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Marques A, Cavaco P, Torre C, Sepodes B, Rocha J. Tumor mutational burden in colorectal cancer: Implications for treatment. Crit Rev Oncol Hematol 2024; 197:104342. [PMID: 38614266 DOI: 10.1016/j.critrevonc.2024.104342] [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: 01/26/2024] [Revised: 03/27/2024] [Accepted: 03/29/2024] [Indexed: 04/15/2024] Open
Abstract
Although immune checkpoint inhibitors have revolutionized the treatment of several advanced solid cancers, in colorectal cancer, the transformative benefit of these innovative medicines is currently limited to those with deficient mismatch repair or high microsatellite instability. Tumor mutational burden (TMB) has emerged as a potential predictor of immunotherapy benefit, but the lack of standardization in its assessment and reporting has hindered the introduction of this biomarker in routine clinical practice. Here, we compiled 45 colorectal cancer studies utilizing numerical thresholds for high-TMB. In this group of studies, TMB cut-offs ranged from 6.88 to 41 mut/Mb and were most often set at 10, 17, or 20 mut/Mb. Additionally, we observed divergent TMB definitions and inconsistent disclosure of specific methodological details, which collectively emphasize the substantial lack of harmonization within the field. Ongoing efforts to harmonize TMB assessment will be critical to validate TMB as a predictive marker of immunotherapy response.
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Affiliation(s)
- Adriana Marques
- Research Institute for Medicines (iMed.ULisboa), Lisboa 1649-003, Portugal; Faculdade de Farmácia, Universidade de Lisboa, Lisboa 1649-003, Portugal
| | - Patrícia Cavaco
- Research Institute for Medicines (iMed.ULisboa), Lisboa 1649-003, Portugal; Faculdade de Farmácia, Universidade de Lisboa, Lisboa 1649-003, Portugal; Pharmacy Department, Centro Hospitalar de Lisboa Ocidental, Lisboa 1449-005, Portugal
| | - Carla Torre
- Research Institute for Medicines (iMed.ULisboa), Lisboa 1649-003, Portugal; Faculdade de Farmácia, Universidade de Lisboa, Lisboa 1649-003, Portugal
| | - Bruno Sepodes
- Research Institute for Medicines (iMed.ULisboa), Lisboa 1649-003, Portugal; Faculdade de Farmácia, Universidade de Lisboa, Lisboa 1649-003, Portugal
| | - João Rocha
- Research Institute for Medicines (iMed.ULisboa), Lisboa 1649-003, Portugal; Faculdade de Farmácia, Universidade de Lisboa, Lisboa 1649-003, Portugal.
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Matzinger M, Schmücker A, Yelagandula R, Stejskal K, Krššáková G, Berger F, Mechtler K, Mayer RL. Micropillar arrays, wide window acquisition and AI-based data analysis improve comprehensiveness in multiple proteomic applications. Nat Commun 2024; 15:1019. [PMID: 38310095 PMCID: PMC10838342 DOI: 10.1038/s41467-024-45391-z] [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: 03/02/2023] [Accepted: 01/19/2024] [Indexed: 02/05/2024] Open
Abstract
Comprehensive proteomic analysis is essential to elucidate molecular pathways and protein functions. Despite tremendous progress in proteomics, current studies still suffer from limited proteomic coverage and dynamic range. Here, we utilize micropillar array columns (µPACs) together with wide-window acquisition and the AI-based CHIMERYS search engine to achieve excellent proteomic comprehensiveness for bulk proteomics, affinity purification mass spectrometry and single cell proteomics. Our data show that µPACs identify ≤50% more peptides and ≤24% more proteins, while offering improved throughput, which is critical for large (clinical) proteomics studies. Combining wide precursor isolation widths of m/z 4-12 with the CHIMERYS search engine identified +51-74% and +59-150% more proteins and peptides, respectively, for single cell, co-immunoprecipitation, and multi-species samples over a conventional workflow at well-controlled false discovery rates. The workflow further offers excellent precision, with CVs <7% for low input bulk samples, and accuracy, with deviations <10% from expected fold changes for regular abundance two-proteome mixes. Compared to a conventional workflow, our entire optimized platform discovered 92% more potential interactors in a protein-protein interaction study on the chromatin remodeler Smarca5/Snf2h. These include previously described Smarca5 binding partners and undescribed ones including Arid1a, another chromatin remodeler with key roles in neurodevelopmental and malignant disorders.
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Affiliation(s)
- Manuel Matzinger
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter, Vienna, Austria.
| | - Anna Schmücker
- Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
- MRC (Medical Research Council) London Institute of Medical Sciences, Du Cane Road, London, W12 0NN, UK
- Institute of Clinical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Ramesh Yelagandula
- Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
- Institute of Molecular Biotechnology (IMBA), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
- Laboratory of Epigenetics, Cell Fate & Disease, Centre for DNA Fingerprinting and Diagnostics (CDFD), Uppal, Hyderabad, India
| | - Karel Stejskal
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter, Vienna, Austria
- Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
- Institute of Molecular Biotechnology (IMBA), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
| | - Gabriela Krššáková
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter, Vienna, Austria
- Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
- Institute of Molecular Biotechnology (IMBA), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
| | - Frédéric Berger
- Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
| | - Karl Mechtler
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter, Vienna, Austria.
- Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria.
- Institute of Molecular Biotechnology (IMBA), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria.
| | - Rupert L Mayer
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter, Vienna, Austria.
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Shang P, Lu J, Song F, Zhao Y, Hong W, He Y, Shen W, Geng L. RNF43 is associated with genomic features and clinical outcome in BRAF mutant colorectal cancer. Front Oncol 2023; 13:1119587. [PMID: 37409251 PMCID: PMC10319416 DOI: 10.3389/fonc.2023.1119587] [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: 12/09/2022] [Accepted: 03/27/2023] [Indexed: 07/07/2023] Open
Abstract
Background Colorectal cancer (CRC) patients with BRAF mutation have very poor prognosis. It is urgent to search for prognostic factors of BRAF mutant CRC. RNF43 is a ENF ubiquitin ligase of Wnt signaling. Mutation of RNF43 has been observed frequently in various types of human cancers. However, few studies have evaluated the role of RNF43 in CRC. The present study aimed to explore the impact of RNF43 mutations on molecular characteristics and prognosis in BRAF mutant CRC. Methods Samples of 261 CRC patients with BRAF mutation were retrospectively analyzed. Tumor tissue and matched peripheral blood samples were collected and subjected to targeted sequencing with a panel of 1021 cancer-related genes. The association of molecular characteristics and survival in patients were then analyzed. 358 CRC patients with BRAF mutation from the cBioPortal dataset were used for further confirmation. Results This study was inspired by a CRC patient with BRAF V600E and RNF43 co-mutation, who achieved a best remission of 70% and a progression free survival (PFS) of 13 months. Genomic analysis indicated that RNF43 mutation affected the genomic characteristics of patients with BRAF mutation, including microsatellite instability (MSI), tumor mutation burden (TMB) and the proportion of common gene mutations. Survival analysis showed that RNF43 mutation was a predictive biomarker for better PFS and OS in BRAF mutant CRC. Conclusion Collectively, we identified that RNF43 mutations were correlated with favorable genomic features, resulting in a better clinical outcome for BRAF mutant CRC patients.
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Affiliation(s)
- Peipei Shang
- Oncology Department, Eastern Hepatobiliary Surgical Hospital, Shanghai, China
| | - Jiongjiong Lu
- Department of Special Treatment, Eastern Hepatobiliary Surgical Hospital, Shanghai, China
| | - Feihong Song
- Department of Special Treatment, Eastern Hepatobiliary Surgical Hospital, Shanghai, China
| | - Yijun Zhao
- Department of Special Treatment, Eastern Hepatobiliary Surgical Hospital, Shanghai, China
| | - Weipeng Hong
- Department of Medical Center, Geneplus-Beijing Ltd., Beijing, China
| | - Yuange He
- Department of Medical Center, Geneplus-Beijing Ltd., Beijing, China
| | - Weidong Shen
- Department of Medical Center, Geneplus-Beijing Ltd., Beijing, China
| | - Li Geng
- Department of Special Treatment, Eastern Hepatobiliary Surgical Hospital, Shanghai, China
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Lebedev T, Kousar R, Patrick B, Usama M, Lee MK, Tan M, Li XG. Targeting ARID1A-Deficient Cancers: An Immune-Metabolic Perspective. Cells 2023; 12:cells12060952. [PMID: 36980292 PMCID: PMC10047504 DOI: 10.3390/cells12060952] [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: 01/01/2023] [Revised: 03/14/2023] [Accepted: 03/16/2023] [Indexed: 03/30/2023] Open
Abstract
Epigenetic remodeling and metabolic reprogramming, two well-known cancer hallmarks, are highly intertwined. In addition to their abilities to confer cancer cell growth advantage, these alterations play a critical role in dynamically shaping the tumor microenvironment and antitumor immunity. Recent studies point toward the interplay between epigenetic regulation and metabolic rewiring as a potentially targetable Achilles' heel in cancer. In this review, we explore the key metabolic mechanisms that underpin the immunomodulatory role of AT-rich interaction domain 1A (ARID1A), the most frequently mutated epigenetic regulator across human cancers. We will summarize the recent advances in targeting ARID1A-deficient cancers by harnessing immune-metabolic vulnerability elicited by ARID1A deficiency to stimulate antitumor immune response, and ultimately, to improve patient outcome.
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Affiliation(s)
- Timofey Lebedev
- Department of Cancer Cell Biology, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Rubina Kousar
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung 110122, Taiwan
- Research Center for Cancer Biology, China Medical University, Taichung 110122, Taiwan
- Institute of Biochemistry and Molecular Biology, College of Life Sciences, China Medical University, Taichung 110122, Taiwan
| | - Bbumba Patrick
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung 110122, Taiwan
- Research Center for Cancer Biology, China Medical University, Taichung 110122, Taiwan
- Institute of Biochemistry and Molecular Biology, College of Life Sciences, China Medical University, Taichung 110122, Taiwan
| | - Muhammad Usama
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung 110122, Taiwan
- Research Center for Cancer Biology, China Medical University, Taichung 110122, Taiwan
- Institute of Biochemistry and Molecular Biology, College of Life Sciences, China Medical University, Taichung 110122, Taiwan
| | - Meng-Kuei Lee
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung 110122, Taiwan
- Research Center for Cancer Biology, China Medical University, Taichung 110122, Taiwan
- Institute of Biochemistry and Molecular Biology, College of Life Sciences, China Medical University, Taichung 110122, Taiwan
| | - Ming Tan
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung 110122, Taiwan
- Research Center for Cancer Biology, China Medical University, Taichung 110122, Taiwan
- Institute of Biochemistry and Molecular Biology, College of Life Sciences, China Medical University, Taichung 110122, Taiwan
| | - Xing-Guo Li
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung 110122, Taiwan
- Research Center for Cancer Biology, China Medical University, Taichung 110122, Taiwan
- Institute of Biochemistry and Molecular Biology, College of Life Sciences, China Medical University, Taichung 110122, Taiwan
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Nguyen VT, Tessema M, Weissman BE. The SWI/SNF Complex: A Frequently Mutated Chromatin Remodeling Complex in Cancer. Cancer Treat Res 2023; 190:211-244. [PMID: 38113003 DOI: 10.1007/978-3-031-45654-1_7] [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: 12/21/2023]
Abstract
The switch/sucrose non-fermenting (SWI/SNF) chromatin remodeling complex is a global regulator of gene expression known to maintain nucleosome-depleted regions at active enhancers and promoters. The mammalian SWI/SNF protein subunits are encoded by 29 genes and 11-15 subunits including an ATPase domain of either SMARCA4 (BRG1) or SMARCA2 (BRM) are assembled into a complex. Based on the distinct subunits, SWI/SNF are grouped into 3 major types (subfamilies): the canonical BRG1/BRM-associated factor (BAF/cBAF), polybromo-associated BAF (PBAF), and non-canonical BAF (GBAF/ncBAF). Pan-cancer genome sequencing studies have shown that nearly 25% of all cancers bear mutations in subunits of the SWI/SNF complex, many of which are loss of function (LOF) mutations, suggesting a tumor suppressor role. Inactivation of SWI/SNF complex subunits causes widespread epigenetic dysfunction, including increased dependence on antagonistic components such as polycomb repressor complexes (PRC1/2) and altered enhancer regulation, likely promoting an oncogenic state leading to cancer. Despite the prevalence of mutations, most SWI/SNF-mutant cancers lack targeted therapeutic strategies. Defining the dependencies created by LOF mutations in SWI/SNF subunits will identify better targets for these cancers.
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Affiliation(s)
- Vinh The Nguyen
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
- Curriculum in Toxicology and Environmental Medicine, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
| | - Mathewos Tessema
- Lung Cancer Program, Lovelace Biomedical Research Institute, Albuquerque, NM, USA
| | - Bernard Ellis Weissman
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA.
- Curriculum in Toxicology and Environmental Medicine, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA.
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA.
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Mandal J, Mandal P, Wang TL, Shih IM. Treating ARID1A mutated cancers by harnessing synthetic lethality and DNA damage response. J Biomed Sci 2022; 29:71. [PMID: 36123603 PMCID: PMC9484255 DOI: 10.1186/s12929-022-00856-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 09/13/2022] [Indexed: 11/10/2022] Open
Abstract
Chromatin remodeling is an essential cellular process for organizing chromatin structure into either open or close configuration at specific chromatin locations by orchestrating and modifying histone complexes. This task is responsible for fundamental cell physiology including transcription, DNA replication, methylation, and damage repair. Aberrations in this activity have emerged as epigenomic mechanisms in cancer development that increase tumor clonal fitness and adaptability amidst various selection pressures. Inactivating mutations in AT-rich interaction domain 1A (ARID1A), a gene encoding a large nuclear protein member belonging to the SWI/SNF chromatin remodeling complex, result in its loss of expression. ARID1A is the most commonly mutated chromatin remodeler gene, exhibiting the highest mutation frequency in endometrium-related uterine and ovarian carcinomas. As a tumor suppressor gene, ARID1A is essential for regulating cell cycle, facilitating DNA damage repair, and controlling expression of genes that are essential for maintaining cellular differentiation and homeostasis in non-transformed cells. Thus, ARID1A deficiency due to somatic mutations propels tumor progression and dissemination. The recent success of PARP inhibitors in treating homologous recombination DNA repair-deficient tumors has engendered keen interest in developing synthetic lethality-based therapeutic strategies for ARID1A-mutated neoplasms. In this review, we summarize recent advances in understanding the biology of ARID1A in cancer development, with special emphasis on its roles in DNA damage repair. We also discuss strategies to harness synthetic lethal mechanisms for future therapeutics against ARID1A-mutated cancers.
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Affiliation(s)
- Jayaprakash Mandal
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | - Tian-Li Wang
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Ie-Ming Shih
- Department of Gynecology and Obstetrics, Johns Hopkins University School of Medicine, Baltimore, USA.
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