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McCool MA, Bryant CJ, Abriola L, Surovtseva YV, Baserga SJ. The cytidine deaminase APOBEC3A regulates nucleolar function to promote cell growth and ribosome biogenesis. PLoS Biol 2024; 22:e3002718. [PMID: 38976757 DOI: 10.1371/journal.pbio.3002718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Accepted: 06/20/2024] [Indexed: 07/10/2024] Open
Abstract
Cancer initiates as a consequence of genomic mutations and its subsequent progression relies in part on increased production of ribosomes to maintain high levels of protein synthesis for unchecked cell growth. Recently, cytidine deaminases have been uncovered as sources of mutagenesis in cancer. In an attempt to form a connection between these 2 cancer driving processes, we interrogated the cytidine deaminase family of proteins for potential roles in human ribosome biogenesis. We identified and validated APOBEC3A and APOBEC4 as novel ribosome biogenesis factors through our laboratory's established screening platform for the discovery of regulators of nucleolar function in MCF10A cells. Through siRNA depletion experiments, we highlight APOBEC3A's requirement in making ribosomes and specific role within the processing and maturation steps that form the large subunit 5.8S and 28S ribosomal (r)RNAs. We demonstrate that a subset of APOBEC3A resides within the nucleolus and associates with critical ribosome biogenesis factors. Mechanistic insight was revealed by transient overexpression of both wild-type and a catalytically dead mutated APOBEC3A, which both increase cell growth and protein synthesis. Through an innovative nuclear RNA sequencing methodology, we identify only modest predicted APOBEC3A C-to-U target sites on the pre-rRNA and pre-mRNAs. Our work reveals a potential direct role for APOBEC3A in ribosome biogenesis likely independent of its editing function. More broadly, we found an additional function of APOBEC3A in cancer pathology through its function in ribosome biogenesis, expanding its relevance as a target for cancer therapeutics.
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Affiliation(s)
- Mason A McCool
- Department of Molecular Biophysics & Biochemistry, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Carson J Bryant
- Department of Molecular Biophysics & Biochemistry, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Laura Abriola
- Yale Center for Molecular Discovery, Yale University, West Haven, Connecticut, United States of America
| | - Yulia V Surovtseva
- Yale Center for Molecular Discovery, Yale University, West Haven, Connecticut, United States of America
| | - Susan J Baserga
- Department of Molecular Biophysics & Biochemistry, Yale University School of Medicine, New Haven, Connecticut, United States of America
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, United States of America
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, Connecticut, United States of America
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2
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Brown GW. The cytidine deaminase APOBEC3C has unique sequence and genome feature preferences. Genetics 2024:iyae092. [PMID: 38946641 DOI: 10.1093/genetics/iyae092] [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: 01/17/2024] [Accepted: 05/22/2024] [Indexed: 07/02/2024] Open
Abstract
APOBEC proteins are cytidine deaminases that restrict the replication of viruses and transposable elements. Several members of the APOBEC3 family, APOBEC3A, APOBEC3B, and APOBEC3H-I, can access the nucleus and cause what is thought to be indiscriminate deamination of the genome, resulting in mutagenesis and genome instability. Although APOBEC3C is also present in the nucleus, the full scope of its deamination target preferences is unknown. By expressing human APOBEC3C in a yeast model system, I have defined the APOBEC3C mutation signature, as well as the preferred genome features of APOBEC3C targets. The APOBEC3C mutation signature is distinct from those of the known cancer genome mutators APOBEC3A and APOBEC3B. APOBEC3C produces DNA strand-coordinated mutation clusters, and APOBEC3C mutations are enriched near the transcription start sites of active genes. Surprisingly, APOBEC3C lacks the bias for the lagging strand of DNA replication that is seen for APOBEC3A and APOBEC3B. The unique preferences of APOBEC3C constitute a mutation profile that will be useful in defining sites of APOBEC3C mutagenesis in human genomes.
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Affiliation(s)
- Grant W Brown
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, ON, Canada M5S 1A8
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON, Canada M5S 3E1
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3
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Martinek R, Lózsa R, Póti Á, Németh E, Várady G, Szabó P, Szüts D. Comprehensive investigation of the mutagenic potential of six pesticides classified by IARC as probably carcinogenic to humans. CHEMOSPHERE 2024; 362:142700. [PMID: 38936485 DOI: 10.1016/j.chemosphere.2024.142700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2024] [Revised: 06/13/2024] [Accepted: 06/23/2024] [Indexed: 06/29/2024]
Abstract
Pesticides are significant environmental pollutants, and many of them possess mutagenic potential, which is closely linked to carcinogenesis. Here we tested the mutagenicity of all six pesticides classified probably carcinogenic (Group 2A) by the International Agency of Research on Cancer: 4,4'-DDT, captafol, dieldrin, diazinon, glyphosate and malathion. Whole genome sequencing of TK6 human lymphoblastoid cell clones following 30-day exposure at subtoxic concentrations revealed a clear mutagenic effect of treatment with captafol or malathion when added at 200 nM or 100 μM initial concentrations, respectively. Each pesticide induced a specific base substitution mutational signature: captafol increased C to A mutations primarily, while malathion induced mostly C to T mutations. 4,4'-DDT, dieldrin, diazinon and glyphosate were not mutagenic. Whereas captafol induced chromosomal instability, H2A.X phosphorylation and cell cycle arrest in G2/M phase, all indicating DNA damage, malathion did not induce DNA damage markers or cell cycle alterations despite its mutagenic effect. Hypersensitivity of REV1 and XPA mutant DT40 chicken cell lines suggests that captafol induces DNA adducts that are bypassed by translesion DNA synthesis and are targets for nucleotide excision repair. The experimentally identified mutational signatures of captafol and malathion could shed light on the mechanism of action of these compounds. The signatures are potentially suitable for detecting past exposure in tumour samples, but the reanalysis of large cancer genome databases did not reveal any evidence of captafol or malathion exposure.
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Affiliation(s)
- Regina Martinek
- Institute of Molecular Life Sciences, HUN-REN Research Centre for Natural Sciences, Magyar Tudósok körútja 2, Budapest, H-1117, Hungary; Doctoral School of Biology, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/C, Budapest, H-1117, Hungary.
| | - Rita Lózsa
- Institute of Molecular Life Sciences, HUN-REN Research Centre for Natural Sciences, Magyar Tudósok körútja 2, Budapest, H-1117, Hungary.
| | - Ádám Póti
- Institute of Molecular Life Sciences, HUN-REN Research Centre for Natural Sciences, Magyar Tudósok körútja 2, Budapest, H-1117, Hungary.
| | - Eszter Németh
- Institute of Molecular Life Sciences, HUN-REN Research Centre for Natural Sciences, Magyar Tudósok körútja 2, Budapest, H-1117, Hungary.
| | - György Várady
- Institute of Molecular Life Sciences, HUN-REN Research Centre for Natural Sciences, Magyar Tudósok körútja 2, Budapest, H-1117, Hungary.
| | - Pál Szabó
- Institute of Molecular Life Sciences, HUN-REN Research Centre for Natural Sciences, Magyar Tudósok körútja 2, Budapest, H-1117, Hungary.
| | - Dávid Szüts
- Institute of Molecular Life Sciences, HUN-REN Research Centre for Natural Sciences, Magyar Tudósok körútja 2, Budapest, H-1117, Hungary.
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Hakobyan A, Meyenberg M, Vardazaryan N, Hancock J, Vulliard L, Loizou JI, Menche J. Pan-cancer analysis of the interplay between mutational signatures and cellular signaling. iScience 2024; 27:109873. [PMID: 38783997 PMCID: PMC11112613 DOI: 10.1016/j.isci.2024.109873] [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: 07/18/2023] [Revised: 12/19/2023] [Accepted: 04/29/2024] [Indexed: 05/25/2024] Open
Abstract
Cancer is a multi-faceted disease with intricate relationships between mutagenic processes, alterations in cellular signaling, and the tissue microenvironment. To date, these processes have been largely studied in isolation. A systematic understanding of how they interact and influence each other is lacking. Here, we present a framework for systematically characterizing the interaction between pairs of mutational signatures and between signatures and signaling pathway alterations. We applied this framework to large-scale data from TCGA and PCAWG and identified multiple positive and negative interactions, both cross֊tissue and tissue֊specific, that provide new insights into the molecular routes observed in tumorigenesis and their respective drivers. This framework allows for a more fine-grained dissection of common and distinct etiology of mutational signatures. We further identified several interactions with both positive and negative impacts on patient survival, demonstrating their clinical relevance and potential for improving personalized cancer care.
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Affiliation(s)
- Anna Hakobyan
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT25.3, 1090 Vienna, Austria
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Dr.-Bohr-Gasse 9, 1030 Vienna, Austria
- University of Vienna, Center for Molecular Biology, Department of Structural and Computational Biology, Dr.-Bohr-Gasse 9, 1030 Vienna, Austria
| | - Mathilde Meyenberg
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT25.3, 1090 Vienna, Austria
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Dr.-Bohr-Gasse 9, 1030 Vienna, Austria
- University of Vienna, Center for Molecular Biology, Department of Structural and Computational Biology, Dr.-Bohr-Gasse 9, 1030 Vienna, Austria
- Center for Cancer Research, Comprehensive Cancer Center, Medical University of Vienna, Spitalgasse 23, BT86/E 01, 1090 Vienna, Austria
| | - Nelli Vardazaryan
- Armenian Bioinformatics Institute, 3/6 Nelson Stepanyan, 0062 Yerevan, Armenia
| | - Joel Hancock
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT25.3, 1090 Vienna, Austria
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Dr.-Bohr-Gasse 9, 1030 Vienna, Austria
- University of Vienna, Center for Molecular Biology, Department of Structural and Computational Biology, Dr.-Bohr-Gasse 9, 1030 Vienna, Austria
| | - Loan Vulliard
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT25.3, 1090 Vienna, Austria
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Dr.-Bohr-Gasse 9, 1030 Vienna, Austria
- University of Vienna, Center for Molecular Biology, Department of Structural and Computational Biology, Dr.-Bohr-Gasse 9, 1030 Vienna, Austria
| | - Joanna I. Loizou
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT25.3, 1090 Vienna, Austria
- Center for Cancer Research, Comprehensive Cancer Center, Medical University of Vienna, Spitalgasse 23, BT86/E 01, 1090 Vienna, Austria
| | - Jörg Menche
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT25.3, 1090 Vienna, Austria
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Dr.-Bohr-Gasse 9, 1030 Vienna, Austria
- University of Vienna, Center for Molecular Biology, Department of Structural and Computational Biology, Dr.-Bohr-Gasse 9, 1030 Vienna, Austria
- Faculty of Mathematics, University of Vienna, Oskar-Morgenstern-Platz 1, 1090 Vienna, Austria
- Ludwig Boltzmann Institute for Network Medicine at the University of Vienna, Augasse 2-6, 1090 Vienna, Austria
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5
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Ji Q, Zheng Y, Zhou L, Chen F, Li W. Unveiling divergent treatment prognoses in IDHwt-GBM subtypes through multiomics clustering: a swift dual MRI-mRNA model for precise subtype prediction. J Transl Med 2024; 22:578. [PMID: 38890658 PMCID: PMC11186189 DOI: 10.1186/s12967-024-05401-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2024] [Accepted: 06/13/2024] [Indexed: 06/20/2024] Open
Abstract
BACKGROUND IDH1-wildtype glioblastoma multiforme (IDHwt-GBM) is a highly heterogeneous and aggressive brain tumour characterised by a dismal prognosis and significant challenges in accurately predicting patient outcomes. To address these issues and personalise treatment approaches, we aimed to develop and validate robust multiomics molecular subtypes of IDHwt-GBM. Through this, we sought to uncover the distinct molecular signatures underlying these subtypes, paving the way for improved diagnosis and targeted therapy for this challenging disease. METHODS To identify stable molecular subtypes among 184 IDHwt-GBM patients from TCGA, we used the consensus clustering method to consolidate the results from ten advanced multiomics clustering approaches based on mRNA, lncRNA, and mutation data. We developed subtype prediction models using the PAM and machine learning algorithms based on mRNA and MRI data for enhanced clinical utility. These models were validated in five independent datasets, and an online interactive system was created. We conducted a comprehensive assessment of the clinical impact, drug treatment response, and molecular associations of the IDHwt-GBM subtypes. RESULTS In the TCGA cohort, two molecular subtypes, class 1 and class 2, were identified through multiomics clustering of IDHwt-GBM patients. There was a significant difference in survival between Class 1 and Class 2 patients, with a hazard ratio (HR) of 1.68 [1.15-2.47]. This difference was validated in other datasets (CGGA: HR = 1.75[1.04, 2.94]; CPTAC: HR = 1.79[1.09-2.91]; GALSS: HR = 1.66[1.09-2.54]; UCSF: HR = 1.33[1.00-1.77]; UPENN HR = 1.29[1.04-1.58]). Additionally, class 2 was more sensitive to treatment with radiotherapy combined with temozolomide, and this sensitivity was validated in the GLASS cohort. Correspondingly, class 2 and class 1 exhibited significant differences in mutation patterns, enriched pathways, programmed cell death (PCD), and the tumour immune microenvironment. Class 2 had more mutation signatures associated with defective DNA mismatch repair (P = 0.0021). Enriched pathways of differentially expressed genes in class 1 and class 2 (P-adjust < 0.05) were mainly related to ferroptosis, the PD-1 checkpoint pathway, the JAK-STAT signalling pathway, and other programmed cell death and immune-related pathways. The different cell death modes and immune microenvironments were validated across multiple datasets. Finally, our developed survival prediction model, which integrates molecular subtypes, age, and sex, demonstrated clinical benefits based on the decision curve in the test set. We deployed the molecular subtyping prediction model and survival prediction model online, allowing interactive use and facilitating user convenience. CONCLUSIONS Molecular subtypes were identified and verified through multiomics clustering in IDHwt-GBM patients. These subtypes are linked to specific mutation patterns, the immune microenvironment, prognoses, and treatment responses.
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Affiliation(s)
- Qiang Ji
- Department of Neuro-Oncology, Cancer Center, China National Clinical Research Center for Neurological Diseases, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- National Institute for Data Science in Health and Medicine, Capital Medical University, Beijing, China
| | - Yi Zheng
- Department of Neuro-Oncology, Cancer Center, China National Clinical Research Center for Neurological Diseases, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- China National Clinical Research Center for Neurological Diseases, Beijing, China
| | - Lili Zhou
- Department of Neuro-Oncology, Cancer Center, China National Clinical Research Center for Neurological Diseases, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Feng Chen
- Department of Neuro-Oncology, Cancer Center, China National Clinical Research Center for Neurological Diseases, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.
| | - Wenbin Li
- Department of Neuro-Oncology, Cancer Center, China National Clinical Research Center for Neurological Diseases, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.
- National Institute for Data Science in Health and Medicine, Capital Medical University, Beijing, China.
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6
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Fingerman DF, O'Leary DR, Hansen AR, Tran T, Harris BR, DeWeerd RA, Hayer KE, Fan J, Chen E, Tennakoon M, Meroni A, Szeto JH, Devenport J, LaVigne D, Weitzman MD, Shalem O, Bednarski J, Vindigni A, Zhao X, Green AM. The SMC5/6 complex prevents genotoxicity upon APOBEC3A-mediated replication stress. EMBO J 2024:10.1038/s44318-024-00137-x. [PMID: 38886582 DOI: 10.1038/s44318-024-00137-x] [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: 01/22/2024] [Revised: 05/09/2024] [Accepted: 05/17/2024] [Indexed: 06/20/2024] Open
Abstract
Mutational patterns caused by APOBEC3 cytidine deaminase activity are evident throughout human cancer genomes. In particular, the APOBEC3A family member is a potent genotoxin that causes substantial DNA damage in experimental systems and human tumors. However, the mechanisms that ensure genome stability in cells with active APOBEC3A are unknown. Through an unbiased genome-wide screen, we define the Structural Maintenance of Chromosomes 5/6 (SMC5/6) complex as essential for cell viability when APOBEC3A is active. We observe an absence of APOBEC3A mutagenesis in human tumors with SMC5/6 dysfunction, consistent with synthetic lethality. Cancer cells depleted of SMC5/6 incur substantial genome damage from APOBEC3A activity during DNA replication. Further, APOBEC3A activity results in replication tract lengthening which is dependent on PrimPol, consistent with re-initiation of DNA synthesis downstream of APOBEC3A-induced lesions. Loss of SMC5/6 abrogates elongated replication tracts and increases DNA breaks upon APOBEC3A activity. Our findings indicate that replication fork lengthening reflects a DNA damage response to APOBEC3A activity that promotes genome stability in an SMC5/6-dependent manner. Therefore, SMC5/6 presents a potential therapeutic vulnerability in tumors with active APOBEC3A.
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Affiliation(s)
- Dylan F Fingerman
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Genome Integrity, Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA
| | - David R O'Leary
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Genome Integrity, Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Ava R Hansen
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Genome Integrity, Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA
- Drexel University College of Medicine, Philadelphia, PA, USA
| | - Thi Tran
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Genome Integrity, Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Brooke R Harris
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Genome Integrity, Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Rachel A DeWeerd
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Genome Integrity, Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Katharina E Hayer
- Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Jiayi Fan
- Molecular Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Emily Chen
- Molecular Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
- School of Agriculture and Life Sciences, Cornell University, Ithaca, NY, USA
| | - Mithila Tennakoon
- Center for Genome Integrity, Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Alice Meroni
- Center for Genome Integrity, Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Julia H Szeto
- Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Jessica Devenport
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Genome Integrity, Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Danielle LaVigne
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Genome Integrity, Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Matthew D Weitzman
- Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Ophir Shalem
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Jeffrey Bednarski
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Genome Integrity, Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Alessandro Vindigni
- Center for Genome Integrity, Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Xiaolan Zhao
- Molecular Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Abby M Green
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA.
- Center for Genome Integrity, Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA.
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Jakobsdottir GM, Dentro SC, Bristow RG, Wedge DC. AmplificationTimeR: an R package for timing sequential amplification events. Bioinformatics 2024; 40:btae281. [PMID: 38656989 PMCID: PMC11153944 DOI: 10.1093/bioinformatics/btae281] [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: 08/08/2023] [Revised: 02/23/2024] [Accepted: 04/23/2024] [Indexed: 04/26/2024] Open
Abstract
MOTIVATION Few methods exist for timing individual amplification events in regions of focal amplification. Current methods are also limited in the copy number states that they are able to time. Here we introduce AmplificationTimeR, a method for timing higher level copy number gains and inferring the most parsimonious order of events for regions that have undergone both single gains and whole genome duplication. Our method is an extension of established approaches for timing genomic gains. RESULTS We can time more copy number states, and in states covered by other methods our results are comparable to previously published methods. AVAILABILITY AND IMPLEMENTATION AmplificationTimer is freely available as an R package hosted at https://github.com/Wedge-lab/AmplificationTimeR.
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Affiliation(s)
- G Maria Jakobsdottir
- Division of Cancer Sciences, University of Manchester, Manchester Academic Health Science Centre, Manchester M13 9PL, United Kingdom
- Christie Hospital, The Christie NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester M20 4BX, United Kingdom
| | - Stefan C Dentro
- Division of AI in Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Christie Hospital, The Christie NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester M20 4BX, United Kingdom
| | - Robert G Bristow
- Division of Cancer Sciences, University of Manchester, Manchester Academic Health Science Centre, Manchester M13 9PL, United Kingdom
- CRUK Manchester Institute and Manchester Cancer Research Centre, Manchester M20 4GJ, United Kingdom
- Christie Hospital, The Christie NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester M20 4BX, United Kingdom
| | - David C Wedge
- Division of Cancer Sciences, University of Manchester, Manchester Academic Health Science Centre, Manchester M13 9PL, United Kingdom
- Christie Hospital, The Christie NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester M20 4BX, United Kingdom
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8
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Graham JH, Schlachetzki JCM, Yang X, Breuss MW. Genomic Mosaicism of the Brain: Origin, Impact, and Utility. Neurosci Bull 2024; 40:759-776. [PMID: 37898991 PMCID: PMC11178748 DOI: 10.1007/s12264-023-01124-8] [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: 05/04/2023] [Accepted: 07/16/2023] [Indexed: 10/31/2023] Open
Abstract
Genomic mosaicism describes the phenomenon where some but not all cells within a tissue harbor unique genetic mutations. Traditionally, research focused on the impact of genomic mosaicism on clinical phenotype-motivated by its involvement in cancers and overgrowth syndromes. More recently, we increasingly shifted towards the plethora of neutral mosaic variants that can act as recorders of cellular lineage and environmental exposures. Here, we summarize the current state of the field of genomic mosaicism research with a special emphasis on our current understanding of this phenomenon in brain development and homeostasis. Although the field of genomic mosaicism has a rich history, technological advances in the last decade have changed our approaches and greatly improved our knowledge. We will provide current definitions and an overview of contemporary detection approaches for genomic mosaicism. Finally, we will discuss the impact and utility of genomic mosaicism.
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Affiliation(s)
- Jared H Graham
- Department of Pediatrics, Section of Clinical Genetics and Metabolism, University of Colorado School of Medicine, Aurora, 80045-2581, CO, USA
| | - Johannes C M Schlachetzki
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, 92093-0021, San Diego, CA, USA
| | - Xiaoxu Yang
- Department of Neurosciences, University of California San Diego, La Jolla, 92093-0021, San Diego, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, 92123, CA, USA
| | - Martin W Breuss
- Department of Pediatrics, Section of Clinical Genetics and Metabolism, University of Colorado School of Medicine, Aurora, 80045-2581, CO, USA.
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9
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Maciejowski J, Mohamed T. APOBEC3 upregulation drives gemcitabine resistance. NATURE CANCER 2024; 5:818-820. [PMID: 38778178 DOI: 10.1038/s43018-024-00755-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2024]
Affiliation(s)
| | - Taha Mohamed
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
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10
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Battuello P, Corti G, Bartolini A, Lorenzato A, Sogari A, Russo M, Di Nicolantonio F, Bardelli A, Crisafulli G. Mutational signatures of colorectal cancers according to distinct computational workflows. Brief Bioinform 2024; 25:bbae249. [PMID: 38783705 PMCID: PMC11116831 DOI: 10.1093/bib/bbae249] [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: 02/20/2024] [Revised: 04/15/2024] [Accepted: 05/13/2024] [Indexed: 05/25/2024] Open
Abstract
Tumor mutational signatures have gained prominence in cancer research, yet the lack of standardized methods hinders reproducibility and robustness. Leveraging colorectal cancer (CRC) as a model, we explored the influence of computational parameters on mutational signature analyses across 230 CRC cell lines and 152 CRC patients. Results were validated in three independent datasets: 483 endometrial cancer patients stratified by mismatch repair (MMR) status, 35 lung cancer patients by smoking status and 12 patient-derived organoids (PDOs) annotated for colibactin exposure. Assessing various bioinformatic tools, reference datasets and input data sizes including whole genome sequencing, whole exome sequencing and a pan-cancer gene panel, we demonstrated significant variability in the results. We report that the use of distinct algorithms and references led to statistically different results, highlighting how arbitrary choices may induce variability in the mutational signature contributions. Furthermore, we found a differential contribution of mutational signatures between coding and intergenic regions and defined the minimum number of somatic variants required for reliable mutational signature assignment. To facilitate the identification of the most suitable workflows, we developed Comparative Mutational Signature analysis on Coding and Extragenic Regions (CoMSCER), a bioinformatic tool which allows researchers to easily perform comparative mutational signature analysis by coupling the results from several tools and public reference datasets and to assess mutational signature contributions in coding and non-coding genomic regions. In conclusion, our study provides a comparative framework to elucidate the impact of distinct computational workflows on mutational signatures.
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Affiliation(s)
- Paolo Battuello
- Department of Oncology, Molecular Biotechnology Center, University of Turin, Piazza Nizza 44, 10126, Turin, Italy
- Genomics of Cancer and Targeted Therapies Unit, IFOM ETS, The AIRC Institute of Molecular Oncology, Via Adamello 16, 20139, Milan, Italy
| | - Giorgio Corti
- Department of Oncology, Molecular Biotechnology Center, University of Turin, Piazza Nizza 44, 10126, Turin, Italy
- Candiolo Cancer Institute, FPO - IRCCS, Strada Provinciale 142 - km 3.95, 10060, Candiolo, Turin, Italy
| | - Alice Bartolini
- Candiolo Cancer Institute, FPO - IRCCS, Strada Provinciale 142 - km 3.95, 10060, Candiolo, Turin, Italy
| | - Annalisa Lorenzato
- Department of Oncology, Molecular Biotechnology Center, University of Turin, Piazza Nizza 44, 10126, Turin, Italy
| | - Alberto Sogari
- Department of Oncology, Molecular Biotechnology Center, University of Turin, Piazza Nizza 44, 10126, Turin, Italy
- Genomics of Cancer and Targeted Therapies Unit, IFOM ETS, The AIRC Institute of Molecular Oncology, Via Adamello 16, 20139, Milan, Italy
| | - Mariangela Russo
- Department of Oncology, Molecular Biotechnology Center, University of Turin, Piazza Nizza 44, 10126, Turin, Italy
- Genomics of Cancer and Targeted Therapies Unit, IFOM ETS, The AIRC Institute of Molecular Oncology, Via Adamello 16, 20139, Milan, Italy
| | - Federica Di Nicolantonio
- Department of Oncology, Molecular Biotechnology Center, University of Turin, Piazza Nizza 44, 10126, Turin, Italy
- Candiolo Cancer Institute, FPO - IRCCS, Strada Provinciale 142 - km 3.95, 10060, Candiolo, Turin, Italy
| | - Alberto Bardelli
- Department of Oncology, Molecular Biotechnology Center, University of Turin, Piazza Nizza 44, 10126, Turin, Italy
- Genomics of Cancer and Targeted Therapies Unit, IFOM ETS, The AIRC Institute of Molecular Oncology, Via Adamello 16, 20139, Milan, Italy
| | - Giovanni Crisafulli
- Genomics of Cancer and Targeted Therapies Unit, IFOM ETS, The AIRC Institute of Molecular Oncology, Via Adamello 16, 20139, Milan, Italy
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11
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Hu H, Gao R, Gao W, Gao B, Jiang Z, Zhou M, Wang G, Jiang T. SVDF: enhancing structural variation detect from long-read sequencing via automatic filtering strategies. Brief Bioinform 2024; 25:bbae336. [PMID: 38980375 PMCID: PMC11232458 DOI: 10.1093/bib/bbae336] [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: 05/06/2024] [Revised: 06/03/2024] [Accepted: 06/27/2024] [Indexed: 07/10/2024] Open
Abstract
Structural variation (SV) is an important form of genomic variation that influences gene function and expression by altering the structure of the genome. Although long-read data have been proven to better characterize SVs, SVs detected from noisy long-read data still include a considerable portion of false-positive calls. To accurately detect SVs in long-read data, we present SVDF, a method that employs a learning-based noise filtering strategy and an SV signature-adaptive clustering algorithm, for effectively reducing the likelihood of false-positive events. Benchmarking results from multiple orthogonal experiments demonstrate that, across different sequencing platforms and depths, SVDF achieves higher calling accuracy for each sample compared to several existing general SV calling tools. We believe that, with its meticulous and sensitive SV detection capability, SVDF can bring new opportunities and advancements to cutting-edge genomic research.
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Affiliation(s)
- Heng Hu
- College of Life Sciences, Northeast Forestry University, Harbin 150000, China
| | - Runtian Gao
- College of Life Sciences, Northeast Forestry University, Harbin 150000, China
| | - Wentao Gao
- College of Life Sciences, Northeast Forestry University, Harbin 150000, China
| | - Bo Gao
- Department of Radiology, The Second Affiliated Hospital of Harbin Medical University, Harbin 150000, China
| | - Zhongjun Jiang
- College of Life Sciences, Northeast Forestry University, Harbin 150000, China
| | - Murong Zhou
- College of Life Sciences, Northeast Forestry University, Harbin 150000, China
| | - Guohua Wang
- College of Computer and Control Engineering, Northeast Forestry University, Harbin 150000, China
- State Key Laboratory of Tree Genetics and Breeding, Harbin 150000, China
| | - Tao Jiang
- School of Computer Science and Technology, Harbin Institute of Technology, Harbin 150000, China
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12
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Zhu Z, Dong S, Qin S, Gu K, Zhou Y. ANOS1 accelerates the progression of esophageal cancer identified by multi-omic approaches. Am J Cancer Res 2024; 14:2343-2370. [PMID: 38859828 PMCID: PMC11162658 DOI: 10.62347/spcp3536] [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: 12/19/2023] [Accepted: 04/27/2024] [Indexed: 06/12/2024] Open
Abstract
To assess the role of ANOS1 in esophageal cancer (ESCA) progression, multi-omic analysis and experimental validation were employed. It was revealed that ANOS1 expression is significantly enhanced in ESCA patients and cell lines. The expression level of ANOS1 in ESCA patients can distinguish the malignancy from normal tissue with an area under curve (AUC) >0.75. Moreover, increased expression of ANOS1 is associated with advanced T stage and worse disease-free survival of ESCA patients. Therefore, a clinically applicable nomogram with ANOS1 was established with strong predictive power. Furthermore, high expression of ANOS1 in ESCA is correlated with (i) the enrichment of epithelial-mesenchymal transition by gene set enrichment analysis, (ii) the involvement in hypoxia, angiogenesis, WNT signaling pathway, and TGFβ signaling pathway by gene set variation analysis, (iii) the presence of the small insertion and deletion mutational signature ID9, associated with chromothripsis, in the single-nucleotide polymorphism analysis, (iv) the amplification of 11q13.3 in the copy number variants analysis, (v) the enrichment of cancer-associated fibroblasts and mesenchymal stromal cells in the tumor microenvironment. All the results from multi-omic analysis indicate that ANOS1 plays a pivotal role in accelerating the progression of ESCA. Results from in vivo and in vitro experiments show that the knockdown of ANOS1 hampers the proliferation of ESCA cells, further validating the oncogenic role of ANOS1 in ESCA. Additionally, potential chemotherapeutics with sensitivity were identified in the high-ANOS1 group. In conclusion, ANOS1 accelerates the progression of ESCA.
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Affiliation(s)
- Zuoquan Zhu
- Department of Radiotherapy and Oncology, The Affiliated Hospital of Jiangnan UniversityWuxi 214000, Jiangsu, China
| | - Shikun Dong
- Department of Otorhinolaryngology, Zhongda Hospital, Southeast UniversityNanjing 210009, Jiangsu, China
| | - Shaolei Qin
- Jiangnan UniversityWuxi 214000, Jiangsu, China
| | - Ke Gu
- Department of Radiotherapy and Oncology, The Affiliated Hospital of Jiangnan UniversityWuxi 214000, Jiangsu, China
| | - Yanjun Zhou
- Department of Radiotherapy and Oncology, The Affiliated Hospital of Jiangnan UniversityWuxi 214000, Jiangsu, China
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13
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Maura F, Coffey DG, Stein CK, Braggio E, Ziccheddu B, Sharik ME, Du MT, Tafoya Alvarado Y, Shi CX, Zhu YX, Meermeier EW, Morgan GJ, Landgren O, Bergsagel PL, Chesi M. The genomic landscape of Vk*MYC myeloma highlights shared pathways of transformation between mice and humans. Nat Commun 2024; 15:3844. [PMID: 38714690 PMCID: PMC11076575 DOI: 10.1038/s41467-024-48091-w] [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: 07/12/2023] [Accepted: 04/15/2024] [Indexed: 05/10/2024] Open
Abstract
Multiple myeloma (MM) is a heterogeneous disease characterized by frequent MYC translocations. Sporadic MYC activation in the germinal center of genetically engineered Vk*MYC mice is sufficient to induce plasma cell tumors in which a variety of secondary mutations are spontaneously acquired and selected over time. Analysis of 119 Vk*MYC myeloma reveals recurrent copy number alterations, structural variations, chromothripsis, driver mutations, apolipoprotein B mRNA-editing enzyme, catalytic polypeptide (APOBEC) mutational activity, and a progressive decrease in immunoglobulin transcription that inversely correlates with proliferation. Moreover, we identify frequent insertional mutagenesis by endogenous retro-elements as a murine specific mechanism to activate NF-kB and IL6 signaling pathways shared with human MM. Despite the increased genomic complexity associated with progression, advanced tumors remain dependent on MYC. In summary, here we credential the Vk*MYC mouse as a unique resource to explore MM genomic evolution and describe a fully annotated collection of diverse and immortalized murine MM tumors.
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Affiliation(s)
| | - David G Coffey
- Division of Myeloma, University of Miami, Miami, FL, USA
| | - Caleb K Stein
- Department of Medicine, Division of Hematology and Medical Oncology, Mayo Clinic, Scottsdale, AZ, USA
| | - Esteban Braggio
- Department of Medicine, Division of Hematology and Medical Oncology, Mayo Clinic, Scottsdale, AZ, USA
| | | | - Meaghen E Sharik
- Department of Medicine, Division of Hematology and Medical Oncology, Mayo Clinic, Scottsdale, AZ, USA
| | - Megan T Du
- Department of Medicine, Division of Hematology and Medical Oncology, Mayo Clinic, Scottsdale, AZ, USA
| | - Yuliza Tafoya Alvarado
- Department of Medicine, Division of Hematology and Medical Oncology, Mayo Clinic, Scottsdale, AZ, USA
| | - Chang-Xin Shi
- Department of Medicine, Division of Hematology and Medical Oncology, Mayo Clinic, Scottsdale, AZ, USA
| | - Yuan Xiao Zhu
- Department of Medicine, Division of Hematology and Medical Oncology, Mayo Clinic, Scottsdale, AZ, USA
| | - Erin W Meermeier
- Department of Medicine, Division of Hematology and Medical Oncology, Mayo Clinic, Scottsdale, AZ, USA
| | - Gareth J Morgan
- Myeloma Research Program, NYU Langone, Perlmutter Cancer Center, New York, NY, USA
| | - Ola Landgren
- Division of Myeloma, University of Miami, Miami, FL, USA
| | - P Leif Bergsagel
- Department of Medicine, Division of Hematology and Medical Oncology, Mayo Clinic, Scottsdale, AZ, USA
| | - Marta Chesi
- Department of Medicine, Division of Hematology and Medical Oncology, Mayo Clinic, Scottsdale, AZ, USA.
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14
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Gupta A, Gazzo A, Selenica P, Safonov A, Pareja F, da Silva EM, Brown DN, Zhu Y, Patel J, Blanco-Heredia J, Stefanovska B, Carpenter MA, Pei X, Frosina D, Jungbluth AA, Ladanyi M, Curigliano G, Weigelt B, Riaz N, Powell SN, Razavi P, Harris RS, Reis-Filho JS, Marra A, Chandarlapaty S. APOBEC3 mutagenesis drives therapy resistance in breast cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.29.591453. [PMID: 38746158 PMCID: PMC11092499 DOI: 10.1101/2024.04.29.591453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Acquired genetic alterations commonly drive resistance to endocrine and targeted therapies in metastatic breast cancer 1-7 , however the underlying processes engendering these diverse alterations are largely uncharacterized. To identify the mutational processes operant in breast cancer and their impact on clinical outcomes, we utilized a well-annotated cohort of 3,880 patient samples with paired tumor-normal sequencing data. The mutational signatures associated with apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like 3 (APOBEC3) enzymes were highly prevalent and enriched in post-treatment compared to treatment-naïve hormone receptor-positive (HR+) cancers. APOBEC3 mutational signatures were independently associated with shorter progression-free survival on antiestrogen plus CDK4/6 inhibitor combination therapy in patients with HR+ metastatic breast cancer. Whole genome sequencing (WGS) of breast cancer models and selected paired primary-metastatic samples demonstrated that active APOBEC3 mutagenesis promoted resistance to both endocrine and targeted therapies through characteristic alterations such as RB1 loss-of-function mutations. Evidence of APOBEC3 activity in pre-treatment samples illustrated a pervasive role for this mutational process in breast cancer evolution. The study reveals APOBEC3 mutagenesis to be a frequent mediator of therapy resistance in breast cancer and highlights its potential as a biomarker and target for overcoming resistance.
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15
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Park JE, Smith MA, Van Alsten SC, Walens A, Wu D, Hoadley KA, Troester MA, Love MI. Diffsig: Associating Risk Factors with Mutational Signatures. Cancer Epidemiol Biomarkers Prev 2024; 33:721-730. [PMID: 38426904 PMCID: PMC11062813 DOI: 10.1158/1055-9965.epi-23-0728] [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: 07/03/2023] [Revised: 10/12/2023] [Accepted: 02/28/2024] [Indexed: 03/02/2024] Open
Abstract
BACKGROUND Somatic mutational signatures elucidate molecular vulnerabilities to therapy, and therefore detecting signatures and classifying tumors with respect to signatures has clinical value. However, identifying the etiology of the mutational signatures remains a statistical challenge, with both small sample sizes and high variability in classification algorithms posing barriers. As a result, few signatures have been strongly linked to particular risk factors. METHODS Here, we develop a statistical model, Diffsig, for estimating the association of one or more continuous or categorical risk factors with DNA mutational signatures. Diffsig takes into account the uncertainty associated with assigning signatures to samples as well as multiple risk factors' simultaneous effect on observed DNA mutations. RESULTS We applied Diffsig to breast cancer data to assess relationships between five established breast-relevant mutational signatures and etiologic variables, confirming known mechanisms of cancer development. In simulation, our model was capable of accurately estimating expected associations in a variety of contexts. CONCLUSIONS Diffsig allows researchers to quantify and perform inference on the associations of risk factors with mutational signatures. IMPACT We expect Diffsig to provide more robust associations of risk factors with signatures to lead to better understanding of the tumor development process and improved models of tumorigenesis.
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Affiliation(s)
- Ji-Eun Park
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Markia A. Smith
- Department of Pathology and Laboratory Medicine, School of Medicine, University of North Carolina, Chapel Hill, NC, USA
| | - Sarah C. Van Alsten
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
| | - Andrea Walens
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
| | - Di Wu
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Division of Oral and Craniofacial Health Sciences, Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Katherine A. Hoadley
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Melissa A. Troester
- Department of Pathology and Laboratory Medicine, School of Medicine, University of North Carolina, Chapel Hill, NC, USA
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | - Michael I. Love
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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16
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Li Q, Jiang M, Hong S, Yang J, Wu X, Pang J, Chen Y, Zhao X, Ding X. Comprehensive genomic and clinical analyses identify APOBEC mutational signatures as a brain metastasis risk factor in lung adenocarcinoma patients. Transl Oncol 2024; 43:101921. [PMID: 38402722 PMCID: PMC10904272 DOI: 10.1016/j.tranon.2024.101921] [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: 11/20/2023] [Revised: 02/08/2024] [Accepted: 02/19/2024] [Indexed: 02/27/2024] Open
Abstract
BACKGROUND Lung adenocarcinoma is the most common source of brain metastasis (BM), resulting in significant morbidity and mortality. We aimed to identify patients with high BM risk who possibly benefit from brain-penetrant drugs, prophylactic cranial irradiation, or close brain magnetic resonance imaging surveillance. METHODS Metastatic lung adenocarcinoma patients with extracranial tumor samples profiled by a next-generation sequencing panel targeting 425 tumor-related genes were retrospectively enrolled between February 2008 and July 2021. We compared BM and non-BM patients' genomic and clinical features and studied their associations with BM risk. Two external cohorts were used for result validation and molecular mechanisms investigation, respectively. RESULTS We included 174 eligible patients, including 90 having developed BM by the end of follow-up. Age≤60, EGFR activating mutations, and high-level apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like (APOBEC) mutational signatures were associated with elevated BM risk. Similar findings in BM-free survival were obtained by fitting Fine-Gray subdistribution hazard models addressing competing risks. Increased BM risk related to APOBEC mutational signatures was validated in an external cohort (N = 440). RNA sequencing data analyses performed in another external cohort (N = 230) revealed that expressions of metastasis-related pathways such as transforming growth factor (TGF)β and epithelial-mesenchymal transition (EMT) were upregulated in the patients with high-level APOBEC mutational signatures. CONCLUSION APOBEC mutational signatures related to upregulated TGFβ and EMT, could serve as an independent risk factor for BM and BM-free survival in metastatic lung adenocarcinoma patients. Further investigations are warranted to tailor personalized treatments to improve the susceptible patient's outcomes.
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Affiliation(s)
- Qiang Li
- Cancer Center, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021, China; Cancer Center, Shandong Provincial Hospital, Shandong University, Jinan, 250021, China
| | - Meng Jiang
- Department of Neurosurgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021, China; Department of Neurosurgery, Shandong Provincial Hospital, Shandong University, Jinan, 250021, China
| | - Shiqiang Hong
- Cancer Center, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021, China; Cancer Center, Shandong Provincial Hospital, Shandong University, Jinan, 250021, China
| | - Jing Yang
- Cancer Center, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021, China; Cancer Center, Shandong Provincial Hospital, Shandong University, Jinan, 250021, China
| | - Xiaoying Wu
- Nanjing Geneseeq Technology Inc., Nanjing, 210032, China
| | - Jiaohui Pang
- Nanjing Geneseeq Technology Inc., Nanjing, 210032, China
| | - Yedan Chen
- Nanjing Geneseeq Technology Inc., Nanjing, 210032, China
| | - Xiaotian Zhao
- Nanjing Geneseeq Technology Inc., Nanjing, 210032, China
| | - Xiao Ding
- Cancer Center, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021, China; Cancer Center, Shandong Provincial Hospital, Shandong University, Jinan, 250021, China.
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17
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Dennis M, Hurley A, Bray N, Cordero C, Ilagan J, Mertz TM, Roberts SA. Her2 amplification, Rel-A, and Bach1 can influence APOBEC3A expression in breast cancer cells. PLoS Genet 2024; 20:e1011293. [PMID: 38805570 PMCID: PMC11161071 DOI: 10.1371/journal.pgen.1011293] [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: 05/12/2023] [Revised: 06/07/2024] [Accepted: 05/08/2024] [Indexed: 05/30/2024] Open
Abstract
APOBEC-induced mutations occur in 50% of sequenced human tumors, with APOBEC3A (A3A) being a major contributor to mutagenesis in breast cancer cells. The mechanisms that cause A3A activation and mutagenesis in breast cancers are still unknown. Here, we describe factors that influence basal A3A mRNA transcript levels in breast cancer cells. We found that basal A3A mRNA correlates with A3A protein levels and predicts the amount of APOBEC signature mutations in a panel of breast cancer cell lines, indicating that increased basal transcription may be one mechanism leading to breast cancer mutagenesis. We also show that alteration of ERBB2 expression can drive A3A mRNA levels, suggesting the enrichment of the APOBEC mutation signature in Her2-enriched breast cancer could in part result from elevated A3A transcription. Hierarchical clustering of transcripts in primary breast cancers determined that A3A mRNA was co-expressed with other genes functioning in viral restriction and interferon responses. However, reduction of STAT signaling via inhibitors or shRNA in breast cancer cell lines had only minor impact on A3A abundance. Analysis of single cell RNA-seq from primary tumors indicated that A3A mRNA was highest in infiltrating immune cells within the tumor, indicating that correlations of A3A with STAT signaling in primary tumors may be result from higher immune infiltrates and are not reflective of STAT signaling controlling A3A expression in breast cancer cells. Analysis of ATAC-seq data in multiple breast cancer cell lines identified two transcription factor sites in the APOBEC3A promoter region that could promote A3A transcription. We determined that Rel-A, and Bach1, which have binding sites in these peaks, elevated basal A3A expression. Our findings highlight a complex and variable set of transcriptional activators for A3A in breast cancer cells.
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Affiliation(s)
- Madeline Dennis
- School of Molecular Biosciences and Center for Reproductive Biology, Washington State University, Pullman, Washington, United States of America
| | - Alyssa Hurley
- Department of Microbiology and Molecular Genetics, University of Vermont Cancer Center, University of Vermont, Burlington, Vermont, United States of America
| | - Nicholas Bray
- School of Molecular Biosciences and Center for Reproductive Biology, Washington State University, Pullman, Washington, United States of America
| | - Cameron Cordero
- School of Molecular Biosciences and Center for Reproductive Biology, Washington State University, Pullman, Washington, United States of America
- Department of Microbiology and Molecular Genetics, University of Vermont Cancer Center, University of Vermont, Burlington, Vermont, United States of America
| | - Jose Ilagan
- School of Molecular Biosciences and Center for Reproductive Biology, Washington State University, Pullman, Washington, United States of America
| | - Tony M. Mertz
- School of Molecular Biosciences and Center for Reproductive Biology, Washington State University, Pullman, Washington, United States of America
- Department of Microbiology and Molecular Genetics, University of Vermont Cancer Center, University of Vermont, Burlington, Vermont, United States of America
| | - Steven A. Roberts
- School of Molecular Biosciences and Center for Reproductive Biology, Washington State University, Pullman, Washington, United States of America
- Department of Microbiology and Molecular Genetics, University of Vermont Cancer Center, University of Vermont, Burlington, Vermont, United States of America
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18
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Watson EV, Lee JJK, Gulhan DC, Melloni GEM, Venev SV, Magesh RY, Frederick A, Chiba K, Wooten EC, Naxerova K, Dekker J, Park PJ, Elledge SJ. Chromosome evolution screens recapitulate tissue-specific tumor aneuploidy patterns. Nat Genet 2024; 56:900-912. [PMID: 38388848 PMCID: PMC11096114 DOI: 10.1038/s41588-024-01665-2] [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: 03/16/2022] [Accepted: 01/16/2024] [Indexed: 02/24/2024]
Abstract
Whole chromosome and arm-level copy number alterations occur at high frequencies in tumors, but their selective advantages, if any, are poorly understood. Here, utilizing unbiased whole chromosome genetic screens combined with in vitro evolution to generate arm- and subarm-level events, we iteratively selected the fittest karyotypes from aneuploidized human renal and mammary epithelial cells. Proliferation-based karyotype selection in these epithelial lines modeled tissue-specific tumor aneuploidy patterns in patient cohorts in the absence of driver mutations. Hi-C-based translocation mapping revealed that arm-level events usually emerged in multiples of two via centromeric translocations and occurred more frequently in tetraploids than diploids, contributing to the increased diversity in evolving tetraploid populations. Isogenic clonal lineages enabled elucidation of pro-tumorigenic mechanisms associated with common copy number alterations, revealing Notch signaling potentiation as a driver of 1q gain in breast cancer. We propose that intrinsic, tissue-specific proliferative effects underlie tumor copy number patterns in cancer.
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Affiliation(s)
- Emma V Watson
- Department of Genetics, Harvard Medical School and Department of Medicine, Division of Genetics, Brigham and Women's Hospital, Boston, MA, USA
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Jake June-Koo Lee
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Doga C Gulhan
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Giorgio E M Melloni
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Sergey V Venev
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Rayna Y Magesh
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Abdulrazak Frederick
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Kunitoshi Chiba
- Department of Genetics, Harvard Medical School and Department of Medicine, Division of Genetics, Brigham and Women's Hospital, Boston, MA, USA
| | - Eric C Wooten
- Department of Genetics, Harvard Medical School and Department of Medicine, Division of Genetics, Brigham and Women's Hospital, Boston, MA, USA
| | - Kamila Naxerova
- Department of Genetics, Harvard Medical School and Department of Medicine, Division of Genetics, Brigham and Women's Hospital, Boston, MA, USA
- Center for Systems Biology and Department of Radiology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Job Dekker
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Peter J Park
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
| | - Stephen J Elledge
- Department of Genetics, Harvard Medical School and Department of Medicine, Division of Genetics, Brigham and Women's Hospital, Boston, MA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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19
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Nakauma-González JA, Rijnders M, Noordsij MTW, Martens JWM, van der Veldt AAM, Lolkema MPJ, Boormans JL, van de Werken HJG. Whole-genome mapping of APOBEC mutagenesis in metastatic urothelial carcinoma identifies driver hotspot mutations and a novel mutational signature. CELL GENOMICS 2024; 4:100528. [PMID: 38552621 PMCID: PMC11019362 DOI: 10.1016/j.xgen.2024.100528] [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: 09/15/2023] [Revised: 12/22/2023] [Accepted: 03/06/2024] [Indexed: 04/13/2024]
Abstract
Apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like (APOBEC) enzymes mutate specific DNA sequences and hairpin-loop structures, challenging the distinction between passenger and driver hotspot mutations. Here, we characterized 115 whole genomes of metastatic urothelial carcinoma (mUC) to identify APOBEC mutagenic hotspot drivers. APOBEC-associated mutations were detected in 92% of mUCs and were equally distributed across the genome, while APOBEC hotspot mutations (ApoHMs) were enriched in open chromatin. Hairpin loops were frequent targets of didymi (twins in Greek), two hotspot mutations characterized by the APOBEC SBS2 signature, in conjunction with an uncharacterized mutational context (Ap[C>T]). Next, we developed a statistical framework that identified ApoHMs as drivers in coding and non-coding genomic regions of mUCs. Our results and statistical framework were validated in independent cohorts of 23 non-metastatic UCs and 3,744 samples of 17 metastatic cancers, identifying cancer-type-specific drivers. Our study highlights the role of APOBEC in cancer development and may contribute to developing novel targeted therapy options for APOBEC-driven cancers.
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Affiliation(s)
- J Alberto Nakauma-González
- Cancer Computational Biology Center, Erasmus MC Cancer Institute, University Medical Center Rotterdam, 3015 GD Rotterdam, the Netherlands; Department of Urology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, 3015 GD Rotterdam, the Netherlands; Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, 3015 GD Rotterdam, the Netherlands.
| | - Maud Rijnders
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, 3015 GD Rotterdam, the Netherlands
| | - Minouk T W Noordsij
- Cancer Computational Biology Center, Erasmus MC Cancer Institute, University Medical Center Rotterdam, 3015 GD Rotterdam, the Netherlands
| | - John W M Martens
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, 3015 GD Rotterdam, the Netherlands
| | - Astrid A M van der Veldt
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, 3015 GD Rotterdam, the Netherlands; Department of Radiology & Nuclear Medicine, Erasmus MC, University Medical Center Rotterdam, 3015 GD Rotterdam, the Netherlands
| | - Martijn P J Lolkema
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, 3015 GD Rotterdam, the Netherlands
| | - Joost L Boormans
- Department of Urology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, 3015 GD Rotterdam, the Netherlands
| | - Harmen J G van de Werken
- Cancer Computational Biology Center, Erasmus MC Cancer Institute, University Medical Center Rotterdam, 3015 GD Rotterdam, the Netherlands; Department of Urology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, 3015 GD Rotterdam, the Netherlands; Department of Immunology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, 3015 GD Rotterdam, the Netherlands.
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20
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Hata AN, Larijani M. Targeting APOBECs in cancer: It's about timing. Cancer Cell 2024; 42:497-501. [PMID: 38593778 DOI: 10.1016/j.ccell.2024.03.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 03/08/2024] [Accepted: 03/15/2024] [Indexed: 04/11/2024]
Abstract
APOBEC3 cytidine deaminases have emerged as key drivers of mutagenesis in a wide spectrum of tumor types and are now appreciated to play a causal role in driving tumor evolution and drug resistance. As efforts to develop APOBEC3 inhibitors progress, understanding the timing and consequences of APOBEC3-mediated mutagenesis in distinct clinical contexts will be critical for guiding the development of anti-cancer therapeutic strategies.
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Affiliation(s)
- Aaron N Hata
- Massachusetts General Hospital Cancer Center, Boston, MA, USA; Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
| | - Mani Larijani
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada.
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21
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Heid J, Cutler R, Sun S, Lee M, Maslov AY, Dong X, Sidoli S, Vijg J. Evidence for negative selection in human primary fibroblasts to tolerate high somatic mutation loads upon treatment with multiple low doses of N-ethyl-N-nitrosourea. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.07.588286. [PMID: 38617356 PMCID: PMC11014556 DOI: 10.1101/2024.04.07.588286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
High-throughput sequencing at the single-cell and single-molecule level has shown that mutation rate is much higher in somatic cells than in the germline, with thousands of mutations accumulating with age in most human tissues. While there is now ample evidence that some of these mutations can clonally amplify and lead to disease, most notably cancer, the total burden of mutations a cell can tolerate without functional decline remains unknown. Here we addressed this question by exposing human primary fibroblasts multiple times to low doses of N-ethyl-N-nitrosourea (ENU) and quantitatively analyzing somatic mutation burden using single-cell whole genome sequencing. The results indicate that individual cells can sustain ∼60,000 single-nucleotide variants (SNVs) with only a slight adverse effect on growth rate. We found evidence for selection against potentially deleterious variants in gene coding regions as well as depletion of mutations in sequences associated with genetic pathways expressed in these human fibroblasts, most notably those relevant for maintaining basic cellular function and growth. However, no evidence of negative selection was found for variants in non-coding regions. We conclude that actively proliferating fibroblasts can tolerate very high levels of somatic mutations without major adverse effects on growth rate via negative selection against damaging coding mutations. Since most tissues in adult organisms have very limited capacity to select against mutations based on a growth disadvantage, these results suggest that a causal effect of somatic mutations in aging and disease cannot be ruled out.
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22
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Zhang T, Sang J, Hoang PH, Zhao W, Rosenbaum J, Johnson KE, Klimczak LJ, McElderry J, Klein A, Wirth C, Bergstrom EN, Díaz-Gay M, Vangara R, Colon-Matos F, Hutchinson A, Lawrence SM, Cole N, Zhu B, Przytycka TM, Shi J, Caporaso NE, Homer R, Pesatori AC, Consonni D, Imielinski M, Chanock SJ, Wedge DC, Gordenin DA, Alexandrov LB, Harris RS, Landi MT. APOBEC shapes tumor evolution and age at onset of lung cancer in smokers. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.02.587805. [PMID: 38617360 PMCID: PMC11014539 DOI: 10.1101/2024.04.02.587805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
APOBEC enzymes are part of the innate immunity and are responsible for restricting viruses and retroelements by deaminating cytosine residues1,2. Most solid tumors harbor different levels of somatic mutations attributed to the off-target activities of APOBEC3A (A3A) and/or APOBEC3B (A3B)3-6. However, how APOBEC3A/B enzymes shape the tumor evolution in the presence of exogenous mutagenic processes is largely unknown. Here, by combining deep whole-genome sequencing with multi-omics profiling of 309 lung cancers from smokers with detailed tobacco smoking information, we identify two subtypes defined by low (LAS) and high (HAS) APOBEC mutagenesis. LAS are enriched for A3B-like mutagenesis and KRAS mutations, whereas HAS for A3A-like mutagenesis and TP53 mutations. Unlike APOBEC3A, APOBEC3B expression is strongly associated with an upregulation of the base excision repair pathway. Hypermutation by unrepaired A3A and tobacco smoking mutagenesis combined with TP53-induced genomic instability can trigger senescence7, apoptosis8, and cell regeneration9, as indicated by high expression of pulmonary healing signaling pathway, stemness markers and distal cell-of-origin in HAS. The expected association of tobacco smoking variables (e.g., time to first cigarette) with genomic/epigenomic changes are not observed in HAS, a plausible consequence of frequent cell senescence or apoptosis. HAS have more neoantigens, slower clonal expansion, and older age at onset compared to LAS, particularly in heavy smokers, consistent with high proportions of newly generated, unmutated cells and frequent immuno-editing. These findings show how heterogeneity in mutational burden across co-occurring mutational processes and cell types contributes to tumor development, with important clinical implications.
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Affiliation(s)
- Tongwu Zhang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Jian Sang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Phuc H. Hoang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Wei Zhao
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | | | | | - Leszek J. Klimczak
- Integrative Bioinformatics Support Group, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - John McElderry
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Alyssa Klein
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Christopher Wirth
- Manchester Cancer Research Centre, The University of Manchester, Manchester, UK
| | - Erik N. Bergstrom
- Department of Cellular and Molecular Medicine and Department of Bioengineering and Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Marcos Díaz-Gay
- Department of Cellular and Molecular Medicine and Department of Bioengineering and Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Raviteja Vangara
- Department of Cellular and Molecular Medicine and Department of Bioengineering and Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Frank Colon-Matos
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Amy Hutchinson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Scott M. Lawrence
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Nathan Cole
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Bin Zhu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Teresa M. Przytycka
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Jianxin Shi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Neil E. Caporaso
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Robert Homer
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - Angela C. Pesatori
- Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy
- Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Dario Consonni
- Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
| | | | - Stephen J. Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - David C. Wedge
- Manchester Cancer Research Centre, The University of Manchester, Manchester, UK
| | - Dmitry A. Gordenin
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Ludmil B. Alexandrov
- Department of Cellular and Molecular Medicine and Department of Bioengineering and Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Reuben S. Harris
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX, USA
- Howard Hughes Medical Institute, University of Texas Health San Antonio, San Antonio, TX, USA
| | - Maria Teresa Landi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
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23
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Edsjö A, Gisselsson D, Staaf J, Holmquist L, Fioretos T, Cavelier L, Rosenquist R. Current and emerging sequencing-based tools for precision cancer medicine. Mol Aspects Med 2024; 96:101250. [PMID: 38330674 DOI: 10.1016/j.mam.2024.101250] [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: 11/14/2023] [Accepted: 01/22/2024] [Indexed: 02/10/2024]
Abstract
Current precision cancer medicine is dependent on the analyses of a plethora of clinically relevant genomic aberrations. During the last decade, next-generation sequencing (NGS) has gradually replaced most other methods for precision cancer diagnostics, spanning from targeted tumor-informed assays and gene panel sequencing to global whole-genome and whole-transcriptome sequencing analyses. The shift has been impelled by a clinical need to assess an increasing number of genomic alterations with diagnostic, prognostic and predictive impact, including more complex biomarkers (e.g. microsatellite instability, MSI, and homologous recombination deficiency, HRD), driven by the parallel development of novel targeted therapies and enabled by the rapid reduction in sequencing costs. This review focuses on these sequencing-based methods, puts their emergence in a historic perspective, highlights their clinical utility in diagnostics and decision-making in pediatric and adult cancer, as well as raises challenges for their clinical implementation. Finally, the importance of applying sensitive tools for longitudinal monitoring of treatment response and detection of measurable residual disease, as well as future avenues in the rapidly evolving field of sequencing-based methods are discussed.
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Affiliation(s)
- Anders Edsjö
- Department of Clinical Genetics, Pathology and Molecular Diagnostics, Office for Medical Services, Region Skåne, Lund, Sweden; Division of Pathology, Department of Clinical Sciences, Lund University, Lund, Sweden.
| | - David Gisselsson
- Department of Clinical Genetics, Pathology and Molecular Diagnostics, Office for Medical Services, Region Skåne, Lund, Sweden; Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Johan Staaf
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, Medicon Village, Lund, Sweden
| | - Louise Holmquist
- Department of Clinical Genetics, Pathology and Molecular Diagnostics, Office for Medical Services, Region Skåne, Lund, Sweden
| | - Thoas Fioretos
- Department of Clinical Genetics, Pathology and Molecular Diagnostics, Office for Medical Services, Region Skåne, Lund, Sweden; Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden; Clinical Genomics Lund, Science for Life Laboratory, Lund University, Lund, Sweden
| | - Lucia Cavelier
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden; Clinical Genetics and Genomics, Karolinska University Hospital, Stockholm, Sweden
| | - Richard Rosenquist
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden; Clinical Genetics and Genomics, Karolinska University Hospital, Stockholm, Sweden; Genomic Medicine Center Karolinska, Karolinska University Hospital, Stockholm, Sweden
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24
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O'Leary DR, Hansen AR, Fingerman DF, Tran T, Harris BR, Hayer KE, Fan J, Chen E, Tennakoon M, DeWeerd RA, Meroni A, Szeto JH, Weitzman MD, Shalem O, Bednarski J, Vindigni A, Zhao X, Green AM. The SMC5/6 complex prevents genotoxicity upon APOBEC3A-mediated replication stress. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.28.568952. [PMID: 38077016 PMCID: PMC10705431 DOI: 10.1101/2023.11.28.568952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Mutational patterns caused by APOBEC3 cytidine deaminase activity are evident throughout human cancer genomes. In particular, the APOBEC3A family member is a potent genotoxin that causes substantial DNA damage in experimental systems and human tumors. However, the mechanisms that ensure genome stability in cells with active APOBEC3A are unknown. Through an unbiased genome-wide screen, we define the Structural Maintenance of Chromosomes 5/6 (SMC5/6) complex as essential for cell viability when APOBEC3A is active. We observe an absence of APOBEC3A mutagenesis in human tumors with SMC5/6 dysfunction, consistent with synthetic lethality. Cancer cells depleted of SMC5/6 incur substantial genome damage from APOBEC3A activity during DNA replication. Further, APOBEC3A activity results in replication tract lengthening which is dependent on PrimPol, consistent with re-initiation of DNA synthesis downstream of APOBEC3A-induced lesions. Loss of SMC5/6 abrogates elongated replication tracts and increases DNA breaks upon APOBEC3A activity. Our findings indicate that replication fork lengthening reflects a DNA damage response to APOBEC3A activity that promotes genome stability in an SMC5/6-dependent manner. Therefore, SMC5/6 presents a potential therapeutic vulnerability in tumors with active APOBEC3A.
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25
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Butt Y, Sakhtemani R, Mohamad-Ramshan R, Lawrence MS, Bhagwat AS. Distinguishing preferences of human APOBEC3A and APOBEC3B for cytosines in hairpin loops, and reflection of these preferences in APOBEC-signature cancer genome mutations. Nat Commun 2024; 15:2369. [PMID: 38499553 PMCID: PMC10948833 DOI: 10.1038/s41467-024-46231-w] [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: 07/31/2023] [Accepted: 02/19/2024] [Indexed: 03/20/2024] Open
Abstract
The APOBEC3 enzymes convert cytosines in single-stranded DNA to uracils to protect against viruses and retrotransposons but can contribute to mutations that diversify tumors. To understand the mechanism of mutagenesis, we map the uracils resulting from expression of APOBEC3B or its catalytic carboxy-terminal domain (CTD) in Escherichia coli. Like APOBEC3A, the uracilomes of A3B and A3B-CTD show a preference to deaminate cytosines near transcription start sites and the lagging-strand replication templates and in hairpin loops. Both biochemical activities of the enzymes and genomic uracil distribution show that A3A prefers 3 nt loops the best, while A3B prefers 4 nt loops. Reanalysis of hairpin loop mutations in human tumors finds intrinsic characteristics of both the enzymes, with a much stronger contribution from A3A. We apply Hairpin Signatures 1 and 2, which define A3A and A3B preferences respectively and are orthogonal to published methods, to evaluate their contribution to human tumor mutations.
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Affiliation(s)
- Yasha Butt
- Department of Chemistry, Wayne State University, Detroit, MI, 48202, USA
| | - Ramin Sakhtemani
- Department of Chemistry, Wayne State University, Detroit, MI, 48202, USA
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Michael S Lawrence
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ashok S Bhagwat
- Department of Chemistry, Wayne State University, Detroit, MI, 48202, USA.
- Department of Biochemistry, Microbiology and Immunology, Wayne State University School of Medicine, Detroit, MI, 48201, USA.
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26
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Sanchez A, Ortega P, Sakhtemani R, Manjunath L, Oh S, Bournique E, Becker A, Kim K, Durfee C, Temiz NA, Chen XS, Harris RS, Lawrence MS, Buisson R. Mesoscale DNA features impact APOBEC3A and APOBEC3B deaminase activity and shape tumor mutational landscapes. Nat Commun 2024; 15:2370. [PMID: 38499542 PMCID: PMC10948877 DOI: 10.1038/s41467-024-45909-5] [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: 07/31/2023] [Accepted: 01/09/2024] [Indexed: 03/20/2024] Open
Abstract
Antiviral DNA cytosine deaminases APOBEC3A and APOBEC3B are major sources of mutations in cancer by catalyzing cytosine-to-uracil deamination. APOBEC3A preferentially targets single-stranded DNAs, with a noted affinity for DNA regions that adopt stem-loop secondary structures. However, the detailed substrate preferences of APOBEC3A and APOBEC3B have not been fully established, and the specific influence of the DNA sequence on APOBEC3A and APOBEC3B deaminase activity remains to be investigated. Here, we find that APOBEC3B also selectively targets DNA stem-loop structures, and they are distinct from those subjected to deamination by APOBEC3A. We develop Oligo-seq, an in vitro sequencing-based method to identify specific sequence contexts promoting APOBEC3A and APOBEC3B activity. Through this approach, we demonstrate that APOBEC3A and APOBEC3B deaminase activity is strongly regulated by specific sequences surrounding the targeted cytosine. Moreover, we identify the structural features of APOBEC3B and APOBEC3A responsible for their substrate preferences. Importantly, we determine that APOBEC3B-induced mutations in hairpin-forming sequences within tumor genomes differ from the DNA stem-loop sequences mutated by APOBEC3A. Together, our study provides evidence that APOBEC3A and APOBEC3B can generate distinct mutation landscapes in cancer genomes, driven by their unique substrate selectivity.
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Affiliation(s)
- Ambrocio Sanchez
- Department of Biological Chemistry, School of Medicine, University of California Irvine, Irvine, CA, USA
- Center for Epigenetics and Metabolism, Chao Family Comprehensive Cancer Center, University of California Irvine, Irvine, CA, USA
| | - Pedro Ortega
- Department of Biological Chemistry, School of Medicine, University of California Irvine, Irvine, CA, USA
- Center for Epigenetics and Metabolism, Chao Family Comprehensive Cancer Center, University of California Irvine, Irvine, CA, USA
| | - Ramin Sakhtemani
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Lavanya Manjunath
- Department of Biological Chemistry, School of Medicine, University of California Irvine, Irvine, CA, USA
- Center for Epigenetics and Metabolism, Chao Family Comprehensive Cancer Center, University of California Irvine, Irvine, CA, USA
| | - Sunwoo Oh
- Department of Biological Chemistry, School of Medicine, University of California Irvine, Irvine, CA, USA
- Center for Epigenetics and Metabolism, Chao Family Comprehensive Cancer Center, University of California Irvine, Irvine, CA, USA
| | - Elodie Bournique
- Department of Biological Chemistry, School of Medicine, University of California Irvine, Irvine, CA, USA
- Center for Epigenetics and Metabolism, Chao Family Comprehensive Cancer Center, University of California Irvine, Irvine, CA, USA
| | - Alexandrea Becker
- Department of Biological Chemistry, School of Medicine, University of California Irvine, Irvine, CA, USA
- Center for Epigenetics and Metabolism, Chao Family Comprehensive Cancer Center, University of California Irvine, Irvine, CA, USA
| | - Kyumin Kim
- Molecular and Computational Biology, Departments of Biological Sciences and Chemistry, University of Southern California, Los Angeles, CA, USA
| | - Cameron Durfee
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX, USA
| | - Nuri Alpay Temiz
- Institute for Health Informatics, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
| | - Xiaojiang S Chen
- Molecular and Computational Biology, Departments of Biological Sciences and Chemistry, University of Southern California, Los Angeles, CA, USA
| | - Reuben S Harris
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX, USA
- Howard Hughes Medical Institute, University of Texas Health San Antonio, San Antonio, TX, USA
| | - Michael S Lawrence
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Rémi Buisson
- Department of Biological Chemistry, School of Medicine, University of California Irvine, Irvine, CA, USA.
- Center for Epigenetics and Metabolism, Chao Family Comprehensive Cancer Center, University of California Irvine, Irvine, CA, USA.
- Department of Pharmaceutical Sciences, School of Pharmacy & Pharmaceutical Sciences, University of California Irvine, Irvine, CA, USA.
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27
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Smith NJ, Reddin I, Policelli P, Oh S, Zainal N, Howes E, Jenkins B, Tracy I, Edmond M, Sharpe B, Amendra D, Zheng K, Egawa N, Doorbar J, Rao A, Mahadevan S, Carpenter MA, Harris RS, Ali S, Hanley C, Buisson R, King E, Thomas GJ, Fenton TR. Differentiation signals induce APOBEC3A expression via GRHL3 in squamous epithelia and squamous cell carcinoma. RESEARCH SQUARE 2024:rs.3.rs-3997426. [PMID: 38496447 PMCID: PMC10942551 DOI: 10.21203/rs.3.rs-3997426/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Two APOBEC (apolipoprotein-B mRNA editing enzyme catalytic polypeptide-like) DNA cytosine deaminase enzymes (APOBEC3A and APOBEC3B) generate somatic mutations in cancer, driving tumour development and drug resistance. Here we used single cell RNA sequencing to study APOBEC3A and APOBEC3B expression in healthy and malignant mucosal epithelia, validating key observations with immunohistochemistry, spatial transcriptomics and functional experiments. Whereas APOBEC3B is expressed in keratinocytes entering mitosis, we show that APOBEC3A expression is confined largely to terminally differentiating cells and requires Grainyhead-like transcription factor 3 (GRHL3). Thus, in normal tissue, neither deaminase appears to be expressed at high levels during DNA replication, the cell cycle stage associated with APOBEC-mediated mutagenesis. In contrast, we show that in squamous cell carcinoma tissues, there is expansion of GRHL3 expression and activity to a subset of cells undergoing DNA replication and concomitant extension of APOBEC3A expression to proliferating cells. These findings indicate a mechanism for acquisition of APOBEC3A mutagenic activity in tumours.
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Affiliation(s)
- Nicola J. Smith
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, UK
- School of Biosciences, University of Kent, UK
| | - Ian Reddin
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, UK
- Bio-R Bioinformatics Research Facility, Faculty of Medicine, University of Southampton, UK
| | - Paige Policelli
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, UK
| | - Sunwoo Oh
- Department of Biological Chemistry, School of Medicine, University of California Irvine, Irvine, CA, USA
| | - Nur Zainal
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, UK
| | - Emma Howes
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, UK
| | - Benjamin Jenkins
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, UK
| | - Ian Tracy
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, UK
| | - Mark Edmond
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, UK
| | - Benjamin Sharpe
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, UK
| | - Damian Amendra
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, UK
| | - Ke Zheng
- Department of Pathology, University of Cambridge, UK
| | | | - John Doorbar
- Department of Pathology, University of Cambridge, UK
| | - Anjali Rao
- Gilead Sciences, Research Department, 324 Lakeside Dr. Foster City, CA 94404, USA
| | - Sangeetha Mahadevan
- Gilead Sciences, Research Department, 324 Lakeside Dr. Foster City, CA 94404, USA
| | - Michael A. Carpenter
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX 78229, USA
- Howard Hughes Medical Institute, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Reuben S. Harris
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX 78229, USA
- Howard Hughes Medical Institute, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Simak Ali
- Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital Campus, London, UK
| | - Christopher Hanley
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, UK
| | - Rémi Buisson
- Department of Biological Chemistry, School of Medicine, University of California Irvine, Irvine, CA, USA
| | - Emma King
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, UK
| | - Gareth J. Thomas
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, UK
- Institute for Life Sciences, University of Southampton, UK
| | - Tim R. Fenton
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, UK
- Institute for Life Sciences, University of Southampton, UK
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28
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Simpson JT. Detecting Somatic Mutations Without Matched Normal Samples Using Long Reads. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.26.582089. [PMID: 38464143 PMCID: PMC10925087 DOI: 10.1101/2024.02.26.582089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
DNA sequencing of tumours to identify somatic mutations has become a critical tool to guide the type of treatment given to cancer patients. The gold standard for mutation calling is comparing sequencing data from the tumour to a matched normal sample to avoid mis-classifying inherited SNPs as mutations. This procedure works extremely well, but in certain situations only a tumour sample is available. While approaches have been developed to find mutations without a matched normal, they have limited accuracy or require specific types of input data (e.g. ultra-deep sequencing). Here we explore the application of single molecule long read sequencing to calling somatic mutations without matched normal samples. We develop a simple theoretical framework to show how haplotype phasing is an important source of information for determining whether a variant is a somatic mutation. We then use simulations to assess the range of experimental parameters (tumour purity, sequencing depth) where this approach is effective. These ideas are developed into a prototype somatic mutation caller, smrest, and its use is demonstrated on two highly mutated cancer cell lines. Finally, we argue that this approach has potential to measure clinically important biomarkers that are based on the genome-wide distribution of mutations: tumour mutation burden and mutation signatures.
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Affiliation(s)
- Jared T. Simpson
- Ontario Institute for Cancer Research, Toronto, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
- Department of Computer Science, University of Toronto, Toronto, Canada
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29
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Dopeso H, Gazzo AM, Derakhshan F, Brown DN, Selenica P, Jalali S, Da Cruz Paula A, Marra A, da Silva EM, Basili T, Gusain L, Colon-Cartagena L, Bhaloo SI, Green H, Vanderbilt C, Oesterreich S, Grabenstetter A, Kuba MG, Ross D, Giri D, Wen HY, Zhang H, Brogi E, Weigelt B, Pareja F, Reis-Filho JS. Genomic and epigenomic basis of breast invasive lobular carcinomas lacking CDH1 genetic alterations. NPJ Precis Oncol 2024; 8:33. [PMID: 38347189 PMCID: PMC10861500 DOI: 10.1038/s41698-024-00508-x] [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: 05/10/2023] [Accepted: 12/14/2023] [Indexed: 02/15/2024] Open
Abstract
CDH1 (E-cadherin) bi-allelic inactivation is the hallmark alteration of breast invasive lobular carcinoma (ILC), resulting in its discohesive phenotype. A subset of ILCs, however, lack CDH1 genetic/epigenetic inactivation, and their genetic underpinning is unknown. Through clinical targeted sequencing data reanalysis of 364 primary ILCs, we identified 25 ILCs lacking CDH1 bi-allelic genetic alterations. CDH1 promoter methylation was frequent (63%) in these cases. Targeted sequencing reanalysis revealed 3 ILCs harboring AXIN2 deleterious fusions (n = 2) or loss-of-function mutation (n = 1). Whole-genome sequencing of 3 cases lacking bi-allelic CDH1 genetic/epigenetic inactivation confirmed the AXIN2 mutation and no other cell-cell adhesion genetic alterations but revealed a new CTNND1 (p120) deleterious fusion. AXIN2 knock-out in MCF7 cells resulted in lobular-like features, including increased cellular migration and resistance to anoikis. Taken together, ILCs lacking CDH1 genetic/epigenetic alterations are driven by inactivating alterations in other cell adhesion genes (CTNND1 or AXIN2), endorsing a convergent phenotype in ILC.
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Affiliation(s)
- Higinio Dopeso
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Andrea M Gazzo
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Fatemeh Derakhshan
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | - David N Brown
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Pier Selenica
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sahar Jalali
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Arnaud Da Cruz Paula
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Antonio Marra
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Edaise M da Silva
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Thais Basili
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Laxmi Gusain
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Lorraine Colon-Cartagena
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Shirin Issa Bhaloo
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Hunter Green
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Chad Vanderbilt
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Steffi Oesterreich
- Department of Pharmacology & Chemical Biology, UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Anne Grabenstetter
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - M Gabriela Kuba
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Dara Ross
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Dilip Giri
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Hannah Y Wen
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Hong Zhang
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Edi Brogi
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Britta Weigelt
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Fresia Pareja
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Jorge S Reis-Filho
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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Kawale AS, Ran X, Patel PS, Saxena S, Lawrence MS, Zou L. APOBEC3A induces DNA gaps through PRIMPOL and confers gap-associated therapeutic vulnerability. SCIENCE ADVANCES 2024; 10:eadk2771. [PMID: 38241374 PMCID: PMC10798555 DOI: 10.1126/sciadv.adk2771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 12/20/2023] [Indexed: 01/21/2024]
Abstract
Mutation signatures associated with apolipoprotein B mRNA editing catalytic polypeptide-like 3A/B (APOBEC3A/B) cytidine deaminases are prevalent across cancers, implying their roles as mutagenic drivers during tumorigenesis and tumor evolution. APOBEC3A (A3A) expression induces DNA replication stress and increases the cellular dependency on the ataxia telangiectasia and Rad3-related (ATR) kinase for survival. Nonetheless, how A3A induces DNA replication stress remains unclear. We show that A3A induces replication stress without slowing replication forks. We find that A3A induces single-stranded DNA (ssDNA) gaps through PrimPol-mediated repriming. A3A-induced ssDNA gaps are repaired by multiple pathways involving ATR, RAD51, and translesion synthesis. Both ATR inhibition and trapping of poly(ADP-ribose) polymerase (PARP) on DNA by PARP inhibitor impair the repair of A3A-induced gaps, preferentially killing A3A-expressing cells. When used in combination, PARP and ATR inhibitors selectively kill A3A-expressing cells synergistically in a manner dependent on PrimPol-generated gaps. Thus, A3A-induced replication stress arises from PrimPol-generated ssDNA gaps, which confer a therapeutic vulnerability to gap-targeted DNA repair inhibitors.
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Affiliation(s)
- Ajinkya S. Kawale
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Xiaojuan Ran
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, USA
| | - Parasvi S. Patel
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Sneha Saxena
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Michael S. Lawrence
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Lee Zou
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, USA
- Department of Pathology, Harvard Medical School, Boston, MA, USA
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31
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Dananberg A, Striepen J, Rozowsky JS, Petljak M. APOBEC Mutagenesis in Cancer Development and Susceptibility. Cancers (Basel) 2024; 16:374. [PMID: 38254863 PMCID: PMC10814203 DOI: 10.3390/cancers16020374] [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: 12/20/2023] [Revised: 01/09/2024] [Accepted: 01/11/2024] [Indexed: 01/24/2024] Open
Abstract
APOBEC cytosine deaminases are prominent mutators in cancer, mediating mutations in over 50% of cancers. APOBEC mutagenesis has been linked to tumor heterogeneity, persistent cell evolution, and therapy responses. While emerging evidence supports the impact of APOBEC mutagenesis on cancer progression, the understanding of its contribution to cancer susceptibility and malignant transformation is limited. We examine the existing evidence for the role of APOBEC mutagenesis in carcinogenesis on the basis of the reported associations between germline polymorphisms in genes encoding APOBEC enzymes and cancer risk, insights into APOBEC activities from sequencing efforts of both malignant and non-malignant human tissues, and in vivo studies. We discuss key knowledge gaps and highlight possible ways to gain a deeper understanding of the contribution of APOBEC mutagenesis to cancer development.
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Affiliation(s)
- Alexandra Dananberg
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Josefine Striepen
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Jacob S Rozowsky
- Medical Scientist Training Program, New York University Grossman School of Medicine, New York, NY 10016, USA
- Department of Pathology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Mia Petljak
- Department of Pathology, NYU Grossman School of Medicine, New York, NY 10016, USA
- Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA
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32
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Caswell DR, Gui P, Mayekar MK, Law EK, Pich O, Bailey C, Boumelha J, Kerr DL, Blakely CM, Manabe T, Martinez-Ruiz C, Bakker B, De Dios Palomino Villcas J, I Vokes N, Dietzen M, Angelova M, Gini B, Tamaki W, Allegakoen P, Wu W, Humpton TJ, Hill W, Tomaschko M, Lu WT, Haderk F, Al Bakir M, Nagano A, Gimeno-Valiente F, de Carné Trécesson S, Vendramin R, Barbè V, Mugabo M, Weeden CE, Rowan A, McCoach CE, Almeida B, Green M, Gomez C, Nanjo S, Barbosa D, Moore C, Przewrocka J, Black JRM, Grönroos E, Suarez-Bonnet A, Priestnall SL, Zverev C, Lighterness S, Cormack J, Olivas V, Cech L, Andrews T, Rule B, Jiao Y, Zhang X, Ashford P, Durfee C, Venkatesan S, Temiz NA, Tan L, Larson LK, Argyris PP, Brown WL, Yu EA, Rotow JK, Guha U, Roper N, Yu J, Vogel RI, Thomas NJ, Marra A, Selenica P, Yu H, Bakhoum SF, Chew SK, Reis-Filho JS, Jamal-Hanjani M, Vousden KH, McGranahan N, Van Allen EM, Kanu N, Harris RS, Downward J, Bivona TG, Swanton C. The role of APOBEC3B in lung tumor evolution and targeted cancer therapy resistance. Nat Genet 2024; 56:60-73. [PMID: 38049664 PMCID: PMC10786726 DOI: 10.1038/s41588-023-01592-8] [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: 06/25/2023] [Accepted: 10/25/2023] [Indexed: 12/06/2023]
Abstract
In this study, the impact of the apolipoprotein B mRNA-editing catalytic subunit-like (APOBEC) enzyme APOBEC3B (A3B) on epidermal growth factor receptor (EGFR)-driven lung cancer was assessed. A3B expression in EGFR mutant (EGFRmut) non-small-cell lung cancer (NSCLC) mouse models constrained tumorigenesis, while A3B expression in tumors treated with EGFR-targeted cancer therapy was associated with treatment resistance. Analyses of human NSCLC models treated with EGFR-targeted therapy showed upregulation of A3B and revealed therapy-induced activation of nuclear factor kappa B (NF-κB) as an inducer of A3B expression. Significantly reduced viability was observed with A3B deficiency, and A3B was required for the enrichment of APOBEC mutation signatures, in targeted therapy-treated human NSCLC preclinical models. Upregulation of A3B was confirmed in patients with NSCLC treated with EGFR-targeted therapy. This study uncovers the multifaceted roles of A3B in NSCLC and identifies A3B as a potential target for more durable responses to targeted cancer therapy.
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Affiliation(s)
- Deborah R Caswell
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK.
| | - Philippe Gui
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Manasi K Mayekar
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Emily K Law
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Oriol Pich
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Chris Bailey
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Jesse Boumelha
- Oncogene Biology Laboratory, The Francis Crick Institute, London, UK
| | - D Lucas Kerr
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Collin M Blakely
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Tadashi Manabe
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Carlos Martinez-Ruiz
- Cancer Genome Evolution Research Group, University College London, Cancer Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, UCL Cancer Institute, London, UK
| | - Bjorn Bakker
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | | | - Natalie I Vokes
- Department of Thoracic and Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Michelle Dietzen
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Genome Evolution Research Group, University College London, Cancer Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, UCL Cancer Institute, London, UK
| | - Mihaela Angelova
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Beatrice Gini
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Whitney Tamaki
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Paul Allegakoen
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Wei Wu
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Timothy J Humpton
- p53 and Metabolism Laboratory, The Francis Crick Institute, London, UK
- CRUK Beatson Institute, Glasgow, UK
- Glasgow Caledonian University, Glasgow, UK
| | - William Hill
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Mona Tomaschko
- Oncogene Biology Laboratory, The Francis Crick Institute, London, UK
| | - Wei-Ting Lu
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Franziska Haderk
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Maise Al Bakir
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Ai Nagano
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | | | | | - Roberto Vendramin
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Vittorio Barbè
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Miriam Mugabo
- Cancer Research UK Lung Cancer Centre of Excellence, UCL Cancer Institute, London, UK
| | - Clare E Weeden
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Andrew Rowan
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | | | - Bruna Almeida
- The Roger Williams Institute of Hepatology, Foundation for Liver Research, London, UK
- Faculty of Life Sciences & Medicine, King's College London, London, UK
| | - Mary Green
- Experimental Histopathology, The Francis Crick Institute, London, UK
| | - Carlos Gomez
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Shigeki Nanjo
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Dora Barbosa
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Chris Moore
- Oncogene Biology Laboratory, The Francis Crick Institute, London, UK
| | - Joanna Przewrocka
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - James R M Black
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Genome Evolution Research Group, University College London, Cancer Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, UCL Cancer Institute, London, UK
| | - Eva Grönroos
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Alejandro Suarez-Bonnet
- Experimental Histopathology, The Francis Crick Institute, London, UK
- Department of Pathobiology & Population Sciences, The Royal Veterinary College, London, UK
| | - Simon L Priestnall
- Experimental Histopathology, The Francis Crick Institute, London, UK
- Department of Pathobiology & Population Sciences, The Royal Veterinary College, London, UK
| | - Caroline Zverev
- Biological Research Facility, The Francis Crick Institute, London, UK
| | - Scott Lighterness
- Biological Research Facility, The Francis Crick Institute, London, UK
| | - James Cormack
- Biological Research Facility, The Francis Crick Institute, London, UK
| | - Victor Olivas
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Lauren Cech
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Trisha Andrews
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | | | | | | | - Paul Ashford
- Institute of Structural and Molecular Biology, University College London, London, UK
| | - Cameron Durfee
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX, USA
| | - Subramanian Venkatesan
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Nuri Alpay Temiz
- Institute for Health Informatics, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
| | - Lisa Tan
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Lindsay K Larson
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Prokopios P Argyris
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
- School of Dentistry, University of Minnesota, Minneapolis, MN, USA
- College of Dentistry, Ohio State University, Columbus, OH, USA
| | - William L Brown
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Elizabeth A Yu
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Sutter Health Palo Alto Medical Foundation, Department of Pulmonary and Critical Care, Mountain View, CA, USA
| | - Julia K Rotow
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Udayan Guha
- Thoracic and GI Malignancies Branch, NCI, NIH, Bethesda, MD, USA
- NextCure Inc., Beltsville, MD, USA
| | - Nitin Roper
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Johnny Yu
- Biomedical Sciences Program, University of California, San Francisco, San Francisco, CA, USA
| | - Rachel I Vogel
- Department of Obstetrics, Gynecology and Women's Health, University of Minnesota, Minneapolis, MN, USA
| | - Nicholas J Thomas
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Antonio Marra
- Division of Early Drug Development for Innovative Therapy, European Institute of Oncology IRCCS, Milan, Italy
| | - Pier Selenica
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York City, NY, USA
| | - Helena Yu
- Memorial Sloan Kettering Cancer Center, New York City, NY, USA
- Department of Medicine, Weill Cornell College of Medicine, New York City, NY, USA
| | - Samuel F Bakhoum
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York City, NY, USA
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York City, NY, USA
| | - Su Kit Chew
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | | | - Mariam Jamal-Hanjani
- Cancer Research UK Lung Cancer Centre of Excellence, UCL Cancer Institute, London, UK
- Cancer Metastasis Laboratory, University College London Cancer Institute, London, UK
- Department of Medical Oncology, University College London Hospitals, London, UK
| | - Karen H Vousden
- p53 and Metabolism Laboratory, The Francis Crick Institute, London, UK
| | - Nicholas McGranahan
- Cancer Genome Evolution Research Group, University College London, Cancer Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, UCL Cancer Institute, London, UK
| | - Eliezer M Van Allen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Nnennaya Kanu
- Cancer Research UK Lung Cancer Centre of Excellence, UCL Cancer Institute, London, UK
| | - Reuben S Harris
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX, USA
- Howard Hughes Medical Institute, University of Texas Health San Antonio, San Antonio, TX, USA
| | - Julian Downward
- Oncogene Biology Laboratory, The Francis Crick Institute, London, UK
| | - Trever G Bivona
- Departments of Medicine and Cellular and Molecular Pharmacology, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
| | - Charles Swanton
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, UCL Cancer Institute, London, UK
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Stracker TH, Osagie OI, Escorcia FE, Citrin DE. Exploiting the DNA Damage Response for Prostate Cancer Therapy. Cancers (Basel) 2023; 16:83. [PMID: 38201511 PMCID: PMC10777950 DOI: 10.3390/cancers16010083] [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: 10/18/2023] [Revised: 12/14/2023] [Accepted: 12/20/2023] [Indexed: 01/12/2024] Open
Abstract
Prostate cancers that progress despite androgen deprivation develop into castration-resistant prostate cancer, a fatal disease with few treatment options. In this review, we discuss the current understanding of prostate cancer subtypes and alterations in the DNA damage response (DDR) that can predispose to the development of prostate cancer and affect its progression. We identify barriers to conventional treatments, such as radiotherapy, and discuss the development of new therapies, many of which target the DDR or take advantage of recurring genetic alterations in the DDR. We place this in the context of advances in understanding the genetic variation and immune landscape of CRPC that could help guide their use in future treatment strategies. Finally, we discuss several new and emerging agents that may advance the treatment of lethal disease, highlighting selected clinical trials.
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Affiliation(s)
- Travis H. Stracker
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; (O.I.O.); (F.E.E.); (D.E.C.)
| | - Oloruntoba I. Osagie
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; (O.I.O.); (F.E.E.); (D.E.C.)
| | - Freddy E. Escorcia
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; (O.I.O.); (F.E.E.); (D.E.C.)
- Molecular Imaging Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Deborah E. Citrin
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; (O.I.O.); (F.E.E.); (D.E.C.)
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34
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Coxon M, Dennis MA, Dananberg A, Collins C, Wilson H, Meekma J, Savenkova M, Ng D, Osbron C, Mertz T, Goodman A, Duttke S, Maciejowski J, Roberts S. An impaired ubiquitin-proteasome system increases APOBEC3A abundance. NAR Cancer 2023; 5:zcad058. [PMID: 38155930 PMCID: PMC10753533 DOI: 10.1093/narcan/zcad058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 11/21/2023] [Accepted: 12/08/2023] [Indexed: 12/30/2023] Open
Abstract
Apolipoprotein B messenger RNA (mRNA) editing enzyme, catalytic polypeptide-like (APOBEC) cytidine deaminases cause genetic instability during cancer development. Elevated APOBEC3A (A3A) levels result in APOBEC signature mutations; however, mechanisms regulating A3A abundance in breast cancer are unknown. Here, we show that dysregulating the ubiquitin-proteasome system with proteasome inhibitors, including Food and Drug Administration-approved anticancer drugs, increased A3A abundance in breast cancer and multiple myeloma cell lines. Unexpectedly, elevated A3A occurs via an ∼100-fold increase in A3A mRNA levels, indicating that proteasome inhibition triggers a transcriptional response as opposed to or in addition to blocking A3A degradation. This transcriptional regulation is mediated in part through FBXO22, a protein that functions in SKP1-cullin-F-box ubiquitin ligase complexes and becomes dysregulated during carcinogenesis. Proteasome inhibitors increased cellular cytidine deaminase activity, decreased cellular proliferation and increased genomic DNA damage in an A3A-dependent manner. Our findings suggest that proteasome dysfunction, either acquired during cancer development or induced therapeutically, could increase A3A-induced genetic heterogeneity and thereby influence therapeutic responses in patients.
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Affiliation(s)
- Margo Coxon
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164-7520, USA
| | - Madeline A Dennis
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164-7520, USA
| | - Alexandra Dananberg
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Christopher D Collins
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164-7520, USA
| | - Hannah E Wilson
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164-7520, USA
| | - Jordyn Meekma
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164-7520, USA
| | - Marina I Savenkova
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164-7520, USA
| | - Daniel Ng
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164-7520, USA
| | - Chelsea A Osbron
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164-7520, USA
| | - Tony M Mertz
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164-7520, USA
- Department of Microbiology and Molecular Genetics, University of Vermont Cancer Center, University of Vermont, Burlington, VT 05405, USA
| | - Alan G Goodman
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164-7520, USA
| | - Sascha H Duttke
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164-7520, USA
| | - John Maciejowski
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Steven A Roberts
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164-7520, USA
- Department of Microbiology and Molecular Genetics, University of Vermont Cancer Center, University of Vermont, Burlington, VT 05405, USA
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35
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Legrand C, Andriantsoa R, Lichter P, Raddatz G, Lyko F. Time-resolved, integrated analysis of clonally evolving genomes. PLoS Genet 2023; 19:e1011085. [PMID: 38096267 PMCID: PMC10754456 DOI: 10.1371/journal.pgen.1011085] [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: 03/27/2023] [Revised: 12/28/2023] [Accepted: 11/27/2023] [Indexed: 12/29/2023] Open
Abstract
Clonal genome evolution is a key feature of asexually reproducing species and human cancer development. While many studies have described the landscapes of clonal genome evolution in cancer, few determine the underlying evolutionary parameters from molecular data, and even fewer integrate theory with data. We derived theoretical results linking mutation rate, time, expansion dynamics, and biological/clinical parameters. Subsequently, we inferred time-resolved estimates of evolutionary parameters from mutation accumulation, mutational signatures and selection. We then applied this framework to predict the time of speciation of the marbled crayfish, an enigmatic, globally invasive parthenogenetic freshwater crayfish. The results predict that speciation occurred between 1986 and 1990, which is consistent with biological records. We also used our framework to analyze whole-genome sequencing datasets from primary and relapsed glioblastoma, an aggressive brain tumor. The results identified evolutionary subgroups and showed that tumor cell survival could be inferred from genomic data that was generated during the resection of the primary tumor. In conclusion, our framework allowed a time-resolved, integrated analysis of key parameters in clonally evolving genomes, and provided novel insights into the evolutionary age of marbled crayfish and the progression of glioblastoma.
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Affiliation(s)
- Carine Legrand
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany
- Université Paris Cité, Génomes, biologie cellulaire et thérapeutique U944, INSERM, CNRS, Paris, France
| | - Ranja Andriantsoa
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany
| | - Peter Lichter
- Division of Molecular Genetics, German Cancer Research Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Molecular Precision Oncology, National Center for Tumor Diseases, Heidelberg, Germany
| | - Günter Raddatz
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany
| | - Frank Lyko
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany
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36
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Necchi A, Spiess PE, Costa de Padua T, Li R, Grivas P, Huang RSP, Lin DI, Danziger N, Ross JS, Jacob JM, Sager RA, Basnet A, Li G, Graf RP, Pavlick DC, Bratslavsky G. Genomic Profiles and Clinical Outcomes of Penile Squamous Cell Carcinoma With Elevated Tumor Mutational Burden. JAMA Netw Open 2023; 6:e2348002. [PMID: 38150257 PMCID: PMC10753400 DOI: 10.1001/jamanetworkopen.2023.48002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 10/31/2023] [Indexed: 12/28/2023] Open
Abstract
Importance Tumor mutational burden (TMB) is a putative biomarker of efficacy for immune checkpoint inhibitor (ICI) therapies of solid tumors, but not specifically for penile squamous cell carcinoma (PSCC). Objective To characterize biomarker features and ICI therapy outcomes associated with high TMB in PSCC in the routine clinical practice setting. Design, Setting, and Participants In this cohort study, 397 PSCC cases were analyzed to identify genomic alterations in more than 300 cancer-associated genes and genomic signatures, including TMB, using a hybrid capture-based comprehensive genomic profiling assay. Tumor mutational burden was categorized as low (<10 mutations per megabase [mut/Mb]), high (10-19 mut/Mb), or very high (≥20 mut/Mb). Germline status of genetic alterations was predicted using a validated somatic-germline computational method. Clinical outcomes of patients with metastatic PSCC receiving first-line ICI were abstracted using the deidentified nationwide Clinico-Genomic Database (CGDB) from January 1, 2011, through December 31, 2022. Exposure Comprehensive genomic profiling was performed using FoundationOne and FoundationOne CDx assays from Foundation Medicine Inc. Main outcomes and measures The spectrum of genetic alterations by TMB level in PSCC, the percentage of germline genetic alterations, and the outcome (overall survival with routine clinical treatment) by TMB of chemotherapy-naive patients with PSCC who received ICI treatment up front were assessed in this descriptive study. Results Among 397 patients (median [IQR] age, 65 [54-73] years; 266 [67.0%] of European, 83 [20.9%] of admixed American, and 34 [8.5%] of African or other genomic ancestry), the median (IQR) age (eg, 65 [53-73] years for low TMB vs 68 [61-78] years for TMB ≥10 mut/Mb) and genomic ancestry distribution (eg, European 228 of 339 [67.3%] for low TMB vs 38 of 58 [65.5%] for TMB ≥10 mut/Mb) were similar between TMB subgroups. There were 339 PSCC cases (85.4%) with low TMB, 40 cases (10.1%) with high TMB, and 18 cases (4.5%) with very high TMB. Comparisons of TMB of 10 mut/Mb or higher vs low TMB showed an enrichment of genetic alterations in PIK3CA (48.3% vs 18.3%; P < .001) and KMT2D (29.3% vs 7.7%; P < .001) and less frequent genetic alterations in CDKN2A (25.9% vs 45.7%; P = .05). Most genetic alterations did not co-occur. Human papillomavirus identification was more frequent as TMB increased: 28.3% for low TMB, 50.0% for high, and 72.2% for very high. In total, 95 of 1377 genetic alterations (6.9%) were germline. Of 10 patients identified from the CGDB receiving frontline ICIs, median (IQR) follow-up was 9.9 months. Four patients had overall survival with clinical treatment of more than 12 months, including 2 of 3 patients with TMB of 10 mut/Mb or higher. Conclusions and Relevance In this cohort study of advanced metastatic PSCC based on TMB levels, significant differences were observed for biomarkers in nearly 15% of patients with a TMB of 10 mut/Mb or higher. Germline testing and ICI-based therapy should be integrated into the management of selected PSCC cases.
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Affiliation(s)
- Andrea Necchi
- Department of Medical Oncology, IRCCS San Raffaele Hospital, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
| | - Philippe E. Spiess
- Department of GU Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | | | - Roger Li
- Department of GU Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Petros Grivas
- Division of Oncology, Department of Medicine, University of Washington, Seattle
- Fred Hutchinson Cancer Center, Seattle, Washington
| | | | | | | | - Jeffrey S. Ross
- Foundation Medicine, Inc, Cambridge, Massachusetts
- SUNY Upstate Medical University, Syracuse, New York
| | | | | | - Alina Basnet
- SUNY Upstate Medical University, Syracuse, New York
| | - Gerald Li
- Foundation Medicine, Inc, Cambridge, Massachusetts
| | - Ryon P. Graf
- Foundation Medicine, Inc, Cambridge, Massachusetts
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Hernandez KM, Venkat A, Elbers DC, Bihn JR, Brophy MT, Do NV, La J, Liu Q, Prokhorenkov A, Metoki-Shlubsky N, Sung FC, Paller CJ, Fillmore NR, Grossman RL. Prostate cancer patient stratification by molecular signatures in the Veterans Precision Oncology Data Commons. Cold Spring Harb Mol Case Stud 2023; 9:a006298. [PMID: 38050021 PMCID: PMC10815278 DOI: 10.1101/mcs.a006298] [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: 06/06/2023] [Accepted: 10/31/2023] [Indexed: 12/06/2023] Open
Abstract
Veterans are at an increased risk for prostate cancer, a disease with extraordinary clinical and molecular heterogeneity, compared with the general population. However, little is known about the underlying molecular heterogeneity within the veteran population and its impact on patient management and treatment. Using clinical and targeted tumor sequencing data from the National Veterans Affairs health system, we conducted a retrospective cohort study on 45 patients with advanced prostate cancer in the Veterans Precision Oncology Data Commons (VPODC), most of whom were metastatic castration-resistant. We characterized the mutational burden in this cohort and conducted unsupervised clustering analysis to stratify patients by molecular alterations. Veterans with prostate cancer exhibited a mutational landscape broadly similar to prior studies, including KMT2A and NOTCH1 mutations associated with neuroendocrine prostate cancer phenotype, previously reported to be enriched in veterans. We also identified several potential novel mutations in PTEN, MSH6, VHL, SMO, and ABL1 Hierarchical clustering analysis revealed two subgroups containing therapeutically targetable molecular features with novel mutational signatures distinct from those reported in the Catalogue of Somatic Mutations in Cancer database. The clustering approach presented in this study can potentially be used to clinically stratify patients based on their distinct mutational profiles and identify actionable somatic mutations for precision oncology.
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Affiliation(s)
| | - Aarti Venkat
- Department of Medicine, University of Chicago, Chicago, Illinois 60637, USA
- Center for Translational Data Science, University of Chicago, Chicago, Illinois 60637, USA
| | - Danne C Elbers
- VA Cooperative Studies Program, VA Boston Healthcare System, Boston, Massachusetts 02130, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts 02115, USA
- Chobanian and Avedisian School of Medicine, Boston University, Boston, Massachusetts 02118, USA
| | - John R Bihn
- VA Cooperative Studies Program, VA Boston Healthcare System, Boston, Massachusetts 02130, USA
| | - Mary T Brophy
- VA Cooperative Studies Program, VA Boston Healthcare System, Boston, Massachusetts 02130, USA
- Chobanian and Avedisian School of Medicine, Boston University, Boston, Massachusetts 02118, USA
| | - Nhan V Do
- VA Cooperative Studies Program, VA Boston Healthcare System, Boston, Massachusetts 02130, USA
- Chobanian and Avedisian School of Medicine, Boston University, Boston, Massachusetts 02118, USA
| | - Jennifer La
- VA Cooperative Studies Program, VA Boston Healthcare System, Boston, Massachusetts 02130, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Qiong Liu
- Frederick National laboratory for Cancer Research, Frederick, Maryland 21701, USA
| | - Andrew Prokhorenkov
- Center for Translational Data Science, University of Chicago, Chicago, Illinois 60637, USA
| | - Noah Metoki-Shlubsky
- Center for Translational Data Science, University of Chicago, Chicago, Illinois 60637, USA
| | - Feng-Chi Sung
- VA Cooperative Studies Program, VA Boston Healthcare System, Boston, Massachusetts 02130, USA
| | - Channing J Paller
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA;
| | - Nathanael R Fillmore
- VA Cooperative Studies Program, VA Boston Healthcare System, Boston, Massachusetts 02130, USA;
- Department of Medicine, Harvard Medical School, Boston, Massachusetts 02115, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Robert L Grossman
- Department of Medicine, University of Chicago, Chicago, Illinois 60637, USA
- Center for Translational Data Science, University of Chicago, Chicago, Illinois 60637, USA
- Open Commons Consortium, Chicago, Illinois 60611, USA
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38
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Alonso de la Vega A, Temiz NA, Tasakis R, Somogyi K, Salgueiro L, Zimmer E, Ramos M, Diaz-Jimenez A, Chocarro S, Fernández-Vaquero M, Stefanovska B, Reuveni E, Ben-David U, Stenzinger A, Poth T, Heikenwälder M, Papavasiliou N, Harris RS, Sotillo R. Acute expression of human APOBEC3B in mice results in RNA editing and lethality. Genome Biol 2023; 24:267. [PMID: 38001542 PMCID: PMC10668425 DOI: 10.1186/s13059-023-03115-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 11/20/2023] [Indexed: 11/26/2023] Open
Abstract
BACKGROUND RNA editing has been described as promoting genetic heterogeneity, leading to the development of multiple disorders, including cancer. The cytosine deaminase APOBEC3B is implicated in tumor evolution through DNA mutation, but whether it also functions as an RNA editing enzyme has not been studied. RESULTS Here, we engineer a novel doxycycline-inducible mouse model of human APOBEC3B-overexpression to understand the impact of this enzyme in tissue homeostasis and address a potential role in C-to-U RNA editing. Elevated and sustained levels of APOBEC3B lead to rapid alteration of cellular fitness, major organ dysfunction, and ultimately lethality in mice. Importantly, RNA-sequencing of mouse tissues expressing high levels of APOBEC3B identifies frequent UCC-to-UUC RNA editing events that are not evident in the corresponding genomic DNA. CONCLUSIONS This work identifies, for the first time, a new deaminase-dependent function for APOBEC3B in RNA editing and presents a preclinical tool to help understand the emerging role of APOBEC3B as a driver of carcinogenesis.
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Affiliation(s)
- Alicia Alonso de la Vega
- Division of Molecular Thoracic Oncology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
- Ruprecht Karl University of Heidelberg, 69120, Heidelberg, Germany
| | - Nuri Alpay Temiz
- Health Informatics Institute, University of Minnesota, Minneapolis, 55455, USA
| | - Rafail Tasakis
- Division of Immune Diversity, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Kalman Somogyi
- Division of Molecular Thoracic Oncology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Lorena Salgueiro
- Division of Molecular Thoracic Oncology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Eleni Zimmer
- Division of Molecular Thoracic Oncology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
- Ruprecht Karl University of Heidelberg, 69120, Heidelberg, Germany
| | - Maria Ramos
- Division of Molecular Thoracic Oncology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
- Ruprecht Karl University of Heidelberg, 69120, Heidelberg, Germany
| | - Alberto Diaz-Jimenez
- Division of Molecular Thoracic Oncology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
- Ruprecht Karl University of Heidelberg, 69120, Heidelberg, Germany
| | - Sara Chocarro
- Division of Molecular Thoracic Oncology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
- Ruprecht Karl University of Heidelberg, 69120, Heidelberg, Germany
| | - Mirian Fernández-Vaquero
- Ruprecht Karl University of Heidelberg, 69120, Heidelberg, Germany
- Division of Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Bojana Stefanovska
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX, 78229, USA
- Howard Hughes Medical Institute, University of Texas Health San Antonio, San Antonio, TX, 78229, USA
| | - Eli Reuveni
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Uri Ben-David
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Albrecht Stenzinger
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
- Translational Lung Research Center Heidelberg (TRLC), German Center for Lung Research (DZL), Heidelberg, Germany
| | - Tanja Poth
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Mathias Heikenwälder
- Division of Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Nina Papavasiliou
- Division of Immune Diversity, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Reuben S Harris
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX, 78229, USA
- Howard Hughes Medical Institute, University of Texas Health San Antonio, San Antonio, TX, 78229, USA
| | - Rocio Sotillo
- Division of Molecular Thoracic Oncology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany.
- Translational Lung Research Center Heidelberg (TRLC), German Center for Lung Research (DZL), Heidelberg, Germany.
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Liu WJ, Song R, Zou XR, Li DL, Xu Q, Zhang CY. Enzymatic DNA repairing amplification-powered construction of an Au nanoparticle-based nanosensor for single-molecule monitoring of cytosine deaminase activity in cancer cells. Anal Chim Acta 2023; 1281:341895. [PMID: 38783732 DOI: 10.1016/j.aca.2023.341895] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 10/09/2023] [Indexed: 05/25/2024]
Abstract
APOBEC3A (A3A) is a cytidine deaminase with critical roles in molecular diagnostics. Herein, we demonstrate the enzymatic DNA repairing amplification-powered construction of an Au nanoparticle-based nanosensor for single-molecule monitoring of A3A activity in cancer cells. Target A3A can convert cytosine (C) in substrate probe to uracil (U), and then the template binds with substrate probe to form a dsDNA containing U/A base pairs. Uracil DNA glycosylase (UDG) excises the U base to produce an apurinic/apyrimidinic (AP) site that can be cleaved by apurinic/apyrimidic endonuclease 1 (APE1) to obtain the substrate fragment with 3'-OH end. Subsequently, the substrate fragment initiates cyclic enzymatic repairing amplification (ERA), releasing trigger-1 and trigger-2. The resultant trigger-1 can act as the primer to induce multiple cycles of cyclic ERA, producing numerous trigger-1 and trigger-2. The hybridization of trigger-2 with signal probe forms the dsDNA duplexes with an AP site, inducing the cyclic cleavage of signal probes by APE1 to release abundant Cy5 molecules from the AuNPs. Released Cy5 molecules can be easily quantified by single-molecule imaging. This nanosensor allows for specific and sensitive detection of A3A activity with a detection limit of 0.855 aM, and it can further measure kinetic parameters, screen inhibitors, and quantify endogenous A3A activity at the single-cell level, with prospect application in disease diagnostics and therapy.
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Affiliation(s)
- Wen-Jing Liu
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan, 250014, China; School of Chemistry and Chemical Engineering, Southeast University, Nanjing, 211189, China
| | - Rui Song
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan, 250014, China
| | - Xiao-Ran Zou
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan, 250014, China
| | - Dong-Ling Li
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing, 211189, China
| | - Qinfeng Xu
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, 710021, China.
| | - Chun-Yang Zhang
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing, 211189, China.
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40
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Carpenter MA, Temiz NA, Ibrahim MA, Jarvis MC, Brown MR, Argyris PP, Brown WL, Starrett GJ, Yee D, Harris RS. Mutational impact of APOBEC3A and APOBEC3B in a human cell line and comparisons to breast cancer. PLoS Genet 2023; 19:e1011043. [PMID: 38033156 PMCID: PMC10715669 DOI: 10.1371/journal.pgen.1011043] [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: 07/31/2023] [Revised: 12/12/2023] [Accepted: 10/30/2023] [Indexed: 12/02/2023] Open
Abstract
A prominent source of mutation in cancer is single-stranded DNA cytosine deamination by cellular APOBEC3 enzymes, which results in signature C-to-T and C-to-G mutations in TCA and TCT motifs. Although multiple enzymes have been implicated, reports conflict and it is unclear which protein(s) are responsible. Here we report the development of a selectable system to quantify genome mutation and demonstrate its utility by comparing the mutagenic activities of three leading candidates-APOBEC3A, APOBEC3B, and APOBEC3H. The human cell line, HAP1, is engineered to express the thymidine kinase (TK) gene of HSV-1, which confers sensitivity to ganciclovir. Expression of APOBEC3A and APOBEC3B, but not catalytic mutant controls or APOBEC3H, triggers increased frequencies of TK mutation and similar TC-biased cytosine mutation profiles in the selectable TK reporter gene. Whole genome sequences from independent clones enabled an analysis of thousands of single base substitution mutations and extraction of local sequence preferences with APOBEC3A preferring YTCW motifs 70% of the time and APOBEC3B 50% of the time (Y = C/T; W = A/T). Signature comparisons with breast tumor whole genome sequences indicate that most malignancies manifest intermediate percentages of APOBEC3 signature mutations in YTCW motifs, mostly between 50 and 70%, suggesting that both enzymes contribute in a combinatorial manner to the overall mutation landscape. Although the vast majority of APOBEC3A- and APOBEC3B-induced single base substitution mutations occur outside of predicted chromosomal DNA hairpin structures, whole genome sequence analyses and supporting biochemical studies also indicate that both enzymes are capable of deaminating the single-stranded loop regions of DNA hairpins at elevated rates. These studies combine to help resolve a long-standing etiologic debate on the source of APOBEC3 signature mutations in cancer and indicate that future diagnostic and therapeutic efforts should focus on both APOBEC3A and APOBEC3B.
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Affiliation(s)
- Michael A. Carpenter
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, United States of America
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, United States of America
- Howard Hughes Medical Institute, University of Minnesota, Minneapolis, Minnesota, United States of America
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, Texas, United States of America
- Howard Hughes Medical Institute, University of Texas Health San Antonio, San Antonio, Texas, United States of America
| | - Nuri A. Temiz
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, United States of America
- Institute for Health Informatics, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Mahmoud A. Ibrahim
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, Texas, United States of America
| | - Matthew C. Jarvis
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, United States of America
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Margaret R. Brown
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, United States of America
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Prokopios P. Argyris
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, United States of America
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, United States of America
- Howard Hughes Medical Institute, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - William L. Brown
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, United States of America
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Gabriel J. Starrett
- Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland, United States of America
| | - Douglas Yee
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, United States of America
- Department of Medicine, University of Minnesota Medical School, Minneapolis, Minnesota, United States of America
| | - Reuben S. Harris
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, United States of America
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, United States of America
- Howard Hughes Medical Institute, University of Minnesota, Minneapolis, Minnesota, United States of America
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, Texas, United States of America
- Howard Hughes Medical Institute, University of Texas Health San Antonio, San Antonio, Texas, United States of America
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Secrier M, McGrath L, Ng F, Gulati S, Raymond A, Nuttall BRB, Berthe J, Jones EV, Sidders BS, Galon J, Barrett JC, Angell HK. Immune Cell Abundance and T-cell Receptor Landscapes Suggest New Patient Stratification Strategies in Head and Neck Squamous Cell Carcinoma. CANCER RESEARCH COMMUNICATIONS 2023; 3:2133-2145. [PMID: 37819239 PMCID: PMC10588680 DOI: 10.1158/2767-9764.crc-23-0155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 08/04/2023] [Accepted: 09/26/2023] [Indexed: 10/13/2023]
Abstract
Head and neck squamous cell carcinoma (HNSCC) is a molecularly and spatially heterogeneous disease frequently characterized by impairment of immunosurveillance mechanisms. Despite recent success with immunotherapy treatment, disease progression still occurs quickly after treatment in the majority of cases, suggesting the need to improve patient selection strategies. In the quest for biomarkers that may help inform response to checkpoint blockade, we characterized the tumor microenvironment (TME) of 162 HNSCC primary tumors of diverse etiologic and spatial origin, through gene expression and IHC profiling of relevant immune proteins, T-cell receptor (TCR) repertoire analysis, and whole-exome sequencing. We identified five HNSCC TME categories based on immune/stromal composition: (i) cytotoxic, (ii) plasma cell rich, (iii) dendritic cell rich, (iv) macrophage rich, and (v) immune-excluded. Remarkably, the cytotoxic and plasma cell rich subgroups exhibited a phenotype similar to tertiary lymphoid structures (TLS), which have been previously linked to immunotherapy response. We also found an increased richness of the TCR repertoire in these two subgroups and in never smokers. Mutational patterns evidencing APOBEC activity were enriched in the plasma cell high subgroup. Furthermore, specific signal propagation patterns within the Ras/ERK and PI3K/AKT pathways associated with distinct immune phenotypes. While traditionally CD8/CD3 T-cell infiltration and immune checkpoint expression (e.g., PD-L1) have been used in the patient selection process for checkpoint blockade treatment, we suggest that additional biomarkers, such as TCR productive clonality, smoking history, and TLS index, may have the ability to pull out potential responders to benefit from immunotherapeutic agents. SIGNIFICANCE Here we present our findings on the genomic and immune landscape of primary disease in a cohort of 162 patients with HNSCC, benefitting from detailed molecular and clinical characterization. By employing whole-exome sequencing and gene expression analysis of relevant immune markers, TCR profiling, and staining of relevant proteins involved in immune response, we highlight how distinct etiologies, cell intrinsic, and environmental factors combine to shape the landscape of HNSCC primary disease.
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Affiliation(s)
- Maria Secrier
- Translational Medicine, Oncology R&D, AstraZeneca, Cambridge, United Kingdom
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Lara McGrath
- Translational Medicine, Oncology R&D, AstraZeneca, Boston, Massachusetts
| | - Felicia Ng
- Oncology Data Science, Oncology R&D, AstraZeneca, Cambridge, United Kingdom
| | - Sakshi Gulati
- Translational Medicine, Oncology R&D, AstraZeneca, Cambridge, United Kingdom
| | - Amelia Raymond
- Translational Medicine, Oncology R&D, AstraZeneca, Boston, Massachusetts
| | | | - Julie Berthe
- Translational Medicine, Oncology R&D, AstraZeneca, Cambridge, United Kingdom
| | - Emma V. Jones
- Translational Medicine, Oncology R&D, AstraZeneca, Cambridge, United Kingdom
| | - Ben S. Sidders
- Oncology Data Science, Oncology R&D, AstraZeneca, Cambridge, United Kingdom
| | - Jérôme Galon
- INSERM, Laboratory of Integrative Cancer Immunology, Paris, France
- Sorbonne Université, Université Paris Cité, Centre de Recherche des Cordeliers, Paris, France
- Equipe Labellisée Ligue Contre le Cancer, Paris, France
| | - J. Carl Barrett
- Translational Medicine, Oncology R&D, AstraZeneca, Boston, Massachusetts
| | - Helen K. Angell
- Translational Medicine, Oncology R&D, AstraZeneca, Cambridge, United Kingdom
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42
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Burack WR, Li H, Adlowitz D, Spence JM, Rimsza LM, Shadman M, Spier CM, Kaminski MS, Leonard JP, Leblanc ML, Smith SM, Friedberg JW. Subclonal TP53 mutations are frequent and predict resistance to radioimmunotherapy in follicular lymphoma. Blood Adv 2023; 7:5082-5090. [PMID: 37379264 PMCID: PMC10471938 DOI: 10.1182/bloodadvances.2022009467] [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: 12/02/2022] [Revised: 05/12/2023] [Accepted: 06/05/2023] [Indexed: 06/30/2023] Open
Abstract
Although TP53 is commonly mutated in transformed follicular lymphoma, mutations are reported in <5% of pretreatment follicular lymphoma (FL) specimens. We assayed archival follicular B-cell non-Hodgkin lymphoma specimens from a completed clinical trial, Southwest Oncology Group S0016, a phase 3 randomized intergroup trial of CHOP (cyclophosphamide, hydroxydaunorubicin, oncovin, and prednisone) chemotherapy plus R-CHOP (rituximab-CHOP) compared with CHOP chemotherapy plus 131-iodine tositumomab (radioimmunotherapy [RIT]-CHOP). Subclonal TP53 mutations (median allele frequency 0.02) were found in 25% of diagnostic FL specimens and in 27% of a separate validation cohort. In the R-CHOP arm, pathogenic TP53 mutations were not associated with progression-free survival (PFS) (10-year PFS 43% vs 44%). In contrast, among patients with no detectable pathogenic TP53 mutation, RIT-CHOP was associated with a longer PFS than with R-CHOP (10-year PFS 67% vs 44%; hazard ratio = 0.49; P = .008). No relationship was detected between PFS and the extent of activation-induced cytidine deaminase (AICDA)-mediated heterogeneity. In summary, subclonal TP53 mutations are common in FL and are a distinct phenomenon from AICDA-mediated genetic heterogeneity. The absence of a detectable subclonal mutation in TP53 defined a population that particularly benefited from RIT.
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Affiliation(s)
- W. Richard Burack
- Department of Pathology, University of Rochester Medical Center, Rochester, NY
| | - Hongli Li
- Clinical Research Division, Fred Hutchison Cancer Research Center, Seattle, WA
| | - Diana Adlowitz
- Department of Pathology, University of Rochester Medical Center, Rochester, NY
| | - Janice M. Spence
- Department of Pathology, University of Rochester Medical Center, Rochester, NY
| | - Lisa M. Rimsza
- Department of Laboratory Medicine and Pathology, Mayo Clinic in Arizona, Phoenix, AZ
| | - Mazyar Shadman
- Clinical Research Division, Fred Hutchison Cancer Research Center, Seattle, WA
| | | | - Mark S. Kaminski
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI
| | - John P. Leonard
- Department of Medicine, Weill Cornell Medical College, New York, NY
| | - Michael L. Leblanc
- Clinical Research Division, Fred Hutchison Cancer Research Center, Seattle, WA
| | - Sonali M. Smith
- Department of Medicine, University of Chicago School of Medicine, Chicago, IL
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Lee JE, Kim KT, Shin SJ, Cheong JH, Choi YY. Genomic and evolutionary characteristics of metastatic gastric cancer by routes. Br J Cancer 2023; 129:672-682. [PMID: 37422528 PMCID: PMC10421927 DOI: 10.1038/s41416-023-02338-3] [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: 12/05/2022] [Revised: 06/07/2023] [Accepted: 06/19/2023] [Indexed: 07/10/2023] Open
Abstract
BACKGROUND In gastric cancer (GC) patients, metastatic progression through the lymphatic, hematogenous, peritoneal, and ovarian routes, is the ultimate cause of death. However, the genomic and evolutionary characteristics of metastatic GC have not been widely evaluated. METHODS Whole-exome sequencing data were analyzed for 99 primary and paired metastatic gastric cancers from 15 patients who underwent gastrectomy and metastasectomy. RESULTS Hematogenous metastatic tumors were associated with increased chromosomal instability and de novo gain/amplification in cancer driver genes, whereas peritoneal/ovarian metastasis was linked to sustained chromosomal stability and de novo somatic mutations in driver genes. The genomic distance of the hematogenous and peritoneal metastatic tumors was found to be closer to the primary tumors than lymph node (LN) metastasis, while ovarian metastasis was closer to LN and peritoneal metastasis than the primary tumor. Two migration patterns for metastatic GCs were identified; branched and diaspora. Both molecular subtypes of the metastatic tumors, rather than the primary tumor, and their migration patterns were related to patient survival. CONCLUSIONS Genomic characteristics of metastatic gastric cancer is distinctive by routes and associated with patients' prognosis along with genomic evolution pattenrs, indicating that both primary and metastatic gastric cancers require genomic evaluation.
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Affiliation(s)
- Jae Eun Lee
- Portrai Inc., Seoul, Korea
- Department of Surgery, Yonsei University Health System, Yonsei University College of Medicine, Seoul, South Korea
| | - Ki Tae Kim
- Department of Molecular Genetics & Dental Pharmacology, School of Dentistry, Seoul National University, Seoul, South Korea
- Dental Research Institute and Dental Multi-omics Center, Seoul National University, Seoul, South Korea
| | - Su-Jin Shin
- Department of Pathology, Yonsei University Health System, Yonsei University College of Medicine, Seoul, South Korea
| | - Jae-Ho Cheong
- Department of Surgery, Yonsei University Health System, Yonsei University College of Medicine, Seoul, South Korea.
| | - Yoon Young Choi
- Department of Surgery, Soonchunhyang Bucheon Hospital, Soonchunhyang University College of Medicine, Bucheon, South Korea.
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Wick C, Moghadasi SA, Becker JT, Fanunza E, Oh S, Bournique E, Buisson R, Harris RS. Mitochondrial double-stranded RNA triggers induction of the antiviral DNA deaminase APOBEC3A and nuclear DNA damage. J Biol Chem 2023; 299:105073. [PMID: 37474103 PMCID: PMC10457583 DOI: 10.1016/j.jbc.2023.105073] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 06/27/2023] [Accepted: 06/28/2023] [Indexed: 07/22/2023] Open
Abstract
APOBEC3A is an antiviral DNA deaminase often induced by virus infection. APOBEC3A is also a source of cancer mutation in viral and nonviral tumor types. It is therefore critical to identify factors responsible for APOBEC3A upregulation. Here, we test the hypothesis that leaked mitochondrial (mt) double-stranded (ds)RNA is recognized as foreign nucleic acid, which triggers innate immune signaling, APOBEC3A upregulation, and DNA damage. Knockdown of an enzyme responsible for degrading mtdsRNA, the exoribonuclease polynucleotide phosphorylase, results in mtdsRNA leakage into the cytosol and induction of APOBEC3A expression. APOBEC3A upregulation by cytoplasmic mtdsRNA requires RIG-I, MAVS, and STAT2 and is likely part of a broader type I interferon response. Importantly, although mtdsRNA-induced APOBEC3A appears cytoplasmic by subcellular fractionation experiments, its induction triggers an overt DNA damage response characterized by elevated nuclear γ-H2AX staining. Thus, mtdsRNA dysregulation may induce APOBEC3A and contribute to observed genomic instability and mutation signatures in cancer.
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Affiliation(s)
- Chloe Wick
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
| | - Seyed Arad Moghadasi
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
| | - Jordan T Becker
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
| | - Elisa Fanunza
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, Texas, USA; Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, Monserrato, Cagliari, Italy
| | - Sunwoo Oh
- Department of Biological Chemistry, School of Medicine, University of California Irvine, Irvine, California, USA; Center for Epigenetics and Metabolism, Chao Family Comprehensive Cancer Center, University of California Irvine, Irvine, California, USA
| | - Elodie Bournique
- Department of Biological Chemistry, School of Medicine, University of California Irvine, Irvine, California, USA; Center for Epigenetics and Metabolism, Chao Family Comprehensive Cancer Center, University of California Irvine, Irvine, California, USA
| | - Rémi Buisson
- Department of Biological Chemistry, School of Medicine, University of California Irvine, Irvine, California, USA; Center for Epigenetics and Metabolism, Chao Family Comprehensive Cancer Center, University of California Irvine, Irvine, California, USA
| | - Reuben S Harris
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA; Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, Texas, USA; Howard Hughes Medical Institute, University of Texas Health San Antonio, San Antonio, Texas, USA.
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45
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Wang P, Sun S, Lam S, Lockwood WW. New insights into the biology and development of lung cancer in never smokers-implications for early detection and treatment. J Transl Med 2023; 21:585. [PMID: 37653450 PMCID: PMC10472682 DOI: 10.1186/s12967-023-04430-x] [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: 06/16/2023] [Accepted: 08/10/2023] [Indexed: 09/02/2023] Open
Abstract
Lung cancer is the leading cause of cancer deaths worldwide. Despite never smokers comprising between 10 and 25% of all cases, lung cancer in never smokers (LCNS) is relatively under characterized from an etiological and biological perspective. The application of multi-omics techniques on large patient cohorts has significantly advanced the current understanding of LCNS tumor biology. By synthesizing the findings of multi-omics studies on LCNS from a clinical perspective, we can directly translate knowledge regarding tumor biology into implications for patient care. Primarily focused on never smokers with lung adenocarcinoma, this review details the predominance of driver mutations, particularly in East Asian patients, as well as the frequency and importance of germline variants in LCNS. The mutational patterns present in LCNS tumors are thoroughly explored, highlighting the high abundance of the APOBEC signature. Moreover, this review recognizes the spectrum of immune profiles present in LCNS tumors and posits how it can be translated to treatment selection. The recurring and novel insights from multi-omics studies on LCNS tumor biology have a wide range of clinical implications. Risk factors such as exposure to outdoor air pollution, second hand smoke, and potentially diet have a genomic imprint in LCNS at varying degrees, and although they do not encompass all LCNS cases, they can be leveraged to stratify risk. Germline variants similarly contribute to a notable proportion of LCNS, which warrants detailed documentation of family history of lung cancer among never smokers and demonstrates value in developing testing for pathogenic variants in never smokers for early detection in the future. Molecular driver subtypes and specific co-mutations and mutational signatures have prognostic value in LCNS and can guide treatment selection. LCNS tumors with no known driver alterations tend to be stem-like and genes contributing to this state may serve as potential therapeutic targets. Overall, the comprehensive findings of multi-omics studies exert a wide influence on clinical management and future research directions in the realm of LCNS.
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Affiliation(s)
- Peiyao Wang
- Department of Integrative Oncology, British Columbia Cancer Research Institute, Vancouver, BC, Canada
- Interdisciplinary Oncology Program, University of British Columbia, Vancouver, BC, Canada
| | - Sophie Sun
- Department of Medical Oncology, British Columbia Cancer Agency Vancouver, Vancouver, BC, Canada
| | - Stephen Lam
- Department of Integrative Oncology, British Columbia Cancer Research Institute, Vancouver, BC, Canada
| | - William W Lockwood
- Department of Integrative Oncology, British Columbia Cancer Research Institute, Vancouver, BC, Canada.
- Interdisciplinary Oncology Program, University of British Columbia, Vancouver, BC, Canada.
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada.
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46
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Xu S, Tan S, Guo L. Patient-Derived Organoids as a Promising Tool for Multimodal Management of Sarcomas. Cancers (Basel) 2023; 15:4339. [PMID: 37686615 PMCID: PMC10486520 DOI: 10.3390/cancers15174339] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 08/17/2023] [Accepted: 08/21/2023] [Indexed: 09/10/2023] Open
Abstract
The management of sarcomas, a diverse group of cancers arising from connective tissues, presents significant challenges due to their heterogeneity and limited treatment options. Patient-derived sarcoma organoids (PDSOs) have emerged as a promising tool in the multimodal management of sarcomas, offering unprecedented opportunities for personalized medicine and improved treatment strategies. This review aims to explore the potential of PDSOs as a promising tool for multimodal management of sarcomas. We discuss the establishment and characterization of PDSOs, which realistically recapitulate the complexity and heterogeneity of the original tumor, providing a platform for genetic and molecular fidelity, histological resemblance, and functional characterization. Additionally, we discuss the applications of PDSOs in pathological and genetic evaluation, treatment screening and development, and personalized multimodal management. One significant advancement of PDSOs lies in their ability to guide personalized treatment decisions, enabling clinicians to assess the response and efficacy of different therapies in a patient-specific manner. Through continued research and development, PDSOs hold the potential to revolutionize sarcoma management and drive advancements in personalized medicine, biomarker discovery, preclinical modeling, and therapy optimization. The integration of PDSOs into clinical practice can ultimately improve patient outcomes and significantly impact the field of sarcoma treatment.
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Affiliation(s)
- Songfeng Xu
- National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Shenzhen 518116, China;
- Department of Orthopedics, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100021, China
| | - ShihJye Tan
- Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Department of Biology, Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, 1088 Xueyuan Blvd, Biology Building 402, Shenzhen 518055, China
| | - Ling Guo
- Department of Orthopedics, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100021, China
- Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Department of Biology, Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, 1088 Xueyuan Blvd, Biology Building 402, Shenzhen 518055, China
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47
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Gyüre Z, Póti Á, Németh E, Szikriszt B, Lózsa R, Krawczyk M, Richardson AL, Szüts D. Spontaneous mutagenesis in human cells is controlled by REV1-Polymerase ζ and PRIMPOL. Cell Rep 2023; 42:112887. [PMID: 37498746 DOI: 10.1016/j.celrep.2023.112887] [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: 03/17/2023] [Revised: 06/09/2023] [Accepted: 07/13/2023] [Indexed: 07/29/2023] Open
Abstract
Translesion DNA synthesis (TLS) facilitates replication over damaged or difficult-to-replicate templates by employing specialized DNA polymerases. We investigate the effect on spontaneous mutagenesis of three main TLS control mechanisms: REV1 and PCNA ubiquitylation that recruit TLS polymerases and PRIMPOL that creates post-replicative gaps. Using whole-genome sequencing of cultured human RPE-1 cell clones, we find that REV1 and Polymerase ζ are wholly responsible for one component of base substitution mutagenesis that resembles homologous recombination deficiency, whereas the remaining component that approximates oxidative mutagenesis is reduced in PRIMPOL-/- cells. Small deletions in short repeats appear in REV1-/-PCNAK164R/K164R double mutants, revealing an alternative TLS mechanism. Also, 500-5,000 bp deletions appear in REV1-/- and REV3L-/- mutants, and chromosomal instability is detectable in REV1-/-PRIMPOL-/- cells. Our results indicate that TLS protects the genome from deletions and large rearrangements at the expense of being responsible for the majority of spontaneous base substitutions.
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Affiliation(s)
- Zsolt Gyüre
- Institute of Enzymology, Research Centre for Natural Sciences, 1117 Budapest, Hungary; Doctoral School of Molecular Medicine, Semmelweis University, 1085 Budapest, Hungary; Turbine Simulated Cell Technologies, 1027 Budapest, Hungary
| | - Ádám Póti
- Institute of Enzymology, Research Centre for Natural Sciences, 1117 Budapest, Hungary
| | - Eszter Németh
- Institute of Enzymology, Research Centre for Natural Sciences, 1117 Budapest, Hungary
| | - Bernadett Szikriszt
- Institute of Enzymology, Research Centre for Natural Sciences, 1117 Budapest, Hungary
| | - Rita Lózsa
- Institute of Enzymology, Research Centre for Natural Sciences, 1117 Budapest, Hungary
| | - Michał Krawczyk
- Institute of Enzymology, Research Centre for Natural Sciences, 1117 Budapest, Hungary
| | | | - Dávid Szüts
- Institute of Enzymology, Research Centre for Natural Sciences, 1117 Budapest, Hungary; National Laboratory for Drug Research and Development, 1117 Budapest, Hungary.
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48
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Otlu B, Díaz-Gay M, Vermes I, Bergstrom EN, Zhivagui M, Barnes M, Alexandrov LB. Topography of mutational signatures in human cancer. Cell Rep 2023; 42:112930. [PMID: 37540596 PMCID: PMC10507738 DOI: 10.1016/j.celrep.2023.112930] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 05/09/2023] [Accepted: 07/18/2023] [Indexed: 08/06/2023] Open
Abstract
The somatic mutations found in a cancer genome are imprinted by different mutational processes. Each process exhibits a characteristic mutational signature, which can be affected by the genome architecture. However, the interplay between mutational signatures and topographical genomic features has not been extensively explored. Here, we integrate mutations from 5,120 whole-genome-sequenced tumors from 40 cancer types with 516 topographical features from ENCODE to evaluate the effect of nucleosome occupancy, histone modifications, CTCF binding, replication timing, and transcription/replication strand asymmetries on the cancer-specific accumulation of mutations from distinct mutagenic processes. Most mutational signatures are affected by topographical features, with signatures of related etiologies being similarly affected. Certain signatures exhibit periodic behaviors or cancer-type-specific enrichments/depletions near topographical features, revealing further information about the processes that imprinted them. Our findings, disseminated via the COSMIC (Catalog of Somatic Mutations in Cancer) signatures database, provide a comprehensive online resource for exploring the interactions between mutational signatures and topographical features across human cancer.
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Affiliation(s)
- Burçak Otlu
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA 92093, USA; Department of Bioengineering, UC San Diego, La Jolla, CA 92093, USA; Moores Cancer Center, UC San Diego, La Jolla, CA 92037, USA; Department of Health Informatics, Graduate School of Informatics, Middle East Technical University, Ankara 06800, Turkey
| | - Marcos Díaz-Gay
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA 92093, USA; Department of Bioengineering, UC San Diego, La Jolla, CA 92093, USA; Moores Cancer Center, UC San Diego, La Jolla, CA 92037, USA
| | - Ian Vermes
- COSMIC, Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Erik N Bergstrom
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA 92093, USA; Department of Bioengineering, UC San Diego, La Jolla, CA 92093, USA; Moores Cancer Center, UC San Diego, La Jolla, CA 92037, USA
| | - Maria Zhivagui
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA 92093, USA; Department of Bioengineering, UC San Diego, La Jolla, CA 92093, USA; Moores Cancer Center, UC San Diego, La Jolla, CA 92037, USA
| | - Mark Barnes
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA 92093, USA; Department of Bioengineering, UC San Diego, La Jolla, CA 92093, USA; Moores Cancer Center, UC San Diego, La Jolla, CA 92037, USA
| | - Ludmil B Alexandrov
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA 92093, USA; Department of Bioengineering, UC San Diego, La Jolla, CA 92093, USA; Moores Cancer Center, UC San Diego, La Jolla, CA 92037, USA.
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49
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Khandekar A, Vangara R, Barnes M, Díaz-Gay M, Abbasi A, Bergstrom EN, Steele CD, Pillay N, Alexandrov LB. Visualizing and exploring patterns of large mutational events with SigProfilerMatrixGenerator. BMC Genomics 2023; 24:469. [PMID: 37605126 PMCID: PMC10440861 DOI: 10.1186/s12864-023-09584-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 08/14/2023] [Indexed: 08/23/2023] Open
Abstract
BACKGROUND All cancers harbor somatic mutations in their genomes. In principle, mutations affecting between one and fifty base pairs are generally classified as small mutational events. Conversely, large mutational events affect more than fifty base pairs, and, in most cases, they encompass copy-number and structural variants affecting many thousands of base pairs. Prior studies have demonstrated that examining patterns of somatic mutations can be leveraged to provide both biological and clinical insights, thus, resulting in an extensive repertoire of tools for evaluating small mutational events. Recently, classification schemas for examining large-scale mutational events have emerged and shown their utility across the spectrum of human cancers. However, there has been no computationally efficient bioinformatics tool that allows visualizing and exploring these large-scale mutational events. RESULTS Here, we present a new version of SigProfilerMatrixGenerator that now delivers integrated capabilities for examining large mutational events. The tool provides support for examining copy-number variants and structural variants under two previously developed classification schemas and it supports data from numerous algorithms and data modalities. SigProfilerMatrixGenerator is written in Python with an R wrapper package provided for users that prefer working in an R environment. CONCLUSIONS The new version of SigProfilerMatrixGenerator provides the first standardized bioinformatics tool for optimized exploration and visualization of two previously developed classification schemas for copy number and structural variants. The tool is freely available at https://github.com/AlexandrovLab/SigProfilerMatrixGenerator with an extensive documentation at https://osf.io/s93d5/wiki/home/ .
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Affiliation(s)
- Azhar Khandekar
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, 92093, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA, 92093, USA
- Moores Cancer Center, UC San Diego, La Jolla, CA, 92037, USA
| | - Raviteja Vangara
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, 92093, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA, 92093, USA
- Moores Cancer Center, UC San Diego, La Jolla, CA, 92037, USA
| | - Mark Barnes
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, 92093, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA, 92093, USA
- Moores Cancer Center, UC San Diego, La Jolla, CA, 92037, USA
| | - Marcos Díaz-Gay
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, 92093, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA, 92093, USA
- Moores Cancer Center, UC San Diego, La Jolla, CA, 92037, USA
| | - Ammal Abbasi
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, 92093, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA, 92093, USA
- Moores Cancer Center, UC San Diego, La Jolla, CA, 92037, USA
| | - Erik N Bergstrom
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, 92093, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA, 92093, USA
- Moores Cancer Center, UC San Diego, La Jolla, CA, 92037, USA
| | - Christopher D Steele
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, 92093, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA, 92093, USA
- Moores Cancer Center, UC San Diego, La Jolla, CA, 92037, USA
| | - Nischalan Pillay
- Research Department of Pathology, Cancer Institute, University College London, London, WC1E 6BT, UK
- Department of Cellular and Molecular Pathology, Royal National Orthopaedic Hospital NHS Trust, Stanmore, HA7 4LP, Middlesex, UK
| | - Ludmil B Alexandrov
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, 92093, USA.
- Department of Bioengineering, UC San Diego, La Jolla, CA, 92093, USA.
- Moores Cancer Center, UC San Diego, La Jolla, CA, 92037, USA.
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50
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Poulsgaard GA, Sørensen SG, Juul RI, Nielsen MM, Pedersen JS. Sequence dependencies and mutation rates of localized mutational processes in cancer. Genome Med 2023; 15:63. [PMID: 37592287 PMCID: PMC10436389 DOI: 10.1186/s13073-023-01217-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: 02/21/2023] [Accepted: 08/02/2023] [Indexed: 08/19/2023] Open
Abstract
BACKGROUND Cancer mutations accumulate through replication errors and DNA damage coupled with incomplete repair. Individual mutational processes often show nucleotide sequence and functional region preferences. As a result, some sequence contexts mutate at much higher rates than others, with additional variation found between functional regions. Mutational hotspots, with recurrent mutations across cancer samples, represent genomic positions with elevated mutation rates, often caused by highly localized mutational processes. METHODS We count the 11-mer genomic sequences across the genome, and using the PCAWG set of 2583 pan-cancer whole genomes, we associate 11-mers with mutational signatures, hotspots of single nucleotide variants, and specific genomic regions. We evaluate the mutation rates of individual and combined sets of 11-mers and derive mutational sequence motifs. RESULTS We show that hotspots generally identify highly mutable sequence contexts. Using these, we show that some mutational signatures are enriched in hotspot sequence contexts, corresponding to well-defined sequence preferences for the underlying localized mutational processes. This includes signature 17b (of unknown etiology) and signatures 62 (POLE deficiency), 7a (UV), and 72 (linked to lymphomas). In some cases, the mutation rate and sequence preference increase further when focusing on certain genomic regions, such as signature 62 in transcribed regions, where the mutation rate is increased up to 9-folds over cancer type and mutational signature average. CONCLUSIONS We summarize our findings in a catalog of localized mutational processes, their sequence preferences, and their estimated mutation rates.
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Affiliation(s)
- Gustav Alexander Poulsgaard
- Department of Clinical Medicine, Aarhus University, Palle Juul-Jensens Boulevard 82, 8200, Aarhus N, Denmark
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, Palle Juul-Jensens Boulevard 99, 8200, Aarhus N, Denmark
| | - Simon Grund Sørensen
- Department of Clinical Medicine, Aarhus University, Palle Juul-Jensens Boulevard 82, 8200, Aarhus N, Denmark
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, Palle Juul-Jensens Boulevard 99, 8200, Aarhus N, Denmark
| | - Randi Istrup Juul
- Department of Clinical Medicine, Aarhus University, Palle Juul-Jensens Boulevard 82, 8200, Aarhus N, Denmark
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, Palle Juul-Jensens Boulevard 99, 8200, Aarhus N, Denmark
| | - Morten Muhlig Nielsen
- Department of Clinical Medicine, Aarhus University, Palle Juul-Jensens Boulevard 82, 8200, Aarhus N, Denmark
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, Palle Juul-Jensens Boulevard 99, 8200, Aarhus N, Denmark
| | - Jakob Skou Pedersen
- Department of Clinical Medicine, Aarhus University, Palle Juul-Jensens Boulevard 82, 8200, Aarhus N, Denmark.
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, Palle Juul-Jensens Boulevard 99, 8200, Aarhus N, Denmark.
- Bioinformatics Research Centre (BiRC), Aarhus University, University City 81, Building 1872, 3Rd Floor, 8000, Aarhus C, Denmark.
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