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Mahyari E, Boggy GJ, McElfresh GW, Kaza M, Benjamin S, Varco-Merth B, Ojha S, Feltham S, Goodwin W, Nkoy C, Duell D, Selseth A, Bennett T, Barber-Axthelm A, Smedley JV, Labriola CS, Axthelm MK, Reeves RK, Okoye AA, Hansen SG, Picker LJ, Bimber BN. Enhanced interpretation of immune cell phenotype and function through a rhesus macaque single-cell atlas. CELL GENOMICS 2025; 5:100849. [PMID: 40233746 DOI: 10.1016/j.xgen.2025.100849] [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: 10/08/2024] [Revised: 02/17/2025] [Accepted: 03/18/2025] [Indexed: 04/17/2025]
Abstract
Single-cell RNA sequencing (scRNA-seq) allows cell classification using genome-wide transcriptional state; however, high-dimensional transcriptomic profiles, and the unsupervised analyses employed to interpret them, provide a systematically different view of biology than well-established functional/lineage definitions of immunocytes. Understanding these differences and limits is essential for accurate interpretation of these rich data. We present the Rhesus Immune Reference Atlas (RIRA), the first immune-focused macaque single-cell multi-tissue atlas. We contrasted transcriptional profiles against immune lineages, using surface protein and marker genes as ground truth. While the pattern of clustering can align with cell type, this is not always true. Especially within T and natural killer (NK) cells, many functionally distinct subsets lack defining markers, and strong shared expression programs, such as cytotoxicity, result in systematic intermingling by unsupervised clustering. We identified gene programs with high discriminatory/diagnostic value, including multi-gene signatures that model T/NK cell maturation. Directly measuring these diagnostic programs complements unsupervised analyses.
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Affiliation(s)
- Eisa Mahyari
- Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR 97006, USA
| | - Gregory J Boggy
- Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR 97006, USA
| | - G W McElfresh
- Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR 97006, USA
| | - Maanasa Kaza
- Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR 97006, USA
| | - Sebastian Benjamin
- Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR 97006, USA
| | - Benjamin Varco-Merth
- Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR 97006, USA; Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR 97006, USA
| | - Sohita Ojha
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR 97006, USA
| | - Shana Feltham
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR 97006, USA
| | - William Goodwin
- Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR 97006, USA; Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR 97006, USA
| | - Candice Nkoy
- Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR 97006, USA; Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR 97006, USA
| | - Derick Duell
- Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR 97006, USA; Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR 97006, USA
| | - Andrea Selseth
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR 97006, USA
| | - Tyler Bennett
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR 97006, USA
| | - Aaron Barber-Axthelm
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR 97006, USA
| | - Jeremy V Smedley
- Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR 97006, USA; Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR 97006, USA
| | - Caralyn S Labriola
- Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR 97006, USA; Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR 97006, USA
| | - Michael K Axthelm
- Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR 97006, USA; Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR 97006, USA
| | - R Keith Reeves
- Division of Innate and Comparative Immunology, Center for Human Systems Immunology, Duke University School of Medicine, Durham, NC, USA; Department of Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Afam A Okoye
- Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR 97006, USA; Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR 97006, USA
| | - Scott G Hansen
- Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR 97006, USA; Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR 97006, USA
| | - Louis J Picker
- Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR 97006, USA; Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR 97006, USA
| | - Benjamin N Bimber
- Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR 97006, USA; Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR 97006, USA.
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Moon SW, Lee JC, Lee JH, Kim TY, Park JH. Clinical and Prognostic Value of VHL in Korean Patients with Rectal Cancer. MEDICINA (KAUNAS, LITHUANIA) 2025; 61:306. [PMID: 40005423 PMCID: PMC11857133 DOI: 10.3390/medicina61020306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2024] [Revised: 01/28/2025] [Accepted: 02/02/2025] [Indexed: 02/27/2025]
Abstract
Background and Objectives: Von Hippel-Lindau (VHL) disease is caused by mutations in the VHL gene and can develop various cancers. Hypoxia-inducible factors 1 and 2 alphas, regulated by the VHL gene, can increase the levels of vascular endothelial growth factor, thereby activating cancer progression. Here, we demonstrated clinical and prognostic values of VHL expression in rectal cancer (RC). Materials and Methods: Von Hippel-Lindau mRNA expression was examined in 60 patients with RC. Furthermore, we evaluated survival to determine the prognostic significance of VHL mRNA expression levels in RC using the Cancer Genome Atlas (TCGA) data. Results: Lower VHL expression was correlated with the recurrence (p = 0.058) and lymphatic invasion (p = 0.078), although it was not statistically significant. In TCGA data, VHL expression level was correlated with the M stage (p = 0.044); however, it had a possible association with lymphatic invasion (p = 0.068) and N stage (p = 0.104). Survival analysis showed that lower VHL gene expression predicted poorer survival in both patients with RC and TCGA data. Conclusions: This study identified a significant correlation between VHL gene expression and RC for the first time using patient tissues and TCGA data, suggesting that the VHL gene expression level could be a potential biomarker or candidate for the treatment of RC. Further studies are required to identify the molecular pathogenesis and clinical characteristics of VHL disease in RC.
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Affiliation(s)
- Sang-Won Moon
- Medical Course, School of Medicine, Keimyung University, Daegu 42601, Republic of Korea; (S.-W.M.); (J.-C.L.)
| | - Jun-Chae Lee
- Medical Course, School of Medicine, Keimyung University, Daegu 42601, Republic of Korea; (S.-W.M.); (J.-C.L.)
| | - Jae-Ho Lee
- Department of Anatomy, School of Medicine & Institute for Medical Science, Keimyung University, Daegu 42601, Republic of Korea;
| | - Tae-Young Kim
- Department of Anatomy, School of Medicine & Institute for Medical Science, Keimyung University, Daegu 42601, Republic of Korea;
| | - Jong Ho Park
- Department of Anatomy, School of Medicine & Institute for Medical Science, Keimyung University, Daegu 42601, Republic of Korea;
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Liu Y, Elmas A, Huang KL. Mutation impact on mRNA versus protein expression across human cancers. Gigascience 2025; 14:giae113. [PMID: 39775839 PMCID: PMC11702362 DOI: 10.1093/gigascience/giae113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2024] [Revised: 09/13/2024] [Accepted: 12/05/2024] [Indexed: 01/11/2025] Open
Abstract
BACKGROUND Cancer mutations are often assumed to alter proteins, thus promoting tumorigenesis. However, how mutations affect protein expression-in addition to gene expression-has rarely been systematically investigated. This is significant as mRNA and protein levels frequently show only moderate correlation, driven by factors such as translation efficiency and protein degradation. Proteogenomic datasets from large tumor cohorts provide an opportunity to systematically analyze the effects of somatic mutations on mRNA and protein abundance and identify mutations with distinct impacts on these molecular levels. RESULTS We conduct a comprehensive analysis of mutation impacts on mRNA- and protein-level expressions of 953 cancer cases with paired genomics and global proteomic profiling across 6 cancer types. Protein-level impacts are validated for 47.2% of the somatic expression quantitative trait loci (seQTLs), including CDH1 and MSH3 truncations, as well as other mutations from likely "long-tail" driver genes. Devising a statistical pipeline for identifying somatic protein-specific QTLs (spsQTLs), we reveal several gene mutations, including NF1 and MAP2K4 truncations and TP53 missenses showing disproportional influence on protein abundance not readily explained by transcriptomics. Cross-validating with data from massively parallel assays of variant effects (MAVE), TP53 missenses associated with high tumor TP53 proteins are more likely to be experimentally confirmed as functional. CONCLUSION This study reveals that somatic mutations can exhibit distinct impacts on mRNA and protein levels, underscoring the necessity of integrating proteogenomic data to comprehensively identify functionally significant cancer mutations. These insights provide a framework for prioritizing mutations for further functional validation and therapeutic targeting.
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Affiliation(s)
- Yuqi Liu
- Department of Genetics and Genomic Sciences, Department of Artificial Intelligence and Human Health, Center for Transformative Disease Modeling, Tisch Cancer Institute, Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Abdulkadir Elmas
- Department of Genetics and Genomic Sciences, Department of Artificial Intelligence and Human Health, Center for Transformative Disease Modeling, Tisch Cancer Institute, Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Kuan-lin Huang
- Department of Genetics and Genomic Sciences, Department of Artificial Intelligence and Human Health, Center for Transformative Disease Modeling, Tisch Cancer Institute, Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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Girnius N, Henstridge AZ, Marks B, Yu JK, Gray GK, Sander C, Zervantonakis IK, Luna A. Cilengitide sensitivity is predicted by overall integrin expression in breast cancer. Breast Cancer Res 2024; 26:187. [PMID: 39707454 DOI: 10.1186/s13058-024-01942-2] [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: 08/30/2024] [Accepted: 12/03/2024] [Indexed: 12/23/2024] Open
Abstract
BACKGROUND Treatment options for triple-negative breast cancer (TNBC) are limited and patients face a poor prognosis. Here, we sought to identify drugs that target TNBC vulnerabilities and understand the biology underlying these responses. We analyzed the Broad Institute DepMap to identify recurrent TNBC vulnerabilities and performed a 45-compound screen on vulnerability-related pathways on a set of up to 8 TNBC cell lines. We identified a subset of cell lines with an ITGAV vulnerability and a differential sensitivity to cilengitide, an integrin inhibitor targeting ITGAV:ITGB3 and ITGAV:ITGB5. Next, we sought to understand cilengitide resistance and response biomarkers. Clinical trials targeting integrins continue enrolling patients, necessitating an understanding of how these drugs affect tumors. METHODS We combined in vitro assays with computational approaches to systematically explore the differential sensitivity to cilengitide and resistance mechanisms. We tested an additional pan-ITGAV inhibitor (GLPG0187) to determine how generalizable our findings on cilengitide sensitivity might be to integrin inhibition. ITGB4, ITGA3, and ITGA6 knockdown experiments assessed the importance of integrin monomers in cell attachment during cilengitide treatment. Additionally, we explored the role of extracellular matrix (ECM) proteins in cilengitide response by performing cell replating experiments and by culturing on collagen, fibronectin, or laminin coated plates. RESULTS We discovered that cell-derived ECM modulates cilengitide sensitivity and exogenous fibronectin addition conferred resistance to all sensitive TNBC cell lines, though fibronectin expression did not correlate with sensitivity. Instead, elevated overall integrin protein levels, not specific integrins, in TNBC cells positively correlated with resistance. This suggested that high pan-integrin expression promotes cilengitide resistance. Thus, we tested cilengitide in six luminal breast cancer cell lines (which have low integrin levels); all were sensitive. Also, pan-ITGAV inhibitor, GLPG0187, showed the same sensitivity profile across our TNBC cell lines, suggesting our findings apply to other integrin inhibitors. CONCLUSIONS Integrin inhibitors are appealing candidates to pursue as anti-cancer drugs because they are generally well-tolerated, but their efficacy is mixed, possibly due to the absence of predictive markers. Cilengitide induces death in breast cancer cells with low integrin abundance, where complementary ECM promotes survival. Thus, integrin inhibition in breast cancer warrants further study.
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Affiliation(s)
- Nomeda Girnius
- Department of Cell Biology, Harvard Medical School, Boston, MA, 02115, USA.
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, USA.
| | - Aylin Z Henstridge
- Department of Cell Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - Benjamin Marks
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - Jeffrey K Yu
- Department of Cell Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - G Kenneth Gray
- Department of Cell Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - Chris Sander
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - Ioannis K Zervantonakis
- Department of Bioengineering, Swanson School of Engineering, University of Pittsburgh, Pittsburgh, PA, 15213, USA
| | - Augustin Luna
- Computational Biology Branch, National Library of Medicine and Developmental Therapeutics Branch, National Cancer Institute, Bethesda, MD, 20892, USA.
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Suehiro T, Ahmad KM, Hoang NTD, Xu B, Komatsu H, Kurachi K, Nikawa H, Mine Y, Matsuki T, Asano K, Fujii M. Activation of platelet-derived growth factor receptors regulate connective tissue growth factor protein levels via the AKT pathway in malignant mesothelioma cells. J Biochem 2024; 176:460-471. [PMID: 39441675 DOI: 10.1093/jb/mvae068] [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: 03/25/2024] [Revised: 08/28/2024] [Accepted: 09/11/2024] [Indexed: 10/25/2024] Open
Abstract
The incidence of malignant mesothelioma (MM), a disease linked to refractory asbestos exposure, continues to increase globally and remains largely resistant to various treatments. Our previous studies have identified a strong correlation between connective tissue growth factor (CTGF) protein expression and MM malignancy, underscoring the importance of understanding CTGF regulation in MM cells. In this study, we demonstrate for the first time that stimulation with platelet-derived growth factor receptor (PDGFR) ligand, PDGF-BB, increases CTGF protein expression levels without affecting CTGF mRNA levels. Inhibition of PDGFR resulted in a reduction of CTGF protein expression, indicating that PDGFR activation is essential in regulating CTGF protein expression in MM cells. PDGF-BB also activated the protein kinase B (AKT) pathway, and inhibition of AKT phosphorylation abolished the PDGFR-induced CTGF protein expression, suggesting that PDGFR acts upstream of CTGF via the AKT pathway. This reinforces the role of CTGF protein as a key regulator of MM malignancy. Additionally, PDGFR activation led to the phosphorylation of mTOR and 4E-BP1, critical regulators of protein synthesis downstream of AKT, suggesting that PDGFR controls CTGF protein expression through the regulation of CTGF mRNA translation.
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Affiliation(s)
- Tomoya Suehiro
- Department of Genomic Oncology and Oral Medicine, Graduate School of Biomedical and Health Science, Hiroshima University, 1-2-3 Kasumi Minami-ku, Hiroshima 734-8553, Japan
| | - Khoja Mouhand Ahmad
- Department of Genomic Oncology and Oral Medicine, Graduate School of Biomedical and Health Science, Hiroshima University, 1-2-3 Kasumi Minami-ku, Hiroshima 734-8553, Japan
| | - Nguyen Truong Duc Hoang
- Oncology Department, Faculty of Medicine, University of Medicine and Pharmacy at Ho Chi Minh City, 217 Hong Bang, Ward 11, District 5, Ho Chi Minh 70000, Vietnam
| | - Bingwen Xu
- Department of Genomic Oncology and Oral Medicine, Graduate School of Biomedical and Health Science, Hiroshima University, 1-2-3 Kasumi Minami-ku, Hiroshima 734-8553, Japan
| | - Honoka Komatsu
- Department of Genomic Oncology and Oral Medicine, Graduate School of Biomedical and Health Science, Hiroshima University, 1-2-3 Kasumi Minami-ku, Hiroshima 734-8553, Japan
| | - Komei Kurachi
- Department of Genomic Oncology and Oral Medicine, Graduate School of Biomedical and Health Science, Hiroshima University, 1-2-3 Kasumi Minami-ku, Hiroshima 734-8553, Japan
| | - Hiroki Nikawa
- Department of Oral Biology and Engineering, Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3 Kasumi Minami-ku, Hiroshima 734-8553, Japan
| | - Yuichi Mine
- Department of Medical Systems Engineering, Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3 Kasumi Minami-ku, Hiroshima 734-8553, Japan
| | - Tohru Matsuki
- Department of Cellular Pathology, Institute for Developmental Research, Aichi Developmental Disability Center, 713-8 Kamiya, Kasugai, Aichi, 480-0304, Japan
| | - Katsura Asano
- Molecular Cellular and Developmental Biology Program, Division of Biology, Kansas State University, 116 Ackert Hall, Manhattan, KS 66506, USA
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan
- Hiroshima Research Center for Healthy Aging, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan
| | - Makiko Fujii
- Department of Genomic Oncology and Oral Medicine, Graduate School of Biomedical and Health Science, Hiroshima University, 1-2-3 Kasumi Minami-ku, Hiroshima 734-8553, Japan
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Verhey TB, Seo H, Gillmor A, Thoppey-Manoharan V, Schriemer D, Morrissy S. mosaicMPI: a framework for modular data integration across cohorts and -omics modalities. Nucleic Acids Res 2024; 52:e53. [PMID: 38813827 PMCID: PMC11229337 DOI: 10.1093/nar/gkae442] [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: 09/02/2023] [Revised: 04/26/2024] [Accepted: 05/10/2024] [Indexed: 05/31/2024] Open
Abstract
Advances in molecular profiling have facilitated generation of large multi-modal datasets that can potentially reveal critical axes of biological variation underlying complex diseases. Distilling biological meaning, however, requires computational strategies that can perform mosaic integration across diverse cohorts and datatypes. Here, we present mosaicMPI, a framework for discovery of low to high-resolution molecular programs representing both cell types and states, and integration within and across datasets into a network representing biological themes. Using existing datasets in glioblastoma, we demonstrate that this approach robustly integrates single cell and bulk programs across multiple platforms. Clinical and molecular annotations from cohorts are statistically propagated onto this network of programs, yielding a richly characterized landscape of biological themes. This enables deep understanding of individual tumor samples, systematic exploration of relationships between modalities, and generation of a reference map onto which new datasets can rapidly be mapped. mosaicMPI is available at https://github.com/MorrissyLab/mosaicMPI.
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Affiliation(s)
- Theodore B Verhey
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta, Canada
- Charbonneau Cancer institute, University of Calgary, Calgary, Alberta, Canada
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Alberta, Canada
| | - Heewon Seo
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta, Canada
- Charbonneau Cancer institute, University of Calgary, Calgary, Alberta, Canada
| | - Aaron Gillmor
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta, Canada
- Charbonneau Cancer institute, University of Calgary, Calgary, Alberta, Canada
| | - Varsha Thoppey-Manoharan
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta, Canada
- Charbonneau Cancer institute, University of Calgary, Calgary, Alberta, Canada
| | - David Schriemer
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta, Canada
- Charbonneau Cancer institute, University of Calgary, Calgary, Alberta, Canada
| | - Sorana Morrissy
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta, Canada
- Charbonneau Cancer institute, University of Calgary, Calgary, Alberta, Canada
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Alberta, Canada
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Gillette MA, Jimenez CR, Carr SA. Clinical Proteomics: A Promise Becoming Reality. Mol Cell Proteomics 2024; 23:100688. [PMID: 38281326 PMCID: PMC10926064 DOI: 10.1016/j.mcpro.2023.100688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2024] Open
Affiliation(s)
- Michael A Gillette
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA; Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Connie R Jimenez
- Amsterdam University Medical Center, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Steven A Carr
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA
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Liu Y, Elmas A, Huang KL. Mutation Impact on mRNA Versus Protein Expression across Human Cancers. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.13.566942. [PMID: 38014015 PMCID: PMC10680725 DOI: 10.1101/2023.11.13.566942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Cancer mutations are often assumed to alter proteins, thus promoting tumorigenesis. However, how mutations affect protein expression has rarely been systematically investigated. We conduct a comprehensive analysis of mutation impacts on mRNA- and protein-level expressions of 953 cancer cases with paired genomics and global proteomic profiling across six cancer types. Protein-level impacts are validated for 47.2% of the somatic expression quantitative trait loci (seQTLs), including mutations from likely "long-tail" driver genes. Devising a statistical pipeline for identifying somatic protein-specific QTLs (spsQTLs), we reveal several gene mutations, including NF1 and MAP2K4 truncations and TP53 missenses showing disproportional influence on protein abundance not readily explained by transcriptomics. Cross-validating with data from massively parallel assays of variant effects (MAVE), TP53 missenses associated with high tumor TP53 proteins were experimentally confirmed as functional. Our study demonstrates the importance of considering protein-level expression to validate mutation impacts and identify functional genes and mutations.
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Affiliation(s)
- Yuqi Liu
- Center for Transformative Disease Modeling, Department of Genetics and Genomic Sciences, Tisch Cancer Institute, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Abdulkadir Elmas
- Center for Transformative Disease Modeling, Department of Genetics and Genomic Sciences, Tisch Cancer Institute, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Kuan-lin Huang
- Center for Transformative Disease Modeling, Department of Genetics and Genomic Sciences, Tisch Cancer Institute, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
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