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Mukohara F, Iwata K, Ishino T, Inozume T, Nagasaki J, Ueda Y, Suzawa K, Ueno T, Ikeda H, Kawase K, Saeki Y, Kawashima S, Yamashita K, Kawahara Y, Nakamura Y, Honobe-Tabuchi A, Watanabe H, Dansako H, Kawamura T, Suzuki Y, Honda H, Mano H, Toyooka S, Kawazu M, Togashi Y. Somatic mutations in tumor-infiltrating lymphocytes impact on antitumor immunity. Proc Natl Acad Sci U S A 2024; 121:e2320189121. [PMID: 39167601 DOI: 10.1073/pnas.2320189121] [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: 12/01/2023] [Accepted: 07/05/2024] [Indexed: 08/23/2024] Open
Abstract
Immune checkpoint inhibitors (ICIs) exert clinical efficacy against various types of cancers by reinvigorating exhausted CD8+ T cells that can expand and directly attack cancer cells (cancer-specific T cells) among tumor-infiltrating lymphocytes (TILs). Although some reports have identified somatic mutations in TILs, their effect on antitumor immunity remains unclear. In this study, we successfully established 18 cancer-specific T cell clones, which have an exhaustion phenotype, from the TILs of four patients with melanoma. We conducted whole-genome sequencing for these T cell clones and identified various somatic mutations in them with high clonality. Among the somatic mutations, an SH2D2A loss-of-function frameshift mutation and TNFAIP3 deletion could activate T cell effector functions in vitro. Furthermore, we generated CD8+ T cell-specific Tnfaip3 knockout mice and showed that Tnfaip3 function loss in CD8+ T cell increased antitumor immunity, leading to remarkable response to PD-1 blockade in vivo. In addition, we analyzed bulk CD3+ T cells from TILs in additional 12 patients and identified an SH2D2A mutation in one patient through amplicon sequencing. These findings suggest that somatic mutations in TILs can affect antitumor immunity and suggest unique biomarkers and therapeutic targets.
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Affiliation(s)
- Fumiaki Mukohara
- Department of Tumor Microenvironment, Faculty of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8558, Japan
- Department of General Thoracic Surgery and Breast and Endocrinological Surgery, Dentistry and Pharmaceutical Sciences, Okayama University Graduate School of Medicine, Okayama University, Okayama 700-8558, Japan
| | - Kazuma Iwata
- Department of Tumor Microenvironment, Faculty of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8558, Japan
- Department of General Thoracic Surgery and Breast and Endocrinological Surgery, Dentistry and Pharmaceutical Sciences, Okayama University Graduate School of Medicine, Okayama University, Okayama 700-8558, Japan
| | - Takamasa Ishino
- Department of Tumor Microenvironment, Faculty of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8558, Japan
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan
| | - Takashi Inozume
- Department of Dermatology, Chiba University Graduate School of Medicine, Chiba 260-8670, Japan
- Division of Cell Therapy, Chiba Cancer Research Institute, Chiba 260-8717, Japan
- Department of Dermatology, University of Yamanashi, Yamanashi 409-3898, Japan
| | - Joji Nagasaki
- Department of Tumor Microenvironment, Faculty of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8558, Japan
| | - Youki Ueda
- Department of Tumor Microenvironment, Faculty of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8558, Japan
| | - Ken Suzawa
- Department of General Thoracic Surgery and Breast and Endocrinological Surgery, Dentistry and Pharmaceutical Sciences, Okayama University Graduate School of Medicine, Okayama University, Okayama 700-8558, Japan
| | - Toshihide Ueno
- Division of Cellular Signaling, National Cancer Center Research Institute, Chuo-ku, Tokyo 104-0045, Japan
| | - Hideki Ikeda
- Division of Cell Therapy, Chiba Cancer Research Institute, Chiba 260-8717, Japan
- Department of Respiratory Medicine, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan
| | - Katsushige Kawase
- Division of Cell Therapy, Chiba Cancer Research Institute, Chiba 260-8717, Japan
- Department of Otorhinolaryngology/Head & Neck Surgery, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan
| | - Yuka Saeki
- Department of Dermatology, Chiba University Graduate School of Medicine, Chiba 260-8670, Japan
| | - Shusuke Kawashima
- Department of Dermatology, Chiba University Graduate School of Medicine, Chiba 260-8670, Japan
- Division of Cell Therapy, Chiba Cancer Research Institute, Chiba 260-8717, Japan
| | | | - Yu Kawahara
- Department of Dermatology, Chiba University Graduate School of Medicine, Chiba 260-8670, Japan
- Department of Skin Oncology/Dermatology, Saitama Medical University International Medical Center, Saitama 350-1298, Japan
| | - Yasuhiro Nakamura
- Department of Skin Oncology/Dermatology, Saitama Medical University International Medical Center, Saitama 350-1298, Japan
| | | | - Hiroko Watanabe
- Department of Tumor Microenvironment, Faculty of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8558, Japan
| | - Hiromichi Dansako
- Department of Tumor Microenvironment, Faculty of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8558, Japan
| | - Tatsuyoshi Kawamura
- Department of Dermatology, University of Yamanashi, Yamanashi 409-3898, Japan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8568, Japan
| | - Hiroaki Honda
- Department of Pathology, Tokyo Women's Medical University, Shinjuku-ku, Tokyo 162-8666, Japan
| | - Hiroyuki Mano
- Division of Cellular Signaling, National Cancer Center Research Institute, Chuo-ku, Tokyo 104-0045, Japan
| | - Shinichi Toyooka
- Department of General Thoracic Surgery and Breast and Endocrinological Surgery, Dentistry and Pharmaceutical Sciences, Okayama University Graduate School of Medicine, Okayama University, Okayama 700-8558, Japan
| | - Masahito Kawazu
- Division of Cell Therapy, Chiba Cancer Research Institute, Chiba 260-8717, Japan
- Division of Cellular Signaling, National Cancer Center Research Institute, Chuo-ku, Tokyo 104-0045, Japan
| | - Yosuke Togashi
- Department of Tumor Microenvironment, Faculty of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8558, Japan
- Division of Cell Therapy, Chiba Cancer Research Institute, Chiba 260-8717, Japan
- Kindai University, Faculty of Medicine, Osaka-Sayama, Osaka 589-0014, Japan
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2
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Tee XR, Hazard E, Latorre-Esteves E, Kohrn BF, Ghezelayagh TS, Fredrickson JU, Coombes C, Radke MR, Manhardt E, Katz R, Soong TR, Swisher EM, Norquist BM, Risques RA. Increased TP53 somatic evolution in peritoneal washes of individuals with BRCA1 germline mutations. Gynecol Oncol 2024; 190:18-27. [PMID: 39128337 DOI: 10.1016/j.ygyno.2024.07.690] [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: 03/09/2024] [Revised: 07/30/2024] [Accepted: 07/31/2024] [Indexed: 08/13/2024]
Abstract
BACKGROUND Individuals with germline BRCA1 and BRCA2 pathogenic variants (BRCA carriers) are at high risk of developing high grade serous ovarian carcinoma (HGSC). HGSC is predominantly driven by TP53 mutations, but mutations in this gene are also commonly found in non-cancerous tissue as a feature of normal human aging. We hypothesized that HGSC predisposition in BRCA carriers may be related to increased TP53 somatic evolution, which could be detectable by ultra-deep sequencing of TP53 mutations in gynecological liquid biopsies. METHODS Duplex sequencing was used to identify TP53 mutations with high sensitivity in peritoneal washes and cervical liquid-based cytology (LBC) collected at surgery from 60 individuals including BRCA1 and BRCA2 carriers, and non-carriers. TP53 mutation pathogenicity was compared across groups and with TP53 cancer mutations. RESULTS TP53 mutations were more abundant in cervical LBC than in peritoneal washes but increased with age in both sample types. In peritoneal washes, but not in cervical LBC, pathogenic TP53 mutation burden was increased in BRCA1 carriers compared to non-carriers, independently of age. Five individuals shared identical pathogenic TP53 mutations in peritoneal washes and cervical LBC, but not in blood. CONCLUSIONS Ultra-deep sequencing of TP53 mutations in peritoneal washes collected at surgery reveals increased burden of pathogenic TP53 mutations in BRCA1 carriers. This excess of pathogenic TP53 mutations might be linked to the elevated risk of HGSC in these individuals. In some patients, concordant TP53 mutations were found in peritoneal washes and cervical LBCs, but the cell of origin remains unknown and deserves further investigation.
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Affiliation(s)
- Xin Ray Tee
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, USA
| | - Emma Hazard
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, USA
| | - Elena Latorre-Esteves
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, USA
| | - Brendan F Kohrn
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, USA
| | - Talayeh S Ghezelayagh
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, USA; Department of Obstetrics and Gynecology, University of Washington, Seattle, USA
| | - Jeanne Uy Fredrickson
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, USA
| | - CoohleenAnn Coombes
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, USA
| | - Marc R Radke
- Department of Obstetrics and Gynecology, University of Washington, Seattle, USA
| | - Enna Manhardt
- Department of Obstetrics and Gynecology, University of Washington, Seattle, USA
| | - Ronit Katz
- Department of Obstetrics and Gynecology, University of Washington, Seattle, USA
| | - T Rinda Soong
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Elizabeth M Swisher
- Department of Obstetrics and Gynecology, University of Washington, Seattle, USA
| | - Barbara M Norquist
- Department of Obstetrics and Gynecology, University of Washington, Seattle, USA
| | - Rosa Ana Risques
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, USA.
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3
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Renz PF, Ghoshdastider U, Baghai Sain S, Valdivia-Francia F, Khandekar A, Ormiston M, Bernasconi M, Duré C, Kretz JA, Lee M, Hyams K, Forny M, Pohly M, Ficht X, Ellis SJ, Moor AE, Sendoel A. In vivo single-cell CRISPR uncovers distinct TNF programmes in tumour evolution. Nature 2024; 632:419-428. [PMID: 39020166 PMCID: PMC11306103 DOI: 10.1038/s41586-024-07663-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 06/04/2024] [Indexed: 07/19/2024]
Abstract
The tumour evolution model posits that malignant transformation is preceded by randomly distributed driver mutations in cancer genes, which cause clonal expansions in phenotypically normal tissues. Although clonal expansions can remodel entire tissues1-3, the mechanisms that result in only a small number of clones transforming into malignant tumours remain unknown. Here we develop an in vivo single-cell CRISPR strategy to systematically investigate tissue-wide clonal dynamics of the 150 most frequently mutated squamous cell carcinoma genes. We couple ultrasound-guided in utero lentiviral microinjections, single-cell RNA sequencing and guide capture to longitudinally monitor clonal expansions and document their underlying gene programmes at single-cell transcriptomic resolution. We uncover a tumour necrosis factor (TNF) signalling module, which is dependent on TNF receptor 1 and involving macrophages, that acts as a generalizable driver of clonal expansions in epithelial tissues. Conversely, during tumorigenesis, the TNF signalling module is downregulated. Instead, we identify a subpopulation of invasive cancer cells that switch to an autocrine TNF gene programme associated with epithelial-mesenchymal transition. Finally, we provide in vivo evidence that the autocrine TNF gene programme is sufficient to mediate invasive properties and show that the TNF signature correlates with shorter overall survival of patients with squamous cell carcinoma. Collectively, our study demonstrates the power of applying in vivo single-cell CRISPR screening to mammalian tissues, unveils distinct TNF programmes in tumour evolution and highlights the importance of understanding the relationship between clonal expansions in epithelia and tumorigenesis.
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Affiliation(s)
- Peter F Renz
- Institute for Regenerative Medicine (IREM), University of Zurich, Schlieren-Zurich, Switzerland
| | - Umesh Ghoshdastider
- Institute for Regenerative Medicine (IREM), University of Zurich, Schlieren-Zurich, Switzerland
| | - Simona Baghai Sain
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Fabiola Valdivia-Francia
- Institute for Regenerative Medicine (IREM), University of Zurich, Schlieren-Zurich, Switzerland
- Life Science Zurich Graduate School, Molecular Life Science Program, University of Zurich and ETH Zurich, Zurich, Switzerland
| | - Ameya Khandekar
- Max Perutz Labs, Vienna BioCenter Campus (VBC), Vienna, Austria
- Center for Molecular Biology, Department of Microbiology, Immunobiology and Genetics, University of Vienna, Vienna, Austria
| | - Mark Ormiston
- Institute for Regenerative Medicine (IREM), University of Zurich, Schlieren-Zurich, Switzerland
| | - Martino Bernasconi
- Institute for Regenerative Medicine (IREM), University of Zurich, Schlieren-Zurich, Switzerland
| | - Clara Duré
- Institute for Regenerative Medicine (IREM), University of Zurich, Schlieren-Zurich, Switzerland
- Life Science Zurich Graduate School, Molecular Life Science Program, University of Zurich and ETH Zurich, Zurich, Switzerland
| | - Jonas A Kretz
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Minkyoung Lee
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Katie Hyams
- Institute for Regenerative Medicine (IREM), University of Zurich, Schlieren-Zurich, Switzerland
| | - Merima Forny
- Institute for Regenerative Medicine (IREM), University of Zurich, Schlieren-Zurich, Switzerland
| | - Marcel Pohly
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Xenia Ficht
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Stephanie J Ellis
- Max Perutz Labs, Vienna BioCenter Campus (VBC), Vienna, Austria
- Center for Molecular Biology, Department of Microbiology, Immunobiology and Genetics, University of Vienna, Vienna, Austria
| | - Andreas E Moor
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.
| | - Ataman Sendoel
- Institute for Regenerative Medicine (IREM), University of Zurich, Schlieren-Zurich, Switzerland.
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Tandukar B, Deivendran D, Chen L, Cruz-Pacheco N, Sharma H, Xu A, Bandari AK, Chen DB, George C, Marty A, Cho RJ, Cheng J, Saylor D, Gerami P, Arron ST, Bastian BC, Shain AH. Genetic evolution of keratinocytes to cutaneous squamous cell carcinoma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.23.604673. [PMID: 39091884 PMCID: PMC11291049 DOI: 10.1101/2024.07.23.604673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
We performed multi-omic profiling of epidermal keratinocytes, precancerous actinic keratoses, and squamous cell carcinomas to understand the molecular transitions during skin carcinogenesis. Single-cell mutational analyses showed that most keratinocytes in normal skin had lower mutation burdens than melanocytes and fibroblasts, however keratinocytes with TP53 or NOTCH1 mutations had substantially higher mutation burdens, suggesting that these mutations prime keratinocytes for transformation by increasing their mutation rate. Mutational profiling and spatial transcriptomics on squamous cell carcinomas adjacent to actinic keratoses revealed TERT promoter and CDKN2A mutations emerging in actinic keratoses, whereas additional mutations inactivating ARID2 and activating the MAPK-pathway delineated the transition to squamous cell carcinomas. Spatial variation in gene expression patterns was common in both tumor and immune cells, with high expression of checkpoint molecules at the invasive front of tumors. In conclusion, this study documents key events during the evolution of cutaneous squamous cell carcinoma.
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Affiliation(s)
- Bishal Tandukar
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Delahny Deivendran
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Limin Chen
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Noel Cruz-Pacheco
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Harsh Sharma
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Albert Xu
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Aravind K. Bandari
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Daniel B. Chen
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
- School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Christopher George
- Department of Dermatology, Erasmus MC, Rotterdam, Netherlands
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Dermatology, School of Medicine, Stanford University, Palo Alto, CA, USA
| | - Annika Marty
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
- Institute of Physiology, University of Zurich, Zurich, Switzerland
| | - Raymond J. Cho
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA
| | - Jeffrey Cheng
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA
| | - Drew Saylor
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA
| | - Pedram Gerami
- Department of Dermatology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | | | - Boris C. Bastian
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
| | - A. Hunter Shain
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
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5
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Cristalli C, Scotlandi K. Targeting DNA Methylation Machinery in Pediatric Solid Tumors. Cells 2024; 13:1209. [PMID: 39056791 PMCID: PMC11275080 DOI: 10.3390/cells13141209] [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: 05/20/2024] [Revised: 07/08/2024] [Accepted: 07/16/2024] [Indexed: 07/28/2024] Open
Abstract
DNA methylation is a key epigenetic regulatory mechanism that plays a critical role in a variety of cellular processes, including the regulation of cell fate during development, maintenance of cell identity, and genome stability. DNA methylation is tightly regulated by enzymatic reactions and its deregulation plays an important role in the development of cancer. Specific DNA methylation alterations have been found in pediatric solid tumors, providing new insights into the development of these tumors. In addition, DNA methylation profiles have greatly contributed to tune the diagnosis of pediatric solid tumors and to define subgroups of patients with different risks of progression, leading to the reduction in unwanted toxicity and the improvement of treatment efficacy. This review highlights the dysregulated DNA methylome in pediatric solid tumors and how this information provides promising targets for epigenetic therapies, particularly inhibitors of DNMT enzymes (DNMTis). Opportunities and limitations are considered, including the ability of DNMTis to induce viral mimicry and immune signaling by tumors. Besides intrinsic action against cancer cells, DNMTis have the potential to sensitize immune-cold tumors to immunotherapies and may represent a remarkable option to improve the treatment of challenging pediatric solid tumors.
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Affiliation(s)
- Camilla Cristalli
- Laboratory of Experimental Oncology, IRCCS Istituto Ortopedico Rizzoli, Via di Barbiano, 1/10, 40136 Bologna, Italy
| | - Katia Scotlandi
- Laboratory of Experimental Oncology, IRCCS Istituto Ortopedico Rizzoli, Via di Barbiano, 1/10, 40136 Bologna, Italy
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6
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Maeda H, Kakiuchi N. Clonal expansion in normal tissues. Cancer Sci 2024; 115:2117-2124. [PMID: 38623936 PMCID: PMC11247609 DOI: 10.1111/cas.16183] [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: 02/07/2024] [Revised: 03/24/2024] [Accepted: 04/01/2024] [Indexed: 04/17/2024] Open
Abstract
Cancer originates from a single ancestral cell that acquires a driver mutation, which confers a growth or survival advantage, followed by the acquisition of additional driver mutations by descendant cells. Recently, it has become evident that somatic cell mutations accumulate in normal tissues with aging and exposure to environmental factors, such as alcohol, smoking, and UV rays, increases the mutation rate. Clones harboring driver mutations expand with age, leading to tissue remodeling. Lineage analysis of myeloproliferative neoplasms and der(1;16)-positive breast cancer revealed that driver mutations were acquired early in our lives and that the development of cancer takes decades, unveiling the previously unknown early process of cancer development. Evidence that clonal hematopoiesis affects various diseases, including nonneoplastic diseases, highlights the potential role of the identification and functional analysis of mutated clones in unraveling unknown pathologies. In this review, we summarize the recent updates on clonal expansion in normal tissues and the natural history of cancer revealed through lineage analysis of noncancerous and cancerous tissues.
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Affiliation(s)
- Hirona Maeda
- Department of Pathology and Tumor Biology, Graduate School of MedicineKyoto UniversityKyotoJapan
- Department of Diagnostic PathologyKyoto University HospitalKyotoJapan
| | - Nobuyuki Kakiuchi
- Department of Pathology and Tumor Biology, Graduate School of MedicineKyoto UniversityKyotoJapan
- The Hakubi Center for Advanced ResearchKyoto UniversityKyotoJapan
- Department of Gastroenterology and Hepatology, Graduate School of MedicineKyoto UniversityKyotoJapan
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7
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Ghezelayagh TS, Kohrn BF, Fredrickson J, Krimmel-Morrison JD, Latorre-Esteves E, Tee XR, Radke MR, Manhardt E, Norquist BM, Katz R, Swisher EM, Risques RA. TP53 somatic evolution in cervical liquid-based cytology and blood from individuals with and without ovarian cancer and BRCA1 or BRCA2 germline mutations. Oncogene 2024; 43:2421-2430. [PMID: 38918516 DOI: 10.1038/s41388-024-03089-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 06/14/2024] [Accepted: 06/17/2024] [Indexed: 06/27/2024]
Abstract
Somatic TP53 mutations are prevalent in normal tissue but little is known about their association with cancer risk. Cervical liquid-based cytology (LBC), commonly known as Pap test, provides an accessible gynecological sample to test the value of TP53 somatic mutations as a biomarker for high-grade serous ovarian cancer (HGSC), a cancer type mostly driven by TP53 mutations. We used ultra-deep duplex sequencing to analyze TP53 mutations in LBC and blood samples from 70 individuals (30 with and 40 without HGSC) undergoing gynecologic surgery, 30 carrying BRCA1 or BRCA2 germline pathogenic variants (BRCApv). Only 30% of the tumor mutations were found in LBC samples. However, TP53 pathogenic mutations were identified in nearly all LBC and blood samples, with only 5.4% of mutations in LBC (20/368) also found in the corresponding blood sample. TP53 mutations were more abundant in LBC than in blood and increased with age in both sample types. BRCApv carriers with HGSC had more TP53 clonal expansions in LBC than BRCApv carriers without cancer. Our results show that, while not useful for direct cancer detection, LBC samples capture TP53 mutation burden in the gynecological tract, presenting potential value for cancer risk assessment in individuals at higher hereditary risk for ovarian cancer.
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Affiliation(s)
- Talayeh S Ghezelayagh
- Department of Obstetrics & Gynecology, University of Washington, Seattle, WA, USA
- Department of Obstetrics & Gynecology, Stanford University, Palo Alto, CA, USA
| | - Brendan F Kohrn
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Jeanne Fredrickson
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | | | - Elena Latorre-Esteves
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Xin-Ray Tee
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Marc R Radke
- Department of Obstetrics & Gynecology, University of Washington, Seattle, WA, USA
| | - Enna Manhardt
- Department of Obstetrics & Gynecology, University of Washington, Seattle, WA, USA
| | - Barbara M Norquist
- Department of Obstetrics & Gynecology, University of Washington, Seattle, WA, USA
| | - Ronit Katz
- Department of Obstetrics & Gynecology, University of Washington, Seattle, WA, USA
| | - Elizabeth M Swisher
- Department of Obstetrics & Gynecology, University of Washington, Seattle, WA, USA
| | - Rosa Ana Risques
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA.
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8
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Monnat RJ. James German and the Quest to Understand Human RECQ Helicase Deficiencies. Cells 2024; 13:1077. [PMID: 38994931 PMCID: PMC11240319 DOI: 10.3390/cells13131077] [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: 04/19/2024] [Revised: 05/10/2024] [Accepted: 06/14/2024] [Indexed: 07/13/2024] Open
Abstract
James German's work to establish the natural history and cancer risk associated with Bloom syndrome (BS) has had a strong influence on the generation of scientists and clinicians working to understand other RECQ deficiencies and heritable cancer predisposition syndromes. I summarize work by us and others below, inspired by James German's precedents with BS, to understand and compare BS with the other heritable RECQ deficiency syndromes with a focus on Werner syndrome (WS). What we know, unanswered questions and new opportunities are discussed, as are potential ways to treat or modify WS-associated disease mechanisms and pathways.
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Affiliation(s)
- Raymond J Monnat
- Departments of Laboratory Medicine/Pathology and Genome Sciences, University of Washington, Seattle, WA 98195, USA
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9
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Zhang S, Xiao X, Yi Y, Wang X, Zhu L, Shen Y, Lin D, Wu C. Tumor initiation and early tumorigenesis: molecular mechanisms and interventional targets. Signal Transduct Target Ther 2024; 9:149. [PMID: 38890350 PMCID: PMC11189549 DOI: 10.1038/s41392-024-01848-7] [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: 01/01/2024] [Revised: 04/23/2024] [Accepted: 04/27/2024] [Indexed: 06/20/2024] Open
Abstract
Tumorigenesis is a multistep process, with oncogenic mutations in a normal cell conferring clonal advantage as the initial event. However, despite pervasive somatic mutations and clonal expansion in normal tissues, their transformation into cancer remains a rare event, indicating the presence of additional driver events for progression to an irreversible, highly heterogeneous, and invasive lesion. Recently, researchers are emphasizing the mechanisms of environmental tumor risk factors and epigenetic alterations that are profoundly influencing early clonal expansion and malignant evolution, independently of inducing mutations. Additionally, clonal evolution in tumorigenesis reflects a multifaceted interplay between cell-intrinsic identities and various cell-extrinsic factors that exert selective pressures to either restrain uncontrolled proliferation or allow specific clones to progress into tumors. However, the mechanisms by which driver events induce both intrinsic cellular competency and remodel environmental stress to facilitate malignant transformation are not fully understood. In this review, we summarize the genetic, epigenetic, and external driver events, and their effects on the co-evolution of the transformed cells and their ecosystem during tumor initiation and early malignant evolution. A deeper understanding of the earliest molecular events holds promise for translational applications, predicting individuals at high-risk of tumor and developing strategies to intercept malignant transformation.
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Affiliation(s)
- Shaosen Zhang
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
- Key Laboratory of Cancer Genomic Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
| | - Xinyi Xiao
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
- Key Laboratory of Cancer Genomic Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
| | - Yonglin Yi
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
- Key Laboratory of Cancer Genomic Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
| | - Xinyu Wang
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
- Key Laboratory of Cancer Genomic Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
| | - Lingxuan Zhu
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
- Key Laboratory of Cancer Genomic Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
- Changping Laboratory, 100021, Beijing, China
| | - Yanrong Shen
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
- Key Laboratory of Cancer Genomic Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
| | - Dongxin Lin
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China.
- Key Laboratory of Cancer Genomic Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China.
- Changping Laboratory, 100021, Beijing, China.
- Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, 211166, China.
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Guangzhou, 510060, China.
| | - Chen Wu
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China.
- Key Laboratory of Cancer Genomic Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China.
- Changping Laboratory, 100021, Beijing, China.
- Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, 211166, China.
- CAMS Oxford Institute, Chinese Academy of Medical Sciences, 100006, Beijing, China.
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10
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Bryant D, Barberan-Martin S, Maeshima R, Del Valle Torres I, Rabii M, Baird W, Sauvadet A, Demetriou C, Jones P, Knöpfel N, Michailidis F, Riachi M, Bennett DC, Zecchin D, Pittman A, Polubothu S, Hart S, Kinsler VA. RNA Therapy for Oncogenic NRAS-Driven Nevi Induces Apoptosis. J Invest Dermatol 2024:S0022-202X(24)00449-4. [PMID: 38897541 DOI: 10.1016/j.jid.2024.04.031] [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: 11/10/2023] [Revised: 04/04/2024] [Accepted: 04/16/2024] [Indexed: 06/21/2024]
Abstract
RAS proteins regulate cell division, differentiation, and apoptosis through multiple downstream effector pathways. Oncogenic RAS variants are the commonest drivers in cancers; however, they also drive many benign lesions predisposing to malignancy, such as melanocytic nevi, thyroid nodules, and colonic polyps. Reversal of these benign lesions could reduce cancer incidence; however, the effects of oncogenic RAS have been notoriously difficult to target with downstream pathway inhibitors. In this study, we show effective suppression of oncogenic and currently undruggable NRASQ61K in primary cells from melanocytic nevi using small interfering RNA targeted to the recurrent causal variant. This results in striking reduction in expression of ARL6IP1, a known inhibitor of endoplasmic reticulum stress-induced apoptosis not previously linked to NRAS. We go on to show that a single dose of small interfering RNA in primary cells triggers an apoptotic cascade, in contrast to treatment with a MAPK/extracellular signal-regulated kinase kinase inhibitor. Protective packaging of the targeted small interfering RNA into lipid nanoparticles permits successful delivery into a humanized mouse model of melanocytic nevi and results in variant NRAS knockdown in vivo. These data show that RAS-induced protection from apoptosis is involved in persistence of NRAS-driven melanocytic nevi and anticipate that targeted small interfering RNA could form the basis of clinical trials for RAS-driven benign tumors.
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Affiliation(s)
- Dale Bryant
- Mosaicism and Precision Medicine Laboratory, The Francis Crick Institute, London, United Kingdom; Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Sara Barberan-Martin
- Mosaicism and Precision Medicine Laboratory, The Francis Crick Institute, London, United Kingdom; Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Ruhina Maeshima
- Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Ignacio Del Valle Torres
- Mosaicism and Precision Medicine Laboratory, The Francis Crick Institute, London, United Kingdom; Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Mohammad Rabii
- Mosaicism and Precision Medicine Laboratory, The Francis Crick Institute, London, United Kingdom; Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - William Baird
- Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Aimie Sauvadet
- Mosaicism and Precision Medicine Laboratory, The Francis Crick Institute, London, United Kingdom; Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Charalambos Demetriou
- Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Phoebe Jones
- Mosaicism and Precision Medicine Laboratory, The Francis Crick Institute, London, United Kingdom; Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Nicole Knöpfel
- Mosaicism and Precision Medicine Laboratory, The Francis Crick Institute, London, United Kingdom; Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London, United Kingdom; Paediatric Dermatology, Great Ormond Street Hospital for Children, London, United Kingdom
| | - Fanourios Michailidis
- Mosaicism and Precision Medicine Laboratory, The Francis Crick Institute, London, United Kingdom; Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Melissa Riachi
- Mosaicism and Precision Medicine Laboratory, The Francis Crick Institute, London, United Kingdom; Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | | | - Davide Zecchin
- Mosaicism and Precision Medicine Laboratory, The Francis Crick Institute, London, United Kingdom; Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Alan Pittman
- St George's University of London, London, United Kingdom
| | - Satyamaanasa Polubothu
- Mosaicism and Precision Medicine Laboratory, The Francis Crick Institute, London, United Kingdom; Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London, United Kingdom; Paediatric Dermatology, Great Ormond Street Hospital for Children, London, United Kingdom
| | - Stephen Hart
- Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Veronica A Kinsler
- Mosaicism and Precision Medicine Laboratory, The Francis Crick Institute, London, United Kingdom; Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London, United Kingdom; Paediatric Dermatology, Great Ormond Street Hospital for Children, London, United Kingdom.
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11
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Lundgren S, Myllymäki M, Järvinen T, Keränen MAI, Theodoropoulos J, Smolander J, Kim D, Salmenniemi U, Walldin G, Savola P, Kelkka T, Rajala H, Hellström-Lindberg E, Itälä-Remes M, Kankainen M, Mustjoki S. Somatic mutations associate with clonal expansion of CD8 + T cells. SCIENCE ADVANCES 2024; 10:eadj0787. [PMID: 38848368 PMCID: PMC11160466 DOI: 10.1126/sciadv.adj0787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 05/06/2024] [Indexed: 06/09/2024]
Abstract
Somatic mutations in T cells can cause cancer but also have implications for immunological diseases and cell therapies. The mutation spectrum in nonmalignant T cells is unclear. Here, we examined somatic mutations in CD4+ and CD8+ T cells from 90 patients with hematological and immunological disorders and used T cell receptor (TCR) and single-cell sequencing to link mutations with T cell expansions and phenotypes. CD8+ cells had a higher mutation burden than CD4+ cells. Notably, the biggest variant allele frequency (VAF) of non-synonymous variants was higher than synonymous variants in CD8+ T cells, indicating non-random occurrence. The non-synonymous VAF in CD8+ T cells strongly correlated with the TCR frequency, but not age. We identified mutations in pathways essential for T cell function and often affected lymphoid neoplasia. Single-cell sequencing revealed cytotoxic TEMRA phenotypes of mutated T cells. Our findings suggest that somatic mutations contribute to CD8+ T cell expansions without malignant transformation.
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Affiliation(s)
- Sofie Lundgren
- Hematology Research Unit Helsinki, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
- Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, Helsinki, Finland
| | - Mikko Myllymäki
- Hematology Research Unit Helsinki, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
- Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, Helsinki, Finland
| | - Timo Järvinen
- Hematology Research Unit Helsinki, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
- Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, Helsinki, Finland
- Medical and Clinical Genetics, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Mikko A. I. Keränen
- Hematology Research Unit Helsinki, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
- Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, Helsinki, Finland
- Department of Hematology, Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
| | - Jason Theodoropoulos
- Hematology Research Unit Helsinki, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
- Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, Helsinki, Finland
| | - Johannes Smolander
- Hematology Research Unit Helsinki, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
- Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, Helsinki, Finland
| | - Daehong Kim
- Hematology Research Unit Helsinki, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
- Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, Helsinki, Finland
| | - Urpu Salmenniemi
- Department of Hematology, Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
- Stem Cell Transplantation Unit, Turku University Hospital, Turku, Finland
| | - Gunilla Walldin
- Center for Hematology and Regenerative Medicine, Department of Medicine, Karolinska Institute and Karolinska University Hospital, Stockholm, Sweden
| | - Paula Savola
- Hematology Research Unit Helsinki, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
- Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, Helsinki, Finland
- Department of Clinical Chemistry, HUS Diagnostic Center, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | - Tiina Kelkka
- Hematology Research Unit Helsinki, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
- Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, Helsinki, Finland
| | - Hanna Rajala
- Hematology Research Unit Helsinki, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
- Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, Helsinki, Finland
- Department of Hematology, Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
| | - Eva Hellström-Lindberg
- Center for Hematology and Regenerative Medicine, Department of Medicine, Karolinska Institute and Karolinska University Hospital, Stockholm, Sweden
| | - Maija Itälä-Remes
- Stem Cell Transplantation Unit, Turku University Hospital, Turku, Finland
| | - Matti Kankainen
- Hematology Research Unit Helsinki, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
- Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, Helsinki, Finland
- Medical and Clinical Genetics, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Satu Mustjoki
- Hematology Research Unit Helsinki, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
- Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, Helsinki, Finland
- ICAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland
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12
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Xin T, Gallini S, Wei H, Gonzalez DG, Matte-Martone C, Machida H, Fujiwara H, Pasolli HA, Suozzi KC, Gonzalez LE, Regot S, Greco V. Oncogenic Kras induces spatiotemporally specific tissue deformation through converting pulsatile into sustained ERK activation. Nat Cell Biol 2024; 26:859-867. [PMID: 38689013 DOI: 10.1038/s41556-024-01413-y] [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: 12/08/2022] [Accepted: 03/28/2024] [Indexed: 05/02/2024]
Abstract
Tissue regeneration and maintenance rely on coordinated stem cell behaviours. This orchestration can be impaired by oncogenic mutations leading to cancer. However, it is largely unclear how oncogenes perturb stem cells' orchestration to disrupt tissue. Here we used intravital imaging to investigate the mechanisms by which oncogenic Kras mutation causes tissue disruption in the hair follicle. Through longitudinally tracking hair follicles in live mice, we found that KrasG12D, a mutation that can lead to squamous cell carcinoma, induces epithelial tissue deformation in a spatiotemporally specific manner, linked with abnormal cell division and migration. Using a reporter mouse capture real-time ERK signal dynamics at the single-cell level, we discovered that KrasG12D, but not a closely related mutation HrasG12V, converts ERK signal in stem cells from pulsatile to sustained. Finally, we demonstrated that interrupting sustained ERK signal reverts KrasG12D-induced tissue deformation through modulating specific features of cell migration and division.
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Affiliation(s)
- Tianchi Xin
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA.
| | - Sara Gallini
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Haoyang Wei
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - David G Gonzalez
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | | | - Hiroki Machida
- Laboratory for Tissue Microenvironment, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
- Graduate School of Medicine, Osaka University, Suita, Japan
| | - Hironobu Fujiwara
- Laboratory for Tissue Microenvironment, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
- Graduate School of Medicine, Osaka University, Suita, Japan
| | - H Amalia Pasolli
- Electron Microscopy Resource Center, The Rockefeller University, New York, NY, USA
| | - Kathleen C Suozzi
- Department of Dermatology, Yale School of Medicine, New Haven, CT, USA
| | - Lauren E Gonzalez
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Sergi Regot
- Department of Molecular Biology and Genetics, Johns Hopkins School of Medicine, Baltimore, MD, USA.
| | - Valentina Greco
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA.
- Department of Dermatology, Yale School of Medicine, New Haven, CT, USA.
- Department of Cell Biology, Yale Stem Cell Center, Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA.
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13
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Duffy MJ, Crown J. Circulating tumor DNA (ctDNA): can it be used as a pan-cancer early detection test? Crit Rev Clin Lab Sci 2024; 61:241-253. [PMID: 37936529 DOI: 10.1080/10408363.2023.2275150] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 10/21/2023] [Indexed: 11/09/2023]
Abstract
Circulating tumor DNA (ctDNA, DNA shed by cancer cells) is emerging as one of the most transformative cancer biomarkers discovered to-date. Although potentially useful at all the phases of cancer detection and patient management, one of its most exciting possibilities is as a relatively noninvasive pan-cancer screening test. Preliminary findings with ctDNA tests such as Galleri or CancerSEEK suggest that they have high specificity (> 99.0%) for malignancy. Their sensitivity varies depending on the type of cancer and stage of disease but it is generally low in patients with stage I disease. A major advantage of ctDNA over existing screening strategies is the potential ability to detect multiple cancer types in a single test. A limitation of most studies published to-date is that they are predominantly case-control investigations that were carried out in patients with a previous diagnosis of malignancy and that used apparently healthy subjects as controls. Consequently, the reported sensitivities, specificities and positive predictive values might be lower if the tests are used for screening in asymptomatic populations, that is, in the population where these tests are likely be employed. To demonstrate clinical utility in an asymptomatic population, these tests must be shown to reduce cancer mortality without causing excessive overdiagnosis in a large randomized prospective randomized trial. Such trials are currently ongoing for Galleri and CancerSEEK.
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Affiliation(s)
- Michael J Duffy
- UCD School of Medicine, Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
- UCD Clinical Research Centre, St. Vincent's University Hospital, Dublin, Ireland
| | - John Crown
- Department of Medical Oncology, St Vincent's University Hospital, Dublin, Ireland
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14
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Grimes K, Jeong H, Amoah A, Xu N, Niemann J, Raeder B, Hasenfeld P, Stober C, Rausch T, Benito E, Jann JC, Nowak D, Emini R, Hoenicka M, Liebold A, Ho A, Shuai S, Geiger H, Sanders AD, Korbel JO. Cell-type-specific consequences of mosaic structural variants in hematopoietic stem and progenitor cells. Nat Genet 2024; 56:1134-1146. [PMID: 38806714 PMCID: PMC11176070 DOI: 10.1038/s41588-024-01754-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 04/17/2024] [Indexed: 05/30/2024]
Abstract
The functional impact and cellular context of mosaic structural variants (mSVs) in normal tissues is understudied. Utilizing Strand-seq, we sequenced 1,133 single-cell genomes from 19 human donors of increasing age, and discovered the heterogeneous mSV landscapes of hematopoietic stem and progenitor cells. While mSVs are continuously acquired throughout life, expanded subclones in our cohort are confined to individuals >60. Cells already harboring mSVs are more likely to acquire additional somatic structural variants, including megabase-scale segmental aneuploidies. Capitalizing on comprehensive single-cell micrococcal nuclease digestion with sequencing reference data, we conducted high-resolution cell-typing for eight hematopoietic stem and progenitor cells. Clonally expanded mSVs disrupt normal cellular function by dysregulating diverse cellular pathways, and enriching for myeloid progenitors. Our findings underscore the contribution of mSVs to the cellular and molecular phenotypes associated with the aging hematopoietic system, and establish a foundation for deciphering the molecular links between mSVs, aging and disease susceptibility in normal tissues.
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Affiliation(s)
- Karen Grimes
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Hyobin Jeong
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, Republic of Korea
| | - Amanda Amoah
- Institute of Molecular Medicine, Ulm University, Ulm, Germany
| | - Nuo Xu
- Department of Human Cell Biology and Genetics, School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Julian Niemann
- Institute of Molecular Medicine, Ulm University, Ulm, Germany
| | - Benjamin Raeder
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Patrick Hasenfeld
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Catherine Stober
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Tobias Rausch
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Molecular Medicine Partnership Unit (MMPU), European Molecular Biology Laboratory, University of Heidelberg, Heidelberg, Germany
- Bridging Research Division on Mechanisms of Genomic Variation and Data Science, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Eva Benito
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Johann-Christoph Jann
- Department of Hematology and Oncology, Medical Faculty Mannheim of the Heidelberg University, Mannheim, Germany
| | - Daniel Nowak
- Department of Hematology and Oncology, Medical Faculty Mannheim of the Heidelberg University, Mannheim, Germany
| | - Ramiz Emini
- Department of Cardiothoracic and Vascular Surgery, Ulm University Hospital, Ulm, Germany
| | - Markus Hoenicka
- Department of Cardiothoracic and Vascular Surgery, Ulm University Hospital, Ulm, Germany
| | - Andreas Liebold
- Department of Cardiothoracic and Vascular Surgery, Ulm University Hospital, Ulm, Germany
| | - Anthony Ho
- Molecular Medicine Partnership Unit (MMPU), European Molecular Biology Laboratory, University of Heidelberg, Heidelberg, Germany
- Department of Medicine V, Hematology, Oncology and Rheumatology, University of Heidelberg, Heidelberg, Germany
| | - Shimin Shuai
- Department of Human Cell Biology and Genetics, School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Hartmut Geiger
- Institute of Molecular Medicine, Ulm University, Ulm, Germany
| | - Ashley D Sanders
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany.
- Berlin Institute of Health (BIH) at Charité-Universitätsmedizin Berlin, Berlin, Germany.
- Charité-Universitätsmedizin Berlin, Berlin, Germany.
| | - Jan O Korbel
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
- Molecular Medicine Partnership Unit (MMPU), European Molecular Biology Laboratory, University of Heidelberg, Heidelberg, Germany.
- Bridging Research Division on Mechanisms of Genomic Variation and Data Science, German Cancer Research Center (DKFZ), Heidelberg, Germany.
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15
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Montégut L, López-Otín C, Kroemer G. Aging and cancer. Mol Cancer 2024; 23:106. [PMID: 38760832 PMCID: PMC11102267 DOI: 10.1186/s12943-024-02020-z] [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: 04/19/2024] [Accepted: 05/09/2024] [Indexed: 05/19/2024] Open
Abstract
Aging and cancer exhibit apparent links that we will examine in this review. The null hypothesis that aging and cancer coincide because both are driven by time, irrespective of the precise causes, can be confronted with the idea that aging and cancer share common mechanistic grounds that are referred to as 'hallmarks'. Indeed, several hallmarks of aging also contribute to carcinogenesis and tumor progression, but some of the molecular and cellular characteristics of aging may also reduce the probability of developing lethal cancer, perhaps explaining why very old age (> 90 years) is accompanied by a reduced incidence of neoplastic diseases. We will also discuss the possibility that the aging process itself causes cancer, meaning that the time-dependent degradation of cellular and supracellular functions that accompanies aging produces cancer as a byproduct or 'age-associated disease'. Conversely, cancer and its treatment may erode health and drive the aging process, as this has dramatically been documented for cancer survivors diagnosed during childhood, adolescence, and young adulthood. We conclude that aging and cancer are connected by common superior causes including endogenous and lifestyle factors, as well as by a bidirectional crosstalk, that together render old age not only a risk factor of cancer but also an important parameter that must be considered for therapeutic decisions.
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Affiliation(s)
- Léa Montégut
- Centre de Recherche des Cordeliers, Equipe labellisée par la Ligue contre le cancer, Inserm U1138, Université Paris Cité, Sorbonne Université, Paris, France
- Metabolomics and Cell Biology Platforms, Gustave Roussy Institut, Villejuif, France
| | - Carlos López-Otín
- Centre de Recherche des Cordeliers, Equipe labellisée par la Ligue contre le cancer, Inserm U1138, Université Paris Cité, Sorbonne Université, Paris, France
- Facultad de Ciencias de la Vida y la Naturaleza, Universidad Nebrija, Madrid, Spain
| | - Guido Kroemer
- Centre de Recherche des Cordeliers, Equipe labellisée par la Ligue contre le cancer, Inserm U1138, Université Paris Cité, Sorbonne Université, Paris, France.
- Metabolomics and Cell Biology Platforms, Gustave Roussy Institut, Villejuif, France.
- Institut du Cancer Paris CARPEM, Department of Biology, Hôpital Européen Georges Pompidou, AP-HP, Paris, France.
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16
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Muyas F, Sauer CM, Valle-Inclán JE, Li R, Rahbari R, Mitchell TJ, Hormoz S, Cortés-Ciriano I. De novo detection of somatic mutations in high-throughput single-cell profiling data sets. Nat Biotechnol 2024; 42:758-767. [PMID: 37414936 PMCID: PMC11098751 DOI: 10.1038/s41587-023-01863-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 06/07/2023] [Indexed: 07/08/2023]
Abstract
Characterization of somatic mutations at single-cell resolution is essential to study cancer evolution, clonal mosaicism and cell plasticity. Here, we describe SComatic, an algorithm designed for the detection of somatic mutations in single-cell transcriptomic and ATAC-seq (assay for transposase-accessible chromatin sequence) data sets directly without requiring matched bulk or single-cell DNA sequencing data. SComatic distinguishes somatic mutations from polymorphisms, RNA-editing events and artefacts using filters and statistical tests parameterized on non-neoplastic samples. Using >2.6 million single cells from 688 single-cell RNA-seq (scRNA-seq) and single-cell ATAC-seq (scATAC-seq) data sets spanning cancer and non-neoplastic samples, we show that SComatic detects mutations in single cells accurately, even in differentiated cells from polyclonal tissues that are not amenable to mutation detection using existing methods. Validated against matched genome sequencing and scRNA-seq data, SComatic achieves F1 scores between 0.6 and 0.7 across diverse data sets, in comparison to 0.2-0.4 for the second-best performing method. In summary, SComatic permits de novo mutational signature analysis, and the study of clonal heterogeneity and mutational burdens at single-cell resolution.
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Affiliation(s)
- Francesc Muyas
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, UK
| | - Carolin M Sauer
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, UK
| | - Jose Espejo Valle-Inclán
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, UK
| | - Ruoyan Li
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Raheleh Rahbari
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Thomas J Mitchell
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Cambridge University Hospitals NHS Foundation Trust and NIHR Cambridge Biomedical Research Centre, Cambridge, UK
- Department of Surgery, University of Cambridge, Cambridge, UK
| | - Sahand Hormoz
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Isidro Cortés-Ciriano
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, UK.
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17
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Detecting somatic mutations in single-cell data sets. Nat Biotechnol 2024; 42:706-707. [PMID: 37414937 DOI: 10.1038/s41587-023-01883-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/08/2023]
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18
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Laisné M, Rodgers B, Benlamara S, Wicinski J, Nicolas A, Djerroudi L, Gupta N, Ferry L, Kirsh O, Daher D, Philippe C, Okada Y, Charafe-Jauffret E, Cristofari G, Meseure D, Vincent-Salomon A, Ginestier C, Defossez PA. A novel bioinformatic approach reveals cooperation between Cancer/Testis genes in basal-like breast tumors. Oncogene 2024; 43:1369-1385. [PMID: 38467851 PMCID: PMC11065691 DOI: 10.1038/s41388-024-03002-7] [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: 07/26/2023] [Revised: 02/22/2024] [Accepted: 03/01/2024] [Indexed: 03/13/2024]
Abstract
Breast cancer is the most prevalent type of cancer in women worldwide. Within breast tumors, the basal-like subtype has the worst prognosis, prompting the need for new tools to understand, detect, and treat these tumors. Certain germline-restricted genes show aberrant expression in tumors and are known as Cancer/Testis genes; their misexpression has diagnostic and therapeutic applications. Here we designed a new bioinformatic approach to examine Cancer/Testis gene misexpression in breast tumors. We identify several new markers in Luminal and HER-2 positive tumors, some of which predict response to chemotherapy. We then use machine learning to identify the two Cancer/Testis genes most associated with basal-like breast tumors: HORMAD1 and CT83. We show that these genes are expressed by tumor cells and not by the microenvironment, and that they are not expressed by normal breast progenitors; in other words, their activation occurs de novo. We find these genes are epigenetically repressed by DNA methylation, and that their activation upon DNA demethylation is irreversible, providing a memory of past epigenetic disturbances. Simultaneous expression of both genes in breast cells in vitro has a synergistic effect that increases stemness and activates a transcriptional profile also observed in double-positive tumors. Therefore, we reveal a functional cooperation between Cancer/Testis genes in basal breast tumors; these findings have consequences for the understanding, diagnosis, and therapy of the breast tumors with the worst outcomes.
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Affiliation(s)
- Marthe Laisné
- Université Paris Cité, CNRS, Epigenetics and Cell Fate, F-75013, Paris, France
| | - Brianna Rodgers
- Université Paris Cité, CNRS, Epigenetics and Cell Fate, F-75013, Paris, France
| | - Sarah Benlamara
- Université Paris Cité, CNRS, Epigenetics and Cell Fate, F-75013, Paris, France
| | - Julien Wicinski
- CRCM, Inserm, CNRS, Institut Paoli-Calmettes, Aix-Marseille University, Epithelial Stem Cells and Cancer Laboratory, Equipe Labellisée LIGUE Contre le Cancer, Marseille, France
| | - André Nicolas
- Platform of Experimental Pathology, Department of Diagnostic and Theranostic Medicine, Institut Curie-Hospital, 75005, Paris, France
| | - Lounes Djerroudi
- Department of Pathology, Institut Curie, 26 Rue d'Ulm, 75005, Paris, France
| | - Nikhil Gupta
- Université Paris Cité, CNRS, Epigenetics and Cell Fate, F-75013, Paris, France
| | - Laure Ferry
- Université Paris Cité, CNRS, Epigenetics and Cell Fate, F-75013, Paris, France
| | - Olivier Kirsh
- Université Paris Cité, CNRS, Epigenetics and Cell Fate, F-75013, Paris, France
| | - Diana Daher
- Université Paris Cité, CNRS, Epigenetics and Cell Fate, F-75013, Paris, France
| | | | - Yuki Okada
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan
| | - Emmanuelle Charafe-Jauffret
- CRCM, Inserm, CNRS, Institut Paoli-Calmettes, Aix-Marseille University, Epithelial Stem Cells and Cancer Laboratory, Equipe Labellisée LIGUE Contre le Cancer, Marseille, France
| | | | - Didier Meseure
- Platform of Experimental Pathology, Department of Diagnostic and Theranostic Medicine, Institut Curie-Hospital, 75005, Paris, France
| | | | - Christophe Ginestier
- CRCM, Inserm, CNRS, Institut Paoli-Calmettes, Aix-Marseille University, Epithelial Stem Cells and Cancer Laboratory, Equipe Labellisée LIGUE Contre le Cancer, Marseille, France
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19
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Rückert T, Romagnani C. Extrinsic and intrinsic drivers of natural killer cell clonality. Immunol Rev 2024; 323:80-106. [PMID: 38506411 DOI: 10.1111/imr.13324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2024]
Abstract
Clonal expansion of antigen-specific lymphocytes is the fundamental mechanism enabling potent adaptive immune responses and the generation of immune memory. Accompanied by pronounced epigenetic remodeling, the massive proliferation of individual cells generates a critical mass of effectors for the control of acute infections, as well as a pool of memory cells protecting against future pathogen encounters. Classically associated with the adaptive immune system, recent work has demonstrated that innate immune memory to human cytomegalovirus (CMV) infection is stably maintained as large clonal expansions of natural killer (NK) cells, raising questions on the mechanisms for clonal selection and expansion in the absence of re-arranged antigen receptors. Here, we discuss clonal NK cell memory in the context of the mechanisms underlying clonal competition of adaptive lymphocytes and propose alternative selection mechanisms that might decide on the clonal success of their innate counterparts. We propose that the integration of external cues with cell-intrinsic sources of heterogeneity, such as variegated receptor expression, transcriptional states, and somatic variants, compose a bottleneck for clonal selection, contributing to the large size of memory NK cell clones.
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Affiliation(s)
- Timo Rückert
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Immunology, Berlin, Germany
| | - Chiara Romagnani
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Immunology, Berlin, Germany
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20
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Fukumoto T, Umakoshi H, Iwahashi N, Ogasawara T, Yokomoto-Umakoshi M, Kaneko H, Fujita M, Uchida N, Nakao H, Kawamura N, Matsuda Y, Sakamoto R, Miyazawa T, Seki M, Eto M, Oda Y, Suzuki Y, Ogawa S, Ogawa Y. Steroids-producing nodules: a two-layered adrenocortical nodular structure as a precursor lesion of cortisol-producing adenoma. EBioMedicine 2024; 103:105087. [PMID: 38570222 PMCID: PMC11121169 DOI: 10.1016/j.ebiom.2024.105087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 03/11/2024] [Accepted: 03/12/2024] [Indexed: 04/05/2024] Open
Abstract
BACKGROUND The human adrenal cortex consists of three functionally and structurally distinct layers; zona glomerulosa, zona fasciculata (zF), and zona reticularis (zR), and produces adrenal steroid hormones in a layer-specific manner; aldosterone, cortisol, and adrenal androgens, respectively. Cortisol-producing adenomas (CPAs) occur mostly as a result of somatic mutations associated with the protein kinase A pathway. However, how CPAs develop after adrenocortical cells acquire genetic mutations, remains poorly understood. METHODS We conducted integrated approaches combining the detailed histopathologic studies with genetic, RNA-sequencing, and spatially resolved transcriptome (SRT) analyses for the adrenal cortices adjacent to human adrenocortical tumours. FINDINGS Histopathological analysis revealed an adrenocortical nodular structure that exhibits the two-layered zF- and zR-like structure. The nodular structures harbour GNAS somatic mutations, known as a driver mutation of CPAs, and confer cell proliferative and autonomous steroidogenic capacities, which we termed steroids-producing nodules (SPNs). RNA-sequencing coupled with SRT analysis suggests that the expansion of the zF-like structure contributes to the formation of CPAs, whereas the zR-like structure is characterised by a macrophage-mediated immune response. INTERPRETATION We postulate that CPAs arise from a precursor lesion, SPNs, where two distinct cell populations might contribute differently to adrenocortical tumorigenesis. Our data also provide clues to the molecular mechanisms underlying the layered structures of human adrenocortical tissues. FUNDING KAKENHI, The Uehara Memorial Foundation, Daiwa Securities Health Foundation, Kaibara Morikazu Medical Science Promotion Foundation, Secom Science and Technology Foundation, ONO Medical Research Foundation, and Japan Foundation for Applied Enzymology.
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Affiliation(s)
- Tazuru Fukumoto
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Hironobu Umakoshi
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan.
| | - Norifusa Iwahashi
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Tatsuki Ogasawara
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Maki Yokomoto-Umakoshi
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Hiroki Kaneko
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Masamichi Fujita
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Naohiro Uchida
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Hiroshi Nakao
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Namiko Kawamura
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Yayoi Matsuda
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Ryuichi Sakamoto
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Takashi Miyazawa
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Masahide Seki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Masatoshi Eto
- Department of Urology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Yoshinao Oda
- Department of Anatomic Pathology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Seishi Ogawa
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yoshihiro Ogawa
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan.
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21
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Chatsirisupachai K, de Magalhães JP. Somatic mutations in human ageing: New insights from DNA sequencing and inherited mutations. Ageing Res Rev 2024; 96:102268. [PMID: 38490496 DOI: 10.1016/j.arr.2024.102268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 02/19/2024] [Accepted: 03/06/2024] [Indexed: 03/17/2024]
Abstract
The accumulation of somatic mutations is a driver of cancer and has long been associated with ageing. Due to limitations in quantifying mutation burden with age in non-cancerous tissues, the impact of somatic mutations in other ageing phenotypes is unclear. Recent advances in DNA sequencing technologies have allowed the large-scale quantification of somatic mutations in ageing tissues. These studies have revealed a gradual accumulation of mutations in normal tissues with age as well as a substantial clonal expansion driven mostly by cancer-related mutations. Nevertheless, it is difficult to envision how the burden and stochastic nature of age-related somatic mutations identified so far can explain most ageing phenotypes that develop gradually. Studies across species have also found that longer-lived species have lower somatic mutation rates, though these could be due to selective pressures acting on other phenotypes such as perhaps cancer. Recent studies in patients with higher somatic mutation burden and no signs of accelerated ageing further question the role of somatic mutations in ageing. Overall, with a few exceptions like cancer, recent DNA sequencing studies and inherited mutations do not support the idea that somatic mutations accumulating with age drive ageing phenotypes, and the phenotypic role, if any, of somatic mutations in ageing remains unclear.
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Affiliation(s)
- Kasit Chatsirisupachai
- Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool L7 8TX, UK; European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - João Pedro de Magalhães
- Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool L7 8TX, UK; Institute of Inflammation and Ageing, University of Birmingham, Queen Elizabeth Hospital, Mindelsohn Way, Birmingham, UK.
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22
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Wu GL, Tan X, Yang Q. Recent Advances on NIR-II Light-Enhanced Chemodynamic Therapy. Adv Healthc Mater 2024; 13:e2303451. [PMID: 37983596 DOI: 10.1002/adhm.202303451] [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: 10/11/2023] [Revised: 11/16/2023] [Indexed: 11/22/2023]
Abstract
Chemodynamic therapy (CDT) is a particular oncological therapeutic strategy by generates the highly toxic hydroxyl radical (•OH) from the dismutation of endogenous hydrogen peroxide (H2O2) via Fenton or Fenton-like reactions. However, single CDT therapies have been limited by unsatisfactory efficacy. Enhanced chemodynamic therapy (ECDT) triggered by near-infrared (NIR) is a novel therapeutic modality based on light energy to improve the efficiency of Fenton or Fenton-like reactions. However, the limited penetration and imaging capability of the visible (400-650 nm) and traditional NIR-I region (650-900 nm) light-amplified CDT restrict the prospects for its clinical application. Combined with the high penetration/high precision imaging characteristics of the second near-infrared (NIR-II,) nanoplatform, it is expected to kill deep tumors efficiently while imaging the treatment process in real-time, and more notably, the NIR-II region radiation with wavelengths above 1000 nm can minimize the irradiation damage to normal tissues. Such NIR-II ECDT nanoplatforms have greatly improved the effectiveness of CDT therapy and demonstrated extraordinary potential for clinical applications. Accordingly, various strategies have been explored in the past years to improve the efficiency of NIR-II Enhanced CDT. In this review, the mechanisms and strategies used to improve the performance of NIR-II-enhanced CDT are outlined.
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Affiliation(s)
- Gui-Long Wu
- Center for Molecular Imaging Probe, Hunan Province Key Laboratory of Tumor Cellular and Molecular Pathology, Cancer Research Institute, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
- MOE Key Lab of Rare Pediatric Diseases, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
| | - Xiaofeng Tan
- Center for Molecular Imaging Probe, Hunan Province Key Laboratory of Tumor Cellular and Molecular Pathology, Cancer Research Institute, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
- MOE Key Lab of Rare Pediatric Diseases, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
- National Health Commission Key Laboratory of Birth Defect Research and Prevention, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, Hunan, 410008, China
| | - Qinglai Yang
- Center for Molecular Imaging Probe, Hunan Province Key Laboratory of Tumor Cellular and Molecular Pathology, Cancer Research Institute, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
- MOE Key Lab of Rare Pediatric Diseases, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
- National Health Commission Key Laboratory of Birth Defect Research and Prevention, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, Hunan, 410008, China
- Department of Hepatopancreatobiliary Surgery, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
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23
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Perdomo S, Abedi-Ardekani B, de Carvalho AC, Ferreiro-Iglesias A, Gaborieau V, Cattiaux T, Renard H, Chopard P, Carreira C, Spanu A, Nikmanesh A, Cardoso Penha RC, Antwi SO, Ashton-Prolla P, Canova C, Chitapanarux T, Cox R, Curado MP, de Oliveira JC, Dzamalala C, Fabianova E, Ferri L, Fitzgerald R, Foretova L, Gallinger S, Goldstein AM, Holcatova I, Huertas A, Janout V, Jarmalaite S, Kaneva R, Kowalski LP, Kulis T, Lagiou P, Lissowska J, Malekzadeh R, Mates D, McCorrmack V, Menya D, Mhatre S, Mmbaga BT, de Moricz A, Nyirády P, Ognjanovic M, Papadopoulou K, Polesel J, Purdue MP, Rascu S, Rebolho Batista LM, Reis RM, Ribeiro Pinto LF, Rodríguez-Urrego PA, Sangkhathat S, Sangrajrang S, Shibata T, Stakhovsky E, Świątkowska B, Vaccaro C, Vasconcelos de Podesta JR, Vasudev NS, Vilensky M, Yeung J, Zaridze D, Zendehdel K, Scelo G, Chanudet E, Wang J, Fitzgerald S, Latimer C, Moody S, Humphreys L, Alexandrov LB, Stratton MR, Brennan P. The Mutographs biorepository: A unique genomic resource to study cancer around the world. CELL GENOMICS 2024; 4:100500. [PMID: 38325367 PMCID: PMC10943582 DOI: 10.1016/j.xgen.2024.100500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 10/24/2023] [Accepted: 01/10/2024] [Indexed: 02/09/2024]
Abstract
Large-scale biorepositories and databases are essential to generate equitable, effective, and sustainable advances in cancer prevention, early detection, cancer therapy, cancer care, and surveillance. The Mutographs project has created a large genomic dataset and biorepository of over 7,800 cancer cases from 30 countries across five continents with extensive demographic, lifestyle, environmental, and clinical information. Whole-genome sequencing is being finalized for over 4,000 cases, with the primary goal of understanding the causes of cancer at eight anatomic sites. Genomic, exposure, and clinical data will be publicly available through the International Cancer Genome Consortium Accelerating Research in Genomic Oncology platform. The Mutographs sample and metadata biorepository constitutes a legacy resource for new projects and collaborations aiming to increase our current research efforts in cancer genomic epidemiology globally.
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Affiliation(s)
- Sandra Perdomo
- Genomic Epidemiology Branch, International Agency for Research on Cancer (IARC/WHO), Lyon, France
| | - Behnoush Abedi-Ardekani
- Genomic Epidemiology Branch, International Agency for Research on Cancer (IARC/WHO), Lyon, France
| | - Ana Carolina de Carvalho
- Genomic Epidemiology Branch, International Agency for Research on Cancer (IARC/WHO), Lyon, France
| | - Aida Ferreiro-Iglesias
- Genomic Epidemiology Branch, International Agency for Research on Cancer (IARC/WHO), Lyon, France
| | - Valérie Gaborieau
- Genomic Epidemiology Branch, International Agency for Research on Cancer (IARC/WHO), Lyon, France
| | - Thomas Cattiaux
- Genomic Epidemiology Branch, International Agency for Research on Cancer (IARC/WHO), Lyon, France
| | - Hélène Renard
- Genomic Epidemiology Branch, International Agency for Research on Cancer (IARC/WHO), Lyon, France
| | - Priscilia Chopard
- Genomic Epidemiology Branch, International Agency for Research on Cancer (IARC/WHO), Lyon, France
| | - Christine Carreira
- Evidence Synthesis and Classification Branch, International Agency for Research on Cancer (IARC/WHO), Lyon, France
| | - Andreea Spanu
- Genomic Epidemiology Branch, International Agency for Research on Cancer (IARC/WHO), Lyon, France
| | - Arash Nikmanesh
- Genomic Epidemiology Branch, International Agency for Research on Cancer (IARC/WHO), Lyon, France
| | | | - Samuel O Antwi
- Division of Epidemiology, Department of Quantitative Health Sciences, Mayo Clinic, Jacksonville, FL, USA; Division of Gastroenterology and Hepatology, Department of Internal Medicine, Mayo Clinic, Jacksonville, FL, USA
| | - Patricia Ashton-Prolla
- Experimental Research Center, Genomic Medicine Laboratory, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil; Post-Graduate Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Cristina Canova
- Unit of Biostatistics, Epidemiology and Public Health, Department of Cardio-Thoraco-Vascular Sciences and Public Health, University of Padua, Padova, Italy
| | - Taned Chitapanarux
- Department of Internal Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Riley Cox
- Ontario Tumour Bank, Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Maria Paula Curado
- Department of Epidemiology, A.C. Camargo Cancer Center, São Paulo, Brazil
| | | | | | | | - Lorenzo Ferri
- Departments of Surgery and Oncology, McGill University, Montreal, QC, Canada
| | | | - Lenka Foretova
- Department of Cancer Epidemiology and Genetics, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Steven Gallinger
- Mount Sinai Hospital; Ontario Institute for Cancer Research (OICR), Toronto, ON, Canada
| | - Alisa M Goldstein
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Ivana Holcatova
- Institute of Public Health & Preventive Medicine, 2nd Faculty of Medicine, Charles University, Prague, Czech Republic; Department of Oncology, 2nd Faculty of Medicine, Charles University and Motol University Hospital, Prague, Czech Republic
| | | | - Vladimir Janout
- Faculty of Health Sciences, Palacky University, Olomouc, Czech Republic
| | - Sonata Jarmalaite
- Laboratory of Genetic Diagnostic, National Cancer Institute, Vilnius, Lithuania; Department of Botany and Genetics, Institute of Biosciences, Vilnius University, Vilnius, Lithuania
| | - Radka Kaneva
- Molecular Medicine Center, Department of Medical Chemistry and Biochemistry, Medical Faculty, Medical University of Sofia, Sofia, Bulgaria
| | - Luiz Paulo Kowalski
- Department of Epidemiology, A.C. Camargo Cancer Center, São Paulo, Brazil; University of São Paulo Medical School, São Paulo, Brazil
| | - Tomislav Kulis
- Department of Urology, University Hospital Center Zagreb, Zagreb, Croatia; University of Zagreb School of Medicine, Zagreb, Croatia
| | - Pagona Lagiou
- National and Kapodistrian University of Athens, Athens, Greece
| | - Jolanta Lissowska
- The Maria Sklodowska-Cure National Research Institute of Oncology, Warsaw, Poland
| | - Reza Malekzadeh
- Digestive Disease Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Dana Mates
- Occupational Health and Toxicology, National Center for Environmental Risk Monitoring, National Institute of Public Health, Bucharest, Romania
| | - Valerie McCorrmack
- Environment and Lifestyle Epidemiology Branch, International Agency for Research on Cancer (IARC/WHO), Lyon, France
| | - Diana Menya
- Moi University, School of Public Health, Eldoret, Kenya
| | - Sharayu Mhatre
- Division of Molecular Epidemiology and Population Genomics, Centre for Cancer Epidemiology, Tata Memorial Centre, Mumbai, India
| | | | - André de Moricz
- Kilimanjaro Clinical Research Institute, Kilimanjaro Christian Medical Centre & Kilimanjaro Christian Medical University College, Moshi, Tanzania
| | | | - Miodrag Ognjanovic
- IOCPR- International Organization for Cancer Prevention and Research, Serbia, Belgrade
| | | | - Jerry Polesel
- Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Aviano, Italy
| | - Mark P Purdue
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Stefan Rascu
- Urology Department, "Carol Davila" University of Medicine and Pharmacy - "Prof. Dr. Th. Burghele" Clinical Hospital, Bucharest, Romania
| | | | - Rui Manuel Reis
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil; Life and Health Sciences Research Institute (ICVS), School of Medicine, Minho University, Braga, Portugal
| | | | | | - Surasak Sangkhathat
- Translational Medicine Research Center, Faculty of Medicine, Prince of Songkla University, Hat Yai, Thailand
| | | | - Tatsuhiro Shibata
- Laboratory of Molecular Medicine, The Institute of Medical Science, The University of Tokyo, Minato-ku, Japan; Division of Cancer Genomics, National Cancer Center Research Institute, Chuo-ku, Japan
| | | | - Beata Świątkowska
- Department of Environmental Epidemiology, Nofer Institute of Occupational Medicine, Łódź, Poland
| | - Carlos Vaccaro
- Instituto Medicina Traslacional e Ingenieria Biomedica - CONICET, Buenos Aires, Argentina
| | | | - Naveen S Vasudev
- Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK
| | - Marta Vilensky
- Instituto de Oncología Angel Roffo, Universidad de Buenos Aires, Buenos Aires, Argentina
| | | | - David Zaridze
- Clinical Epidemiology, N.N. Blokhin National Medical Research Centre of Oncology, Moscow, Russia
| | - Kazem Zendehdel
- Cancer Research Center, Cancer Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Ghislaine Scelo
- Observational & Pragmatic Research Institute Pte., Ltd., Singapore, Singapore
| | - Estelle Chanudet
- Department of Pathology, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Jingwei Wang
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Cambridge, UK
| | - Stephen Fitzgerald
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Cambridge, UK
| | - Calli Latimer
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Cambridge, UK
| | - Sarah Moody
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Cambridge, UK
| | - Laura Humphreys
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Cambridge, UK
| | - Ludmil B Alexandrov
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA; Department of Bioengineering, University of California San Diego, La Jolla, CA, USA; Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Michael R Stratton
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Cambridge, UK
| | - Paul Brennan
- Genomic Epidemiology Branch, International Agency for Research on Cancer (IARC/WHO), Lyon, France.
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24
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Kapadia CD, Goodell MA. Tissue mosaicism following stem cell aging: blood as an exemplar. NATURE AGING 2024; 4:295-308. [PMID: 38438628 DOI: 10.1038/s43587-024-00589-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 02/07/2024] [Indexed: 03/06/2024]
Abstract
Loss of stem cell regenerative potential underlies aging of all tissues. Somatic mosaicism, the emergence of cellular patchworks within tissues, increases with age and has been observed in every organ yet examined. In the hematopoietic system, as in most tissues, stem cell aging through a variety of mechanisms occurs in lockstep with the emergence of somatic mosaicism. Here, we draw on insights from aging hematopoiesis to illustrate fundamental principles of stem cell aging and somatic mosaicism. We describe the generalizable changes intrinsic to aged stem cells and their milieu that provide the backdrop for somatic mosaicism to emerge. We discuss genetic and nongenetic mechanisms that can result in tissue somatic mosaicism and existing methodologies to detect such clonal outgrowths. Finally, we propose potential avenues to modify mosaicism during aging, with the ultimate aim of increasing tissue resiliency.
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Affiliation(s)
- Chiraag D Kapadia
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, USA
| | - Margaret A Goodell
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA.
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, USA.
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25
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Stańkowska W, Sarkisyan D, Bruhn-Olszewska B, Duzowska K, Bieńkowski M, Jąkalski M, Wójcik-Zalewska M, Davies H, Drężek-Chyła K, Pęksa R, Harazin-Lechowska A, Ambicka A, Przewoźnik M, Adamczyk A, Sasim K, Makarewicz W, Matuszewski M, Biernat W, Järhult JD, Lipcsey M, Hultström M, Frithiof R, Jaszczyński J, Ryś J, Genovese G, Piotrowski A, Filipowicz N, Dumanski JP. Tumor Predisposing Post-Zygotic Chromosomal Alterations in Bladder Cancer-Insights from Histologically Normal Urothelium. Cancers (Basel) 2024; 16:961. [PMID: 38473323 DOI: 10.3390/cancers16050961] [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: 11/30/2023] [Revised: 01/15/2024] [Accepted: 02/23/2024] [Indexed: 03/14/2024] Open
Abstract
Bladder urothelial carcinoma (BLCA) is the 10th most common cancer with a low survival rate and strong male bias. We studied the field cancerization in BLCA using multi-sample- and multi-tissue-per-patient protocol for sensitive detection of autosomal post-zygotic chromosomal alterations and loss of chromosome Y (LOY). We analysed 277 samples of histologically normal urothelium, 145 tumors and 63 blood samples from 52 males and 15 females, using the in-house adapted Mosaic Chromosomal Alterations (MoChA) pipeline. This approach allows identification of the early aberrations in urothelium from BLCA patients. Overall, 45% of patients exhibited at least one alteration in at least one normal urothelium sample. Recurrence analysis resulted in 16 hotspots composed of either gains and copy number neutral loss of heterozygosity (CN-LOH) or deletions and CN-LOH, encompassing well-known and new BLCA cancer driver genes. Conservative assessment of LOY showed 29%, 27% and 18% of LOY-cells in tumors, blood and normal urothelium, respectively. We provide a proof of principle that our approach can characterize the earliest alterations preconditioning normal urothelium to BLCA development. Frequent LOY in blood and urothelium-derived tissues suggest its involvement in BLCA.
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Affiliation(s)
- Wiktoria Stańkowska
- 3P-Medicine Laboratory, Medical University of Gdańsk, M. Sklodowskiej-Curie 3A, 80-210 Gdańsk, Poland
| | - Daniil Sarkisyan
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, BMC, Husargatan 3, 751 08 Uppsala, Sweden
| | - Bożena Bruhn-Olszewska
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, BMC, Husargatan 3, 751 08 Uppsala, Sweden
| | - Katarzyna Duzowska
- 3P-Medicine Laboratory, Medical University of Gdańsk, M. Sklodowskiej-Curie 3A, 80-210 Gdańsk, Poland
| | - Michał Bieńkowski
- Department of Pathomorphology, Medical University of Gdańsk, M. Sklodowskiej-Curie 3A, 80-210 Gdańsk, Poland
| | - Marcin Jąkalski
- 3P-Medicine Laboratory, Medical University of Gdańsk, M. Sklodowskiej-Curie 3A, 80-210 Gdańsk, Poland
| | - Magdalena Wójcik-Zalewska
- 3P-Medicine Laboratory, Medical University of Gdańsk, M. Sklodowskiej-Curie 3A, 80-210 Gdańsk, Poland
| | - Hanna Davies
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, BMC, Husargatan 3, 751 08 Uppsala, Sweden
| | - Kinga Drężek-Chyła
- 3P-Medicine Laboratory, Medical University of Gdańsk, M. Sklodowskiej-Curie 3A, 80-210 Gdańsk, Poland
| | - Rafał Pęksa
- Department of Pathomorphology, Medical University of Gdańsk, M. Sklodowskiej-Curie 3A, 80-210 Gdańsk, Poland
| | - Agnieszka Harazin-Lechowska
- Department of Tumor Pathology, Maria Skłodowska-Curie National Research Institute of Oncology, Garncarska 11, 31-115 Kraków, Poland
| | - Aleksandra Ambicka
- Department of Tumor Pathology, Maria Skłodowska-Curie National Research Institute of Oncology, Garncarska 11, 31-115 Kraków, Poland
| | - Marcin Przewoźnik
- Department of Tumor Pathology, Maria Skłodowska-Curie National Research Institute of Oncology, Garncarska 11, 31-115 Kraków, Poland
| | - Agnieszka Adamczyk
- Department of Tumor Pathology, Maria Skłodowska-Curie National Research Institute of Oncology, Garncarska 11, 31-115 Kraków, Poland
| | - Karol Sasim
- Clinic of Urology and Oncological Urology, Specialist Hospital of Kościerzyna, Piechowskiego 36, 83-400 Kościerzyna, Poland
| | - Wojciech Makarewicz
- Clinic of General and Oncological Surgery, Specialist Hospital of Kościerzyna, Piechowskiego 36, 83-400 Kościerzyna, Poland
| | - Marcin Matuszewski
- Department and Clinic of Urology, Medical University of Gdańsk, M. Sklodowskiej-Curie 3A, 80-210 Gdańsk, Poland
| | - Wojciech Biernat
- Department of Pathomorphology, Medical University of Gdańsk, M. Sklodowskiej-Curie 3A, 80-210 Gdańsk, Poland
| | - Josef D Järhult
- Zoonosis Science Center, Department of Medical Sciences, Uppsala University, Akademiska Sjukhuset, 751 85 Uppsala, Sweden
| | - Miklós Lipcsey
- Department of Surgical Sciences, Anesthesiology and Intensive Care, Uppsala University, Akademiska Sjukhuset, 751 85 Uppsala, Sweden
- Hedenstierna Laboratory, Department of Surgical Sciences, Uppsala University, Akademiska Sjukhuset, 751 85 Uppsala, Sweden
| | - Michael Hultström
- Department of Surgical Sciences, Anesthesiology and Intensive Care, Uppsala University, Akademiska Sjukhuset, 751 85 Uppsala, Sweden
- Integrative Physiology, Department of Medical Cell Biology, Uppsala University, BMC, Husargatan 3, 751 08 Uppsala, Sweden
| | - Robert Frithiof
- Department of Surgical Sciences, Anesthesiology and Intensive Care, Uppsala University, Akademiska Sjukhuset, 751 85 Uppsala, Sweden
| | - Janusz Jaszczyński
- Department of Urology, Maria Skłodowska-Curie National Research Institute of Oncology, Garncarska 11, 31-115 Kraków, Poland
| | - Janusz Ryś
- Department of Tumor Pathology, Maria Skłodowska-Curie National Research Institute of Oncology, Garncarska 11, 31-115 Kraków, Poland
| | - Giulio Genovese
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Arkadiusz Piotrowski
- 3P-Medicine Laboratory, Medical University of Gdańsk, M. Sklodowskiej-Curie 3A, 80-210 Gdańsk, Poland
- Department of Biology and Pharmaceutical Botany, Medical University of Gdańsk, Hallera 107, 80-416 Gdańsk, Poland
| | - Natalia Filipowicz
- 3P-Medicine Laboratory, Medical University of Gdańsk, M. Sklodowskiej-Curie 3A, 80-210 Gdańsk, Poland
| | - Jan P Dumanski
- 3P-Medicine Laboratory, Medical University of Gdańsk, M. Sklodowskiej-Curie 3A, 80-210 Gdańsk, Poland
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, BMC, Husargatan 3, 751 08 Uppsala, Sweden
- Department of Biology and Pharmaceutical Botany, Medical University of Gdańsk, Hallera 107, 80-416 Gdańsk, Poland
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26
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Xiao R, Xu D, Zhang M, Chen Z, Cheng L, Du S, Lu M, Zhou T, Li R, Bai F, Huang Y. Aneuploid embryonic stem cells drive teratoma metastasis. Nat Commun 2024; 15:1087. [PMID: 38316790 PMCID: PMC10844504 DOI: 10.1038/s41467-024-45265-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 01/18/2024] [Indexed: 02/07/2024] Open
Abstract
Aneuploidy, a deviation of the chromosome number from euploidy, is one of the hallmarks of cancer. High levels of aneuploidy are generally correlated with metastasis and poor prognosis in cancer patients. However, the causality of aneuploidy in cancer metastasis remains to be explored. Here we demonstrate that teratomas derived from aneuploid murine embryonic stem cells (ESCs), but not from isogenic diploid ESCs, disseminated to multiple organs, for which no additional copy number variations were required. Notably, no cancer driver gene mutations were identified in any metastases. Aneuploid circulating teratoma cells were successfully isolated from peripheral blood and showed high capacities for migration and organ colonization. Single-cell RNA sequencing of aneuploid primary teratomas and metastases identified a unique cell population with high stemness that was absent in diploid ESCs-derived teratomas. Further investigation revealed that aneuploid cells displayed decreased proteasome activity and overactivated endoplasmic reticulum (ER) stress during differentiation, thereby restricting the degradation of proteins produced from extra chromosomes in the ESC state and causing differentiation deficiencies. Noticeably, both proteasome activator Oleuropein and ER stress inhibitor 4-PBA can effectively inhibit aneuploid teratoma metastasis.
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Affiliation(s)
- Rong Xiao
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Medical Genetics, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China
| | - Deshu Xu
- Biomedical Pioneering Innovation Center (BIOPIC), Beijing Advanced Innovation Center for Genomics (ICG), School of Life Sciences, Peking University, Beijing, 100871, China
| | - Meili Zhang
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Medical Genetics, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China
| | - Zhanghua Chen
- Biomedical Pioneering Innovation Center (BIOPIC), Beijing Advanced Innovation Center for Genomics (ICG), School of Life Sciences, Peking University, Beijing, 100871, China
| | - Li Cheng
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Medical Genetics, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China
| | - Songjie Du
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Medical Genetics, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China
| | - Mingfei Lu
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Medical Genetics, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China
| | - Tonghai Zhou
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Medical Genetics, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China
| | - Ruoyan Li
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Fan Bai
- Biomedical Pioneering Innovation Center (BIOPIC), Beijing Advanced Innovation Center for Genomics (ICG), School of Life Sciences, Peking University, Beijing, 100871, China.
| | - Yue Huang
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Medical Genetics, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China.
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27
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Huang AY, Zhou Z, Talukdar M, Miller MB, Chhouk B, Enyenihi L, Rosen I, Stronge E, Zhao B, Kim D, Choi J, Khoshkhoo S, Kim J, Ganz J, Travaglini K, Gabitto M, Hodge R, Kaplan E, Lein E, De Jager PL, Bennett DA, Lee EA, Walsh CA. Somatic cancer driver mutations are enriched and associated with inflammatory states in Alzheimer's disease microglia. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.03.574078. [PMID: 38260600 PMCID: PMC10802273 DOI: 10.1101/2024.01.03.574078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Alzheimer's disease (AD) is an age-associated neurodegenerative disorder characterized by progressive neuronal loss and pathological accumulation of the misfolded proteins amyloid-β and tau1,2. Neuroinflammation mediated by microglia and brain-resident macrophages plays a crucial role in AD pathogenesis1-5, though the mechanisms by which age, genes, and other risk factors interact remain largely unknown. Somatic mutations accumulate with age and lead to clonal expansion of many cell types, contributing to cancer and many non-cancer diseases6,7. Here we studied somatic mutation in normal aged and AD brains by three orthogonal methods and in three independent AD cohorts. Analysis of bulk RNA sequencing data from 866 samples from different brain regions revealed significantly higher (~two-fold) overall burdens of somatic single-nucleotide variants (sSNVs) in AD brains compared to age-matched controls. Molecular-barcoded deep (>1000X) gene panel sequencing of 311 prefrontal cortex samples showed enrichment of sSNVs and somatic insertions and deletions (sIndels) in cancer driver genes in AD brain compared to control, with recurrent, and often multiple, mutations in genes implicated in clonal hematopoiesis (CH)8,9. Pathogenic sSNVs were enriched in CSF1R+ microglia of AD brains, and the high proportion of microglia (up to 40%) carrying some sSNVs in cancer driver genes suggests mutation-driven microglial clonal expansion (MiCE). Analysis of single-nucleus RNA sequencing (snRNAseq) from temporal neocortex of 62 additional AD cases and controls exhibited nominally increased mosaic chromosomal alterations (mCAs) associated with CH10,11. Microglia carrying mCA showed upregulated pro-inflammatory genes, resembling the transcriptomic features of disease-associated microglia (DAM) in AD. Our results suggest that somatic driver mutations in microglia are common with normal aging but further enriched in AD brain, driving MiCE with inflammatory and DAM signatures. Our findings provide the first insights into microglial clonal dynamics in AD and identify potential new approaches to AD diagnosis and therapy.
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Affiliation(s)
- August Yue Huang
- Division of Genetics and Genomics and Manton Center for Orphan Diseases, Boston Children’s Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Zinan Zhou
- Division of Genetics and Genomics and Manton Center for Orphan Diseases, Boston Children’s Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Maya Talukdar
- Division of Genetics and Genomics and Manton Center for Orphan Diseases, Boston Children’s Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard-MIT MD/PhD Program, Boston, MA, USA
| | - Michael B. Miller
- Division of Genetics and Genomics and Manton Center for Orphan Diseases, Boston Children’s Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Neuropathology, Department of Pathology, Brigham and Women’s Hospital, Boston, MA, USA
| | - Brian Chhouk
- Division of Genetics and Genomics and Manton Center for Orphan Diseases, Boston Children’s Hospital, Boston, MA, USA
| | - Liz Enyenihi
- Division of Genetics and Genomics and Manton Center for Orphan Diseases, Boston Children’s Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard-MIT MD/PhD Program, Boston, MA, USA
| | - Ila Rosen
- Division of Genetics and Genomics and Manton Center for Orphan Diseases, Boston Children’s Hospital, Boston, MA, USA
| | - Edward Stronge
- Division of Genetics and Genomics and Manton Center for Orphan Diseases, Boston Children’s Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard-MIT MD/PhD Program, Boston, MA, USA
| | - Boxun Zhao
- Division of Genetics and Genomics and Manton Center for Orphan Diseases, Boston Children’s Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Dachan Kim
- Division of Genetics and Genomics and Manton Center for Orphan Diseases, Boston Children’s Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- Department of Otorhinolaryngology, Severance Hospital, Yonsei University Health System, Yonsei University College of Medicine, Seoul, South Korea
| | - Jaejoon Choi
- Division of Genetics and Genomics and Manton Center for Orphan Diseases, Boston Children’s Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sattar Khoshkhoo
- Division of Genetics and Genomics and Manton Center for Orphan Diseases, Boston Children’s Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Neurology, Brigham and Women’s Hospital, Boston, MA, USA
| | - Junho Kim
- Division of Genetics and Genomics and Manton Center for Orphan Diseases, Boston Children’s Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biological Sciences, Sungkyunkwan University, Suwon, South Korea
| | - Javier Ganz
- Division of Genetics and Genomics and Manton Center for Orphan Diseases, Boston Children’s Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | | | | | - Eitan Kaplan
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Ed Lein
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Philip L. De Jager
- Center for Translational and Computational Neuroimmunology, Department of Neurology and the Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY, USA
| | - David A. Bennett
- Rush Alzheimer’s Disease Center, Rush University Medical College, Chicago, IL, USA
| | - Eunjung Alice Lee
- Division of Genetics and Genomics and Manton Center for Orphan Diseases, Boston Children’s Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Christopher A. Walsh
- Division of Genetics and Genomics and Manton Center for Orphan Diseases, Boston Children’s Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Howard Hughes Medical Institute, Boston, MA USA
- Departments of Neurology, Harvard Medical School, Boston, MA, USA
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28
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Shah A. Rethinking cancer initiation: The role of large-scale mutational events. Genes Chromosomes Cancer 2024; 63:e23213. [PMID: 37950638 DOI: 10.1002/gcc.23213] [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: 06/08/2023] [Revised: 10/24/2023] [Accepted: 10/27/2023] [Indexed: 11/13/2023] Open
Abstract
Cancer initiation is revisited in light of recent discoveries in cancer pathogenesis. Of note is the detection of mutated cancer genes in benign conditions. More significantly, somatic clones, which harbor mutations in cancer genes, arise in normal tissues from early development through adulthood, but seldom do they transform into cancer. Further, clustered mutational events-kataegis, chromothripsis and chromoplexy-are widespread in cancer, generating point mutations and chromosomal rearrangements in a single cellular catastrophe. These observations are contrary to the prevailing somatic mutation theory, which states that a cancer is caused by the gradual accumulation of mutations over time. A different perspective is proposed within the framework of Waddington's epigenetic landscape wherein tumorigenesis is viewed primarily as a disruption of cell development. Cell types are defined by their specific gene-expression profiles, determined by the gene regulatory network, and can be regarded as attractor states of the network dynamics: they represent specific, self-stabilizing patterns of gene activities across the genome. However, large-scale mutational events reshape the landscape topology, creating abnormal "unphysiological" attractors. This is the crux of the process of initiation. Initiation primes the cell for conversion into a tumor phenotype by oncogenes and tumor suppressor genes, which drive cell proliferation and clonal diversification. This view of tumorigenesis calls for a different approach to therapy.
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Affiliation(s)
- Amil Shah
- Department of Medicine, University of British Columbia, Vancouver, Canada
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29
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Weeks LD, Ebert BL. Causes and consequences of clonal hematopoiesis. Blood 2023; 142:2235-2246. [PMID: 37931207 PMCID: PMC10862247 DOI: 10.1182/blood.2023022222] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 10/25/2023] [Accepted: 10/25/2023] [Indexed: 11/08/2023] Open
Abstract
ABSTRACT Clonal hematopoiesis (CH) is described as the outsized contribution of expanded clones of hematopoietic stem and progenitor cells (HSPCs) to blood cell production. The prevalence of CH increases dramatically with age. CH can be caused by somatic mutations in individual genes or by gains and/or losses of larger chromosomal segments. CH is a premalignant state; the somatic mutations detected in CH are the initiating mutations for hematologic malignancies, and CH is a strong predictor of the development of blood cancers. Moreover, CH is associated with nonmalignant disorders and increased overall mortality. The somatic mutations that drive clonal expansion of HSPCs can alter the function of terminally differentiated blood cells, including the release of elevated levels of inflammatory cytokines. These cytokines may then contribute to a broad range of inflammatory disorders that increase in prevalence with age. Specific somatic mutations in the peripheral blood in coordination with blood count parameters can powerfully predict the development of hematologic malignancies and overall mortality in CH. In this review, we summarize the current understanding of CH nosology and origins. We provide an overview of available tools for risk stratification and discuss management strategies for patients with CH presenting to hematology clinics.
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Affiliation(s)
- Lachelle D. Weeks
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Center for Early Detection and Interception of Blood Cancers, Dana-Farber Cancer Institute, Boston, MA
- Department of Medicine, Harvard Medical School, Boston, MA
| | - Benjamin L. Ebert
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Center for Early Detection and Interception of Blood Cancers, Dana-Farber Cancer Institute, Boston, MA
- Department of Medicine, Harvard Medical School, Boston, MA
- Howard Hughes Medical Institute, Boston, MA
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30
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Huang KK, Ma H, Chong RHH, Uchihara T, Lian BSX, Zhu F, Sheng T, Srivastava S, Tay ST, Sundar R, Tan ALK, Ong X, Lee M, Ho SWT, Lesluyes T, Ashktorab H, Smoot D, Van Loo P, Chua JS, Ramnarayanan K, Lau LHS, Gotoda T, Kim HS, Ang TL, Khor C, Lee JWJ, Tsao SKK, Yang WL, Teh M, Chung H, So JBY, Yeoh KG, Tan P. Spatiotemporal genomic profiling of intestinal metaplasia reveals clonal dynamics of gastric cancer progression. Cancer Cell 2023; 41:2019-2037.e8. [PMID: 37890493 PMCID: PMC10729843 DOI: 10.1016/j.ccell.2023.10.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 08/08/2023] [Accepted: 10/06/2023] [Indexed: 10/29/2023]
Abstract
Intestinal metaplasia (IM) is a pre-malignant condition of the gastric mucosa associated with increased gastric cancer (GC) risk. Analyzing 1,256 gastric samples (1,152 IMs) across 692 subjects from a prospective 10-year study, we identify 26 IM driver genes in diverse pathways including chromatin regulation (ARID1A) and intestinal homeostasis (SOX9). Single-cell and spatial profiles highlight changes in tissue ecology and IM lineage heterogeneity, including an intestinal stem-cell dominant cellular compartment linked to early malignancy. Expanded transcriptome profiling reveals expression-based molecular subtypes of IM associated with incomplete histology, antral/intestinal cell types, ARID1A mutations, inflammation, and microbial communities normally associated with the healthy oral tract. We demonstrate that combined clinical-genomic models outperform clinical-only models in predicting IMs likely to transform to GC. By highlighting strategies for accurately identifying IM patients at high GC risk and a role for microbial dysbiosis in IM progression, our results raise opportunities for GC precision prevention and interception.
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Affiliation(s)
- Kie Kyon Huang
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Haoran Ma
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Roxanne Hui Heng Chong
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore
| | - Tomoyuki Uchihara
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Benedict Shi Xiang Lian
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Feng Zhu
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore
| | - Taotao Sheng
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - Supriya Srivastava
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore
| | - Su Ting Tay
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Raghav Sundar
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore 169857, Singapore; Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore; Department of Haematology-Oncology, National University Health System, Singapore 119074, Singapore
| | - Angie Lay Keng Tan
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Xuewen Ong
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Minghui Lee
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Shamaine Wei Ting Ho
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | | | | | - Duane Smoot
- Department of Internal Medicine, Meharry Medical College, Nashville, TN, USA
| | - Peter Van Loo
- The Francis Crick Institute, London, UK; Department of Genetics, 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
| | - Joy Shijia Chua
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore
| | - Kalpana Ramnarayanan
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Louis Ho Shing Lau
- Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, Hong Kong
| | - Takuji Gotoda
- Division of Gastroenterology and Hepatology, Department of Medicine, Nihon University School of Medicine, Tokyo, Japan
| | - Hyun Soo Kim
- Department of Internal Medicine, Yonsei University Wonju College of Medicine, Seoul, Korea
| | - Tiing Leong Ang
- Department of Gastroenterology & Hepatology, Changi General Hospital, Singapore 529889, Singapore
| | - Christopher Khor
- Department of Gastroenterology & Hepatology, Singapore General Hospital, Singapore 169854, Singapore
| | - Jonathan Wei Jie Lee
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore; iHealthtech, National University of Singapore, Singapore, Singapore; SynCTI, National University of Singapore, Singapore 117599, Singapore; Department of Gastroenterology & Hepatology, National University Hospital, Singapore 119074, Singapore
| | - Stephen Kin Kwok Tsao
- Department of Gastroenterology & Hepatology, Tan Tock Seng Hospital, Singapore 308433, Singapore
| | - Wei Lyn Yang
- Department of Gastroenterology & Hepatology, Tan Tock Seng Hospital, Singapore 308433, Singapore
| | - Ming Teh
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore
| | - Hyunsoo Chung
- Department of Internal Medicine, Seoul National University Hospital, Seoul, Korea.
| | - Jimmy Bok Yan So
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore; NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore; Division of Surgical Oncology, National University Cancer Institute of Singapore (NCIS), Singapore, Singapore.
| | - Khay Guan Yeoh
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore; Department of Gastroenterology & Hepatology, National University Hospital, Singapore 119074, Singapore.
| | - Patrick Tan
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore 169857, Singapore; Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore; Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore; Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117593, Singapore; Cellular and Molecular Research, National Cancer Centre, Singapore, Singapore; Singhealth/Duke-NUS Institute of Precision Medicine, National Heart Centre Singapore, Singapore 168752, Singapore.
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31
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Koch Z, Li A, Evans DS, Cummings S, Ideker T. Somatic mutation as an explanation for epigenetic aging. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.08.569638. [PMID: 38106096 PMCID: PMC10723383 DOI: 10.1101/2023.12.08.569638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
DNA methylation marks have recently been used to build models known as "epigenetic clocks" which predict calendar age. As methylation of cytosine promotes C-to-T mutations, we hypothesized that the methylation changes observed with age should reflect the accrual of somatic mutations, and the two should yield analogous aging estimates. In analysis of multimodal data from 9,331 human individuals, we find that CpG mutations indeed coincide with changes in methylation, not only at the mutated site but also with pervasive remodeling of the methylome out to ±10 kilobases. This one-to-many mapping enables mutation-based predictions of age that agree with epigenetic clocks, including which individuals are aging faster or slower than expected. Moreover, genomic loci where mutations accumulate with age also tend to have methylation patterns that are especially predictive of age. These results suggest a close coupling between the accumulation of sporadic somatic mutations and the widespread changes in methylation observed over the course of life.
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Affiliation(s)
- Zane Koch
- Program in Bioinformatics and Systems Biology, University of California San Diego, La Jolla CA, 92093, USA
| | - Adam Li
- Program in Bioinformatics and Systems Biology, University of California San Diego, La Jolla CA, 92093, USA
| | - Daniel S. Evans
- California Pacific Medical Center Research Institute, San Francisco CA 94158, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, 94158
| | - Steven Cummings
- California Pacific Medical Center Research Institute, San Francisco CA 94158, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, 94158
| | - Trey Ideker
- Program in Bioinformatics and Systems Biology, University of California San Diego, La Jolla CA, 92093, USA
- Department of Medicine, University of California San Diego, La Jolla California, 92093, USA
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32
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Newcomb G, Farkas L. Endothelial cell clonality, heterogeneity and dysfunction in pulmonary arterial hypertension. Front Med (Lausanne) 2023; 10:1304766. [PMID: 38126077 PMCID: PMC10731016 DOI: 10.3389/fmed.2023.1304766] [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: 09/29/2023] [Accepted: 11/23/2023] [Indexed: 12/23/2023] Open
Abstract
Our understanding of the pathophysiology of pulmonary arterial hypertension (PAH) has evolved over recent years, with the recognition that endothelial cell (EC) dysfunction and inflammation play an integral role in the development of this disease. ECs within the pulmonary vasculature play a unique role in maintaining vascular integrity and barrier function, regulating gas exchange, and contributing to vascular tone. Using single-cell transcriptomics, research has shown that there are multiple, unique EC subpopulations with different phenotypes. In response to injury or certain stressors such as hypoxia, there can be a dysregulated response with aberrant endothelial injury repair involving other pulmonary vascular cells and even immune cells. This aberrant signaling cascade is potentially a primary driver of pulmonary arterial remodeling in PAH. Recent studies have examined the role of EC clonal expansion, immune dysregulation, and genetic mutations in the pathogenesis of PAH. This review summarizes the existing literature on EC subpopulations and the intricate mechanisms through which ECs develop aberrant physiologic phenotypes and contribute to PAH. Our goal is to provide a framework for understanding the unique pulmonary EC biology and pathophysiology that is involved in the development of PAH.
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Affiliation(s)
- Geoffrey Newcomb
- Department of Internal Medicine, Division of Pulmonary, Critical Care, and Sleep Medicine, The Ohio State University Wexner Medical Center, Columbus, OH, United States
- Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, United States
| | - Laszlo Farkas
- Department of Internal Medicine, Division of Pulmonary, Critical Care, and Sleep Medicine, The Ohio State University Wexner Medical Center, Columbus, OH, United States
- Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, United States
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33
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Balmain A. Peto's paradox revisited: black box vs mechanistic approaches to understanding the roles of mutations and promoting factors in cancer. Eur J Epidemiol 2023; 38:1251-1258. [PMID: 36512199 PMCID: PMC10757908 DOI: 10.1007/s10654-022-00933-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 10/10/2022] [Indexed: 12/15/2022]
Affiliation(s)
- Allan Balmain
- Helen Diller Family Comprehensive Cancer Center, University of California, San FranciscoSan Francisco, CA, 1450 3rd Street94143, USA.
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34
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Davey Smith G, Hofman A, Brennan P. Chance, ignorance, and the paradoxes of cancer: Richard Peto on developing preventative strategies under uncertainty. Eur J Epidemiol 2023; 38:1227-1237. [PMID: 38147198 DOI: 10.1007/s10654-023-01090-5] [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] [Accepted: 12/08/2023] [Indexed: 12/27/2023]
Abstract
During the early 1980s both cancer biology and epidemiological methods were being transformed. In 1984 the leading cancer epidemiologist Richard Peto - who, in 1981, had published the landmark Causes of Cancer with Richard Doll - wrote a short chapter on "The need for ignorance in cancer research", in which the worlds of epidemiology and speculative Darwinian biology met. His reflections on how evolutionary theory related to cancer have become known as "Peto's paradox", whilst his articulation of "black box epidemiology" provided the logic of subsequent practice in the field. We reprint this sparkling and prescient example of biologically-informed epidemiological theorising at its best in this issue of the European Journal of Epidemiology, together with four commentaries that focus on different aspects of its rich content. Here were provide some contextual background to the 1984 chapter, and our own speculations regarding various paradoxes in cancer epidemiology. We suggest that one reason for the relative lack of progress in indentifying novel modifiable causes of cancer over the last 40 years may reflect such exposures being ubiquitous within environments, and discuss the lessons for epidemiology that would follow from this.
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Affiliation(s)
- George Davey Smith
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, BS8 2BN, UK.
| | - Albert Hofman
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, USA
| | - Paul Brennan
- Genomic Epidemiology Branch, IARC - International Agency for Research on Cancer, Lyon, France
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35
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Liu CY, Girish N, Gomez ML, Kalski M, Bernard JK, Simons BD, Polk DB. Wound-healing plasticity enables clonal expansion of founder progenitor cells in colitis. Dev Cell 2023; 58:2309-2325.e7. [PMID: 37652012 PMCID: PMC10872951 DOI: 10.1016/j.devcel.2023.08.011] [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: 04/12/2022] [Revised: 05/30/2023] [Accepted: 08/05/2023] [Indexed: 09/02/2023]
Abstract
Chronic colonic injury and inflammation pose high risks for field cancerization, wherein injury-associated mutations promote stem cell fitness and gradual clonal expansion. However, the long-term stability of some colitis-associated mutational fields could suggest alternate origins. Here, studies of acute murine colitis reveal a punctuated mechanism of massive, neutral clonal expansion during normal wound healing. Through three-dimensional (3D) imaging, quantitative fate mapping, and single-cell transcriptomics, we show that epithelial wound repair begins with the loss of structural constraints on regeneration, forming fused labyrinthine channels containing epithelial cells reprogrammed to a non-proliferative plastic state. A small but highly proliferative set of epithelial founder progenitor cells (FPCs) subsequently emerges and undergoes extensive cell division, enabling fluid-like lineage mixing and spreading across the colonic surface. Crypt budding restores the glandular organization, imprinting the pattern of clonal expansion. The emergence and functions of FPCs within a critical window of plasticity represent regenerative targets with implications for preneoplasia.
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Affiliation(s)
- Cambrian Y Liu
- Department of Medicine, The University of Chicago, Chicago, IL 60637, USA; Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Children's Hospital Los Angeles, Los Angeles, CA 90027, USA.
| | - Nandini Girish
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Children's Hospital Los Angeles, Los Angeles, CA 90027, USA; Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA 92093, USA
| | - Marie L Gomez
- Program in Biomedical and Biological Sciences, Keck School of Medicine of the University of Southern California, Los Angeles, CA 90033, USA
| | - Martin Kalski
- Department of Medicine, The University of Chicago, Chicago, IL 60637, USA
| | - Jessica K Bernard
- Program in Craniofacial Biology, Herman Ostrow School of Dentistry of the University of Southern California, Los Angeles, CA 90033, USA
| | - Benjamin D Simons
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK; Department of Applied Mathematics and Theoretical Physics, Centre for Mathematical Sciences, University of Cambridge, Cambridge CB3 0WA, UK; Wellcome Trust, Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
| | - D Brent Polk
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Children's Hospital Los Angeles, Los Angeles, CA 90027, USA; Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA 92093, USA; Department of Biochemistry and Molecular Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, CA 90033, USA; Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Rady Children's Hospital, San Diego, CA 92123, USA.
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36
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Derks LLM, van Boxtel R. Stem cell mutations, associated cancer risk, and consequences for regenerative medicine. Cell Stem Cell 2023; 30:1421-1433. [PMID: 37832550 PMCID: PMC10624213 DOI: 10.1016/j.stem.2023.09.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 09/05/2023] [Accepted: 09/20/2023] [Indexed: 10/15/2023]
Abstract
Mutation accumulation in stem cells has been associated with cancer risk. However, the presence of numerous mutant clones in healthy tissues has raised the question of what limits cancer initiation. Here, we review recent developments in characterizing mutation accumulation in healthy tissues and compare mutation rates in stem cells during development and adult life with corresponding cancer risk. A certain level of mutagenesis within the stem cell pool might be beneficial to limit the size of malignant clones through competition. This knowledge impacts our understanding of carcinogenesis with potential consequences for the use of stem cells in regenerative medicine.
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Affiliation(s)
- Lucca L M Derks
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, the Netherlands; Oncode Institute, Jaarbeursplein 6, 3521 AL Utrecht, the Netherlands
| | - Ruben van Boxtel
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, the Netherlands; Oncode Institute, Jaarbeursplein 6, 3521 AL Utrecht, the Netherlands.
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37
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Bansaccal N, Vieugue P, Sarate R, Song Y, Minguijon E, Miroshnikova YA, Zeuschner D, Collin A, Allard J, Engelman D, Delaunois AL, Liagre M, de Groote L, Timmerman E, Van Haver D, Impens F, Salmon I, Wickström SA, Sifrim A, Blanpain C. The extracellular matrix dictates regional competence for tumour initiation. Nature 2023; 623:828-835. [PMID: 37968399 PMCID: PMC7615367 DOI: 10.1038/s41586-023-06740-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 10/11/2023] [Indexed: 11/17/2023]
Abstract
The skin epidermis is constantly renewed throughout life1,2. Disruption of the balance between renewal and differentiation can lead to uncontrolled growth and tumour initiation3. However, the ways in which oncogenic mutations affect the balance between renewal and differentiation and lead to clonal expansion, cell competition, tissue colonization and tumour development are unknown. Here, through multidisciplinary approaches that combine in vivo clonal analysis using intravital microscopy, single-cell analysis and functional analysis, we show how SmoM2-a constitutively active oncogenic mutant version of Smoothened (SMO) that induces the development of basal cell carcinoma-affects clonal competition and tumour initiation in real time. We found that expressing SmoM2 in the ear epidermis of mice induced clonal expansion together with tumour initiation and invasion. By contrast, expressing SmoM2 in the back-skin epidermis led to a clonal expansion that induced lateral cell competition without dermal invasion and tumour formation. Single-cell analysis showed that oncogene expression was associated with a cellular reprogramming of adult interfollicular cells into an embryonic hair follicle progenitor (EHFP) state in the ear but not in the back skin. Comparisons between the ear and the back skin revealed that the dermis has a very different composition in these two skin types, with increased stiffness and a denser collagen I network in the back skin. Decreasing the expression of collagen I in the back skin through treatment with collagenase, chronic UV exposure or natural ageing overcame the natural resistance of back-skin basal cells to undergoing EHFP reprogramming and tumour initiation after SmoM2 expression. Altogether, our study shows that the composition of the extracellular matrix regulates how susceptible different regions of the body are to tumour initiation and invasion.
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Affiliation(s)
- Nordin Bansaccal
- Laboratory of Stem Cells and Cancer, Université Libre de Bruxelles, Brussels, Belgium
| | - Pauline Vieugue
- Laboratory of Stem Cells and Cancer, Université Libre de Bruxelles, Brussels, Belgium
| | - Rahul Sarate
- Laboratory of Stem Cells and Cancer, Université Libre de Bruxelles, Brussels, Belgium
| | - Yura Song
- Laboratory of Stem Cells and Cancer, Université Libre de Bruxelles, Brussels, Belgium
| | - Esmeralda Minguijon
- Department of Pathology, CUB Hôpital Erasme, Hôpital Universitaire de Bruxelles, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Yekaterina A Miroshnikova
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
- Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Dagmar Zeuschner
- Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Amandine Collin
- DIAPath, Center for Microscopy and Molecular Imaging (CMMI), Université Libre de Bruxelles (ULB), Gosselies, Belgium
| | - Justine Allard
- DIAPath, Center for Microscopy and Molecular Imaging (CMMI), Université Libre de Bruxelles (ULB), Gosselies, Belgium
| | - Dan Engelman
- Laboratory of Stem Cells and Cancer, Université Libre de Bruxelles, Brussels, Belgium
| | - Anne-Lise Delaunois
- Laboratory of Stem Cells and Cancer, Université Libre de Bruxelles, Brussels, Belgium
| | - Mélanie Liagre
- Laboratory of Stem Cells and Cancer, Université Libre de Bruxelles, Brussels, Belgium
| | - Leona de Groote
- Laboratory of Stem Cells and Cancer, Université Libre de Bruxelles, Brussels, Belgium
| | - Evy Timmerman
- VIB Center for Medical Biotechnology, VIB Proteomics Core, Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Delphi Van Haver
- VIB Center for Medical Biotechnology, VIB Proteomics Core, Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Francis Impens
- VIB Center for Medical Biotechnology, VIB Proteomics Core, Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Isabelle Salmon
- Department of Pathology, CUB Hôpital Erasme, Hôpital Universitaire de Bruxelles, Université Libre de Bruxelles (ULB), Brussels, Belgium
- DIAPath, Center for Microscopy and Molecular Imaging (CMMI), Université Libre de Bruxelles (ULB), Gosselies, Belgium
| | - Sara A Wickström
- Max Planck Institute for Molecular Biomedicine, Münster, Germany
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | | | - Cédric Blanpain
- Laboratory of Stem Cells and Cancer, Université Libre de Bruxelles, Brussels, Belgium.
- WELBIO, Université Libre de Bruxelles (ULB), Brussels, Belgium.
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38
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Olafsson S, Rodriguez E, Lawson ARJ, Abascal F, Huber AR, Suembuel M, Jones PH, Gerdes S, Martincorena I, Weidinger S, Campbell PJ, Anderson CA. Effects of psoriasis and psoralen exposure on the somatic mutation landscape of the skin. Nat Genet 2023; 55:1892-1900. [PMID: 37884686 PMCID: PMC10632143 DOI: 10.1038/s41588-023-01545-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Accepted: 09/20/2023] [Indexed: 10/28/2023]
Abstract
Somatic mutations are hypothesized to play a role in many non-neoplastic diseases. We performed whole-exome sequencing of 1,182 microbiopsies dissected from lesional and nonlesional epidermis from 111 patients with psoriasis to search for evidence that somatic mutations in keratinocytes may influence the disease process. Lesional skin remained highly polyclonal, showing no evidence of large-scale spread of clones carrying potentially pathogenic mutations. The mutation rate of keratinocytes was similarly only modestly affected by the disease. We found evidence of positive selection in previously reported driver genes NOTCH1, NOTCH2, TP53, FAT1 and PPM1D and also identified mutations in four genes (GXYLT1, CHEK2, ZFP36L2 and EEF1A1) that we hypothesize are selected for in squamous epithelium irrespective of disease status. Finally, we describe a mutational signature of psoralens-a class of chemicals previously found in some sunscreens and which are used as part of PUVA (psoralens and ultraviolet-A) photochemotherapy treatment for psoriasis.
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Affiliation(s)
| | - Elke Rodriguez
- Department of Dermatology and Allergy, University Hospital Schleswig-Holstein, Kiel, Germany
| | | | | | | | - Melike Suembuel
- Department of Dermatology and Allergy, University Hospital Schleswig-Holstein, Kiel, Germany
| | | | - Sascha Gerdes
- Department of Dermatology and Allergy, University Hospital Schleswig-Holstein, Kiel, Germany
| | | | - Stephan Weidinger
- Department of Dermatology and Allergy, University Hospital Schleswig-Holstein, Kiel, Germany
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Pradeu T, Daignan-Fornier B, Ewald A, Germain PL, Okasha S, Plutynski A, Benzekry S, Bertolaso M, Bissell M, Brown JS, Chin-Yee B, Chin-Yee I, Clevers H, Cognet L, Darrason M, Farge E, Feunteun J, Galon J, Giroux E, Green S, Gross F, Jaulin F, Knight R, Laconi E, Larmonier N, Maley C, Mantovani A, Moreau V, Nassoy P, Rondeau E, Santamaria D, Sawai CM, Seluanov A, Sepich-Poore GD, Sisirak V, Solary E, Yvonnet S, Laplane L. Reuniting philosophy and science to advance cancer research. Biol Rev Camb Philos Soc 2023; 98:1668-1686. [PMID: 37157910 PMCID: PMC10869205 DOI: 10.1111/brv.12971] [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: 09/22/2022] [Revised: 04/24/2023] [Accepted: 04/25/2023] [Indexed: 05/10/2023]
Abstract
Cancers rely on multiple, heterogeneous processes at different scales, pertaining to many biomedical fields. Therefore, understanding cancer is necessarily an interdisciplinary task that requires placing specialised experimental and clinical research into a broader conceptual, theoretical, and methodological framework. Without such a framework, oncology will collect piecemeal results, with scant dialogue between the different scientific communities studying cancer. We argue that one important way forward in service of a more successful dialogue is through greater integration of applied sciences (experimental and clinical) with conceptual and theoretical approaches, informed by philosophical methods. By way of illustration, we explore six central themes: (i) the role of mutations in cancer; (ii) the clonal evolution of cancer cells; (iii) the relationship between cancer and multicellularity; (iv) the tumour microenvironment; (v) the immune system; and (vi) stem cells. In each case, we examine open questions in the scientific literature through a philosophical methodology and show the benefit of such a synergy for the scientific and medical understanding of cancer.
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Affiliation(s)
- Thomas Pradeu
- CNRS UMR5164 ImmunoConcEpT, University of Bordeaux, 146 rue Leo Saignat, Bordeaux 33076, France
- CNRS UMR8590, Institut d’Histoire et Philosophie des Sciences et des Technique, University Paris I Panthéon-Sorbonne, 13 rue du Four, Paris 75006, France
| | - Bertrand Daignan-Fornier
- CNRS UMR 5095 Institut de Biochimie et Génétique Cellulaires, University of Bordeaux, 1 rue Camille St Saens, Bordeaux 33077, France
| | - Andrew Ewald
- Departments of Cell Biology and Oncology, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Pierre-Luc Germain
- Department of Health Sciences and Technology, Institute for Neurosciences, Eidgenössische Technische Hochschule (ETH) Zürich, Universitätstrasse 2, Zürich 8092, Switzerland
- Department of Molecular Life Sciences, Laboratory of Statistical Bioinformatics, Universität Zürich, Winterthurerstrasse 190, Zurich 8057, Switzerland
| | - Samir Okasha
- Department of Philosophy, University of Bristol, Cotham House, Bristol, BS6 6JL, UK
| | - Anya Plutynski
- Department of Philosophy, Washington University in St. Louis, and Associate with Division of Biology and Biomedical Sciences, St. Louis, MO 63105, USA
| | - Sébastien Benzekry
- Computational Pharmacology and Clinical Oncology (COMPO) Unit, Inria Sophia Antipolis-Méditerranée, Cancer Research Center of Marseille, Inserm UMR1068, CNRS UMR7258, Aix Marseille University UM105, 27, bd Jean Moulin, Marseille 13005, France
| | - Marta Bertolaso
- Research Unit of Philosophy of Science and Human Development, Università Campus Bio-Medico di Roma, Via Àlvaro del Portillo, 21-00128, Rome, Italy
- Centre for Cancer Biomarkers, University of Bergen, Bergen 5007, Norway
| | - Mina Bissell
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA 94720, USA
| | - Joel S. Brown
- Department of Integrated Mathematical Oncology, Moffitt Cancer Center, Tampa, FL, USA
| | - Benjamin Chin-Yee
- Division of Hematology, Department of Medicine, Schulich School of Medicine and Dentistry, Western University, 800 Commissioners Rd E, London, ON, Canada
- Rotman Institute of Philosophy, Western University, 1151 Richmond Street North, London, ON, Canada
| | - Ian Chin-Yee
- Department of Pathology and Laboratory Medicine, Schulich School of Medicine and Dentistry, Western University, 800 Commissioners Rd E, London, ON, Canada
| | - Hans Clevers
- Pharma, Research and Early Development (pRED) of F. Hoffmann-La Roche Ltd, Grenzacherstrasse 124, Basel 4070, Switzerland
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center, Uppsalalaan 8, Utrecht 3584 CT, The Netherlands
| | - Laurent Cognet
- CNRS UMR 5298, Laboratoire Photonique Numérique et Nanosciences, University of Bordeaux, Rue François Mitterrand, Talence 33400, France
| | - Marie Darrason
- Department of Pneumology and Thoracic Oncology, University Hospital of Lyon, 165 Chem. du Grand Revoyet, 69310 Pierre Bénite, Lyon, France
- Lyon Institute of Philosophical Research, Lyon 3 Jean Moulin University, 1 Av. des Frères Lumière, Lyon 69007, France
| | - Emmanuel Farge
- Mechanics and Genetics of Embryonic and Tumor Development group, Institut Curie, CNRS, UMR168, Inserm, Centre Origines et conditions d’apparition de la vie (OCAV) Paris Sciences Lettres Research University, Sorbonne University, Institut Curie, 11 rue Pierre et Marie Curie, Paris 75005, France
| | - Jean Feunteun
- INSERM U981, Gustave Roussy, 114 Rue Edouard Vaillant, Villejuif 94800, France
| | - Jérôme Galon
- INSERM UMRS1138, Integrative Cancer Immunology, Cordelier Research Center, Sorbonne Université, Université Paris Cité, 15 rue de l’École de Médecine, Paris 75006, France
| | - Elodie Giroux
- Lyon Institute of Philosophical Research, Lyon 3 Jean Moulin University, 1 Av. des Frères Lumière, Lyon 69007, France
| | - Sara Green
- Section for History and Philosophy of Science, Department of Science Education, University of Copenhagen, Rådmandsgade 64, Copenhagen 2200, Denmark
| | - Fridolin Gross
- CNRS UMR5164 ImmunoConcEpT, University of Bordeaux, 146 rue Leo Saignat, Bordeaux 33076, France
| | - Fanny Jaulin
- INSERM U1279, Gustave Roussy, 114 Rue Edouard Vaillant, Villejuif 94800, France
| | - Rob Knight
- Department of Bioengineering, University of California San Diego, 3223 Voigt Dr, La Jolla, CA 92093, USA
- Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Ezio Laconi
- Department of Biomedical Sciences, School of Medicine, University of Cagliari, Via Università 40, Cagliari 09124, Italy
| | - Nicolas Larmonier
- CNRS UMR5164 ImmunoConcEpT, University of Bordeaux, 146 rue Leo Saignat, Bordeaux 33076, France
| | - Carlo Maley
- Arizona Cancer Evolution Center, Arizona State University, 427 East Tyler Mall, Tempe, AZ 85287, USA
- School of Life Sciences, Arizona State University, 427 East Tyler Mall, Tempe, AZ 85287, USA
- Biodesign Center for Biocomputing, Security and Society, Arizona State University, 1001 S McAllister Ave, Tempe, AZ 85287, USA
- Biodesign Center for Mechanisms of Evolution, Arizona State University, 1001 S McAllister Ave, Tempe, AZ 85287, USA
- Center for Evolution and Medicine, Arizona State University, 427 East Tyler Mall, Tempe, AZ 85287, USA
| | - Alberto Mantovani
- Department of Biomedical Sciences, Humanitas University, 4 Via Rita Levi Montalcini, 20090 Pieve Emanuele, Milan, Italy
- Department of Immunology and Inflammation, Istituto Clinico Humanitas Humanitas Cancer Center (IRCCS) Humanitas Research Hospital, Via Manzoni 56, Rozzano, Milan 20089, Italy
- The William Harvey Research Institute, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Violaine Moreau
- INSERM UMR1312, Bordeaux Institute of Oncology (BRIC), University of Bordeaux, 146 Rue Léo Saignat, Bordeaux 33076, France
| | - Pierre Nassoy
- CNRS UMR 5298, Laboratoire Photonique Numérique et Nanosciences, University of Bordeaux, Rue François Mitterrand, Talence 33400, France
| | - Elena Rondeau
- INSERM U1111, ENS Lyon and Centre International de Recherche en Infectionlogie (CIRI), 46 Allée d’Italie, Lyon 69007, France
| | - David Santamaria
- Molecular Mechanisms of Cancer Program, Centro de Investigación del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC)-University of Salamanca, Salamanca 37007, Spain
| | - Catherine M. Sawai
- INSERM UMR1312, Bordeaux Institute of Oncology (BRIC), University of Bordeaux, 146 Rue Léo Saignat, Bordeaux 33076, France
| | - Andrei Seluanov
- Department of Biology and Medicine, University of Rochester, Rochester, NY 14627, USA
| | | | - Vanja Sisirak
- CNRS UMR5164 ImmunoConcEpT, University of Bordeaux, 146 rue Leo Saignat, Bordeaux 33076, France
| | - Eric Solary
- INSERM U1287, Gustave Roussy, 114 Rue Edouard Vaillant, Villejuif 94800, France
- Département d’hématologie, Gustave Roussy, 114 Rue Edouard Vaillant, Villejuif 94800, France
- Université Paris-Saclay, Faculté de Médecine, 63 Rue Gabriel Péri, Le Kremlin-Bicêtre 94270, France
| | - Sarah Yvonnet
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Blegdamsvej 3B, Copenhagen DK-2200, Denmark
| | - Lucie Laplane
- CNRS UMR8590, Institut d’Histoire et Philosophie des Sciences et des Technique, University Paris I Panthéon-Sorbonne, 13 rue du Four, Paris 75006, France
- INSERM U1287, Gustave Roussy, 114 Rue Edouard Vaillant, Villejuif 94800, France
- Center for Biology and Society, College of Liberal Arts and Sciences, Arizona State University, 1100 S McAllister Ave, Tempe, AZ 85281, USA
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40
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Baron M, Tagore M, Wall P, Zheng F, Barkley D, Yanai I, Yang J, Kiuru M, White RM, Ideker T. Desmosome mutations impact the tumor microenvironment to promote melanoma proliferation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.19.558457. [PMID: 37786690 PMCID: PMC10541613 DOI: 10.1101/2023.09.19.558457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
Desmosomes are transmembrane protein complexes that contribute to cell-cell adhesion in epithelia and other tissues. Here, we report the discovery of frequent genetic alterations in the desmosome in human cancers, with the strongest signal seen in cutaneous melanoma where desmosomes are mutated in over 70% of cases. In primary but not metastatic melanoma biopsies, the burden of coding mutations on desmosome genes associates with a strong reduction in desmosome gene expression. Analysis by spatial transcriptomics suggests that these expression decreases occur in keratinocytes in the microenvironment rather than in primary melanoma tumor cells. In further support of a microenvironmental origin, we find that loss-of-function knockdowns of the desmosome in keratinocytes yield markedly increased proliferation of adjacent melanocytes in keratinocyte/melanocyte co-cultures. Thus, gradual accumulation of desmosome mutations in neighboring cells may prime melanocytes for neoplastic transformation.
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Affiliation(s)
- Maayan Baron
- Department of Medicine, University of California San Diego, La Jolla, CA USA
| | - Mohita Tagore
- Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Patrick Wall
- Department of Medicine, University of California San Diego, La Jolla, CA USA
| | - Fan Zheng
- Department of Medicine, University of California San Diego, La Jolla, CA USA
| | - Dalia Barkley
- Institute for Computational Medicine, NYU School of Medicine, New York, NY USA
| | - Itai Yanai
- Institute for Computational Medicine, NYU School of Medicine, New York, NY USA
| | - Jing Yang
- Department of Pharmacology, University of California San Diego, La Jolla, CA USA
| | - Maija Kiuru
- Depts. of Dermatology and Pathology, University of California Davis, Sacramento, CA USA
| | - Richard M White
- Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Trey Ideker
- Department of Medicine, University of California San Diego, La Jolla, CA USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA USA
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41
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Panzeri I, Fagnocchi L, Apostle S, Tompkins M, Wolfrum E, Madaj Z, Hostetter G, Liu Y, Schaefer K, Chih-Hsiang Y, Bergsma A, Drougard A, Dror E, Chandler D, Schramek D, Triche TJ, Pospisilik JA. Developmental priming of cancer susceptibility. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.12.557446. [PMID: 37745326 PMCID: PMC10515831 DOI: 10.1101/2023.09.12.557446] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
DNA mutations are necessary drivers of cancer, yet only a small subset of mutated cells go on to cause the disease. To date, the mechanisms that determine which rare subset of cells transform and initiate tumorigenesis remain unclear. Here, we take advantage of a unique model of intrinsic developmental heterogeneity (Trim28+/D9) and demonstrate that stochastic early life epigenetic variation can trigger distinct cancer-susceptibility 'states' in adulthood. We show that these developmentally primed states are characterized by differential methylation patterns at typically silenced heterochromatin, and that these epigenetic signatures are detectable as early as 10 days of age. The differentially methylated loci are enriched for genes with known oncogenic potential. These same genes are frequently mutated in human cancers, and their dysregulation correlates with poor prognosis. These results provide proof-of-concept that intrinsic developmental heterogeneity can prime individual, life-long cancer risk.
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Affiliation(s)
- Ilaria Panzeri
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
- Department of Epigenetics, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Luca Fagnocchi
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
| | - Stefanos Apostle
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
| | - Megan Tompkins
- Vivarium and Transgenics Core, Van Andel Institute, Grand Rapids, MI, USA
| | - Emily Wolfrum
- Bioinformatics and Biostatistics Core, Van Andel Institute, Grand Rapids, MI, USA
| | - Zachary Madaj
- Bioinformatics and Biostatistics Core, Van Andel Institute, Grand Rapids, MI, USA
| | - Galen Hostetter
- Pathology and Biorepository Core, Van Andel Institute, Grand Rapids, MI, USA
| | - Yanqing Liu
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
| | - Kristen Schaefer
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
- Department of Genetics and Genome Science, Case Western Reserve University, Cleveland, Ohio, USA
| | - Yang Chih-Hsiang
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
- Department of Epigenetics, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA USA
| | - Alexis Bergsma
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
- Parkinson’s Disease Center, Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI, USA
| | - Anne Drougard
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
| | - Erez Dror
- Department of Epigenetics, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | | | - Darrell Chandler
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
| | - Daniel Schramek
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Timothy J. Triche
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
| | - J. Andrew Pospisilik
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
- Department of Epigenetics, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
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42
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Borgsmüller N, Valecha M, Kuipers J, Beerenwinkel N, Posada D. Single-cell phylogenies reveal changes in the evolutionary rate within cancer and healthy tissues. CELL GENOMICS 2023; 3:100380. [PMID: 37719146 PMCID: PMC10504633 DOI: 10.1016/j.xgen.2023.100380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 05/03/2023] [Accepted: 07/18/2023] [Indexed: 09/19/2023]
Abstract
Cell lineages accumulate somatic mutations during organismal development, potentially leading to pathological states. The rate of somatic evolution within a cell population can vary due to multiple factors, including selection, a change in the mutation rate, or differences in the microenvironment. Here, we developed a statistical test called the Poisson Tree (PT) test to detect varying evolutionary rates among cell lineages, leveraging the phylogenetic signal of single-cell DNA sequencing (scDNA-seq) data. We applied the PT test to 24 healthy and cancer samples, rejecting a constant evolutionary rate in 11 out of 15 cancer and five out of nine healthy scDNA-seq datasets. In six cancer datasets, we identified subclonal mutations in known driver genes that could explain the rate accelerations of particular cancer lineages. Our findings demonstrate the efficacy of scDNA-seq for studying somatic evolution and suggest that cell lineages often evolve at different rates within cancer and healthy tissues.
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Affiliation(s)
- Nico Borgsmüller
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, 4058 Basel, Switzerland
| | - Monica Valecha
- CINBIO, Universidade de Vigo, 36310 Vigo, Spain
- Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Vigo, Spain
| | - Jack Kuipers
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, 4058 Basel, Switzerland
| | - Niko Beerenwinkel
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, 4058 Basel, Switzerland
| | - David Posada
- CINBIO, Universidade de Vigo, 36310 Vigo, Spain
- Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Vigo, Spain
- Department of Biochemistry, Genetics, and Immunology, Universidade de Vigo, 36310 Vigo, Spain
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43
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D’Arino A, Caputo S, Eibenschutz L, Piemonte P, Buccini P, Frascione P, Bellei B. Skin Cancer Microenvironment: What We Can Learn from Skin Aging? Int J Mol Sci 2023; 24:14043. [PMID: 37762344 PMCID: PMC10531546 DOI: 10.3390/ijms241814043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 08/30/2023] [Accepted: 09/09/2023] [Indexed: 09/29/2023] Open
Abstract
Aging is a natural intrinsic process associated with the loss of fibrous tissue, a slower cell turnover, and a reduction in immune system competence. In the skin, the continuous exposition of environmental factors superimposes extrinsic damage, mainly due to ultraviolet radiation causing photoaging. Although not usually considered a pathogenic event, photoaging affects cutaneous biology, increasing the risk of skin carcinogenesis. At the cellular level, aging is typified by the rise of senescence cells a condition characterized by reduced or absent capacity to proliferate and aberrant hyper-secretory activity. Senescence has a double-edged sword in cancer biology given that senescence prevents the uncontrolled proliferation of damaged cells and favors their clearance by paracrine secretion. Nevertheless, the cumulative insults and the poor clearance of injured cells in the elderly increase cancer incidence. However, there are not conclusive data proving that aged skin represents a permissive milieu for tumor onset. On the other hand, tumor cells are capable of activating resident fibroblasts onto a pro-tumorigenic phenotype resembling those of senescent fibroblasts suggesting that aged fibroblasts might facilitate cancer progression. This review discusses changes that occur during aging that can prime neoplasm or increase the aggressiveness of melanoma and non-melanoma skin cancer.
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Affiliation(s)
- Andrea D’Arino
- Oncologic and Preventative Dermatology, San Gallicano Dermatological Institute, Istituto di Ricovero e Cura a Carattere Scientifico IRCCS, 00141 Rome, Italy
| | - Silvia Caputo
- Laboratory of Cutaneous Physiopathology and Integrated Center of Metabolomics Research, San Gallicano Dermatological Institute, Istituto di Ricovero e Cura a Carattere Scientifico IRCCS, 00141 Rome, Italy
| | - Laura Eibenschutz
- Oncologic and Preventative Dermatology, San Gallicano Dermatological Institute, Istituto di Ricovero e Cura a Carattere Scientifico IRCCS, 00141 Rome, Italy
| | - Paolo Piemonte
- Oncologic and Preventative Dermatology, San Gallicano Dermatological Institute, Istituto di Ricovero e Cura a Carattere Scientifico IRCCS, 00141 Rome, Italy
| | - Pierluigi Buccini
- Oncologic and Preventative Dermatology, San Gallicano Dermatological Institute, Istituto di Ricovero e Cura a Carattere Scientifico IRCCS, 00141 Rome, Italy
| | - Pasquale Frascione
- Oncologic and Preventative Dermatology, San Gallicano Dermatological Institute, Istituto di Ricovero e Cura a Carattere Scientifico IRCCS, 00141 Rome, Italy
| | - Barbara Bellei
- Laboratory of Cutaneous Physiopathology and Integrated Center of Metabolomics Research, San Gallicano Dermatological Institute, Istituto di Ricovero e Cura a Carattere Scientifico IRCCS, 00141 Rome, Italy
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44
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Marongiu F, Cheri S, Laconi E. Clones of aging: When better fitness can be dangerous. Eur J Cell Biol 2023; 102:151340. [PMID: 37423036 DOI: 10.1016/j.ejcb.2023.151340] [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: 02/28/2023] [Revised: 05/29/2023] [Accepted: 07/05/2023] [Indexed: 07/11/2023] Open
Abstract
The biological and clinical significance of aberrant clonal expansions in aged tissues is being intensely discussed. Evidence is accruing that these clones often result from the normal dynamics of cell turnover in our tissues. The aged tissue microenvironment is prone to favour the emergence of specific clones with higher fitness partly because of an overall decline in cell intrinsic regenerative potential of surrounding counterparts. Thus, expanding clones in aged tissues need not to be mechanistically associated with the development of cancer, albeit this is a possibility. We suggest that growth pattern is a critical phenotypic attribute that impacts on the fate of such clonal proliferations. The acquisition of a better proliferative fitness, coupled with a defect in tissue pattern formation, could represent a dangerous mix setting the stage for their evolution towards neoplasia.
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Affiliation(s)
- Fabio Marongiu
- Department of Biomedical Sciences, University of Cagliari, Italy
| | - Samuele Cheri
- Department of Biomedical Sciences, University of Cagliari, Italy
| | - Ezio Laconi
- Department of Biomedical Sciences, University of Cagliari, Italy.
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45
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Igarashi T, Mazevet M, Yasuhara T, Yano K, Mochizuki A, Nishino M, Yoshida T, Yoshida Y, Takamatsu N, Yoshimi A, Shiraishi K, Horinouchi H, Kohno T, Hamamoto R, Adachi J, Zou L, Shiotani B. An ATR-PrimPol pathway confers tolerance to oncogenic KRAS-induced and heterochromatin-associated replication stress. Nat Commun 2023; 14:4991. [PMID: 37591859 PMCID: PMC10435487 DOI: 10.1038/s41467-023-40578-2] [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: 05/11/2023] [Accepted: 08/02/2023] [Indexed: 08/19/2023] Open
Abstract
Activation of the KRAS oncogene is a source of replication stress, but how this stress is generated and how it is tolerated by cancer cells remain poorly understood. Here we show that induction of KRASG12V expression in untransformed cells triggers H3K27me3 and HP1-associated chromatin compaction in an RNA transcription dependent manner, resulting in replication fork slowing and cell death. Furthermore, elevated ATR expression is necessary and sufficient for tolerance of KRASG12V-induced replication stress to expand replication stress-tolerant cells (RSTCs). PrimPol is phosphorylated at Ser255, a potential Chk1 substrate site, under KRASG12V-induced replication stress and promotes repriming to maintain fork progression and cell survival in an ATR/Chk1-dependent manner. However, ssDNA gaps are generated at heterochromatin by PrimPol-dependent repriming, leading to genomic instability. These results reveal a role of ATR-PrimPol in enabling precancerous cells to survive KRAS-induced replication stress and expand clonally with accumulation of genomic instability.
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Affiliation(s)
- Taichi Igarashi
- Laboratory of Genome Stress Signaling, National Cancer Center Research Institute, Chuo-ku, Tokyo, 104-0045, Japan
- Department of Biosciences, School of Science, Kitasato University, Minami-ku, Sagamihara-city, Kanagawa, 252-0373, Japan
| | - Marianne Mazevet
- Laboratory of Genome Stress Signaling, National Cancer Center Research Institute, Chuo-ku, Tokyo, 104-0045, Japan
| | - Takaaki Yasuhara
- Department of Late Effects Studies, Radiation Biology Center, Graduate School of Biostudies, Kyoto University, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Kimiyoshi Yano
- Laboratory of Genome Stress Signaling, National Cancer Center Research Institute, Chuo-ku, Tokyo, 104-0045, Japan
| | - Akifumi Mochizuki
- Division of Genome Biology, National Cancer Center Research Institute, Chuo-ku, Tokyo, 104-0045, Japan
- Department of Respiratory Medicine, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo, 113-8519, Japan
| | - Makoto Nishino
- Division of Genome Biology, National Cancer Center Research Institute, Chuo-ku, Tokyo, 104-0045, Japan
| | - Tatsuya Yoshida
- Department of Thoracic Oncology, National Cancer Center Hospital, Chuo-ku, Tokyo, 104-0045, Japan
| | - Yukihiro Yoshida
- Department of Thoracic Surgery, National Cancer Center Hospital, Chuo-ku, Tokyo, 104-0045, Japan
| | - Nobuhiko Takamatsu
- Department of Biosciences, School of Science, Kitasato University, Minami-ku, Sagamihara-city, Kanagawa, 252-0373, Japan
| | - Akihide Yoshimi
- Department of Biosciences, School of Science, Kitasato University, Minami-ku, Sagamihara-city, Kanagawa, 252-0373, Japan
- Division of Cancer RNA Research, National Cancer Center Research Institute, Chuo-ku, Tokyo, 104-0045, Japan
| | - Kouya Shiraishi
- Division of Genome Biology, National Cancer Center Research Institute, Chuo-ku, Tokyo, 104-0045, Japan
- Department of Clinical Genomics, National Cancer Center Research Institute, Chuo-ku, Tokyo, 104-0045, Japan
| | - Hidehito Horinouchi
- Department of Thoracic Oncology, National Cancer Center Hospital, Chuo-ku, Tokyo, 104-0045, Japan
| | - Takashi Kohno
- Division of Genome Biology, National Cancer Center Research Institute, Chuo-ku, Tokyo, 104-0045, Japan
| | - Ryuji Hamamoto
- Division of Medical AI Research and Development, National Cancer Center Research Institute, Chuo-ku, Tokyo, 104-0045, Japan
| | - Jun Adachi
- Laboratory of Proteomics for Drug Discovery, Laboratory of Clinical and Analytical Chemistry, Center for Drug Design Research, National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki-city, Osaka, 567-0085, Japan
| | - Lee Zou
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA, 02129, USA
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02115, USA
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, 27708, USA
| | - Bunsyo Shiotani
- Laboratory of Genome Stress Signaling, National Cancer Center Research Institute, Chuo-ku, Tokyo, 104-0045, Japan.
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46
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Yao P, Xiao P, Huang Z, Tang M, Tang X, Yang G, Zhang Q, Li X, Yang Z, Xie C, Gong H, Wang G, Liu Y, Wang X, Li H, Jia D, Dai L, Chen L, Chen C, Liu Y, Xiao H, Zhang Y, Wang Y. Protein-level mutant p53 reporters identify druggable rare precancerous clones in noncancerous tissues. NATURE CANCER 2023; 4:1176-1192. [PMID: 37537298 DOI: 10.1038/s43018-023-00608-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 06/29/2023] [Indexed: 08/05/2023]
Abstract
Detecting and targeting precancerous cells in noncancerous tissues is a major challenge for cancer prevention. Massive stabilization of mutant p53 (mutp53) proteins is a cancer-specific event that could potentially mark precancerous cells, yet in vivo protein-level mutp53 reporters are lacking. Here we developed two transgenic protein-level mutp53 reporters, p53R172H-Akaluc and p53-mCherry, that faithfully mimic the dynamics and function of mutp53 proteins in vivo. Using these reporters, we identified and traced rare precancerous clones in deep noncancerous tissues in various cancer models. In classic mutp53-driven thymic lymphoma models, we found that precancerous clones exhibit broad chromosome number variations, upregulate precancerous stage-specific genes such as Ybx3 and enhance amino acid transport and metabolism. Inhibiting amino acid transporters downstream of Ybx3 at the early but not late stage effectively suppresses tumorigenesis and prolongs survival. Together, these protein-level mutp53 reporters reveal undercharacterized features and vulnerabilities of precancerous cells during early tumorigenesis, paving the way for precision cancer prevention.
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Affiliation(s)
- Pengle Yao
- Department of Neurosurgery, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Peng Xiao
- Department of Neurosurgery, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Zongyao Huang
- Department of Neurosurgery, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Min Tang
- Department of Neurosurgery, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Xiwen Tang
- Department of Neurosurgery, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Gaoxia Yang
- Department of Neurosurgery, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Qi Zhang
- Department of Neurosurgery, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Xinpei Li
- Department of Neurosurgery, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Zhengnan Yang
- Department of Neurosurgery, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Chuanxing Xie
- Department of Neurosurgery, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Hui Gong
- National Clinical Research Center for Geriatrics, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Guihua Wang
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University, Chengdu, China
| | - Yutong Liu
- Department of Neurosurgery, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Xiuxuan Wang
- National Clinical Research Center for Geriatrics, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Huifang Li
- Core Facilities of West China Hospital, Sichuan University, Chengdu, China
| | - Da Jia
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University, Chengdu, China
| | - Lunzhi Dai
- National Clinical Research Center for Geriatrics, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Lu Chen
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University, Chengdu, China
| | - Chong Chen
- Department of Neurosurgery, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Yu Liu
- Department of Neurosurgery, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Hengyi Xiao
- National Clinical Research Center for Geriatrics, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Yan Zhang
- National Clinical Research Center for Geriatrics, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Yuan Wang
- Department of Neurosurgery, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China.
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47
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Nishimura T, Kakiuchi N, Yoshida K, Sakurai T, Kataoka TR, Kondoh E, Chigusa Y, Kawai M, Sawada M, Inoue T, Takeuchi Y, Maeda H, Baba S, Shiozawa Y, Saiki R, Nakagawa MM, Nannya Y, Ochi Y, Hirano T, Nakagawa T, Inagaki-Kawata Y, Aoki K, Hirata M, Nanki K, Matano M, Saito M, Suzuki E, Takada M, Kawashima M, Kawaguchi K, Chiba K, Shiraishi Y, Takita J, Miyano S, Mandai M, Sato T, Takeuchi K, Haga H, Toi M, Ogawa S. Evolutionary histories of breast cancer and related clones. Nature 2023; 620:607-614. [PMID: 37495687 PMCID: PMC10432280 DOI: 10.1038/s41586-023-06333-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 06/15/2023] [Indexed: 07/28/2023]
Abstract
Recent studies have documented frequent evolution of clones carrying common cancer mutations in apparently normal tissues, which are implicated in cancer development1-3. However, our knowledge is still missing with regard to what additional driver events take place in what order, before one or more of these clones in normal tissues ultimately evolve to cancer. Here, using phylogenetic analyses of multiple microdissected samples from both cancer and non-cancer lesions, we show unique evolutionary histories of breast cancers harbouring der(1;16), a common driver alteration found in roughly 20% of breast cancers. The approximate timing of early evolutionary events was estimated from the mutation rate measured in normal epithelial cells. In der(1;16)(+) cancers, the derivative chromosome was acquired from early puberty to late adolescence, followed by the emergence of a common ancestor by the patient's early 30s, from which both cancer and non-cancer clones evolved. Replacing the pre-existing mammary epithelium in the following years, these clones occupied a large area within the premenopausal breast tissues by the time of cancer diagnosis. Evolution of multiple independent cancer founders from the non-cancer ancestors was common, contributing to intratumour heterogeneity. The number of driver events did not correlate with histology, suggesting the role of local microenvironments and/or epigenetic driver events. A similar evolutionary pattern was also observed in another case evolving from an AKT1-mutated founder. Taken together, our findings provide new insight into how breast cancer evolves.
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Affiliation(s)
- Tomomi Nishimura
- Department of Pathology and Tumour Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Department of Next-generation Clinical Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Department of Breast Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Nobuyuki Kakiuchi
- Department of Pathology and Tumour Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- The Hakubi Center for Advanced Research, Kyoto University, Kyoto, Japan
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Kenichi Yoshida
- Department of Pathology and Tumour Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Division of Cancer Evolution, National Cancer Center Research Institute, Tokyo, Japan
| | - Takaki Sakurai
- Department of Diagnostic Pathology, Kyoto University Hospital, Kyoto, Japan
- Department of Diagnostic Pathology, Osaka Red Cross Hospital, Osaka, Japan
| | - Tatsuki R Kataoka
- Department of Diagnostic Pathology, Kyoto University Hospital, Kyoto, Japan
- Department of Pathology, Iwate Medical University, Iwate, Japan
| | - Eiji Kondoh
- Department of Gynecology and Obstetrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Department of Obstetrics and Gynecology Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Yoshitsugu Chigusa
- Department of Gynecology and Obstetrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Masahiko Kawai
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | | | | | - Yasuhide Takeuchi
- Department of Pathology and Tumour Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Department of Diagnostic Pathology, Kyoto University Hospital, Kyoto, Japan
| | - Hirona Maeda
- Department of Pathology and Tumour Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Department of Diagnostic Pathology, Kyoto University Hospital, Kyoto, Japan
| | - Satoko Baba
- Pathology Project for Molecular Targets, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
- Division of Pathology, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
- Department of Pathology, Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Yusuke Shiozawa
- Department of Pathology and Tumour Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Ryunosuke Saiki
- Department of Pathology and Tumour Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Masahiro M Nakagawa
- Department of Pathology and Tumour Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Department of Next-generation Clinical Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yasuhito Nannya
- Department of Pathology and Tumour Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Division of Hematopoietic Disease Control, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Yotaro Ochi
- Department of Pathology and Tumour Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Tomonori Hirano
- Department of Pathology and Tumour Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan
| | - Tomoe Nakagawa
- Department of Pathology and Tumour Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan
| | - Yukiko Inagaki-Kawata
- Department of Pathology and Tumour Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Department of Breast Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Kosuke Aoki
- Department of Pathology and Tumour Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Masahiro Hirata
- Department of Diagnostic Pathology, Kyoto University Hospital, Kyoto, Japan
| | - Kosaku Nanki
- Department of Organoid Medicine, Sakaguchi Laboratory, Keio University School of Medicine, Tokyo, Japan
| | - Mami Matano
- Department of Organoid Medicine, Sakaguchi Laboratory, Keio University School of Medicine, Tokyo, Japan
| | - Megumu Saito
- Department of Organoid Medicine, Sakaguchi Laboratory, Keio University School of Medicine, Tokyo, Japan
- Osaka Research Center for Drug Discovery, Otsuka Pharmaceutical Company, Limited, Osaka, Japan
| | - Eiji Suzuki
- Department of Breast Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Breast Surgery Department, Kobe City Medical Center General Hospital, Hyogo, Japan
| | - Masahiro Takada
- Department of Breast Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Masahiro Kawashima
- Department of Breast Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Kosuke Kawaguchi
- Department of Breast Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Kenichi Chiba
- Division of Genome Analysis Platform Development, National Cancer Center Research Institute, Tokyo, Japan
| | - Yuichi Shiraishi
- Division of Genome Analysis Platform Development, National Cancer Center Research Institute, Tokyo, Japan
| | - Junko Takita
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Satoru Miyano
- Department of Integrated Analytics, M&D Data Science Center, Tokyo Medical and Dental University, Tokyo, Japan
- Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Masaki Mandai
- Department of Gynecology and Obstetrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Toshiro Sato
- Department of Organoid Medicine, Sakaguchi Laboratory, Keio University School of Medicine, Tokyo, Japan
| | - Kengo Takeuchi
- Pathology Project for Molecular Targets, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
- Division of Pathology, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
- Department of Pathology, Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Hironori Haga
- Department of Diagnostic Pathology, Kyoto University Hospital, Kyoto, Japan
| | - Masakazu Toi
- Department of Breast Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Seishi Ogawa
- Department of Pathology and Tumour Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan.
- Department of Medicine, Centre for Haematology and Regenerative Medicine, Karolinska Institute, Stockholm, Sweden.
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48
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Rane JK, Frankell AM, Weeden CE, Swanton C. Clonal Evolution in Healthy and Premalignant Tissues: Implications for Early Cancer Interception Strategies. Cancer Prev Res (Phila) 2023; 16:369-378. [PMID: 36930945 PMCID: PMC7614725 DOI: 10.1158/1940-6207.capr-22-0469] [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: 01/13/2023] [Revised: 02/17/2023] [Accepted: 03/14/2023] [Indexed: 03/19/2023]
Abstract
Histologically normal human tissues accumulate significant mutational burden with age. The extent and spectra of mutagenesis are comparable both in rapidly proliferating and post-mitotic tissues and in stem cells compared with their differentiated progeny. Some of these mutations provide increased fitness, giving rise to clones which, at times, can replace the entire surface area of tissues. Compared with cancer, somatic mutations in histologically normal tissues are primarily single-nucleotide variations. Interestingly though, the presence of these mutations and positive clonal selection in isolation remains a poor indicator of potential future cancer transformation in solid tissues. Common clonally expanded mutations in histologically normal tissues also do not always represent the most frequent early mutations in cancers of corresponding tissues, indicating differences in selection pressures. Preliminary evidence implies that stroma and immune system co-evolve with age, which may impact selection dynamics. In this review, we will explore the mutational landscape of histologically normal and premalignant human somatic tissues in detail and discuss cell-intrinsic and environmental factors that can determine the fate of positively selected mutations within them. Precisely pinpointing these determinants of cancer transformation would aid development of early cancer interventional and prevention strategies.
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Affiliation(s)
- Jayant K. Rane
- University College London Cancer Institute, London, UK
- Department of Clinical Oncology, University College London Hospitals, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Alexander M. Frankell
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Clare E. Weeden
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Charles Swanton
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Department of Medical Oncology, University College London Hospitals, London, UK
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49
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Aoyama M, Homma T, Koharazawa R, Suhara Y, Semba K. Effect of lonidamine derivatives on the inhibition of transformed cell area expansion. Biochem Biophys Rep 2023; 34:101480. [PMID: 37180755 PMCID: PMC10172748 DOI: 10.1016/j.bbrep.2023.101480] [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: 02/10/2023] [Revised: 04/13/2023] [Accepted: 04/26/2023] [Indexed: 05/16/2023] Open
Abstract
Expansion of transformed cell area is regulated by the surrounding nontransformed cells. Lonidamine (LND) was recently found to regulate transformed cell area expansion through suppressing the cell motility of nontransformed cells; however, the structure-activity relationship between LND and this inhibitory activity has yet to be elucidated. We synthesized several LND derivatives and evaluated their inhibitory activity against the expansion of transformed cell area and found that the halogenation pattern on the benzene ring moiety, the carboxylic acid moiety, and the overall hydrophobicity of the molecule were correlated with inhibition activity. We also found that the localization of the tight junction protein, zonula occludens-1 (ZO-1), in nontransformed cells was significantly altered after treatment with the LND derivatives that displayed inhibitory activity. Further studies with LND derivatives and monitoring the localization of ZO-1 may help to develop more active compounds for suppressing transformed cell area expansion and lead to new anticancer treatments.
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Affiliation(s)
- Megumi Aoyama
- Department of Life Science and Medical Bioscience, School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480, Japan
- Corresponding author.
| | - Taiki Homma
- Department of Bioscience and Engineering, College of Systems Engineering and Science, Shibaura Institute of Technology, 307 Fukasaku, Minuma-ku, Saitama, 337-8570, Japan
| | - Ryohto Koharazawa
- Department of Bioscience and Engineering, College of Systems Engineering and Science, Shibaura Institute of Technology, 307 Fukasaku, Minuma-ku, Saitama, 337-8570, Japan
| | - Yoshitomo Suhara
- Department of Bioscience and Engineering, College of Systems Engineering and Science, Shibaura Institute of Technology, 307 Fukasaku, Minuma-ku, Saitama, 337-8570, Japan
| | - Kentaro Semba
- Department of Life Science and Medical Bioscience, School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480, Japan
- Translational Research Center, Fukushima Medical University, 1 Hikarigaoka, Fukushima, 960-1295, Japan
- Corresponding author. Department of Life Science and Medical Bioscience, School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480, Japan.
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50
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Griffin GK, Booth CAG, Togami K, Chung SS, Ssozi D, Verga JA, Bouyssou JM, Lee YS, Shanmugam V, Hornick JL, LeBoeuf NR, Morgan EA, Bernstein BE, Hovestadt V, van Galen P, Lane AA. Ultraviolet radiation shapes dendritic cell leukaemia transformation in the skin. Nature 2023:10.1038/s41586-023-06156-8. [PMID: 37286599 PMCID: PMC10284703 DOI: 10.1038/s41586-023-06156-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 05/02/2023] [Indexed: 06/09/2023]
Abstract
Tumours most often arise from progression of precursor clones within a single anatomical niche. In the bone marrow, clonal progenitors can undergo malignant transformation to acute leukaemia, or differentiate into immune cells that contribute to disease pathology in peripheral tissues1-4. Outside the marrow, these clones are potentially exposed to a variety of tissue-specific mutational processes, although the consequences of this are unclear. Here we investigate the development of blastic plasmacytoid dendritic cell neoplasm (BPDCN)-an unusual form of acute leukaemia that often presents with malignant cells isolated to the skin5. Using tumour phylogenomics and single-cell transcriptomics with genotyping, we find that BPDCN arises from clonal (premalignant) haematopoietic precursors in the bone marrow. We observe that BPDCN skin tumours first develop at sun-exposed anatomical sites and are distinguished by clonally expanded mutations induced by ultraviolet (UV) radiation. A reconstruction of tumour phylogenies reveals that UV damage can precede the acquisition of alterations associated with malignant transformation, implicating sun exposure of plasmacytoid dendritic cells or committed precursors during BPDCN pathogenesis. Functionally, we find that loss-of-function mutations in Tet2, the most common premalignant alteration in BPDCN, confer resistance to UV-induced cell death in plasmacytoid, but not conventional, dendritic cells, suggesting a context-dependent tumour-suppressive role for TET2. These findings demonstrate how tissue-specific environmental exposures at distant anatomical sites can shape the evolution of premalignant clones to disseminated cancer.
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Affiliation(s)
- Gabriel K Griffin
- Department of Pathology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA.
| | | | - Katsuhiro Togami
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Sun Sook Chung
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Daniel Ssozi
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Hematology, Brigham and Women's Hospital, Boston, MA, USA
| | - Julia A Verga
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Juliette M Bouyssou
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Yoke Seng Lee
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Hematology, Brigham and Women's Hospital, Boston, MA, USA
| | - Vignesh Shanmugam
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Jason L Hornick
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Nicole R LeBoeuf
- Department of Dermatology, Center for Cutaneous Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Boston, MA, USA
| | | | - Bradley E Bernstein
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA
| | - Volker Hovestadt
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA.
| | - Peter van Galen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Division of Hematology, Brigham and Women's Hospital, Boston, MA, USA.
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA.
| | - Andrew A Lane
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA.
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