultad de Medicina y Ciencia, Universidad San Sebastián, Valdivia, Chile.
- Integrative Biology Group, Valdivia, Chile.
- Millennium Nucleus of Ion Channel-Associated Diseases (MiNICAD), Valdivia, Chile.
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14
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Wang Y, Muraleetharan A, Langiu M, Gregory KJ, Hellyer SD. SCA44- and SCAR13-associated GRM1 mutations affect metabotropic glutamate receptor 1 function through distinct mechanisms. Br J Pharmacol 2024. [PMID: 39030902 DOI: 10.1111/bph.16510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2024] [Revised: 05/09/2024] [Accepted: 06/18/2024] [Indexed: 07/22/2024] Open
Abstract
BACKGROUND AND PURPOSE Metabotropic glutamate receptor 1 (mGlu1) is a promising therapeutic target for neurodegenerative CNS disorders including spinocerebellar ataxias (SCAs). Clinical reports have identified naturally-occurring mGlu1 mutations in rare SCA subtypes and linked symptoms to mGlu1 mutations. However, how mutations alter mGlu1 function remains unknown, as does amenability of receptor function to pharmacological rescue. Here, we explored SCA-associated mutation effects on mGlu1 cell surface expression, canonical signal transduction and allosteric ligand pharmacology. EXPERIMENTAL APPROACH Orthosteric agonists, positive allosteric modulators (PAMs) and negative allosteric modulators (NAMs) were assessed at two functional endpoints (iCa2+ mobilisation and inositol 1-phosphate [IP1] accumulation) in FlpIn Trex HEK293A cell lines expressing five mutant mGlu1 subtypes. Key pharmacological parameters including ligand potency, affinity and cooperativity were derived using operational models of agonism and allostery. KEY RESULTS mGlu1 mutants exhibited differential impacts on mGlu1 expression, with a C-terminus truncation significantly reducing surface expression. Mutations differentially influenced orthosteric ligand affinity, efficacy and functional cooperativity between allosteric and orthosteric ligands. Loss-of-function mutations L454F and N885del reduced orthosteric affinity and efficacy, respectively. A gain-of-function Y792C mutant mGlu1 displayed enhanced constitutive activity in IP1 assays, which manifested as reduced orthosteric agonist activity. The mGlu1 PAMs restored glutamate potency in iCa2+ mobilisation for loss-of-function mutations and mGlu1 NAMs displayed enhanced inverse agonist activity at Y792C relative to wild-type mGlu1. CONCLUSION AND IMPLICATIONS Collectively, these data highlight distinct mechanisms by which mGlu1 mutations affect receptor function and show allosteric modulators may present a therapeutic strategy to restore aberrant mGlu1 function in rare SCA subtypes.
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Affiliation(s)
- Yuyang Wang
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
| | - Ashwin Muraleetharan
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
| | - Monica Langiu
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
| | - Karen J Gregory
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
- ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
| | - Shane D Hellyer
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
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15
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Hudák A, Pusztai D, Letoha A, Letoha T. Mutual Inhibition of Antithrombin III and SARS-CoV-2 Cellular Attachment to Syndecans: Implications for COVID-19 Treatment and Vaccination. Int J Mol Sci 2024; 25:7534. [PMID: 39062776 PMCID: PMC11277105 DOI: 10.3390/ijms25147534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2024] [Revised: 07/07/2024] [Accepted: 07/08/2024] [Indexed: 07/28/2024] Open
Abstract
Antithrombin III (ATIII) is a potent endogenous anticoagulant that binds to heparan sulfate proteoglycans (HSPGs) on endothelial cells' surfaces. Among these HSPGs, syndecans (SDCs) are crucial as transmembrane receptors bridging extracellular ligands with intracellular signaling pathways. Specifically, syndecan-4 (SDC4) has been identified as a key receptor on endothelial cells for transmitting the signaling effects of ATIII. Meanwhile, SDCs have been implicated in facilitating the cellular internalization of SARS-CoV-2. Given the complex interactions between ATIII and SDC4, our study analyzed the impact of ATIII on the virus entry into host cells. While ATIII binds to all SDC isoforms, it shows the strongest affinity for SDC4. SDCs' heparan sulfate chains primarily influence ATIII's SDC attachment, although other parts might also play a role in ATIII's dominant affinity toward SDC4. ATIII significantly reduces SARS-CoV-2's cellular entry into cell lines expressing SDCs, suggesting a competitive inhibition mechanism at the SDC binding sites, particularly SDC4. Conversely, the virus or its spike protein decreases the availability of SDCs on the cell surface, reducing ATIII's cellular attachment and hence contributing to a procoagulant environment characteristic of COVID-19.
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Affiliation(s)
- Anett Hudák
- Pharmacoidea Ltd., 6726 Szeged, Hungary; (A.H.); (D.P.)
| | - Dávid Pusztai
- Pharmacoidea Ltd., 6726 Szeged, Hungary; (A.H.); (D.P.)
| | - Annamária Letoha
- Department of Medicine, Albert Szent-Györgyi Clinical Center, Faculty of Medicine, University of Szeged, 6720 Szeged, Hungary;
| | - Tamás Letoha
- Pharmacoidea Ltd., 6726 Szeged, Hungary; (A.H.); (D.P.)
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16
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Wang X, Zhang Y, Li Z, Duan Z, Guo M, Wang Z, Zhu F, Xue W. PROSCA: an online platform for humanized scaffold mining facilitating rational protein engineering. Nucleic Acids Res 2024; 52:W272-W279. [PMID: 38738624 PMCID: PMC11223824 DOI: 10.1093/nar/gkae384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 04/23/2024] [Accepted: 04/29/2024] [Indexed: 05/14/2024] Open
Abstract
Protein scaffolds with small size, high stability and low immunogenicity show important applications in the field of protein engineering and design. However, no relevant computational platform has been reported yet to mining such scaffolds with the desired properties from massive protein structures in human body. Here, we developed PROSCA, a structure-based online platform dedicated to explore the space of the entire human proteome, and to discovery new privileged protein scaffolds with potential engineering value that have never been noticed. PROSCA accepts structure of protein as an input, which can be subsequently aligned with a certain class of protein structures (e.g. the human proteome either from experientially resolved or AlphaFold2 predicted structures, and the human proteins belonging to specific families or domains), and outputs humanized protein scaffolds which are structurally similar with the input protein as well as other related important information such as families, sequences, structures and expression level in human tissues. Through PROSCA, the user can also get excellent experience in visualizations of protein structures and expression overviews, and download the figures and tables of results which can be customized according to the user's needs. Along with the advanced protein engineering and selection technologies, PROSCA will facilitate the rational design of new functional proteins with privileged scaffolds. PROSCA is freely available at https://idrblab.org/prosca/.
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Affiliation(s)
- Xiaona Wang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
- Department of Intensive Care Medicine, Army Medical Center of PLA, Chongqing 401331, China
| | - Yintao Zhang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Zengpeng Li
- State Key Laboratory Breeding Base of Marine Genetic Resources, Third Institute of Oceanography Ministry of Natural Resources, Xiamen 361005, China
| | - Zixin Duan
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Menghan Guo
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Zhen Wang
- Department of Intensive Care Medicine, Army Medical Center of PLA, Chongqing 401331, China
| | - Feng Zhu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Weiwei Xue
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
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17
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Qiao Y, Chen Z, Li W, Li H, Zhou L. Clinical significance of TROAP in endometrial cancer and the antiproliferative and proapoptotic effects of TROAP knockdown in endometrial cancer cells: integrated utilization of bioinformatic analysis and in vitro test verification. NAUNYN-SCHMIEDEBERG'S ARCHIVES OF PHARMACOLOGY 2024:10.1007/s00210-024-03260-y. [PMID: 38967825 DOI: 10.1007/s00210-024-03260-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 06/24/2024] [Indexed: 07/06/2024]
Abstract
Trophinin-associated protein (TROAP), a cytoplasmic protein essential for spindle assembly and centrosome integrity during mitosis, has been reported to serve as an oncogene in various tumors. However, its role in endometrial cancer (EC) progression is still undefined. TROAP expression in EC was analyzed via GEPIA and HPA databases. The diagnostic and prognostic values of TROAP were examined by ROC curve analysis and Kaplan-Meier plotter, respectively. Cell proliferation was evaluated using CCK-8 and EdU incorporation assays. Apoptosis was assessed using TUNEL and flow cytometry assays. GSEA was performed to explore TROAP-related pathways in EC. Expression of TROAP, proliferating cell nuclear antigen (PCNA), Ki-67, cleaved-caspase-3 (cl-caspase-3), caspase-3, active β-catenin, and total β-catenin was detected using western blot analysis. TROAP was upregulated in EC. TROAP served as a potential diagnostic and prognostic marker in EC patients. TROAP silencing suppressed proliferation and enhanced apoptosis in EC cells. GSEA revealed that EC and Wnt signaling pathways were related to the expression of TROAP. We further demonstrated that TROAP knockout repressed the Wnt/β-catenin pathway in EC cells. Moreover, SKL2001, a Wnt/β-catenin activator, partially abrogated the effects of TROAP silencing on EC cell proliferation and apoptosis, while the signaling inhibitor XAV-939 had the opposite effect. In conclusion, TROAP knockout retarded proliferation and elicited apoptosis in EC cells by blocking the Wnt/β-catenin pathway.
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Affiliation(s)
- Yan Qiao
- Department of Radiation Oncology, Huai'an Hospital Affiliated to Xuzhou Medical University, Huai'an, 223001, China
| | - Zheng Chen
- Department of Radiation Oncology, Huai'an Hospital Affiliated to Xuzhou Medical University, Huai'an, 223001, China
| | - Wei Li
- Department of Radiation Oncology, Huai'an Hospital Affiliated to Xuzhou Medical University, Huai'an, 223001, China
| | - Hongliang Li
- Department of Radiation Oncology, Huai'an Hospital Affiliated to Xuzhou Medical University, Huai'an, 223001, China
| | - Liqing Zhou
- Department of Radiation Oncology, Huai'an Hospital Affiliated to Xuzhou Medical University, Huai'an, 223001, China.
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Zhang S, Jiang Z, Wang P, Jiang W, Ding W, Zhong L. TCBIR/CD320: a potential therapeutic target upregulated in endothelial cells and associated with immune cell infiltration in liver hepatocellular carcinoma. Discov Oncol 2024; 15:255. [PMID: 38955924 PMCID: PMC11219609 DOI: 10.1007/s12672-024-01122-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Accepted: 06/25/2024] [Indexed: 07/04/2024] Open
Abstract
CD320, which is a transmembrane protein responsible for facilitating the absorption of vitamin B12, plays a key role in this process. However, the relationships between CD320 and immune cell infiltration levels remain unclear, with limited studies investigating the diagnostic and prognostic significance of CD320 in hepatocellular carcinoma. We used various databases, including the TIMER, GEPIA, UALCAN and TCGA databases to investigate the expression levels of CD320 in hepatocellular carcinoma. Subsequently, we analyzed the prognosis of hepatocellular carcinoma patients with different expression levels of CD320. Furthermore, we also performed Western blot, immunohistochemistry, and immunofluorescence analyses to validate the results of the database analysis. Finally, the functions of CD320 in hepatocellular carcinoma were also confirmed via relevant cell experiments and angiogenesis assays. We found that CD320 expression was significantly upregulated in tumor vascular endothelial cells. Moreover, the knockdown of CD320 led to a reduction in angiogenesis in endothelial cells. Increased expression of CD320 was also correlated with a poor prognosis in patients with hepatocellular carcinoma, which suggested that CD320 may be a potential prognostic marker. Finally, TIMER analysis demonstrated that the infiltration of six immune cell types was significantly associated with high expression levels of CD320 in hepatocellular carcinoma. Herein, we demonstrated that CD320 may play an important role in angiogenesis in hepatocellular carcinoma. These findings suggested that CD320 may be a potential clinical prognostic marker and immunotherapy target for hepatocellular carcinoma.
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Affiliation(s)
- Shubin Zhang
- Department of Hepatobiliary & Pancreatic Surgery, The First Affiliated Hospital of Shandong Second Medical University, School of Clinical Medicine, Weifang People's Hospital, Shandong Second Medical University, No. 151 Guangwen Street, Weifang, 261041, Shandong, China
- Department of General Surgery, The Third People's Hospital of Shenzhen, The Second Hospital Affiliated of Southern University of Science and Technology, Guangdong, China
- Department of General Surgery, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhongyi Jiang
- Department of Hepatobiliary & Pancreatic Surgery, The First Affiliated Hospital of Shandong Second Medical University, School of Clinical Medicine, Weifang People's Hospital, Shandong Second Medical University, No. 151 Guangwen Street, Weifang, 261041, Shandong, China
- Department of General Surgery, The Third People's Hospital of Shenzhen, The Second Hospital Affiliated of Southern University of Science and Technology, Guangdong, China
- Department of General Surgery, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Pusen Wang
- Department of Hepatobiliary & Pancreatic Surgery, The First Affiliated Hospital of Shandong Second Medical University, School of Clinical Medicine, Weifang People's Hospital, Shandong Second Medical University, No. 151 Guangwen Street, Weifang, 261041, Shandong, China
- Department of General Surgery, The Third People's Hospital of Shenzhen, The Second Hospital Affiliated of Southern University of Science and Technology, Guangdong, China
- Department of General Surgery, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Weihao Jiang
- Department of General Surgery, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wei Ding
- Department of Hepatobiliary & Pancreatic Surgery, The First Affiliated Hospital of Shandong Second Medical University, School of Clinical Medicine, Weifang People's Hospital, Shandong Second Medical University, No. 151 Guangwen Street, Weifang, 261041, Shandong, China.
| | - Lin Zhong
- Department of Hepatobiliary & Pancreatic Surgery, The First Affiliated Hospital of Shandong Second Medical University, School of Clinical Medicine, Weifang People's Hospital, Shandong Second Medical University, No. 151 Guangwen Street, Weifang, 261041, Shandong, China.
- Department of General Surgery, The Third People's Hospital of Shenzhen, The Second Hospital Affiliated of Southern University of Science and Technology, Guangdong, China.
- Department of General Surgery, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
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Badhwar A, Hirschberg Y, Valle‐Tamayo N, Iulita MF, Udeh‐Momoh CT, Matton A, Tarawneh RM, Rissman RA, Ledreux A, Winston CN, Haqqani AS. Assessment of brain-derived extracellular vesicle enrichment for blood biomarker analysis in age-related neurodegenerative diseases: An international overview. Alzheimers Dement 2024; 20:4411-4422. [PMID: 38864416 PMCID: PMC11247682 DOI: 10.1002/alz.13823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 02/09/2024] [Accepted: 02/17/2024] [Indexed: 06/13/2024]
Abstract
INTRODUCTION Brain-derived extracellular vesicles (BEVs) in blood allows for minimally-invasive investigations of central nervous system (CNS) -specific markers of age-related neurodegenerative diseases (NDDs). Polymer-based EV- and immunoprecipitation (IP)-based BEV-enrichment protocols from blood have gained popularity. We systematically investigated protocol consistency across studies, and determined CNS-specificity of proteins associated with these protocols. METHODS NDD articles investigating BEVs in blood using polymer-based and/or IP-based BEV enrichment protocols were systematically identified, and protocols compared. Proteins used for BEV-enrichment and/or post-enrichment were assessed for CNS- and brain-cell-type-specificity, extracellular domains (ECD+), and presence in EV-databases. RESULTS A total of 82.1% of studies used polymer-based (ExoQuick) EV-enrichment, and 92.3% used L1CAM for IP-based BEV-enrichment. Centrifugation times differed across studies. A total of 26.8% of 82 proteins systematically identified were CNS-specific: 50% ECD+, 77.3% were listed in EV-databases. CONCLUSIONS We identified protocol steps requiring standardization, and recommend additional CNS-specific proteins that can be used for BEV-enrichment or as BEV-biomarkers. HIGHLIGHTS Across NDDs, we identified protocols commonly used for EV/BEV enrichment from blood. We identified protocol steps showing variability that require harmonization. We assessed CNS-specificity of proteins used for BEV-enrichment or found in BEV cargo. CNS-specific EV proteins with ECD+ or without were identified. We recommend evaluation of blood-BEV enrichment using these additional ECD+ proteins.
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Affiliation(s)
- AmanPreet Badhwar
- Département de pharmacologie et physiologieInstitut de Génie BiomédicalFaculté de Médecine, Université de MontréalMontréalQuebecCanada
- Multiomics Investigation of Neurodegenerative Diseases (MIND) lab, Centre de recherche de l'Institut Universitaire de GériatrieMontréalQuebecCanada
| | - Yael Hirschberg
- Centre for ProteomicsUniversity of AntwerpAntwerpBelgium
- Health Unit, Flemish Institute for Technological Research (VITO)MolBelgium
| | - Natalia Valle‐Tamayo
- Sant Pau Memory Unit, Department of NeurologyHospital de la Santa Creu i Sant Pau, Biomedical Research Institute Sant PauCalle San QuintíBarcelonaSpain
| | - M. Florencia Iulita
- Sant Pau Memory Unit, Department of NeurologyHospital de la Santa Creu i Sant Pau, Biomedical Research Institute Sant PauCalle San QuintíBarcelonaSpain
| | - Chinedu T. Udeh‐Momoh
- Ageing Epidemiology research unit, School of Public Health, Imperial College LondonLondonUK
- Division of Clinical GeriatricsDepartment of NeurobiologyCare Sciences and Society, Center for Alzheimer Research, Karolinska InstitutetSolnaSweden
- Global Brain Health InstituteUniversity of San Francisco Joan and Sanford I. Weill Neurosciences buildingSan FranciscoCaliforniaUSA
- Imarisha Centre for Brain Health and AgingBrain and Mind InstituteAga Khan UniversityNairobiKenya
| | - Anna Matton
- Ageing Epidemiology research unit, School of Public Health, Imperial College LondonLondonUK
- Division of Clinical GeriatricsDepartment of NeurobiologyCare Sciences and Society, Center for Alzheimer Research, Karolinska InstitutetSolnaSweden
- Division of NeurogeriatricsDepartment of Neurobiology, Care Sciences and SocietyCenter for Alzheimer Research, Karolinska Institutet, SolnaNobels vägSweden
| | - Rawan M. Tarawneh
- Department of NeurologyCenter for Memory and AgingUniversity of New MexicoAlbuquerqueNew MexicoUSA
| | - Robert A. Rissman
- VA San Diego Healthcare SystemSan DiegoCaliforniaUSA
- Department of Physiology and NeuroscienceAlzheimer's Therapeutic Research InstituteKeck School of Medicine of the University of Southern CaliforniaSan DiegoCaliforniaUSA
| | - Aurélie Ledreux
- Department of NeurosurgerySchool of MedicineUniversity of Colorado Anschutz Medical CampusAuroraColoradoUSA
| | - Charisse N. Winston
- Department of Physiology and NeuroscienceAlzheimer's Therapeutic Research InstituteKeck School of Medicine of the University of Southern CaliforniaSan DiegoCaliforniaUSA
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20
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Paquette A, Ahuna K, Hwang YM, Pearl J, Liao H, Shannon P, Kadam L, Lapehn S, Bucher M, Roper R, Funk C, MacDonald J, Bammler T, Baloni P, Brockway H, Mason WA, Bush N, Lewinn KZ, Karr CJ, Stamatoyannopoulos J, Muglia LJ, Jones H, Sadovsky Y, Myatt L, Sathyanarayana S, Price ND. A genome scale transcriptional regulatory model of the human placenta. SCIENCE ADVANCES 2024; 10:eadf3411. [PMID: 38941464 PMCID: PMC11212735 DOI: 10.1126/sciadv.adf3411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 05/28/2024] [Indexed: 06/30/2024]
Abstract
Gene regulation is essential to placental function and fetal development. We built a genome-scale transcriptional regulatory network (TRN) of the human placenta using digital genomic footprinting and transcriptomic data. We integrated 475 transcriptomes and 12 DNase hypersensitivity datasets from placental samples to globally and quantitatively map transcription factor (TF)-target gene interactions. In an independent dataset, the TRN model predicted target gene expression with an out-of-sample R2 greater than 0.25 for 73% of target genes. We performed siRNA knockdowns of four TFs and achieved concordance between the predicted gene targets in our TRN and differences in expression of knockdowns with an accuracy of >0.7 for three of the four TFs. Our final model contained 113,158 interactions across 391 TFs and 7712 target genes and is publicly available. We identified 29 TFs which were significantly enriched as regulators for genes previously associated with preterm birth, and eight of these TFs were decreased in preterm placentas.
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Affiliation(s)
- Alison Paquette
- University of Washington, Seattle, WA, USA
- Seattle Children’s Research Institute, Seattle, WA, USA
| | - Kylia Ahuna
- Oregon Health and Sciences University, Portland, OR, USA
| | | | | | - Hanna Liao
- University of Washington, Seattle, WA, USA
| | | | - Leena Kadam
- Oregon Health and Sciences University, Portland, OR, USA
| | | | - Matthew Bucher
- Oregon Health and Sciences University, Portland, OR, USA
| | - Ryan Roper
- Institute for Systems Biology, Seattle, WA, USA
| | - Cory Funk
- Institute for Systems Biology, Seattle, WA, USA
| | | | | | | | - Heather Brockway
- Department of Physiology and Aging, University of Florida, Gainesville, FL, USA
| | - W. Alex Mason
- University of Tennessee Health Sciences Center, Memphis, TN, USA
| | - Nicole Bush
- University of California San Francisco, San Francisco, CA, USA
| | - Kaja Z. Lewinn
- University of California San Francisco, San Francisco, CA, USA
| | | | | | - Louis J. Muglia
- The Burroughs Wellcome Fund, Research Triangle Park, NC, USA
- Cincinnati Children’s Hospital Medical Center and Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | | | - Yoel Sadovsky
- Magee Womens Research Institute, Pittsburgh, PA, USA
- University of Pittsburgh, Pittsburgh, PA, USA
| | - Leslie Myatt
- Oregon Health and Sciences University, Portland, OR, USA
| | - Sheela Sathyanarayana
- University of Washington, Seattle, WA, USA
- Seattle Children’s Research Institute, Seattle, WA, USA
| | - Nathan D. Price
- Institute for Systems Biology, Seattle, WA, USA
- Thorne HealthTech, New York City, NY, USA
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21
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Al-Odat OS, Nelson E, Budak-Alpdogan T, Jonnalagadda SC, Desai D, Pandey MK. Discovering Potential in Non-Cancer Medications: A Promising Breakthrough for Multiple Myeloma Patients. Cancers (Basel) 2024; 16:2381. [PMID: 39001443 PMCID: PMC11240591 DOI: 10.3390/cancers16132381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Revised: 06/20/2024] [Accepted: 06/24/2024] [Indexed: 07/16/2024] Open
Abstract
MM is a common type of cancer that unfortunately leads to a significant number of deaths each year. The majority of the reported MM cases are detected in the advanced stages, posing significant challenges for treatment. Additionally, all MM patients eventually develop resistance or experience relapse; therefore, advances in treatment are needed. However, developing new anti-cancer drugs, especially for MM, requires significant financial investment and a lengthy development process. The study of drug repurposing involves exploring the potential of existing drugs for new therapeutic uses. This can significantly reduce both time and costs, which are typically a major concern for MM patients. The utilization of pre-existing non-cancer drugs for various myeloma treatments presents a highly efficient and cost-effective strategy, considering their prior preclinical and clinical development. The drugs have shown promising potential in targeting key pathways associated with MM progression and resistance. Thalidomide exemplifies the success that can be achieved through this strategy. This review delves into the current trends, the challenges faced by conventional therapies for MM, and the importance of repurposing drugs for MM. This review highlights a noncomprehensive list of conventional therapies that have potentially significant anti-myeloma properties and anti-neoplastic effects. Additionally, we offer valuable insights into the resources that can help streamline and accelerate drug repurposing efforts in the field of MM.
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Affiliation(s)
- Omar S. Al-Odat
- Department of Biomedical Sciences, Cooper Medical School of Rowan University, Camden, NJ 08103, USA; (O.S.A.-O.); (E.N.)
- Department of Chemistry and Biochemistry, Rowan University, Glassboro, NJ 08028, USA;
| | - Emily Nelson
- Department of Biomedical Sciences, Cooper Medical School of Rowan University, Camden, NJ 08103, USA; (O.S.A.-O.); (E.N.)
- Department of Chemistry and Biochemistry, Rowan University, Glassboro, NJ 08028, USA;
| | | | | | - Dhimant Desai
- Department of Pharmacology, Penn State Neuroscience Institute, Penn State College of Medicine, Hershey, PA 17033, USA;
| | - Manoj K. Pandey
- Department of Biomedical Sciences, Cooper Medical School of Rowan University, Camden, NJ 08103, USA; (O.S.A.-O.); (E.N.)
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Jaatinen K, Shah P, Mazhari R, Hayden Z, Wargowsky R, Jepson T, Toma I, Perkins J, McCaffrey TA. RNAseq of INOCA patients identifies innate, invariant, and acquired immune changes: potential autoimmune microvascular dysfunction. Front Cardiovasc Med 2024; 11:1385457. [PMID: 38978787 PMCID: PMC11228317 DOI: 10.3389/fcvm.2024.1385457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 05/31/2024] [Indexed: 07/10/2024] Open
Abstract
Background Ischemia with non-obstructive coronary arteries (INOCA) is a major clinical entity that involves potentially 20%-30% of patients with chest pain. INOCA is typically attributed either to coronary microvascular disease and/or vasospasm, but is likely distinct from classical coronary artery disease (CAD). Objectives To gain insights into the etiology of INOCA and CAD, RNA sequencing of whole blood from patients undergoing both stress testing and elective invasive coronary angiography (ICA) was conducted. Methods Stress testing and ICA of 177 patients identified 40 patients (23%) with INOCA compared to 39 controls (stress-, ICA-). ICA+ patients divided into 38 stress- and 60 stress+. RNAseq was performed by Illumina with ribosomal RNA depletion. Transcriptome changes were analyzed by DeSeq2 and curated by manual and automated methods. Results Differentially expressed genes for INOCA were associated with elevated levels of transcripts related to mucosal-associated invariant T (MAIT) cells, plasmacytoid dendritic cells (pcDC), and memory B cells, and were associated with autoimmune diseases such as rheumatoid arthritis. Decreased transcripts were associated with neutrophils, but neutrophil transcripts, per se, were not less abundant in INOCA. CAD transcripts were more related to T cell functions. Conclusions Elevated transcripts related to pcDC, MAIT, and memory B cells suggest an autoimmune component to INOCA. Reduced neutrophil transcripts are likely attributed to chronic activation leading to increased translation and degradation. Thus, INOCA could result from stimulation of B cell, pcDC, invariant T cell, and neutrophil activation that compromises cardiac microvascular function.
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Affiliation(s)
- Kevin Jaatinen
- Department of Medicine, Division of Genomic Medicine, The George Washington University, Washington, DC, United States
| | - Palak Shah
- INOVA Heart and Vascular Institute, Fairfax, VA, United States
| | - Ramesh Mazhari
- Department of Medicine, Division of Cardiology, The George Washington University, Washington, DC, United States
| | - Zane Hayden
- Department of Medicine, Division of Genomic Medicine, The George Washington University, Washington, DC, United States
| | - Richard Wargowsky
- Department of Medicine, Division of Genomic Medicine, The George Washington University, Washington, DC, United States
| | - Tisha Jepson
- Department of Medicine, Division of Genomic Medicine, The George Washington University, Washington, DC, United States
- The St. Laurent Institute, Woburn, MA, United States
- True Bearing Diagnostics, Washington, DC, United States
| | - Ian Toma
- Department of Medicine, Division of Genomic Medicine, The George Washington University, Washington, DC, United States
- Department of Clinical Research and Leadership, The George Washington University, Washington, DC, United States
| | - John Perkins
- Department of Medicine, Division of Genomic Medicine, The George Washington University, Washington, DC, United States
| | - Timothy A. McCaffrey
- Department of Medicine, Division of Genomic Medicine, The George Washington University, Washington, DC, United States
- True Bearing Diagnostics, Washington, DC, United States
- Department of Microbiology, Immunology, and Tropical Medicine, The George Washington University, Washington, DC, United States
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Park C, Weerakkody JS, Schneider R, Miao S, Pitt D. CNS cell-derived exosome signatures as blood-based biomarkers of neurodegenerative diseases. Front Neurosci 2024; 18:1426700. [PMID: 38966760 PMCID: PMC11222337 DOI: 10.3389/fnins.2024.1426700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Accepted: 06/07/2024] [Indexed: 07/06/2024] Open
Abstract
Molecular biomarkers require the reproducible capture of disease-associated changes and are ideally sensitive, specific and accessible with minimal invasiveness to patients. Exosomes are a subtype of extracellular vesicles that have gained attention as potential biomarkers. They are released by all cell types and carry molecular cargo that reflects the functional state of the cells of origin. These characteristics make them an attractive means of measuring disease-related processes within the central nervous system (CNS), as they cross the blood-brain barrier (BBB) and can be captured in peripheral blood. In this review, we discuss recent progress made toward identifying blood-based protein and RNA biomarkers of several neurodegenerative diseases from circulating, CNS cell-derived exosomes. Given the lack of standardized methodology for exosome isolation and characterization, we discuss the challenges of capturing and quantifying the molecular content of exosome populations from blood for translation to clinical use.
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Affiliation(s)
- Calvin Park
- Columbia University Irving Medical Center, Columbia University, New York, NY, United States
| | | | | | - Sheng Miao
- Yale School of Medicine, Yale University, New Haven, CT, United States
| | - David Pitt
- Yale School of Medicine, Yale University, New Haven, CT, United States
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24
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Xie J, Chen Y, Luo S, Yang W, Lin Y, Wang L, Ding X, Tong M, Yu R. Tracing unknown tumor origins with a biological-pathway-based transformer model. CELL REPORTS METHODS 2024; 4:100797. [PMID: 38889685 PMCID: PMC11228371 DOI: 10.1016/j.crmeth.2024.100797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 02/01/2024] [Accepted: 05/21/2024] [Indexed: 06/20/2024]
Abstract
Cancer of unknown primary (CUP) represents metastatic cancer where the primary site remains unidentified despite standard diagnostic procedures. To determine the tumor origin in such cases, we developed BPformer, a deep learning method integrating the transformer model with prior knowledge of biological pathways. Trained on transcriptomes from 10,410 primary tumors across 32 cancer types, BPformer achieved remarkable accuracy rates of 94%, 92%, and 89% in primary tumors and primary and metastatic sites of metastatic tumors, respectively, surpassing existing methods. Additionally, BPformer was validated in a retrospective study, demonstrating consistency with tumor sites diagnosed through immunohistochemistry and histopathology. Furthermore, BPformer was able to rank pathways based on their contribution to tumor origin identification, which helped to classify oncogenic signaling pathways into those that are highly conservative among different cancers versus those that are highly variable depending on their origins.
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Affiliation(s)
- Jiajing Xie
- National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, Fujian 361102, China
| | - Ying Chen
- School of Informatics, Xiamen University, Xiamen, Fujian 361005, China
| | - Shijie Luo
- National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, Fujian 361102, China
| | - Wenxian Yang
- Aginome Scientific, Xiamen, Fujian 361005, China
| | - Yuxiang Lin
- National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, Fujian 361102, China
| | - Liansheng Wang
- National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, Fujian 361102, China; School of Informatics, Xiamen University, Xiamen, Fujian 361005, China
| | - Xin Ding
- Department of Pathology, Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian 361004, China.
| | - Mengsha Tong
- National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, Fujian 361102, China; State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian 361102, China.
| | - Rongshan Yu
- National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, Fujian 361102, China; School of Informatics, Xiamen University, Xiamen, Fujian 361005, China; Aginome Scientific, Xiamen, Fujian 361005, China.
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25
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Dai P, Zou M, Cai Z, Zeng X, Zhang X, Liang M. pH Homeodynamics and Male Fertility: A Coordinated Regulation of Acid-Based Balance during Sperm Journey to Fertilization. Biomolecules 2024; 14:685. [PMID: 38927088 PMCID: PMC11201807 DOI: 10.3390/biom14060685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2024] [Revised: 06/03/2024] [Accepted: 06/10/2024] [Indexed: 06/28/2024] Open
Abstract
pH homeostasis is crucial for spermatogenesis, sperm maturation, sperm physiological function, and fertilization in mammals. HCO3- and H+ are the most significant factors involved in regulating pH homeostasis in the male reproductive system. Multiple pH-regulating transporters and ion channels localize in the testis, epididymis, and spermatozoa, such as HCO3- transporters (solute carrier family 4 and solute carrier family 26 transporters), carbonic anhydrases, and H+-transport channels and enzymes (e.g., Na+-H+ exchangers, monocarboxylate transporters, H+-ATPases, and voltage-gated proton channels). Hormone-mediated signals impose an influence on the production of some HCO3- or H+ transporters, such as NBCe1, SLC4A2, MCT4, etc. Additionally, ion channels including sperm-specific cationic channels for Ca2+ (CatSper) and K+ (SLO3) are directly or indirectly regulated by pH, exerting specific actions on spermatozoa. The slightly alkaline testicular pH is conducive to spermatogenesis, whereas the epididymis's low HCO3- concentration and acidic lumen are favorable for sperm maturation and storage. Spermatozoa pH increases substantially after being fused with seminal fluid to enhance motility. In the female reproductive tract, sperm are subjected to increasing concentrations of HCO3- in the uterine and fallopian tube, causing a rise in the intracellular pH (pHi) of spermatozoa, leading to hyperpolarization of sperm plasma membranes, capacitation, hyperactivation, acrosome reaction, and ultimately fertilization. The physiological regulation initiated by SLC26A3, SLC26A8, NHA1, sNHE, and CFTR localized in sperm is proven for certain to be involved in male fertility. This review intends to present the key factors and characteristics of pHi regulation in the testes, efferent duct, epididymis, seminal fluid, and female reproductive tract, as well as the associated mechanisms during the sperm journey to fertilization, proposing insights into outstanding subjects and future research trends.
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Affiliation(s)
| | | | | | | | - Xiaoning Zhang
- Institute of Reproductive Medicine, Medical School, Nantong University, Nantong 226019, China; (P.D.); (M.Z.); (Z.C.); (X.Z.)
| | - Min Liang
- Institute of Reproductive Medicine, Medical School, Nantong University, Nantong 226019, China; (P.D.); (M.Z.); (Z.C.); (X.Z.)
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Caon E, Martins M, Hodgetts H, Blanken L, Vilia MG, Levi A, Thanapirom K, Al-Akkad W, Abu-Hanna J, Baselli G, Hall AR, Luong TV, Taanman JW, Vacca M, Valenti L, Romeo S, Mazza G, Pinzani M, Rombouts K. Exploring the impact of the PNPLA3 I148M variant on primary human hepatic stellate cells using 3D extracellular matrix models. J Hepatol 2024; 80:941-956. [PMID: 38365182 DOI: 10.1016/j.jhep.2024.01.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 01/24/2024] [Accepted: 01/27/2024] [Indexed: 02/18/2024]
Abstract
BACKGROUND & AIMS The PNPLA3 rs738409 C>G (encoding for I148M) variant is a risk locus for the fibrogenic progression of chronic liver diseases, a process driven by hepatic stellate cells (HSCs). We investigated how the PNPLA3 I148M variant affects HSC biology using transcriptomic data and validated findings in 3D-culture models. METHODS RNA sequencing was performed on 2D-cultured primary human HSCs and liver biopsies of individuals with obesity, genotyped for the PNPLA3 I148M variant. Data were validated in wild-type (WT) or PNPLA3 I148M variant-carrying HSCs cultured on 3D extracellular matrix (ECM) scaffolds from human healthy and cirrhotic livers, with/without TGFB1 or cytosporone B (Csn-B) treatment. RESULTS Transcriptomic analyses of liver biopsies and HSCs highlighted shared PNPLA3 I148M-driven dysregulated pathways related to mitochondrial function, antioxidant response, ECM remodelling and TGFB1 signalling. Analogous pathways were dysregulated in WT/PNPLA3-I148M HSCs cultured in 3D liver scaffolds. Mitochondrial dysfunction in PNPLA3-I148M cells was linked to respiratory chain complex IV insufficiency. Antioxidant capacity was lower in PNPLA3-I148M HSCs, while reactive oxygen species secretion was increased in PNPLA3-I148M HSCs and higher in bioengineered cirrhotic vs. healthy scaffolds. TGFB1 signalling followed the same trend. In PNPLA3-I148M cells, expression and activation of the endogenous TGFB1 inhibitor NR4A1 were decreased: treatment with the Csn-B agonist increased total NR4A1 in HSCs cultured in healthy but not in cirrhotic 3D scaffolds. NR4A1 regulation by TGFB1/Csn-B was linked to Akt signalling in PNPLA3-WT HSCs and to Erk signalling in PNPLA3-I148M HSCs. CONCLUSION HSCs carrying the PNPLA3 I148M variant have impaired mitochondrial function, antioxidant responses, and increased TGFB1 signalling, which dampens antifibrotic NR4A1 activity. These features are exacerbated by cirrhotic ECM, highlighting the dual impact of the PNPLA3 I148M variant and the fibrotic microenvironment in progressive chronic liver diseases. IMPACT AND IMPLICATIONS Hepatic stellate cells (HSCs) play a key role in the fibrogenic process associated with chronic liver disease. The PNPLA3 genetic mutation has been linked with increased risk of fibrogenesis, but its role in HSCs requires further investigation. Here, by using comparative transcriptomics and a novel 3D in vitro model, we demonstrate the impact of the PNPLA3 genetic mutation on primary human HSCs' behaviour, and we show that it affects the cell's mitochondrial function and antioxidant response, as well as the antifibrotic gene NR4A1. Our publicly available transcriptomic data, 3D platform and our findings on NR4A1 could facilitate the discovery of targets to develop more effective treatments for chronic liver diseases.
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Affiliation(s)
- Elisabetta Caon
- Regenerative Medicine and Fibrosis Group, Institute for Liver and Digestive Health, University College London, Royal Free Campus, London, UK
| | - Maria Martins
- Regenerative Medicine and Fibrosis Group, Institute for Liver and Digestive Health, University College London, Royal Free Campus, London, UK
| | - Harry Hodgetts
- Regenerative Medicine and Fibrosis Group, Institute for Liver and Digestive Health, University College London, Royal Free Campus, London, UK
| | - Lieke Blanken
- Regenerative Medicine and Fibrosis Group, Institute for Liver and Digestive Health, University College London, Royal Free Campus, London, UK
| | - Maria Giovanna Vilia
- Regenerative Medicine and Fibrosis Group, Institute for Liver and Digestive Health, University College London, Royal Free Campus, London, UK
| | - Ana Levi
- Regenerative Medicine and Fibrosis Group, Institute for Liver and Digestive Health, University College London, Royal Free Campus, London, UK
| | - Kessarin Thanapirom
- Regenerative Medicine and Fibrosis Group, Institute for Liver and Digestive Health, University College London, Royal Free Campus, London, UK
| | - Walid Al-Akkad
- Regenerative Medicine and Fibrosis Group, Institute for Liver and Digestive Health, University College London, Royal Free Campus, London, UK
| | - Jeries Abu-Hanna
- Research Department of Surgical Biotechnology, Division of Surgery and Interventional Science, University College London, London, UK
| | - Guido Baselli
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy
| | - Andrew R Hall
- Sheila Sherlock Liver Centre, Royal Free London NHS Foundation Trust, London, UK; Department of Cellular Pathology, Royal Free London NHS Foundation Trust, London, UK
| | - Tu Vinh Luong
- Sheila Sherlock Liver Centre, Royal Free London NHS Foundation Trust, London, UK; Department of Cellular Pathology, Royal Free London NHS Foundation Trust, London, UK
| | - Jan-Willem Taanman
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, London UK
| | - Michele Vacca
- Laboratory of Hepatic Metabolism and NAFLD, Roger Williams Institute of Hepatology, London, UK; Clinica Medica "Frugoni", Interdisciplinary Department of Medicine, University of Bari "Aldo Moro", Bari, Italy
| | - Luca Valenti
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy; Precision Medicine, Biological Resource Center, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Stefano Romeo
- Department of Molecular and Clinical Medicine, Institute of Medicine, Sahlgrenska Academy, Wallenberg Laboratory, University of Gothenburg, Gothenburg, Sweden
| | - Giuseppe Mazza
- Regenerative Medicine and Fibrosis Group, Institute for Liver and Digestive Health, University College London, Royal Free Campus, London, UK
| | - Massimo Pinzani
- Regenerative Medicine and Fibrosis Group, Institute for Liver and Digestive Health, University College London, Royal Free Campus, London, UK
| | - Krista Rombouts
- Regenerative Medicine and Fibrosis Group, Institute for Liver and Digestive Health, University College London, Royal Free Campus, London, UK.
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Stehle IF, Imventarza JA, Woerz F, Hoffmann F, Boldt K, Beyer T, Quinn PM, Ueffing M. Human CRB1 and CRB2 form homo- and heteromeric protein complexes in the retina. Life Sci Alliance 2024; 7:e202302440. [PMID: 38570189 PMCID: PMC10992996 DOI: 10.26508/lsa.202302440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 03/26/2024] [Accepted: 03/26/2024] [Indexed: 04/05/2024] Open
Abstract
Crumbs homolog 1 (CRB1) is one of the key genes linked to retinitis pigmentosa and Leber congenital amaurosis, which are characterized by a high clinical heterogeneity. The Crumbs family member CRB2 has a similar protein structure to CRB1, and in zebrafish, Crb2 has been shown to interact through the extracellular domain. Here, we show that CRB1 and CRB2 co-localize in the human retina and human iPSC-derived retinal organoids. In retina-specific pull-downs, CRB1 was enriched in CRB2 samples, supporting a CRB1-CRB2 interaction. Furthermore, novel interactors of the crumbs complex were identified, representing a retina-derived protein interaction network. Using co-immunoprecipitation, we further demonstrate that human canonical CRB1 interacts with CRB1 and CRB2, but not with CRB3, which lacks an extracellular domain. Next, we explored how missense mutations in the extracellular domain affect CRB1-CRB2 interactions. We observed no or a mild loss of CRB1-CRB2 interaction, when interrogating various CRB1 or CRB2 missense mutants in vitro. Taken together, our results show a stable interaction of human canonical CRB2 and CRB1 in the retina.
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Affiliation(s)
- Isabel F Stehle
- https://ror.org/03a1kwz48 Institute for Ophthalmic Research, Eberhard Karls University Tübingen, Tübingen, Germany
| | - Joel A Imventarza
- Department of Ophthalmology, Vagelos College of Physicians & Surgeons, Columbia University; New York, NY, USA
| | - Franziska Woerz
- https://ror.org/03a1kwz48 Institute for Ophthalmic Research, Eberhard Karls University Tübingen, Tübingen, Germany
| | - Felix Hoffmann
- https://ror.org/03a1kwz48 Institute for Ophthalmic Research, Eberhard Karls University Tübingen, Tübingen, Germany
| | - Karsten Boldt
- https://ror.org/03a1kwz48 Institute for Ophthalmic Research, Eberhard Karls University Tübingen, Tübingen, Germany
| | - Tina Beyer
- https://ror.org/03a1kwz48 Institute for Ophthalmic Research, Eberhard Karls University Tübingen, Tübingen, Germany
| | - Peter Mj Quinn
- Department of Ophthalmology, Vagelos College of Physicians & Surgeons, Columbia University; New York, NY, USA
| | - Marius Ueffing
- https://ror.org/03a1kwz48 Institute for Ophthalmic Research, Eberhard Karls University Tübingen, Tübingen, Germany
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28
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Boesch DJ, Singla A, Han Y, Kramer DA, Liu Q, Suzuki K, Juneja P, Zhao X, Long X, Medlyn MJ, Billadeau DD, Chen Z, Chen B, Burstein E. Structural organization of the retriever-CCC endosomal recycling complex. Nat Struct Mol Biol 2024; 31:910-924. [PMID: 38062209 PMCID: PMC11260360 DOI: 10.1038/s41594-023-01184-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 11/17/2023] [Indexed: 12/19/2023]
Abstract
The recycling of membrane proteins from endosomes to the cell surface is vital for cell signaling and survival. Retriever, a trimeric complex of vacuolar protein-sorting-associated protein (VPS)35L, VPS26C and VPS29, together with the CCC complex comprising coiled-coil domain-containing (CCDC)22, CCDC93 and copper metabolism domain-containing (COMMD) proteins, plays a crucial role in this process. The precise mechanisms underlying retriever assembly and its interaction with CCC have remained elusive. Here, we present a high-resolution structure of retriever in humans determined using cryogenic electron microscopy. The structure reveals a unique assembly mechanism, distinguishing it from its remotely related paralog retromer. By combining AlphaFold predictions and biochemical, cellular and proteomic analyses, we further elucidate the structural organization of the entire retriever-CCC complex across evolution and uncover how cancer-associated mutations in humans disrupt complex formation and impair membrane protein homeostasis. These findings provide a fundamental framework for understanding the biological and pathological implications associated with retriever-CCC-mediated endosomal recycling.
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Affiliation(s)
- Daniel J Boesch
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, USA
| | - Amika Singla
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Yan Han
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Daniel A Kramer
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, USA
| | - Qi Liu
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Kohei Suzuki
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Puneet Juneja
- Cryo-EM Facility, Office of Biotechnology, Iowa State University, Ames, IA, USA
| | - Xuefeng Zhao
- Information Technology Services, Iowa State University, Ames, IA, USA
| | - Xin Long
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Michael J Medlyn
- Division of Oncology Research, College of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Daniel D Billadeau
- Division of Oncology Research, College of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Zhe Chen
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA.
| | - Baoyu Chen
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, USA.
| | - Ezra Burstein
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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29
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Kuo YP, Nombela-Arrieta C, Carja O. A theory of evolutionary dynamics on any complex population structure reveals stem cell niche architecture as a spatial suppressor of selection. Nat Commun 2024; 15:4666. [PMID: 38821923 PMCID: PMC11143212 DOI: 10.1038/s41467-024-48617-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 05/02/2024] [Indexed: 06/02/2024] Open
Abstract
How the spatial arrangement of a population shapes its evolutionary dynamics has been of long-standing interest in population genetics. Most previous studies assume a small number of demes or symmetrical structures that, most often, act as well-mixed populations. Other studies use network theory to study more heterogeneous spatial structures, however they usually assume small, regular networks, or strong constraints on the strength of selection considered. Here we build network generation algorithms, conduct evolutionary simulations and derive general analytic approximations for probabilities of fixation in populations with complex spatial structure. We build a unifying evolutionary theory across network families and derive the relevant selective parameter, which is a combination of network statistics, predictive of evolutionary dynamics. We also illustrate how to link this theory with novel datasets of spatial organization and use recent imaging data to build the cellular spatial networks of the stem cell niches of the bone marrow. Across a wide variety of parameters, we find these networks to be strong suppressors of selection, delaying mutation accumulation in this tissue. We also find that decreases in stem cell population size also decrease the suppression strength of the tissue spatial structure.
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Affiliation(s)
- Yang Ping Kuo
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
- Joint Carnegie Mellon University-University of Pittsburgh Ph.D. Program in Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
| | - César Nombela-Arrieta
- Department of Medical Oncology and Hematology, University and University Hospital Zurich, Zurich, Switzerland
| | - Oana Carja
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA.
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30
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Reyes Alcaraz V, Pattappa G, Miura S, Angele P, Blunk T, Rudert M, Hiraki Y, Shukunami C, Docheva D. A Narrative Review of the Roles of Chondromodulin-I (Cnmd) in Adult Cartilage Tissue. Int J Mol Sci 2024; 25:5839. [PMID: 38892027 PMCID: PMC11173128 DOI: 10.3390/ijms25115839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 05/13/2024] [Accepted: 05/16/2024] [Indexed: 06/21/2024] Open
Abstract
Articular cartilage is crucial for joint function but its avascularity limits intrinsic repair, leading to conditions like osteoarthritis (OA). Chondromodulin-I (Cnmd) has emerged as a key molecule in cartilage biology, with potential implications for OA therapy. Cnmd is primarily expressed in cartilage and plays an important role in chondrocyte proliferation, cartilage homeostasis, and the blocking of angiogenesis. In vivo and in vitro studies on Cnmd, also suggest an involvement in bone repair and in delaying OA progression. Its downregulation correlates with OA severity, indicating its potential as a therapeutic target. Further research is needed to fully understand the mode of action of Cnmd and its beneficial implications for managing OA. This comprehensive review aims to elucidate the molecular characteristics of Cnmd, from its expression pattern, role in cartilage maintenance, callus formation during bone repair and association with OA.
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Affiliation(s)
- Viviana Reyes Alcaraz
- Department of Musculoskeletal Tissue Regeneration, Orthopaedic Hospital König-Ludwig-Haus, University of Würzburg, 97070 Würzburg, Germany; (V.R.A.); (G.P.)
| | - Girish Pattappa
- Department of Musculoskeletal Tissue Regeneration, Orthopaedic Hospital König-Ludwig-Haus, University of Würzburg, 97070 Würzburg, Germany; (V.R.A.); (G.P.)
| | - Shigenori Miura
- Department of Molecular Biology and Biochemistry, Division of Dental Sciences, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima 734-8553, Japan; (S.M.); (C.S.)
| | - Peter Angele
- Laboratory of Experimental Trauma Surgery, Department of Trauma Surgery, University Hospital Regensburg, 93053 Regensburg, Germany;
| | - Torsten Blunk
- Department of Trauma, Hand, Plastic and Reconstructive Surgery, University Hospital Würzburg, 97080 Würzburg, Germany;
| | - Maximilian Rudert
- Department of Orthopaedics, Orthopaedic Hospital König-Ludwig-Haus, University of Würzburg, 97070 Würzburg, Germany;
| | - Yuji Hiraki
- Department of Cellular Differentiation, Institute for Frontier Medical Sciences, Kyoto University, Kyoto 606-8501, Japan;
| | - Chisa Shukunami
- Department of Molecular Biology and Biochemistry, Division of Dental Sciences, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima 734-8553, Japan; (S.M.); (C.S.)
| | - Denitsa Docheva
- Department of Musculoskeletal Tissue Regeneration, Orthopaedic Hospital König-Ludwig-Haus, University of Würzburg, 97070 Würzburg, Germany; (V.R.A.); (G.P.)
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31
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Peters-Clarke TM, Coon JJ, Riley NM. Instrumentation at the Leading Edge of Proteomics. Anal Chem 2024; 96:7976-8010. [PMID: 38738990 DOI: 10.1021/acs.analchem.3c04497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2024]
Affiliation(s)
- Trenton M Peters-Clarke
- Department of Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Department of Biomolecular Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
| | - Joshua J Coon
- Department of Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Department of Biomolecular Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Morgridge Institute for Research, Madison, Wisconsin 53715, United States
| | - Nicholas M Riley
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
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32
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Sefik E, Duan K, Li Y, Sholar B, Evans L, Pincus J, Ammar Z, Murphy MM, Klaiman C, Saulnier CA, Pulver SL, Goldman-Yassen AE, Guo Y, Walker EF, Li L, Mulle JG, Shultz S. Structural deviations of the posterior fossa and the cerebellum and their cognitive links in a neurodevelopmental deletion syndrome. Mol Psychiatry 2024:10.1038/s41380-024-02584-8. [PMID: 38744992 DOI: 10.1038/s41380-024-02584-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 04/16/2024] [Accepted: 04/23/2024] [Indexed: 05/16/2024]
Abstract
High-impact genetic variants associated with neurodevelopmental disorders provide biologically-defined entry points for mechanistic investigation. The 3q29 deletion (3q29Del) is one such variant, conferring a 40-100-fold increased risk for schizophrenia, as well as high risk for autism and intellectual disability. However, the mechanisms leading to neurodevelopmental disability remain largely unknown. Here, we report the first in vivo quantitative neuroimaging study in individuals with 3q29Del (N = 24) and neurotypical controls (N = 1608) using structural MRI. Given prior radiology reports of posterior fossa abnormalities in 3q29Del, we focused our investigation on the cerebellum and its tissue-types and lobules. Additionally, we compared the prevalence of cystic/cyst-like malformations of the posterior fossa between 3q29Del and controls and examined the association between neuroanatomical findings and quantitative traits to probe gene-brain-behavior relationships. 3q29Del participants had smaller cerebellar cortex volumes than controls, before and after correction for intracranial volume (ICV). An anterior-posterior gradient emerged in finer grained lobule-based and voxel-wise analyses. 3q29Del participants also had larger cerebellar white matter volumes than controls following ICV-correction and displayed elevated rates of posterior fossa arachnoid cysts and mega cisterna magna findings independent of cerebellar volume. Cerebellar white matter and subregional gray matter volumes were associated with visual-perception and visual-motor integration skills as well as IQ, while cystic/cyst-like malformations yielded no behavioral link. In summary, we find that abnormal development of cerebellar structures may represent neuroimaging-based biomarkers of cognitive and sensorimotor function in 3q29Del, adding to the growing evidence identifying cerebellar pathology as an intersection point between syndromic and idiopathic forms of neurodevelopmental disabilities.
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Affiliation(s)
- Esra Sefik
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
- Department of Psychology, Emory University, Atlanta, GA, USA
| | - Kuaikuai Duan
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
- Tri-institutional Center for Translational Research in Neuroimaging and Data Science, Georgia State University, Georgia Institute of Technology, Emory University, Atlanta, GA, USA
| | - Yiheng Li
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Brittney Sholar
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
- Marcus Autism Center, Children's Healthcare of Atlanta and Emory University School of Medicine, Atlanta, GA, USA
| | - Lindsey Evans
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
- Marcus Autism Center, Children's Healthcare of Atlanta and Emory University School of Medicine, Atlanta, GA, USA
| | - Jordan Pincus
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
- Marcus Autism Center, Children's Healthcare of Atlanta and Emory University School of Medicine, Atlanta, GA, USA
| | - Zeena Ammar
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
- Marcus Autism Center, Children's Healthcare of Atlanta and Emory University School of Medicine, Atlanta, GA, USA
| | - Melissa M Murphy
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Cheryl Klaiman
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
- Marcus Autism Center, Children's Healthcare of Atlanta and Emory University School of Medicine, Atlanta, GA, USA
| | - Celine A Saulnier
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
- Neurodevelopmental Assessment & Consulting Services, Atlanta, GA, USA
| | - Stormi L Pulver
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
- Marcus Autism Center, Children's Healthcare of Atlanta and Emory University School of Medicine, Atlanta, GA, USA
| | - Adam E Goldman-Yassen
- Department of Radiology, Children's Healthcare of Atlanta, Atlanta, GA, USA
- Department of Radiology and Imaging Sciences, Emory University School of Medicine, Atlanta, GA, USA
| | - Ying Guo
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Elaine F Walker
- Department of Psychology, Emory University, Atlanta, GA, USA
| | - Longchuan Li
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
- Marcus Autism Center, Children's Healthcare of Atlanta and Emory University School of Medicine, Atlanta, GA, USA
| | - Jennifer G Mulle
- Department of Psychiatry, Robert Wood Johnson Medical School, Rutgers University, New Brunswick, NJ, USA.
| | - Sarah Shultz
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA.
- Marcus Autism Center, Children's Healthcare of Atlanta and Emory University School of Medicine, Atlanta, GA, USA.
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33
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Bradburn DA, Reis JC, Arthanari H, Cyert MS. A novel motif in calcimembrin/C16orf74 dictates multimeric dephosphorylation by calcineurin. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.12.593783. [PMID: 38798520 PMCID: PMC11118366 DOI: 10.1101/2024.05.12.593783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Calcineurin (CN), the only Ca 2+ -calmodulin activated protein phosphatase, dephosphorylates substrates within membrane-associated Ca 2+ microdomains. CN binds to substrates and regulators via short linear motifs (SLIMs), PxIxIT and LxVP. PxIxIT binding to CN is Ca 2+ independent and affects its distribution, while LxVP associates only with the active enzyme and promotes catalysis. 31 human proteins contain one or more composite 'LxVPxIxIT' motifs, whose functional properties have not been examined. Here we report studies of calcimembrin/C16orf74 (CLMB), a largely uncharacterized protein containing a composite motif that binds and directs CN to membranes. We demonstrate that CLMB associates with membranes via N-myristoylation and dynamic S-acylation and is dephosphorylated by CN on Thr44. The LxVP and PxIxIT portions of the CLMB composite sequence, together with Thr44 phosphorylation, confer high affinity PxIxIT-mediated binding to CN (KD∼8.9 nM) via an extended, 33 LxVPxIxITxx(p)T 44 sequence. This binding promotes CLMB-based targeting of CN to membranes, but also protects Thr44 from dephosphorylation. Thus, we propose that CN dephosphorylates CLMB in multimeric complexes, where one CLMB molecule recruits CN to membranes via PxIxIT binding, allowing others to engage through their LxVP motif for dephosphorylation. This unique mechanism makes dephosphorylation sensitive to CLMB:CN ratios and is supported by in vivo and in vitro analyses. CLMB overexpression is associated with poor prognoses for several cancers, suggesting that it promotes oncogenesis by shaping CN signaling.
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34
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Turanli B, Gulfidan G, Aydogan OO, Kula C, Selvaraj G, Arga KY. Genome-scale metabolic models in translational medicine: the current status and potential of machine learning in improving the effectiveness of the models. Mol Omics 2024; 20:234-247. [PMID: 38444371 DOI: 10.1039/d3mo00152k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2024]
Abstract
The genome-scale metabolic model (GEM) has emerged as one of the leading modeling approaches for systems-level metabolic studies and has been widely explored for a broad range of organisms and applications. Owing to the development of genome sequencing technologies and available biochemical data, it is possible to reconstruct GEMs for model and non-model microorganisms as well as for multicellular organisms such as humans and animal models. GEMs will evolve in parallel with the availability of biological data, new mathematical modeling techniques and the development of automated GEM reconstruction tools. The use of high-quality, context-specific GEMs, a subset of the original GEM in which inactive reactions are removed while maintaining metabolic functions in the extracted model, for model organisms along with machine learning (ML) techniques could increase their applications and effectiveness in translational research in the near future. Here, we briefly review the current state of GEMs, discuss the potential contributions of ML approaches for more efficient and frequent application of these models in translational research, and explore the extension of GEMs to integrative cellular models.
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Affiliation(s)
- Beste Turanli
- Marmara University, Faculty of Engineering, Department of Bioengineering, Istanbul, Turkey.
- Health Biotechnology Joint Research and Application Center of Excellence, Istanbul, Turkey
| | - Gizem Gulfidan
- Marmara University, Faculty of Engineering, Department of Bioengineering, Istanbul, Turkey.
| | - Ozge Onluturk Aydogan
- Marmara University, Faculty of Engineering, Department of Bioengineering, Istanbul, Turkey.
| | - Ceyda Kula
- Marmara University, Faculty of Engineering, Department of Bioengineering, Istanbul, Turkey.
- Health Biotechnology Joint Research and Application Center of Excellence, Istanbul, Turkey
| | - Gurudeeban Selvaraj
- Concordia University, Centre for Research in Molecular Modeling & Department of Chemistry and Biochemistry, Quebec, Canada
- Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha Dental College and Hospital, Department of Biomaterials, Bioinformatics Unit, Chennai, India
| | - Kazim Yalcin Arga
- Marmara University, Faculty of Engineering, Department of Bioengineering, Istanbul, Turkey.
- Health Biotechnology Joint Research and Application Center of Excellence, Istanbul, Turkey
- Marmara University, Genetic and Metabolic Diseases Research and Investigation Center, Istanbul, Turkey
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35
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D'Atri I, Martin ER, Yang L, Sears E, Baple E, Crosby AH, Chilton JK, Oguro-Ando A. Unraveling the CLCC1 interactome: Impact of the Asp25Glu variant and its interaction with SigmaR1 at the Mitochondrial-Associated ER Membrane (MAM). Neurosci Lett 2024; 830:137778. [PMID: 38621504 DOI: 10.1016/j.neulet.2024.137778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 03/23/2024] [Accepted: 04/12/2024] [Indexed: 04/17/2024]
Abstract
The endoplasmic reticulum (ER) plays an indispensable role in cellular processes, including maintenance of calcium homeostasis, and protein folding, synthesized and processing. Disruptions in these processes leading to ER stress and the accumulation of misfolded proteins can instigate the unfolded protein response (UPR), culminating in either restoration of balanced proteostasis or apoptosis. A key player in this intricate balance is CLCC1, an ER-resident chloride channel, whose essential role extends to retinal development, regulation of ER stress, and UPR. The importance of CLCC1 is further underscored by its interaction with proteins localized to mitochondria-associated endoplasmic reticulum membranes (MAMs), where it participates in UPR induction by MAM proteins. In previous research, we identified a p.(Asp25Glu) pathogenic CLCC1 variant associated with retinitis pigmentosa (RP) (CLCC1 hg38 NC_000001.11; NM_001048210.3, c.75C > A; UniprotKB Q96S66). In attempt to decipher the impact of this variant function, we leveraged liquid chromatography-mass spectrometry (LC-MS) to identify likely CLCC1-interacting proteins. We discovered that the CLCC1 interactome is substantially composed of proteins that localize to ER compartments and that the Asp25Glu variant results in noticeable loss and gain of specific protein interactors. Intriguingly, the analysis suggests that the CLCC1Asp25Glu mutant protein exhibits a propensity for increased interactions with cytoplasmic proteins compared to its wild-type counterpart. To corroborate our LC-MS data, we further scrutinized two novel CLCC1 interactors, Calnexin and SigmaR1, chaperone proteins that localize to the ER and MAMs. Through microscopy, we demonstrate that CLCC1 co-localizes with both proteins, thereby validating our initial findings. Moreover, our results reveal that CLCC1 co-localizes with SigmaR1 not merely at the ER, but also at MAMs. These findings reinforce the notion of CLCC1 interacting with MAM proteins at the ER-mitochondria interface, setting the stage for further exploration into how these interactions impact ER or mitochondria function and lead to retinal degenerative disease when impaired.
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Affiliation(s)
- Ilaria D'Atri
- School of Physiology, Pharmacology and Neuroscience, University of Bristol, BS8 1TD, United Kingdom; University of Exeter Medical School, University of Exeter, Exeter, United Kingdom
| | - Emily-Rose Martin
- University of Exeter Medical School, University of Exeter, Exeter, United Kingdom
| | - Liming Yang
- University of Exeter Medical School, University of Exeter, Exeter, United Kingdom
| | - Elizabeth Sears
- University of Exeter Medical School, University of Exeter, Exeter, United Kingdom
| | - Emma Baple
- University of Exeter Medical School, University of Exeter, Exeter, United Kingdom
| | - Andrew H Crosby
- University of Exeter Medical School, University of Exeter, Exeter, United Kingdom
| | - John K Chilton
- Peninsula Medical School, University of Plymouth, Plymouth, United Kingdom
| | - Asami Oguro-Ando
- University of Exeter Medical School, University of Exeter, Exeter, United Kingdom; Laboratory of Pharmacology, Faculty of Pharmaceutical Science, Tokyo University of Science, Japan.
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Yue W, Li X, Zhan X, Wang L, Ma J, Bi M, Wang Q, Gu X, Xie B, Liu T, Guo H, Zhu X, Song C, Qiao J, Li M. PARP inhibitors suppress tumours via centrosome error-induced senescence independent of DNA damage response. EBioMedicine 2024; 103:105129. [PMID: 38640836 PMCID: PMC11052917 DOI: 10.1016/j.ebiom.2024.105129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 04/07/2024] [Accepted: 04/07/2024] [Indexed: 04/21/2024] Open
Abstract
BACKGROUND Poly(ADP-ribose) polymerase (PARP) inhibitors have emerged as promising chemotherapeutic drugs primarily against BRCA1/2-associated tumours, known as synthetic lethality. However, recent clinical trials reported patients' survival benefits from PARP inhibitor treatments, irrelevant to homologous recombination deficiency. Therefore, revealing the therapeutic mechanism of PARP inhibitors beyond DNA damage repair is urgently needed, which can facilitate precision medicine. METHODS A CRISPR-based knock-in technology was used to establish stable BRCA1 mutant cancer cells. The effects of PARP inhibitors on BRCA1 mutant cancer cells were evaluated by biochemical and cell biological experiments. Finally, we validated its in vivo effects in xenograft and patient-derived xenograft (PDX) tumour mice. FINDINGS In this study, we uncovered that the majority of clinical BRCA1 mutations in breast cancers were in and near the middle of the gene, rather than in essential regions for DNA damage repair. Representative mutations such as R1085I and E1222Q caused transient extra spindle poles during mitosis in cancer cells. PAR, which is synthesized by PARP2 but not PARP1 at mitotic centrosomes, clustered these transient extra poles, independent of DNA damage response. Common PARP inhibitors could effectively suppress PARP2-synthesized PAR and induce cell senescence by abrogating the correction of mitotic extra-pole error. INTERPRETATION Our findings uncover an alternative mechanism by which PARP inhibitors efficiently suppress tumours, thereby pointing to a potential new therapeutic strategy for centrosome error-related tumours. FUNDING Funded by National Natural Science Foundation of China (NSFC) (T2225006, 82272948, 82103106), Beijing Municipal Natural Science Foundation (Key program Z220011), and the National Clinical Key Specialty Construction Program, P. R. China (2023).
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Affiliation(s)
- Wei Yue
- State Key Laboratory of Female Fertility Promotion, Centre for Reproductive Medicine, Department of Obstetrics and Gynaecology, Peking University Third Hospital, Beijing, 100191, China; National Clinical Research Centre for Obstetrics and Gynaecology (Peking University Third Hospital), Beijing, 100191, China; Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing 100191, China; Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, 100191, China
| | - Xinyu Li
- State Key Laboratory of Female Fertility Promotion, Centre for Reproductive Medicine, Department of Obstetrics and Gynaecology, Peking University Third Hospital, Beijing, 100191, China; National Clinical Research Centre for Obstetrics and Gynaecology (Peking University Third Hospital), Beijing, 100191, China; Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing 100191, China; Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, 100191, China
| | - Xiaolu Zhan
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, 150081, China
| | - Lei Wang
- Centre for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China; Peking-Tsinghua Centre for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China
| | - Jihong Ma
- State Key Laboratory of Female Fertility Promotion, Centre for Reproductive Medicine, Department of Obstetrics and Gynaecology, Peking University Third Hospital, Beijing, 100191, China; National Clinical Research Centre for Obstetrics and Gynaecology (Peking University Third Hospital), Beijing, 100191, China; Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing 100191, China; Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, 100191, China
| | - Meiyu Bi
- State Key Laboratory of Female Fertility Promotion, Centre for Reproductive Medicine, Department of Obstetrics and Gynaecology, Peking University Third Hospital, Beijing, 100191, China; National Clinical Research Centre for Obstetrics and Gynaecology (Peking University Third Hospital), Beijing, 100191, China; Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing 100191, China; Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, 100191, China
| | - Qilong Wang
- State Key Laboratory of Female Fertility Promotion, Centre for Reproductive Medicine, Department of Obstetrics and Gynaecology, Peking University Third Hospital, Beijing, 100191, China; National Clinical Research Centre for Obstetrics and Gynaecology (Peking University Third Hospital), Beijing, 100191, China; Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing 100191, China; Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, 100191, China
| | - Xiaoyang Gu
- State Key Laboratory of Female Fertility Promotion, Centre for Reproductive Medicine, Department of Obstetrics and Gynaecology, Peking University Third Hospital, Beijing, 100191, China; National Clinical Research Centre for Obstetrics and Gynaecology (Peking University Third Hospital), Beijing, 100191, China; Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing 100191, China; Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, 100191, China
| | - Bingteng Xie
- Key Laboratory of Molecular Medicine and Biological Diagnosis and Treatment (Ministry of Industry and Information Technology), School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Tong Liu
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, 150081, China
| | - Hongyan Guo
- National Clinical Research Centre for Obstetrics and Gynaecology (Peking University Third Hospital), Beijing, 100191, China; Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing 100191, China; Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, 100191, China
| | - Xin Zhu
- State Key Laboratory of Female Fertility Promotion, Centre for Reproductive Medicine, Department of Obstetrics and Gynaecology, Peking University Third Hospital, Beijing, 100191, China; National Clinical Research Centre for Obstetrics and Gynaecology (Peking University Third Hospital), Beijing, 100191, China; Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing 100191, China; Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, 100191, China
| | - Chen Song
- Centre for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China; Peking-Tsinghua Centre for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China
| | - Jie Qiao
- State Key Laboratory of Female Fertility Promotion, Centre for Reproductive Medicine, Department of Obstetrics and Gynaecology, Peking University Third Hospital, Beijing, 100191, China; National Clinical Research Centre for Obstetrics and Gynaecology (Peking University Third Hospital), Beijing, 100191, China; Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing 100191, China; Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, 100191, China
| | - Mo Li
- State Key Laboratory of Female Fertility Promotion, Centre for Reproductive Medicine, Department of Obstetrics and Gynaecology, Peking University Third Hospital, Beijing, 100191, China; National Clinical Research Centre for Obstetrics and Gynaecology (Peking University Third Hospital), Beijing, 100191, China; Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing 100191, China; Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, 100191, China.
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Thakore VP, Patel KD, Vora HH, Patel PS, Jain NK. Up-regulation of extracellular-matrix and inflammation related genes in oral squamous cell carcinoma. Arch Oral Biol 2024; 161:105925. [PMID: 38442470 DOI: 10.1016/j.archoralbio.2024.105925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Revised: 02/16/2024] [Accepted: 02/18/2024] [Indexed: 03/07/2024]
Abstract
OBJECTIVE Oral squamous cell carcinoma (OSCC) is the most prevalent malignancy with late-presentation, site-specific heterogeneity, and high-propensity for recurrence/metastasis that has shown rise in mortality. Lately, research emphasize on dynamic interactions between tumor-cells and extracellular-matrix components within tumor-microenvironment that promote tissue integrity loss and carcinogenesis. Therefore, OSCC clinical-management is still challenging. DESIGN Present study validated clinical utility of a 13 gene-panel in two chief sub-sites of OSCC: Buccal mucosa squamous cell carcinoma (BMSCC) (N = 50) and Tongue squamous cell carcinoma (TSCC) (N = 52) using qRT-PCR. Principal component analysis and binary logistic regression analysis were applied to acquire definite multi gene models. Protein expression analysis was employed using the Human Protein Atlas, UALCAN and TIMER 2.0 databases to explore potential correlation between immune cells and gene-panels. RESULTS Significant up-regulation of CXCL8, CXCL10, FN1, GBP1, IFIT3, ISG15, MMP1, MMP3, MMP10, PLAU, SERPINE1 and SPP1 except OASL was observed in OSCC tissue in comparison of absolute normal controls. Although, this gene-panel could potentially discriminate OSCC tissues from absolute normal controls as solitarily diagnostic and/or predictive biomarkers, models generated also showed substantial discriminating efficacy. Eight-genes were found to be significantly associated with poor-prognosis on clinico-pathological association. Protein-expression confirmed overexpression of gene-panel and added advantage of being secretory-protein. Importantly, up-regulated genes in our study showed significant relation with immune-cells infiltration suggesting their contribution in immune-escape. CONCLUSION Thus, we propose that the 13 gene-panel could pave the way to effective and personalized clinical-management of OSCC in terms of diagnostic and prognostic measures and thereby as therapeutic targets.
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Affiliation(s)
- Vaidehi P Thakore
- Life Science Department, School of Science, Gujarat University, Ahmedabad 380009, Gujarat, India; Cancer Biology Department, The Gujarat Cancer & Research Institute, Civil, Ahmedabad, Gujarat, India
| | - Kinjal D Patel
- Cancer Biology Department, The Gujarat Cancer & Research Institute, Civil, Ahmedabad, Gujarat, India
| | - Hemangini H Vora
- Cancer Biology Department, The Gujarat Cancer & Research Institute, Civil, Ahmedabad, Gujarat, India
| | - Prabhudas S Patel
- Cancer Biology Department, The Gujarat Cancer & Research Institute, Civil, Ahmedabad, Gujarat, India
| | - Nayan K Jain
- Life Science Department, School of Science, Gujarat University, Ahmedabad 380009, Gujarat, India.
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Lin M, Hu L, Shen S, Liu J, Liu Y, Xu Y, Chen H, Sugimoto K, Li J, Kamitsukasa I, Hiwasa T, Wang H, Xu A. Atherosclerosis-related biomarker PABPC1 predicts pan-cancer events. Stroke Vasc Neurol 2024; 9:108-125. [PMID: 37311641 PMCID: PMC11103157 DOI: 10.1136/svn-2022-002246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 05/25/2023] [Indexed: 06/15/2023] Open
Abstract
BACKGROUND Atherosclerosis (AS) and tumours are the leading causes of death worldwide and share common risk factors, detection methods and molecular markers. Therefore, searching for serum markers shared by AS and tumours is beneficial to the early diagnosis of patients. METHODS The sera of 23 patients with AS-related transient ischaemic attack were screened by serological identification of antigens through recombinant cDNA expression cloning (SEREX), and cDNA clones were identified. Pathway function enrichment analysis was performed on cDNA clones to identify their biological pathways and determine whether they were related to AS or tumours. Subsequently, gene-gene and protein-protein interactions were performed and AS-associated markers would be discovered. The expression of AS biomarkers in human normal organs and pan-cancer tumour tissues were explored. Then, immune infiltration level and tumour mutation burden of various immune cells were evaluated. Survival curves analysis could show the expression of AS markers in pan-cancer. RESULTS AS-related sera were screened by SEREX, and 83 cDNA clones with high homology were obtained. Through functional enrichment analysis, it was found that their functions were closely related to AS and tumour functions. After multiple biological information interaction screening and the external cohort validating, poly(A) binding protein cytoplasmic 1 (PABPC1) was found to be a potential AS biomarker. To assess whether PABPC1 was related to pan-cancer, its expression in different tumour pathological stages and ages was screened. Since AS-associated proteins were closely related to cancer immune infiltration, we investigated and found that PABPC1 had the same role in pan-cancer. Finally, analysis of Kaplan-Meier survival curves revealed that high PABPC1 expression in pan-cancer was associated with high risk of death. CONCLUSIONS Through the findings of SEREX and bioinformatics pan-cancer analysis, we concluded that PABPC1 might serve as a potential biomarker for the prediction and diagnosis of AS and pan-cancer.
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Affiliation(s)
- Miao Lin
- Stroke Center, The First Affiliated Hospital, Jinan University, Guangzhou, China
- Department of Anesthesiology, The First Affiliated Hospital, Jinan University, Guangzhou, China
| | - Liubing Hu
- Stroke Center, The First Affiliated Hospital, Jinan University, Guangzhou, China
- Department of Anesthesiology, The First Affiliated Hospital, Jinan University, Guangzhou, China
- The Biomedical Translational Research Institute,Faculty of Medical Science, Jinan University, Guangzhou, China
| | - Si Shen
- Stroke Center, The First Affiliated Hospital, Jinan University, Guangzhou, China
- Department of Radiology, Medical Imaging Center, The First Affiliated Hospital, Jinan University, Guangzhou, China
| | - Jiyue Liu
- Stroke Center, The First Affiliated Hospital, Jinan University, Guangzhou, China
- Department of Anesthesiology, The First Affiliated Hospital, Jinan University, Guangzhou, China
| | - Yanyan Liu
- The Biomedical Translational Research Institute,Faculty of Medical Science, Jinan University, Guangzhou, China
| | - Yixian Xu
- Stroke Center, The First Affiliated Hospital, Jinan University, Guangzhou, China
- Department of Anesthesiology, The First Affiliated Hospital, Jinan University, Guangzhou, China
| | - Honglin Chen
- Stroke Center, The First Affiliated Hospital, Jinan University, Guangzhou, China
- Department of Radiology, Medical Imaging Center, The First Affiliated Hospital, Jinan University, Guangzhou, China
| | - Kazuo Sugimoto
- Department of Biochemistry and Genetics, Graduate School of Medicine, Chiba University, Chiba, Japan
- Department of Neurology, Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Jianshuang Li
- The Biomedical Translational Research Institute,Faculty of Medical Science, Jinan University, Guangzhou, China
| | - Ikuo Kamitsukasa
- Department of Neurology, Chiba Rosai Hospital, Chiba, Japan
- Department of Neurology, Chibaken Saiseikai Narashino Hospital, Chiba, Japan
| | - Takaki Hiwasa
- Department of Biochemistry and Genetics, Graduate School of Medicine, Chiba University, Chiba, Japan
- Department of Neurological Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Hao Wang
- Stroke Center, The First Affiliated Hospital, Jinan University, Guangzhou, China
- Department of Anesthesiology, The First Affiliated Hospital, Jinan University, Guangzhou, China
- Department of Biochemistry and Genetics, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Anding Xu
- Stroke Center, The First Affiliated Hospital, Jinan University, Guangzhou, China
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Hatziapostolou M, Koutsioumpa M, Zaitoun AM, Polytarchou C, Edderkaoui M, Mahurkar-Joshi S, Vadakekolathu J, D'Andrea D, Lay AR, Christodoulou N, Pham T, Yau TO, Vorvis C, Chatterji S, Pandol SJ, Poultsides GA, Dawson DW, Lobo DN, Iliopoulos D. Promoter Methylation Leads to Hepatocyte Nuclear Factor 4A Loss and Pancreatic Cancer Aggressiveness. GASTRO HEP ADVANCES 2024; 3:687-702. [PMID: 39165427 PMCID: PMC11330932 DOI: 10.1016/j.gastha.2024.04.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 04/15/2024] [Indexed: 08/22/2024]
Abstract
Background and Aims Decoding pancreatic ductal adenocarcinoma heterogeneity and the consequent therapeutic selection remains a challenge. We aimed to characterize epigenetically regulated pathways involved in pancreatic ductal adenocarcinoma progression. Methods Global DNA methylation analysis in pancreatic cancer patient tissues and cell lines was performed to identify differentially methylated genes. Targeted bisulfite sequencing and in vitro methylation reporter assays were employed to investigate the direct link between site-specific methylation and transcriptional regulation. A series of in vitro loss-of-function and gain-of function studies and in vivo xenograft and the KPC (LSL-Kras G12D/+ ; LSL-Trp53 R172H/+ ; Pdx1-Cre) mouse models were used to assess pancreatic cancer cell properties. Gene and protein expression analyses were performed in 3 different cohorts of pancreatic cancer patients and correlated to clinicopathological parameters. Results We identify Hepatocyte Nuclear Factor 4A (HNF4A) as a novel target of hypermethylation in pancreatic cancer and demonstrate that site-specific proximal promoter methylation drives HNF4A transcriptional repression. Expression analyses in patients indicate the methylation-associated suppression of HNF4A expression in pancreatic cancer tissues. In vitro and in vivo studies reveal that HNF4A is a novel tumor suppressor in pancreatic cancer, regulating cancer growth and aggressiveness. As evidenced in both the KPC mouse model and human pancreatic cancer tissues, HNF4A expression declines significantly in the early stages of the disease. Most importantly, HNF4 loss correlates with poor overall patient survival. Conclusion HNF4A silencing, mediated by promoter DNA methylation, drives pancreatic cancer development and aggressiveness leading to poor patient survival.
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Affiliation(s)
- Maria Hatziapostolou
- Department of Biosciences, John van Geest Cancer Research Centre, Centre for Systems Health and Integrated Metabolic Research, School of Science and Technology, Nottingham Trent University, Nottingham, UK
| | - Marina Koutsioumpa
- Vatche and Tamar Manoukian Division of Digestive Diseases, Center for Systems Biomedicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California
| | - Abed M. Zaitoun
- Department of Cellular Pathology, Nottingham Digestive Diseases Centre and NIHR Nottingham Biomedical Research Centre, Nottingham University Hospitals and University of Nottingham, Queen’s Medical Centre, Nottingham, UK
| | - Christos Polytarchou
- Department of Biosciences, John van Geest Cancer Research Centre, Centre for Systems Health and Integrated Metabolic Research, School of Science and Technology, Nottingham Trent University, Nottingham, UK
| | - Mouad Edderkaoui
- Departments of Medicine and Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California
| | - Swapna Mahurkar-Joshi
- Vatche and Tamar Manoukian Division of Digestive Diseases, Center for Systems Biomedicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California
| | - Jayakumar Vadakekolathu
- Department of Biosciences, John van Geest Cancer Research Centre, Centre for Systems Health and Integrated Metabolic Research, School of Science and Technology, Nottingham Trent University, Nottingham, UK
| | - Daniel D'Andrea
- Department of Biosciences, John van Geest Cancer Research Centre, Centre for Systems Health and Integrated Metabolic Research, School of Science and Technology, Nottingham Trent University, Nottingham, UK
| | - Anna Rose Lay
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, California
- Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California, Los Angeles, California
| | - Niki Christodoulou
- Department of Biosciences, John van Geest Cancer Research Centre, Centre for Systems Health and Integrated Metabolic Research, School of Science and Technology, Nottingham Trent University, Nottingham, UK
| | - Thuy Pham
- Department of Biosciences, John van Geest Cancer Research Centre, Centre for Systems Health and Integrated Metabolic Research, School of Science and Technology, Nottingham Trent University, Nottingham, UK
| | - Tung-On Yau
- Department of Biosciences, John van Geest Cancer Research Centre, Centre for Systems Health and Integrated Metabolic Research, School of Science and Technology, Nottingham Trent University, Nottingham, UK
| | - Christina Vorvis
- Vatche and Tamar Manoukian Division of Digestive Diseases, Center for Systems Biomedicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California
| | - Suchit Chatterji
- Department of Biosciences, John van Geest Cancer Research Centre, Centre for Systems Health and Integrated Metabolic Research, School of Science and Technology, Nottingham Trent University, Nottingham, UK
| | - Stephen J. Pandol
- Departments of Medicine and Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California
| | - George A. Poultsides
- Department of Surgery, Stanford University School of Medicine, Stanford, California
| | - David W. Dawson
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, California
- Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California, Los Angeles, California
| | - Dileep N. Lobo
- Nottingham Digestive Diseases Centre and NIHR Nottingham Biomedical Research Centre, Nottingham University Hospitals and University of Nottingham, Queen’s Medical Centre, Nottingham, UK
- MRC Versus Arthritis Centre for Musculoskeletal Ageing Research, School of Life Sciences, Queen’s Medical Centre, University of Nottingham, Nottingham, UK
| | - Dimitrios Iliopoulos
- Vatche and Tamar Manoukian Division of Digestive Diseases, Center for Systems Biomedicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California
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Li Q, Li F, Song X, Lu N, Jing X, Wen H, Ma P, Zhang H, Yao W, Wang X, Zhang M. Pan-cancer analysis of ARFs family and ARF5 promoted the progression of hepatocellular carcinoma. Heliyon 2024; 10:e29099. [PMID: 38617932 PMCID: PMC11015141 DOI: 10.1016/j.heliyon.2024.e29099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 03/29/2024] [Accepted: 03/31/2024] [Indexed: 04/16/2024] Open
Abstract
Background ARF family proteins are a kind of small GTPases, which are involved in regulating a variety of basic functions of cells. In recent years, the role and molecular regulatory mechanisms of ARFs in tumor progression have received increasing attention, and research reports on most of their family members are increasing. However, research on the clinical and pathological relevance of ARF5 in cancer, especially in hepatocellular carcinoma, still needs to be improved. Methods RNA-seq data in the Cancer Genome Atlas (TCGA) and genome tissue expression (GTEx) databases were used to analyze the expression and pathological data of ARFs family in Pan-cancer. Kaplan-Meier and Cox regression were used for prognostic analysis of ARF5 and Pan-cancer. Combined with ImmuCellAI database and TIMER2 database, the relationship between ARF5 expression and immune cell tumor infiltration in hepatocellular carcinoma (HCC) was analyzed. WGCNA is used to construct the co-expression gene network related to ARF5 expression in HCC and screen important modules and central genes. GO and KEGG path enrichment analysis were carried out for the genes in the modules with clinical significance. GSEA analysis was performed to take into account the role of genes with small differences. Finally, ceRNA network analysis was used to explore the molecular mechanism of miRNAs and lncRNAs regulating ARF5 expression. Results ARFs family (ARF1, ARF3, ARF4, ARF5, ARF6) are generally highly expressed in Pan-cancer. ARF5 is significantly highly expressed in 29 cancers, and the high expression of ARF5 in HCC patients is significantly negatively correlated with OS, DFI, PFI and DSS, which may lead to cancer deterioration by participating in tumor immune infiltration of HCC. Through WGCNA analysis, the expression of ARF5 in HCC may be involved in many cellular processes that consume a lot of energy, such as ribosome formation, RNA and protein synthesis and lipids, as well as COVID-19, nonalcoholic fatty liver, neurodegenerative diseases and other disease pathways. Conclusion ARFs, especially ARF5, are overexpressed in many human tumors. This study shows for the first time that ARF5 is significantly correlated with the poor prognosis of HCC patients, which may play a role as an oncogene, suggesting that ARF5 has the potential as a biomarker for the diagnosis and treatment of HCC.
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Affiliation(s)
- Qian Li
- The First Affiliated Hospital of Xi'an Medical University, Xi'an, 710077, Shaanxi, China
| | - Fang Li
- Institute of Genetics and Development Biology, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, 710061, Shaanxi, China
| | - Xinqiu Song
- Medical College of Yan'an University, Yan'an, 716000, Shaanxi, China
| | - Ning Lu
- The First Affiliated Hospital of Xi'an Medical University, Xi'an, 710077, Shaanxi, China
| | - Xintao Jing
- Institute of Genetics and Development Biology, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, 710061, Shaanxi, China
| | - Hua Wen
- The First Affiliated Hospital of Xi'an Medical University, Xi'an, 710077, Shaanxi, China
| | - Peihan Ma
- The First Affiliated Hospital of Xi'an Medical University, Xi'an, 710077, Shaanxi, China
| | - Hua Zhang
- The First Affiliated Hospital of Xi'an Medical University, Xi'an, 710077, Shaanxi, China
| | - Wenzhu Yao
- Xi'an Medical University, Xi'an, 710021, Shaanxi, China
| | - Xiaofei Wang
- Biomedical Experimental Center, Xi'an Jiaotong University, Xi'an, 710061, Shaanxi, China
| | - Mingxin Zhang
- The First Affiliated Hospital of Xi'an Medical University, Xi'an, 710077, Shaanxi, China
- Shaanxi University of Traditional Chinese Medicine, Xianyang, 712046, Shaanxi, China
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Xia F, Yang H, Wu H, Zhao B. Spindle component 25 predicts the prognosis and the immunotherapy response of cancers: a pan-cancer analysis. Sci Rep 2024; 14:8452. [PMID: 38605119 PMCID: PMC11009294 DOI: 10.1038/s41598-024-59038-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Accepted: 04/05/2024] [Indexed: 04/13/2024] Open
Abstract
Spindle component 25 (SPC25) is one of the four proteins that make up the nuclear division cycle 80 (NDC80) complex, the other three components being Ndc80p, Nuf2p, and spindle component 24. Deregulation of the components of this complex can lead to uncontrolled proliferation and reduced apoptosis. However, the prognostic and immunotherapeutic value of SPC25 in pan-cancer remains unclear. Data from the UCSC Xena, TIMER2.0, and TCGA were analyzed to investigate the overall differential expression of SPC25 across multiple cancer types. The survival prognosis, clinical features, and genetic changes of SPC25 were also evaluated. Finally, the relationship between SPC25 and immunotherapy response was further explored through Gene Set Enrichment Analysis, tumor microenvironment, and immune cell infiltration. The transcription and protein expression of SPC25 were significantly increased in most cancer types and had prognostic value for the survival of certain cancer patients such as ACC, CESC, KIRC, KIRP, LIHC, LUAD, MESO, STAD, THYM, and UCEC. In some cancer types, SPC25 expression was also markedly correlated with the TMB, MSI, and clinical characteristics. Gene Set Enrichment Analysis showed that SPC25 was significantly associated with immune-related pathways. In addition, it was also confirmed that the expression level of SPC25 was strongly correlated with immune cell infiltration, immune checkpoint genes, immune regulatory genes, Ferroptosis-related genes, Cuproptosis-related genes, and lactate metabolism-related genes. This study comprehensively explored the potential value of SPC25 as a prognostic and immunotherapeutic marker for pan-cancer, providing new direction and evidence for cancer therapy.
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Affiliation(s)
- Fengjuan Xia
- Department of Neurology of the First People's Hospital of Zhaoqing, China, Zhaoqing, 526000, China
| | - Haixia Yang
- Oncology Center of the First People's Hospital of Zhaoqing, Zhaoqing, 526000, China
| | - Huangjian Wu
- Oncology Center of the First People's Hospital of Zhaoqing, Zhaoqing, 526000, China
| | - Bo Zhao
- Center for Pain Medicine of the First People's Hospital of Zhaoqing, Zhaoqing, 526000, China.
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Higashi T, Hayashi H, Hanamatsu Y, Saigo C, Matsuhashi N, Takeuchi T. Expression of IZUMO2 in colorectal cancer in association with clinicopathological features. Pathol Res Pract 2024; 256:155263. [PMID: 38484656 DOI: 10.1016/j.prp.2024.155263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Accepted: 03/09/2024] [Indexed: 04/14/2024]
Abstract
IZUMO2 belongs to the testis-expressed IZUMO family of proteins, which are characterized by an N-terminal IZUMO domain. Based on integrated analysis of expression profiles and matched DNA methylation data from a public database, IZUMO2 represents a prognosis-related methylation-driven gene in colorectal cancer. However, it remains unclear whether IZUMO2 protein expression is suppressed or overexpressed in colorectal cancer cells. In this study, we aimed to elucidate the expression of the IZUMO2 protein in colorectal cancer, with a focus on the clinicopathological features. Sixty-four colorectal cancer tissue specimens were immunohistochemically stained using specific antibodies against IZUMO2. IZUMO2 immunoreactivity was detected at the invasion front in 30 of the 64 colorectal cancer samples. Kaplan-Meier analysis demonstrated that patients with IZUMO2 immunoreactivity had a relatively shorter overall and progression-free survival (log-rank test, P = 0.046 and 0.019, respectively). IZUMO2 immunoreactivity served as an independent factor predictive of poor progression-free survival in colorectal cancer (P = 0.025) as determined via the Cox proportional hazard regression model. Moreover, IZUMO2 immunoreactivity represented an independent factor for poor overall survival (P = 0.035) and progression-free survival (P = 0.013) in patients with colon cancer. The present findings suggest that IZUMO2 is expressed in many colorectal cancers, especially at the cancer invasion front, and may represent an indicator of poor prognosis in colorectal cancer.
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Affiliation(s)
- Toshiya Higashi
- Department of Gastroenterological Surgery and Pediatric Surgery, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Hirokatsu Hayashi
- Department of Gastroenterological Surgery and Pediatric Surgery, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Yuki Hanamatsu
- Department of Pathology and Translational Research, Gifu University Graduate School of Medicine, Gifu, Japan; Center for One Medicine Innovative Translational Research; COMIT, Gifu University, Gifu, Japan.
| | - Chiemi Saigo
- Department of Pathology and Translational Research, Gifu University Graduate School of Medicine, Gifu, Japan; Center for One Medicine Innovative Translational Research; COMIT, Gifu University, Gifu, Japan; The United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Japan
| | - Nobuhisa Matsuhashi
- Department of Gastroenterological Surgery and Pediatric Surgery, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Tamotsu Takeuchi
- Department of Pathology and Translational Research, Gifu University Graduate School of Medicine, Gifu, Japan; Center for One Medicine Innovative Translational Research; COMIT, Gifu University, Gifu, Japan
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Shen B, Mei J, Xu R, Cai Y, Wan M, Zhou J, Ding J, Zhu Y. B7-H3 is associated with the armored-cold phenotype and predicts poor immune checkpoint blockade response in melanoma. Pathol Res Pract 2024; 256:155267. [PMID: 38520953 DOI: 10.1016/j.prp.2024.155267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 03/09/2024] [Accepted: 03/17/2024] [Indexed: 03/25/2024]
Abstract
Melanoma is the most suitable tumor type for immunotherapy, but not all melanoma patients could respond to immunotherapy. B7 homolog 3 (B7-H3) belongs to the B7 family and is overexpressed in a number of malignant tumors, but the expression pattern of B7-H3 in melanoma has not been well summarized. The expression of B7-H3 was investigated in melanoma and its correlations with features of the tumor microenvironment (TME) by using various public databases, including the Cancer Genome Atlas (TCGA), the GEPIA, and the Human Protein Atlas databases. In addition, the in-house melanoma tissue microarray was applied to validate the results from public databases. Based on the public and in-house cohorts, we found that B7-H3 was overexpressed in melanoma tumor tissues and high B7-H3 expression was related to poor clinical outcome. Moreover, B7-H3 was negatively correlated with levels of tumor-infiltrating lymphocytes (TILs) and positively correlated with collagen infiltration. With clinical translational value, the predictive value of B7-H3 for conventional immunotherapy was detected using the Kaplan-Meier plotter tool, and the results showed that melanoma patients with high B7-H3 expression were insensitive to anti-PD-1 and anti-CTLA-4 immunotherapy. In conclusion, we first investigate the expression of B7-H3 in melanoma and its correlations with the TME features, and indicate B7-H3 as a promising therapeutic target in melanoma patients that are insensitive to conventional immunotherapy.
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Affiliation(s)
- Bozhi Shen
- The First Clinical Medicine College, Nanjing Medical University, Nanjing 211166, China; The Laboratory Center for Basic Medical Sciences, Nanjing Medical University, Nanjing 211166, China
| | - Jie Mei
- The First Clinical Medicine College, Nanjing Medical University, Nanjing 211166, China
| | - Rui Xu
- The First Clinical Medicine College, Nanjing Medical University, Nanjing 211166, China
| | - Yun Cai
- Department of Laboratory Medicine, Changzhou Jintan First People's Hospital, Changzhou 213200, China
| | - Mengyun Wan
- Department of Physiology, Nanjing Medical University, Nanjing 211166, China
| | - Ji Zhou
- Department of Physiology, Nanjing Medical University, Nanjing 211166, China
| | - Junli Ding
- Department of Oncology, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi Medical Center, Nanjing Medical University, Wuxi 214023, China.
| | - Yichao Zhu
- Department of Physiology, Nanjing Medical University, Nanjing 211166, China.
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Ma X, Zhao D, Liu S, Zuo J, Wang W, Wang F, Li Y, Ding Z, Wang J, Wang X. FERMT2 upregulation in CAFs enhances EMT of OSCC and M2 macrophage polarization. Oral Dis 2024; 30:991-1003. [PMID: 37357349 DOI: 10.1111/odi.14610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 04/19/2023] [Accepted: 04/22/2023] [Indexed: 06/27/2023]
Abstract
OBJECTIVES FERMT2 upregulation was associated with malignant tumor behaviors, including epithelial-to-mesenchymal (EMT). This study aimed to characterize the expression profile of FERMT2 in oral squamous cell carcinoma (OSCC) and to explore its involvement in the tumor microenvironment sculptured by oral cancer-associated fibroblasts (OCAFs). MATERIALS Previous bulk-seq (TCGA-HNSC) and single-cell RNA-seq data sets were retrieved for bioinformatic analysis. Human OSCC lines SCC15 and CAL27, primary normal oral fibroblasts (NOFs), OCAFs, and THP-1 cells were used for intro studies. RESULTS FERMT2 expression was significantly higher in CAFs compared with OSCC tumor cells and normal fibroblasts. Higher FERMT2 expression might independently predict unfavorable disease-specific survival (DSS) in patients with OSCC. Knockdown of FERMT2 suppressed the expression and secretion of IGFBP7, SPARC, TIMP3, COL4A1, and IGFBP4 in OCAFs. OCAFs with FERMT2 knockdown had significantly weakened capability to induce the invasion of OSCC cells and the expression of mesenchymal markers. FERMT2 knockdown impaired the inducing effect of OCAFs on the migration of M0 macrophages and the expression of M2 macrophage markers. CONCLUSIONS FERMT2 could modulate the production and secretion of IGFBP7, SPARC, COL4A1, and IGFBP4 in OCAFs, thereby inducing the EMT of OSCC and M2 macrophage polarization.
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Affiliation(s)
- Xiangrui Ma
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China College of Stomatology, Sichuan University, Chengdu, China
- Department of Oral and Maxillofacial Surgery, Binzhou Medical University Hospital, Binzhou, China
| | - Dan Zhao
- Department of Oral and Maxillofacial Surgery, The Affiliated Stomatological Hospital of Southwest Medical University, Luzhou, China
| | - Shan Liu
- Department of Oral and Maxillofacial Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jinhua Zuo
- Department of Oral and Maxillofacial Surgery, Binzhou Medical University Hospital, Binzhou, China
| | - Wenlong Wang
- Department of Oral and Maxillofacial Surgery, Binzhou Medical University Hospital, Binzhou, China
| | - Fang Wang
- Department of Oral and Maxillofacial Surgery, Binzhou Medical University Hospital, Binzhou, China
| | - Yourui Li
- Department of Prosthodontics, Binzhou Medical University Hospital, Binzhou, China
| | - Zhangfan Ding
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China College of Stomatology, Sichuan University, Chengdu, China
- Department of Oral and Maxillofacial Surgery, West China School of Stomatology, Sichuan University, Chengdu, China
| | - Jing Wang
- Department of Oral Medicine, Binzhou Medical University Hospital, Binzhou, China
| | - Xiaoyi Wang
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China College of Stomatology, Sichuan University, Chengdu, China
- Department of Oral and Maxillofacial Surgery, West China School of Stomatology, Sichuan University, Chengdu, China
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Baker BH, Freije S, MacDonald JW, Bammler TK, Benson C, Carroll KN, Enquobahrie DA, Karr CJ, LeWinn KZ, Zhao Q, Bush NR, Sathyanarayana S, Paquette AG. Placental transcriptomic signatures of prenatal and preconceptional maternal stress. Mol Psychiatry 2024; 29:1179-1191. [PMID: 38212375 PMCID: PMC11176062 DOI: 10.1038/s41380-023-02403-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 12/20/2023] [Accepted: 12/22/2023] [Indexed: 01/13/2024]
Abstract
Prenatal exposure to maternal psychological stress is associated with increased risk for adverse birth and child health outcomes. Accumulating evidence suggests that preconceptional maternal stress may also be transmitted intergenerationally to negatively impact offspring. However, understanding of mechanisms linking these exposures to offspring outcomes, particularly those related to placenta, is limited. Using RNA sequencing, we identified placental transcriptomic signatures associated with maternal prenatal stressful life events (SLEs) and childhood traumatic events (CTEs) in 1 029 mother-child pairs in two birth cohorts from Washington state and Memphis, Tennessee. We evaluated individual gene-SLE/CTE associations and performed an ensemble of gene set enrichment analyses combing across 11 popular enrichment methods. Higher number of prenatal SLEs was significantly (FDR < 0.05) associated with increased expression of ADGRG6, a placental tissue-specific gene critical in placental remodeling, and decreased expression of RAB11FIP3, an endocytosis and endocytic recycling gene, and SMYD5, a histone methyltransferase. Prenatal SLEs and maternal CTEs were associated with gene sets related to several biological pathways, including upregulation of protein processing in the endoplasmic reticulum, protein secretion, and ubiquitin mediated proteolysis, and down regulation of ribosome, epithelial mesenchymal transition, DNA repair, MYC targets, and amino acid-related pathways. The directional associations in these pathways corroborate prior non-transcriptomic mechanistic studies of psychological stress and mental health disorders, and have previously been implicated in pregnancy complications and adverse birth outcomes. Accordingly, our findings suggest that maternal exposure to psychosocial stressors during pregnancy as well as the mother's childhood may disrupt placental function, which may ultimately contribute to adverse pregnancy, birth, and child health outcomes.
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Affiliation(s)
- Brennan H Baker
- University of Washington, Seattle, WA, USA.
- Seattle Children's Research Institute, Seattle, WA, USA.
| | | | | | | | - Ciara Benson
- Global Alliance to Prevent Preterm Birth and Stillbirth (GAPPS), Lynnwood, WA, USA
| | | | | | | | - Kaja Z LeWinn
- University of California San Francisco, San Francisco, CA, USA
| | - Qi Zhao
- University of Tennessee Health Sciences Center, Memphis, TN, USA
| | - Nicole R Bush
- University of California San Francisco, San Francisco, CA, USA
| | - Sheela Sathyanarayana
- University of Washington, Seattle, WA, USA
- Seattle Children's Research Institute, Seattle, WA, USA
| | - Alison G Paquette
- University of Washington, Seattle, WA, USA
- Seattle Children's Research Institute, Seattle, WA, USA
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46
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Gerault MA, Granjeaud S, Camoin L, Nordlund P, Dai L. IMPRINTS.CETSA and IMPRINTS.CETSA.app: an R package and a Shiny application for the analysis and interpretation of IMPRINTS-CETSA data. Brief Bioinform 2024; 25:bbae128. [PMID: 38557673 PMCID: PMC10982947 DOI: 10.1093/bib/bbae128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Revised: 02/10/2024] [Accepted: 03/11/2024] [Indexed: 04/04/2024] Open
Abstract
IMPRINTS-CETSA (Integrated Modulation of Protein Interaction States-Cellular Thermal Shift Assay) provides a highly resolved means to systematically study the interactions of proteins with other cellular components, including metabolites, nucleic acids and other proteins, at the proteome level, but no freely available and user-friendly data analysis software has been reported. Here, we report IMPRINTS.CETSA, an R package that provides the basic data processing framework for robust analysis of the IMPRINTS-CETSA data format, from preprocessing and normalization to visualization. We also report an accompanying R package, IMPRINTS.CETSA.app, which offers a user-friendly Shiny interface for analysis and interpretation of IMPRINTS-CETSA results, with seamless features such as functional enrichment and mapping to other databases at a single site. For the hit generation part, the diverse behaviors of protein modulations have been typically segregated with a two-measure scoring method, i.e. the abundance and thermal stability changes. We present a new algorithm to classify modulated proteins in IMPRINTS-CETSA experiments by a robust single-measure scoring. In this way, both the numerical changes and the statistical significances of the IMPRINTS information can be visualized on a single plot. The IMPRINTS.CETSA and IMPRINTS.CETSA.app R packages are freely available on GitHub at https://github.com/nkdailingyun/IMPRINTS.CETSA and https://github.com/mgerault/IMPRINTS.CETSA.app, respectively. IMPRINTS.CETSA.app is also available as an executable program at https://zenodo.org/records/10636134.
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Affiliation(s)
- Marc-Antoine Gerault
- Department of Oncology and Pathology, Karolinska Institutet, 171 77 Stockholm, Sweden
- Aix-Marseille Univ, INSERM, CNRS, Institut Paoli-Calmettes, CRCM, Marseille Protéomique, F-13009 Marseille, France
| | - Samuel Granjeaud
- Aix-Marseille Univ, INSERM, CNRS, Institut Paoli-Calmettes, CRCM, Marseille Protéomique, F-13009 Marseille, France
| | - Luc Camoin
- Aix-Marseille Univ, INSERM, CNRS, Institut Paoli-Calmettes, CRCM, Marseille Protéomique, F-13009 Marseille, France
| | - Pär Nordlund
- Department of Oncology and Pathology, Karolinska Institutet, 171 77 Stockholm, Sweden
- Institute of Molecular and Cell Biology, A*STAR, 138673, Singapore
| | - Lingyun Dai
- Institute of Molecular and Cell Biology, A*STAR, 138673, Singapore
- Department of Geriatrics, and Shenzhen Clinical Research Centre for Geriatrics, The First Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen 518020, China
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47
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Lee S, Cho Y, Li Y, Li R, Brown D, McAuliffe P, Lee AV, Oesterreich S, Zervantonakis IK, Osmanbeyoglu HU. Cancer-cell derived S100A11 promotes macrophage recruitment in ER+ breast cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.21.586041. [PMID: 38585952 PMCID: PMC10996512 DOI: 10.1101/2024.03.21.586041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Macrophages are pivotal in driving breast tumor development, progression, and resistance to treatment, particularly in estrogen receptor-positive (ER+) tumors, where they infiltrate the tumor microenvironment (TME) influenced by cancer cell-secreted factors. By analyzing single-cell RNA-sequencing data from 25 ER+ tumors, we elucidated interactions between cancer cells and macrophages, correlating macrophage density with epithelial cancer cell density. We identified that S100A11, a previously unexplored factor in macrophage-cancer crosstalk, predicts high macrophage density and poor outcomes in ER+ tumors. We found that recombinant S100A11 enhances macrophage infiltration and migration in a dose-dependent manner. Additionally, in 3D models, we showed that S100A11 expression levels in ER+ cancer cells predict macrophage infiltration patterns. Neutralizing S100A11 decreased macrophage recruitment, both in cancer cell lines and in a clinically relevant patient-derived organoid model, underscoring its role as a paracrine regulator of cancer-macrophage interactions in the protumorigenic TME. This study offers novel insights into the interplay between macrophages and cancer cells in ER+ breast tumors, highlighting S100A11 as a potential therapeutic target to modulate the macrophage-rich tumor microenvironment.
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Affiliation(s)
- Sanghoon Lee
- Department of Biomedical Informatics, School of Medicine, University of Pittsburgh, Pittsburgh, 15206, U.S.A
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, 15213 U.S.A
| | - Youngbin Cho
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, 15213 U.S.A
- Department of Bioengineering, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, U.S.A
| | - Yiting Li
- Women’s Cancer Research Center, University of Pittsburgh Medical Center (UPMC) Hillman Cancer Center (HCC), Magee-Womens Research Institute, Pittsburgh, PA, 15213, U.S.A
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, U.S.A
| | - Ruxuan Li
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, 15213 U.S.A
- Department of Bioengineering, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, U.S.A
| | - Daniel Brown
- Women’s Cancer Research Center, University of Pittsburgh Medical Center (UPMC) Hillman Cancer Center (HCC), Magee-Womens Research Institute, Pittsburgh, PA, 15213, U.S.A
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, U.S.A
| | - Priscilla McAuliffe
- Women’s Cancer Research Center, University of Pittsburgh Medical Center (UPMC) Hillman Cancer Center (HCC), Magee-Womens Research Institute, Pittsburgh, PA, 15213, U.S.A
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, U.S.A
| | - Adrian V Lee
- Women’s Cancer Research Center, University of Pittsburgh Medical Center (UPMC) Hillman Cancer Center (HCC), Magee-Womens Research Institute, Pittsburgh, PA, 15213, U.S.A
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, U.S.A
| | - Steffi Oesterreich
- Women’s Cancer Research Center, University of Pittsburgh Medical Center (UPMC) Hillman Cancer Center (HCC), Magee-Womens Research Institute, Pittsburgh, PA, 15213, U.S.A
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, U.S.A
| | - Ioannis K. Zervantonakis
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, 15213 U.S.A
- Department of Bioengineering, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, U.S.A
| | - Hatice Ulku Osmanbeyoglu
- Department of Biomedical Informatics, School of Medicine, University of Pittsburgh, Pittsburgh, 15206, U.S.A
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, 15213 U.S.A
- Department of Bioengineering, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, U.S.A
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48
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Gatasheh MK, Natarajan SR, Krishnamoorthy R, Alsulami TS, Rajagopal P, Palanisamy CP, Veeraraghavan VP, Jayaraman S. Molecular analysis to identify novel potential biomarkers as drug targets in colorectal cancer therapy: an integrated bioinformatics analysis. Mol Cell Oncol 2024; 11:2326699. [PMID: 38505173 PMCID: PMC10950290 DOI: 10.1080/23723556.2024.2326699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 02/29/2024] [Indexed: 03/21/2024]
Abstract
Colorectal cancer (CRC) is a heterogeneous disease that requires new diagnostic and prognostic markers. Integrated bioinformatics approach to identify novel therapeutic targets associated with CRC. Using GEO2R identified DEGs in CRC, and Funrich software facilitated the visualization of DEGs through Venn diagrams. From a total of 114 enhanced DEGs, potential hub genes were further filtered based on their nodal strength and edges using STRING database. To gain insights into the functional roles of these hub genes, gene ontology and pathway enrichment were conducted thorough g: profiler web server. Subsequently, overall survival plots from GEPIA and oncogenic predictive functions like mRNA expressions for stages and nodal metastasis were employed to identify hub genes in CRC patient samples. Additionally, the cBioPortal and HPA databases also revealed genetic alterations and expression levels in these hub genes in CRC patients, further supporting their involvement in colorectal cancer. Gene expression by RT-PCR shows upregulation of hub genes in HT-29 cells. Finally, our integrated bioinformatic analysis revealed that ABCE1, AURKA, HSPD1, PHKA1, CDK4, and YWHAE as hub genes with potential oncogenic roles in CRC. These genes hold promise as diagnostic and prognostic markers for colorectal tumorigenesis, providing insights into targeted therapies for improved patient outcomes.
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Affiliation(s)
- Mansour K. Gatasheh
- Department of Biochemistry, College of Science, King Saud University, Riyadh, Kingdom of Saudi Arabia
| | - Sathan Raj Natarajan
- Centre of Molecular Medicine and Diagnostics (COMManD), Department of Biochemistry, Saveetha Dental College & Hospitals, Saveetha Institute of Medical & Technical Sciences, SaveethaUniversity, Chennai, India
| | - Rajapandiyan Krishnamoorthy
- Department of Food Science and Nutrition, College of Food and Agriculture Sciences, King Saud University, Riyadh, Kingdom of Saudi Arabia
| | - Tawfiq S Alsulami
- Department of Food Science and Nutrition, College of Food and Agriculture Sciences, King Saud University, Riyadh, Kingdom of Saudi Arabia
| | - Ponnulakshmi Rajagopal
- Department of Central Research Laboratory, Meenakshi Ammal Dental College and Hospital, Meenakshi Academy of Higher Education and Research (Deemed to be University), Chennai, India
| | - Chella Perumal Palanisamy
- Mini-invasive Neurosurgery and Translational Medical Center, Xi’an Central Hospital, Xi’an Jiaotong University, Xi’an, PR China
| | - Vishnu Priya Veeraraghavan
- Centre of Molecular Medicine and Diagnostics (COMManD), Department of Biochemistry, Saveetha Dental College & Hospitals, Saveetha Institute of Medical & Technical Sciences, SaveethaUniversity, Chennai, India
| | - Selvaraj Jayaraman
- Centre of Molecular Medicine and Diagnostics (COMManD), Department of Biochemistry, Saveetha Dental College & Hospitals, Saveetha Institute of Medical & Technical Sciences, SaveethaUniversity, Chennai, India
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49
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Zhao X, Zhang J, Liu J, Yuan J, Wu T, Cheng X. Comprehensive analysis of gene expression profiles of annulus fibrosus subtypes and hub genes in intervertebral disc degeneration. Aging (Albany NY) 2024; 16:5370-5386. [PMID: 38484139 PMCID: PMC11006460 DOI: 10.18632/aging.205653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Accepted: 01/05/2024] [Indexed: 04/06/2024]
Abstract
Intervertebral disc degeneration (IVDD) has been considered a major cause of low back pain. Therefore, further molecular subtypes of IVDD and identification of potential critical genes are urgently needed. First, consensus clustering was used to classify patients with IVDD into two subtypes and key module genes for subtyping were identified using weighted gene co-expression network analysis (WGCNA). Then, key module genes for the disease were identified by WGCNA. Subsequently, SVM and GLM were used to identify hub genes. Based on the above genes, a nomogram was constructed to predict the subtypes of IVDD. Finally, we find that ROM1 is lowered in IVDD and is linked to various cancer prognoses. The present work offers innovative diagnostic and therapeutic biomarkers for molecular subtypes of IVDD.
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Affiliation(s)
- Xiaokun Zhao
- Department of Orthopedics, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - Jian Zhang
- Jiangxi Key Laboratory of Intervertebral Disc Disease, Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - Jiahao Liu
- Institute of Minimally Invasive Orthopedics, Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - Jinghong Yuan
- Department of Orthopedics, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - Tianlong Wu
- Department of Orthopedics, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - Xigao Cheng
- Department of Orthopedics, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, P.R. China
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50
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Mestareehi A, Abu-Farsakh N. Impact of Protein Phosphatase Expressions on the Prognosis of Hepatocellular Carcinoma Patients. ACS OMEGA 2024; 9:10299-10331. [PMID: 38463290 PMCID: PMC10918787 DOI: 10.1021/acsomega.3c07787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 02/02/2024] [Accepted: 02/08/2024] [Indexed: 03/12/2024]
Abstract
The study was conducted to unveil the significance of protein phosphatases in the prognosis of hepatocellular carcinoma (HCC) patients and its related molecular biological attributes as well as to discover novel potential biomarkers for therapeutic significance and diagnostic purposes that may benefit clinical practice. Analyzing a data set from 159 HCC patients using high-throughput phosphoproteomics, we examined the dysregulated expression of protein phosphatases. Employing bioinformatic and pathway analyses, we explored differentially expressed genes linked to protein phosphatases. A protein-protein interaction network was constructed using the search tool for the retrieval of interacting genes/proteins database. We quantified a total of 11,547 phosphorylation sites associated with 4043 phosphoproteins from HCC patients. Within this data set, we identified 105 identified phosphorylation sites associated with protein phosphatases; 28 genes were upregulated and 3 were downregulated in HCC. Enriched pathways using Gene Set Enrichment Analysis encompassed oocyte meiosis, proteoglycans in cancer, the oxytocin signaling pathway, the cGMP-PKG signaling pathway, the vascular smooth muscle, and the cAMP signaling pathway. The Kyoto encyclopedia of genes and genomes (KEGG) analysis highlighted pathways like mitogen-activated protein kinase, AMPK, and PI3K-Akt, indicating potential involvement in HCC progression. Notably, the PPI network identified hub genes, emphasizing their interconnections and potential roles in HCC. In our study, we found significantly upregulated levels of CDC25C, PPP1R13L, and PPP1CA, which emerge as promising avenues. This significant expression could serve as potent diagnostic and prognostic markers to enhance the effectiveness of HCC cancer treatment, offering efficiency and accuracy in patient assessment. The findings regarding protein phosphatases reveal their elevated expression in HCC, correlating with unfavorable prognosis. Moreover, the outcomes of gene ontology and KEGG pathway analyses suggest that protein phosphatases may influence liver cancer by engaging diverse targets and pathways, ultimately fostering the progression of HCC. These results underscore the substantial potential of protein phosphatases as key contributors to HCC's development and advancement. This insight holds promise for identifying therapeutic targets and charting research avenues to enhance the comprehension of the intricate molecular mechanisms underpinning HCC.
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Affiliation(s)
- Aktham Mestareehi
- Department
of Pharmaceutical Sciences, Faculty of Pharmacy, Isra University, P.O. Box 22, Amman 11622, Jordan
- Department
of Pharmaceutical Sciences, School of Pharmacy and Health Sciences, Wayne State University, Detroit, Michigan 48201, United States
- School
of Medicine, The Ohio State University, Columbus, Ohio 43202, United States
| | - Noor Abu-Farsakh
- Department
of Gastroenterology and Hepatology, Internal Medicine Department, Jordan University Hospital, Amman 11942, Jordan
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