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Soon GST, Callea F, Burt AD, Cook S, Terracciano L, Ercan C, Dienes HP, Goodman ZD, Roberts EA, Clouston AD, Gouw ASH, Kleiner DE, Park YN, Chung T, Schirmacher P, Tiniakos D, Dimopoulou K, Weber A, Endhardt K, Torbenson M. Steatohepatitic Hepatocellular Carcinoma:A New Approach to Classifying Morphological Subtypes of Hepatocellular Carcinoma. Hum Pathol 2024:S0046-8177(24)00108-4. [PMID: 38876199 DOI: 10.1016/j.humpath.2024.06.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 06/07/2024] [Accepted: 06/11/2024] [Indexed: 06/16/2024]
Abstract
Histological subtyping of hepatocellular carcinoma (HCC) is challenging in the presence of histological heterogeneity, where distinctly different morphological patterns are present within the same tumor. Current approaches rely on percent cut-offs. We hypothesized that morphologic intratumor heterogeneity is a non-random biological feature and that incorporating recurrent patterns would improve histological subtyping of HCC. Resected HCC were studied and the overall frequency of morphologic intratumor heterogeneity was 45% in 242 specimens. Steatohepatitic HCC (SH-HCC) had the highest frequency of morphologic intratumor heterogeneity (91%); this was confirmed in additional cohorts of SH-HCC from different medical centers (overall frequency of 78% in SH-HCC). Morphologic intratumor heterogeneity in SH-HCC showed distinct and recurrent patterns that could be classified as early, intermediate, and advanced. Incorporating these patterns into the definition of SH-HCC allowed successful resolution of several persistent challenges: the problem of the best cut-off for subtyping SH-HCC, the problem of the relationship between SH-HCC and scirrhous HCC, and the classification for HCC with abundant microvesicular steatosis. This approach also clarified the relationship between SH-HCC and CTNNB1 mutations, showing that CTNNB1 mutations occur late in a subset of SH-HCC. In summary, there is a high frequency of morphologic intratumor heterogeneity in HCC. Incorporating this finding into histological subtyping resolved several persistent problems with the SH-HCC subtype.
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Affiliation(s)
- Gwyneth S T Soon
- Department of Pathology, National University Hospital, Singapore
| | | | - Alastair D Burt
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Sam Cook
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Luigi Terracciano
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20090 Pieve Emanuele -Milan, Italy; IRCCS Humanitas Research Hospital, Via Manzoni 56, 20089 Rozzano -Milan, Italy
| | - Caner Ercan
- Institute of Pathology and Medical Genetics, University Hospital Basel, Basel, Switzerland
| | - Hans-Peter Dienes
- Institute of Pathology, Meduniwien, Medical University of Vienna, 1090 Wien, Austria
| | - Zachary D Goodman
- Center for Liver Diseases, Inova Fairfax Hospital, Falls Church, VA 22042, United States of America
| | - Eve A Roberts
- Division of Gastroenterology, Hepatology and Nutrition, The Hospital for Sick Children, Toronto, Ontario M5G1X8, Canada
| | - Andrew D Clouston
- Centre for Liver Disease Research, School of Medicine (Southern), University of Queensland, Princess Alexandra Hospital, Ipswich Rd Woolloongabba 4109, Australia
| | - Annette S H Gouw
- Department of Pathology and Medical Biology, University Medical Center Groningen, 9700 RB Groningen, The Netherlands
| | - David E Kleiner
- Laboratory of Pathology, National Cancer Institute, National Institutes of Health, Bethesda, United States of America
| | - Young Nyun Park
- Department of Pathology, Yonsei University College of Medicine, Seoul Korea
| | - Taek Chung
- Department of Pathology, Yonsei University College of Medicine, Seoul Korea.
| | - Peter Schirmacher
- Institute of Pathology, University Hospital, Im Neuenheimer Feld 224, 69120 Heidelberg, Germany
| | - Dina Tiniakos
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom; Department of Pathology, Aretaieion Hospital, Medical School, National & Kapodistrian University of Athens, Athens, Greece
| | - Konstantina Dimopoulou
- Department of Pathology, Aretaieion Hospital, Medical School, National & Kapodistrian University of Athens, Athens, Greece
| | - Achim Weber
- Department of Pathology and Molecular Pathology, University Hospital Zurich and University of Zurich, Zurich, Switzerland
| | - Katharina Endhardt
- Department of Pathology and Molecular Pathology, University Hospital Zurich and University of Zurich, Zurich, Switzerland
| | - Michael Torbenson
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States of America.
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2
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Chen J, Kaya NA, Zhang Y, Kendarsari RI, Sekar K, Lee Chong S, Seshachalam VP, Ling WH, Jin Phua CZ, Lai H, Yang H, Lu B, Lim JQ, Ma S, Chew SC, Chua KP, Alvarez JJS, Wu L, Ooi L, Chung AYF, Cheow PC, Kam JH, Kow AWC, Ganpathi IS, Bunchaliew C, Thammasiri J, Koh PS, Ong DBL, Lim J, de Villa VH, Dela Cruz RD, Loh TJ, Wan WK, Leow WQ, Yang Y, Liu J, Skanderup AJ, Pang YH, Soon GST, Madhavan K, Lim TKH, Bonney G, Goh BKP, Chew V, Dan YY, Toh HC, Foo RSY, Tam WL, Zhai W, Chow PKH. A multimodal atlas of hepatocellular carcinoma reveals convergent evolutionary paths and 'bad apple' effect on clinical trajectory. J Hepatol 2024:S0168-8278(24)00352-0. [PMID: 38782118 DOI: 10.1016/j.jhep.2024.05.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Revised: 05/06/2024] [Accepted: 05/14/2024] [Indexed: 05/25/2024]
Abstract
BACKGROUND & AIMS Hepatocellular Carcinoma (HCC) is a highly fatal cancer characterized by high intra-tumor heterogeneity (ITH). A panoramic understanding of its tumor evolution, in relation to its clinical trajectory, may provide novel prognostic and treatment strategies. METHODS Through the Asia-Pacific Hepatocellular Carcinoma (AHCC) trials group (NCT03267641), we recruited one of the largest prospective cohorts of HCC with over 600 whole genome and transcriptome samples from 123 treatment-naïve patients. RESULTS Using a multi-region sampling approach, we revealed seven convergent genetic evolutionary paths governed by the early driver mutations, late copy number variations and viral integrations, which stratify patient clinical trajectories after surgical resection. Furthermore, such evolutionary paths shaped the molecular profiles, leading to distinct transcriptomic subtypes. Most significantly, although we found the coexistence of multiple transcriptomic subtypes within certain tumors, patient prognosis was best predicted by the most aggressive cell fraction of the tumor, rather than by overall degree of transcriptomic ITH level - a phenomenon we termed the 'bad apple' effect. Finally, we found that characteristics throughout early and late tumor evolution provide significant and complementary prognostic power in predicting patient survival. CONCLUSIONS Taken together, our study generated a comprehensive landscape of evolutionary history for HCC and provided a rich multi-omics resource for understanding tumor heterogeneity and clinical trajectories. CLINICAL TRIAL NUMBER NCT03267641 (Observational cohort) IMPACT AND IMPLICATIONS: This prospective study, utilizing comprehensive multi-sector, multi-omics sequencing and clinical data from surgically resected HCC, reveals critical insights into the role of tumor evolution and intra-tumor heterogeneity (ITH) in determining the prognosis of Hepatocellular Carcinoma (HCC). These findings are invaluable for oncology researchers and clinicians, as they underscore the influence of distinct evolutionary paths and the 'bad apple' effect, where the most aggressive tumor fraction dictates disease progression. These insights not only enhance prognostic accuracy post-surgical resection but also pave the way for developing personalized therapies tailored to specific tumor evolutionary and transcriptomic profiles. The co-existence of multiple sub-types within the same tumor prompts a re-appraisal of the utilities of depending on single samples to represent the entire tumor and suggests the need for clinical molecular imaging. This research thus marks a significant step forward in the clinical understanding and management of HCC, underscoring the importance of integrating tumor evolutionary dynamics and multi-omics biomarkers into therapeutic decision-making.
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Affiliation(s)
- Jianbin Chen
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore 138672, Republic of Singapore..
| | - Neslihan Arife Kaya
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore 138672, Republic of Singapore.; School of Biological Sciences, Nanyang Technological University, Singapore 637551, Republic of Singapore
| | - Ying Zhang
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore 138672, Republic of Singapore
| | - Raden Indah Kendarsari
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore 138672, Republic of Singapore
| | - Karthik Sekar
- Program in Clinical and Translational Liver Cancer Research, Division of Medical Science, National Cancer Center Singapore, Republic of Singapore
| | - Shay Lee Chong
- Program in Clinical and Translational Liver Cancer Research, Division of Medical Science, National Cancer Center Singapore, Republic of Singapore
| | - Veerabrahma Pratap Seshachalam
- Program in Clinical and Translational Liver Cancer Research, Division of Medical Science, National Cancer Center Singapore, Republic of Singapore
| | - Wen Huan Ling
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore 138672, Republic of Singapore.; Program in Clinical and Translational Liver Cancer Research, Division of Medical Science, National Cancer Center Singapore, Republic of Singapore
| | - Cheryl Zi Jin Phua
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore 138672, Republic of Singapore
| | - Hannah Lai
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore 138672, Republic of Singapore
| | - Hechuan Yang
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore 138672, Republic of Singapore.; Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, P.R. China
| | - Bingxin Lu
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore 138672, Republic of Singapore.; Cell & Developmental Biology, Division of Biosciences, Faculty of Life Sciences, Bloomsbury, London WC1E 6AP, UK
| | - Jia Qi Lim
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore 138672, Republic of Singapore
| | - Siming Ma
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore 138672, Republic of Singapore
| | - Sin Chi Chew
- Program in Clinical and Translational Liver Cancer Research, Division of Medical Science, National Cancer Center Singapore, Republic of Singapore
| | - Khi Pin Chua
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore 138672, Republic of Singapore
| | - Jacob Josiah Santiago Alvarez
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore 138672, Republic of Singapore
| | - Lingyan Wu
- Program in Clinical and Translational Liver Cancer Research, Division of Medical Science, National Cancer Center Singapore, Republic of Singapore
| | - London Ooi
- Department of Hepatopancreatobiliary and Transplant Surgery, Singapore General Hospital and National Cancer Centre Singapore, Republic of Singapore
| | - Alexander Yaw-Fui Chung
- Department of Hepatopancreatobiliary and Transplant Surgery, Singapore General Hospital and National Cancer Centre Singapore, Republic of Singapore
| | - Peng Chung Cheow
- Department of Hepatopancreatobiliary and Transplant Surgery, Singapore General Hospital and National Cancer Centre Singapore, Republic of Singapore
| | - Juinn Huar Kam
- Department of Hepatopancreatobiliary and Transplant Surgery, Singapore General Hospital and National Cancer Centre Singapore, Republic of Singapore
| | - Alfred Wei-Chieh Kow
- Division of Hepatobiliary & Pancreatic Surgery, Department of Surgery, University Surgical Cluster, National University Health System, Singapore 119228, Republic of Singapore
| | - Iyer Shridhar Ganpathi
- Division of Hepatobiliary & Pancreatic Surgery, Department of Surgery, University Surgical Cluster, National University Health System, Singapore 119228, Republic of Singapore
| | - Chairat Bunchaliew
- Hepato-Pancreato-Biliary Surgery Unit, Department of Surgery, National Cancer Institute, Bangkok, Thailand
| | | | - Peng Soon Koh
- Department of Surgery, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Diana Bee-Lan Ong
- Department of Surgery, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Jasmine Lim
- Department of Surgery, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Vanessa H de Villa
- Department of Surgery and Center for Liver Disease Management and Transplantation, The Medical City, Pasig City, Metro Manila, Philippines
| | | | - Tracy Jiezhen Loh
- Department of Pathology, Singapore General Hospital, Singapore 169608, Republic of Singapore
| | - Wei Keat Wan
- Department of Pathology, Singapore General Hospital, Singapore 169608, Republic of Singapore
| | - Wei Qiang Leow
- Department of Pathology, Singapore General Hospital, Singapore 169608, Republic of Singapore
| | - Yi Yang
- School of Data Science, The Chinese University of Hong Kong-Shenzhen, Shenzhen 518172, China
| | - Jin Liu
- School of Data Science, The Chinese University of Hong Kong-Shenzhen, Shenzhen 518172, China
| | - Anders Jacobsen Skanderup
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore 138672, Republic of Singapore
| | - Yin Huei Pang
- Department of Pathology, National University Health System, Singapore 119074, Republic of Singapore
| | - Gwyneth Shook Ting Soon
- Department of Pathology, National University Health System, Singapore 119074, Republic of Singapore
| | - Krishnakumar Madhavan
- Division of Hepatobiliary & Pancreatic Surgery, Department of Surgery, University Surgical Cluster, National University Health System, Singapore 119228, Republic of Singapore
| | - Tony Kiat-Hon Lim
- Department of Pathology, Singapore General Hospital, Singapore 169608, Republic of Singapore
| | - Glenn Bonney
- Division of Hepatobiliary & Pancreatic Surgery, Department of Surgery, University Surgical Cluster, National University Health System, Singapore 119228, Republic of Singapore
| | - Brian K P Goh
- Department of Hepatopancreatobiliary and Transplant Surgery, Singapore General Hospital and National Cancer Centre Singapore, Republic of Singapore
| | - Valerie Chew
- Translational Immunology Institute (TII), SingHealth Duke-NUS Academic Medical Centre, Singapore, Republic of Singapore
| | - Yock Young Dan
- Division of Gastroenterology and Hepatology, University Medicine Cluster, National University Hospital, Singapore, Republic of Singapore
| | - Han Chong Toh
- Division of Medical Oncology, National Cancer Center Singapore, 169610 Singapore, Republic of Singapore
| | - Roger Sik-Yin Foo
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore 138672, Republic of Singapore.; Cardiovascular Research Institute, National University of Singapore, National University Healthcare System, Singapore 119228, Republic of Singapore
| | - Wai Leong Tam
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore 138672, Republic of Singapore.; Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597, Republic of Singapore; Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Singapore 117599, Republic of Singapore; NUS Center for Cancer Research, Yong Loo Lin School of Medicine, National University Singapore, 14 Medical Drive, Singapore 117599, Republic of Singapore.
| | - Weiwei Zhai
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore 138672, Republic of Singapore.; Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, P.R. China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, P.R. China.
| | - Pierce Kah-Hoe Chow
- Department of Hepatopancreatobiliary and Transplant Surgery, Singapore General Hospital and National Cancer Centre Singapore, Republic of Singapore; Program in Clinical and Translational Liver Cancer Research, Division of Medical Science, National Cancer Center Singapore, Republic of Singapore; SingHealth-Duke-NUS Academic Surgery Program, Duke-NUS Graduate Medical School, Singapore 169857, Republic of Singapore.
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3
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Liu X, Zhang K, Kaya NA, Jia Z, Wu D, Chen T, Liu Z, Zhu S, Hillmer AM, Wuestefeld T, Liu J, Chan YS, Hu Z, Ma L, Jiang L, Zhai W. Tumor phylogeography reveals block-shaped spatial heterogeneity and the mode of evolution in Hepatocellular Carcinoma. Nat Commun 2024; 15:3169. [PMID: 38609353 PMCID: PMC11015015 DOI: 10.1038/s41467-024-47541-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 03/26/2024] [Indexed: 04/14/2024] Open
Abstract
Solid tumors are complex ecosystems with heterogeneous 3D structures, but the spatial intra-tumor heterogeneity (sITH) at the macroscopic (i.e., whole tumor) level is under-explored. Using a phylogeographic approach, we sequence genomes and transcriptomes from 235 spatially informed sectors across 13 hepatocellular carcinomas (HCC), generating one of the largest datasets for studying sITH. We find that tumor heterogeneity in HCC segregates into spatially variegated blocks with large genotypic and phenotypic differences. By dissecting the transcriptomic heterogeneity, we discover that 30% of patients had a "spatially competing distribution" (SCD), where different spatial blocks have distinct transcriptomic subtypes co-existing within a tumor, capturing the critical transition period in disease progression. Interestingly, the tumor regions with more advanced transcriptomic subtypes (e.g., higher cell cycle) often take clonal dominance with a wider geographic range, rejecting neutral evolution for SCD patients. Extending the statistical tests for detecting natural selection to many non-SCD patients reveal varying levels of selective signal across different tumors, implying that many evolutionary forces including natural selection and geographic isolation can influence the overall pattern of sITH. Taken together, tumor phylogeography unravels a dynamic landscape of sITH, pinpointing important evolutionary and clinical consequences of spatial heterogeneity in cancer.
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Affiliation(s)
- Xiaodong Liu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Ke Zhang
- Department of General Surgery, Beijing Ditan Hospital, Capital Medical University, No. 8, Jingshun East Street, Chaoyang District, Beijing, P.R. China
| | - Neslihan A Kaya
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - Zhe Jia
- Department of General Surgery, Beijing Ditan Hospital, Capital Medical University, No. 8, Jingshun East Street, Chaoyang District, Beijing, P.R. China
| | - Dafei Wu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Tingting Chen
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Zhiyuan Liu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Sinan Zhu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Centre for Quantitative Medicine, Program in Health Services and Systems Research, Duke-NUS Medical School, Singapore, Singapore
| | - Axel M Hillmer
- Institute of Pathology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Torsten Wuestefeld
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Jin Liu
- Centre for Quantitative Medicine, Program in Health Services and Systems Research, Duke-NUS Medical School, Singapore, Singapore
| | - Yun Shen Chan
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China
| | - Zheng Hu
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Liang Ma
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
| | - Li Jiang
- Department of General Surgery, Beijing Ditan Hospital, Capital Medical University, No. 8, Jingshun East Street, Chaoyang District, Beijing, P.R. China.
| | - Weiwei Zhai
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China.
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4
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Li Y, Wu X, Fang D, Luo Y. Informing immunotherapy with multi-omics driven machine learning. NPJ Digit Med 2024; 7:67. [PMID: 38486092 PMCID: PMC10940614 DOI: 10.1038/s41746-024-01043-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Accepted: 02/14/2024] [Indexed: 03/18/2024] Open
Abstract
Progress in sequencing technologies and clinical experiments has revolutionized immunotherapy on solid and hematologic malignancies. However, the benefits of immunotherapy are limited to specific patient subsets, posing challenges for broader application. To improve its effectiveness, identifying biomarkers that can predict patient response is crucial. Machine learning (ML) play a pivotal role in harnessing multi-omic cancer datasets and unlocking new insights into immunotherapy. This review provides an overview of cutting-edge ML models applied in omics data for immunotherapy analysis, including immunotherapy response prediction and immunotherapy-relevant tumor microenvironment identification. We elucidate how ML leverages diverse data types to identify significant biomarkers, enhance our understanding of immunotherapy mechanisms, and optimize decision-making process. Additionally, we discuss current limitations and challenges of ML in this rapidly evolving field. Finally, we outline future directions aimed at overcoming these barriers and improving the efficiency of ML in immunotherapy research.
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Affiliation(s)
- Yawei Li
- Department of Preventive Medicine, Northwestern University, Feinberg School of Medicine, Chicago, IL, 60611, USA
- Center for Collaborative AI in Healthcare, Northwestern University, Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Xin Wu
- Department of Medicine, University of Illinois at Chicago, Chicago, IL, 60612, USA
| | - Deyu Fang
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Yuan Luo
- Department of Preventive Medicine, Northwestern University, Feinberg School of Medicine, Chicago, IL, 60611, USA.
- Center for Collaborative AI in Healthcare, Northwestern University, Feinberg School of Medicine, Chicago, IL, 60611, USA.
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Blanco-Heredia J, Souza CA, Trincado JL, Gonzalez-Cao M, Gonçalves-Ribeiro S, Gil SR, Pravdyvets D, Cedeño S, Callari M, Marra A, Gazzo AM, Weigelt B, Pareja F, Vougiouklakis T, Jungbluth AA, Rosell R, Brander C, Tresserra F, Reis-Filho JS, Tiezzi DG, de la Iglesia N, Heyn H, De Mattos-Arruda L. Converging and evolving immuno-genomic routes toward immune escape in breast cancer. Nat Commun 2024; 15:1302. [PMID: 38383522 PMCID: PMC10882008 DOI: 10.1038/s41467-024-45292-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 01/19/2024] [Indexed: 02/23/2024] Open
Abstract
The interactions between tumor and immune cells along the course of breast cancer progression remain largely unknown. Here, we extensively characterize multiple sequential and parallel multiregion tumor and blood specimens of an index patient and a cohort of metastatic triple-negative breast cancers. We demonstrate that a continuous increase in tumor genomic heterogeneity and distinct molecular clocks correlated with resistance to treatment, eventually allowing tumors to escape from immune control. TCR repertoire loses diversity over time, leading to convergent evolution as breast cancer progresses. Although mixed populations of effector memory and cytotoxic single T cells coexist in the peripheral blood, defects in the antigen presentation machinery coupled with subdued T cell recruitment into metastases are observed, indicating a potent immune avoidance microenvironment not compatible with an effective antitumor response in lethal metastatic disease. Our results demonstrate that the immune responses against cancer are not static, but rather follow dynamic processes that match cancer genomic progression, illustrating the complex nature of tumor and immune cell interactions.
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Affiliation(s)
- Juan Blanco-Heredia
- IrsiCaixa, Germans Trias i Pujol University Hospital, Badalona, Spain
- Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Carla Anjos Souza
- IrsiCaixa, Germans Trias i Pujol University Hospital, Badalona, Spain
- Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain
| | - Juan L Trincado
- Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain
- Josep Carreras Leukemia Research Institute, Barcelona, Spain
| | | | | | - Sara Ruiz Gil
- Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain
| | | | - Samandhy Cedeño
- IrsiCaixa, Germans Trias i Pujol University Hospital, Badalona, Spain
| | - Maurizio Callari
- Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, UK
| | - Antonio Marra
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Andrea M Gazzo
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Britta Weigelt
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Fresia Pareja
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Theodore Vougiouklakis
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Achim A Jungbluth
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Rafael Rosell
- Dexeus Institute of Oncology, Quironsalud Group, Barcelona, Spain
| | - Christian Brander
- IrsiCaixa, Germans Trias i Pujol University Hospital, Badalona, Spain
- ICREA, Passeig de Lluís Companys, 23, Barcelona, Spain
- Universitat de Vic-Universitat Central de Catalunya, Catalunya, Spain
| | | | - Jorge S Reis-Filho
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Daniel Guimarães Tiezzi
- Department of Gynecology and Obstetrics - Breast Disease Division and Laboratory for Translational Data Science, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, Brazil
- Advanced Research Center in Medicine (CEPAM), Union of the Colleges of the Great Lakes (UNILAGO), São José do Rio Preto, Brazil
| | | | - Holger Heyn
- Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain
- Omniscope, Barcelona, Spain
| | - Leticia De Mattos-Arruda
- IrsiCaixa, Germans Trias i Pujol University Hospital, Badalona, Spain.
- Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain.
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6
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Wang RY, Kimmel M. A Countable-Type Branching Process Model for the Tug-of-War Cancer Cell Dynamics. Bull Math Biol 2024; 86:18. [PMID: 38236346 DOI: 10.1007/s11538-023-01245-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 12/13/2023] [Indexed: 01/19/2024]
Abstract
We consider a time-continuous Markov branching process of proliferating cells with a countable collection of types. Among-type transitions are inspired by the Tug-of-War process introduced by McFarland et al. (Proc Natl Acad Sci 111(42):15138-15143, 2014) as a mathematical model for competition of advantageous driver mutations and deleterious passenger mutations in cancer cells. We introduce a version of the model in which a driver mutation pushes the type of the cell L-units up, while a passenger mutation pulls it 1-unit down. The distribution of time to divisions depends on the type (fitness) of cell, which is an integer. The extinction probability given any initial cell type is strictly less than 1, which allows us to investigate the transition between types (type transition) in an infinitely long cell lineage of cells. The analysis leads to the result that under driver dominance, the type transition process escapes to infinity, while under passenger dominance, it leads to a limit distribution. Implications in cancer cell dynamics and population genetics are discussed.
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Affiliation(s)
- Ren-Yi Wang
- Department of Statistics, Rice University, Houston, TX, 77005, USA.
| | - Marek Kimmel
- Department of Statistics, Rice University, Houston, TX, 77005, USA
- Department of Systems Biology and Engineering, Silesian University of Technology, 44-100, Gliwice, Poland
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7
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Li H, Yang Z, Tu F, Deng L, Han Y, Fu X, Wang L, Gu D, Werner B, Huang W. Mutation divergence over space in tumour expansion. J R Soc Interface 2023; 20:20230542. [PMID: 37989227 PMCID: PMC10681009 DOI: 10.1098/rsif.2023.0542] [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: 09/16/2023] [Accepted: 10/30/2023] [Indexed: 11/23/2023] Open
Abstract
Mutation accumulation in tumour evolution is one major cause of intra-tumour heterogeneity (ITH), which often leads to drug resistance during treatment. Previous studies with multi-region sequencing have shown that mutation divergence among samples within the patient is common, and the importance of spatial sampling to obtain a complete picture in tumour measurements. However, quantitative comparisons of the relationship between mutation heterogeneity and tumour expansion modes, sampling distances as well as the sampling methods are still few. Here, we investigate how mutations diverge over space by varying the sampling distance and tumour expansion modes using individual-based simulations. We measure ITH by the Jaccard index between samples and quantify how ITH increases with sampling distance, the pattern of which holds in various sampling methods and sizes. We also compare the inferred mutation rates based on the distributions of variant allele frequencies under different tumour expansion modes and sampling sizes. In exponentially fast expanding tumours, a mutation rate can always be inferred for any sampling size. However, the accuracy compared with the true value decreases when the sampling size decreases, where small sampling sizes result in a high estimate of the mutation rate. In addition, such an inference becomes unreliable when the tumour expansion is slow, such as in surface growth.
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Affiliation(s)
- Haiyang Li
- Group of Theoretical Biology, The State Key Laboratory of Bio-control, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, People’s Republic of China
- Evolutionary Dynamics Group, Centre for Cancer Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Zixuan Yang
- Group of Theoretical Biology, The State Key Laboratory of Bio-control, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, People’s Republic of China
| | - Fengyu Tu
- Group of Theoretical Biology, The State Key Laboratory of Bio-control, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, People’s Republic of China
| | - Lijuan Deng
- Group of Theoretical Biology, The State Key Laboratory of Bio-control, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, People’s Republic of China
| | - Yuqing Han
- Group of Theoretical Biology, The State Key Laboratory of Bio-control, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, People’s Republic of China
| | - Xing Fu
- Group of Theoretical Biology, The State Key Laboratory of Bio-control, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, People’s Republic of China
| | - Long Wang
- Group of Theoretical Biology, The State Key Laboratory of Bio-control, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, People’s Republic of China
| | - Di Gu
- The first affiliated hospital of Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Benjamin Werner
- Evolutionary Dynamics Group, Centre for Cancer Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Weini Huang
- Group of Theoretical Biology, The State Key Laboratory of Bio-control, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, People’s Republic of China
- School of Mathematical Sciences, Queen Mary University of London, London, UK
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8
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Niu M, Zhang Y, Luo J, Sinson JC, Thompson AM, Zong C. Characterization of Cancer Evolution Landscape Based on Accurate Detection of Somatic Mutations in Single Tumor Cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.09.561356. [PMID: 37873375 PMCID: PMC10592685 DOI: 10.1101/2023.10.09.561356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Accurate detection of somatic mutations in single tumor cells is greatly desired as it allows us to quantify the single-cell mutation burden and construct the mutation-based phylogenetic tree. Here we developed scNanoSeq chemistry and profiled 842 single cells from 21 human breast cancer samples. The majority of the mutation-based phylogenetic trees comprise a characteristic stem evolution followed by the clonal sweep. We observed the subtype-dependent lengths in the stem evolution. To explain this phenomenon, we propose that the differences are related to different reprogramming required for different subtypes of breast cancer. Furthermore, we reason that the time that the tumor-initiating cell took to acquire the critical clonal-sweep-initiating mutation by random chance set the time limit for the reprogramming process. We refer to this model as a reprogramming and critical mutation co-timing (RCMC) subtype model. Next, in the sweeping clone, we observed that tumor cells undergo a branched evolution with rapidly decreasing selection. In the most recent clades, effectively neutral evolution has been reached, resulting in a substantially large number of mutational heterogeneities. Integrative analysis with 522-713X ultra-deep bulk whole genome sequencing (WGS) further validated this evolution mode. Mutation-based phylogenetic trees also allow us to identify the early branched cells in a few samples, whose phylogenetic trees support the gradual evolution of copy number variations (CNVs). Overall, the development of scNanoSeq allows us to unveil novel insights into breast cancer evolution.
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9
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Guo T, Chen GQ, Li XF, Wang M, Liu KM, Yang XY, Liu SC, Feng YL, Liu PY, Lin H, Xie AY. Small extrachromosomal circular DNA harboring targeted tumor suppressor gene mutations supports intratumor heterogeneity in mouse liver cancer induced by multiplexed CRISPR/Cas9. Genome Med 2023; 15:80. [PMID: 37803452 PMCID: PMC10557318 DOI: 10.1186/s13073-023-01230-2] [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: 06/05/2023] [Accepted: 09/08/2023] [Indexed: 10/08/2023] Open
Abstract
BACKGROUND Primary liver cancer has significant intratumor genetic heterogeneity (IGH), which drives cancer evolution and prevents effective cancer treatment. CRISPR/Cas9-induced mouse liver cancer models can be used to elucidate how IGH is developed. However, as CRISPR/Cas9 could induce chromothripsis and extrachromosomal DNA in cells in addition to targeted mutations, we wondered whether this effect contributes to the development of IGH in CRISPR/Cas9-induced mouse liver cancer. METHODS CRISPR/Cas9-based targeted somatic multiplex-mutagenesis was used to target 34 tumor suppressor genes (TSGs) for induction of primary liver tumors in mice. Target site mutations in tumor cells were analyzed and compared between single-cell clones and their subclones, between different time points of cell proliferation, and between parental clones and single-cell clones derived from mouse subcutaneous allografts. Genomic instability and generation of extrachromosomal circular DNA (eccDNA) was explored as a potential mechanism underlying the oscillation of target site mutations in these liver tumor cells. RESULTS After efficiently inducing autochthonous liver tumors in mice within 30-60 days, analyses of CRISPR/Cas9-induced tumors and single-cell clones derived from tumor nodules revealed multiplexed and heterogeneous mutations at target sites. Many target sites frequently displayed more than two types of allelic variations with varying frequencies in single-cell clones, indicating increased copy number of these target sites. The types and frequencies of targeted TSG mutations continued to change at some target sites between single-cell clones and their subclones. Even the proliferation of a subclone in cell culture and in mouse subcutaneous graft altered the types and frequencies of targeted TSG mutations in the absence of continuing CRISPR/Cas9 genome editing, indicating a new source outside primary chromosomes for the development of IGH in these liver tumors. Karyotyping of tumor cells revealed genomic instability in these cells manifested by high levels of micronuclei and chromosomal aberrations including chromosomal fragments and chromosomal breaks. Sequencing analysis further demonstrated the generation of eccDNA harboring targeted TSG mutations in these tumor cells. CONCLUSIONS Small eccDNAs carrying TSG mutations may serve as an important source supporting intratumor heterogeneity and tumor evolution in mouse liver cancer induced by multiplexed CRISPR/Cas9.
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Affiliation(s)
- Tao Guo
- Innovation Center for Minimally Invasive Technique and Device, Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, 3 East Qingchun Rd, Hangzhou, Zhejiang, 310019, P. R. China
- Institute of Translational Medicine, Zhejiang University School of Medicine and Zhejiang University Cancer Center, 268 Kai Xuan Rd, Hangzhou, Zhejiang, 310029, P. R. China
| | - Guo-Qiao Chen
- Innovation Center for Minimally Invasive Technique and Device, Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, 3 East Qingchun Rd, Hangzhou, Zhejiang, 310019, P. R. China
- Institute of Translational Medicine, Zhejiang University School of Medicine and Zhejiang University Cancer Center, 268 Kai Xuan Rd, Hangzhou, Zhejiang, 310029, P. R. China
| | - Xu-Fan Li
- Innovation Center for Minimally Invasive Technique and Device, Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, 3 East Qingchun Rd, Hangzhou, Zhejiang, 310019, P. R. China
- Institute of Translational Medicine, Zhejiang University School of Medicine and Zhejiang University Cancer Center, 268 Kai Xuan Rd, Hangzhou, Zhejiang, 310029, P. R. China
| | - Meng Wang
- Innovation Center for Minimally Invasive Technique and Device, Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, 3 East Qingchun Rd, Hangzhou, Zhejiang, 310019, P. R. China
- Institute of Translational Medicine, Zhejiang University School of Medicine and Zhejiang University Cancer Center, 268 Kai Xuan Rd, Hangzhou, Zhejiang, 310029, P. R. China
| | - Kun-Ming Liu
- Innovation Center for Minimally Invasive Technique and Device, Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, 3 East Qingchun Rd, Hangzhou, Zhejiang, 310019, P. R. China
- Institute of Translational Medicine, Zhejiang University School of Medicine and Zhejiang University Cancer Center, 268 Kai Xuan Rd, Hangzhou, Zhejiang, 310029, P. R. China
| | - Xiao-Ying Yang
- Innovation Center for Minimally Invasive Technique and Device, Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, 3 East Qingchun Rd, Hangzhou, Zhejiang, 310019, P. R. China
- Institute of Translational Medicine, Zhejiang University School of Medicine and Zhejiang University Cancer Center, 268 Kai Xuan Rd, Hangzhou, Zhejiang, 310029, P. R. China
| | - Si-Cheng Liu
- Innovation Center for Minimally Invasive Technique and Device, Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, 3 East Qingchun Rd, Hangzhou, Zhejiang, 310019, P. R. China
- Institute of Translational Medicine, Zhejiang University School of Medicine and Zhejiang University Cancer Center, 268 Kai Xuan Rd, Hangzhou, Zhejiang, 310029, P. R. China
| | - Yi-Li Feng
- Innovation Center for Minimally Invasive Technique and Device, Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, 3 East Qingchun Rd, Hangzhou, Zhejiang, 310019, P. R. China
- Institute of Translational Medicine, Zhejiang University School of Medicine and Zhejiang University Cancer Center, 268 Kai Xuan Rd, Hangzhou, Zhejiang, 310029, P. R. China
| | - Peng-Yuan Liu
- Innovation Center for Minimally Invasive Technique and Device, Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, 3 East Qingchun Rd, Hangzhou, Zhejiang, 310019, P. R. China.
- Institute of Translational Medicine, Zhejiang University School of Medicine and Zhejiang University Cancer Center, 268 Kai Xuan Rd, Hangzhou, Zhejiang, 310029, P. R. China.
| | - Hui Lin
- Innovation Center for Minimally Invasive Technique and Device, Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, 3 East Qingchun Rd, Hangzhou, Zhejiang, 310019, P. R. China.
| | - An-Yong Xie
- Innovation Center for Minimally Invasive Technique and Device, Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, 3 East Qingchun Rd, Hangzhou, Zhejiang, 310019, P. R. China.
- Institute of Translational Medicine, Zhejiang University School of Medicine and Zhejiang University Cancer Center, 268 Kai Xuan Rd, Hangzhou, Zhejiang, 310029, P. R. China.
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10
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Wang Y, Zhang M, Shi J, Zhu Y, Wang X, Zhang S, Wang F. Cracking the pattern of tumor evolution based on single-cell copy number alterations. Brief Bioinform 2023; 24:bbad341. [PMID: 37791583 DOI: 10.1093/bib/bbad341] [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: 05/13/2023] [Revised: 09/02/2023] [Accepted: 09/11/2023] [Indexed: 10/05/2023] Open
Abstract
Copy number alterations (CNAs) are a key characteristic of tumor development and progression. The accumulation of various CNAs during tumor development plays a critical role in driving tumor evolution. Heterogeneous clones driven by distinct CNAs have different selective advantages, leading to differential patterns of tumor evolution that are essential for developing effective cancer therapies. Recent advances in single-cell sequencing technology have enabled genome-wide copy number profiling of tumor cell populations at single-cell resolution. This has made it possible to explore the evolutionary patterns of CNAs and accurately discover the mechanisms of intra-tumor heterogeneity. Here, we propose a two-step statistical approach that distinguishes neutral, linear, branching and punctuated evolutionary patterns for a tumor cell population based on single-cell copy number profiles. We assessed our approach using a variety of simulated and real single-cell genomic and transcriptomic datasets, demonstrating its high accuracy and robustness in predicting tumor evolutionary patterns. We applied our approach to single-cell DNA sequencing data from 20 breast cancer patients and observed that punctuated evolution is the dominant evolutionary pattern in breast cancer. Similar conclusions were drawn when applying the approach to single-cell RNA sequencing data obtained from 132 various cancer patients. Moreover, we found that differential immune cell infiltration is associated with specific evolutionary patterns. The source code of our study is available at https://github.com/FangWang-SYSU/PTEM.
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Affiliation(s)
- Ying Wang
- Guangdong Cardiovascular Institute,Guangdong Provincial People's Hospital,Guangdong Academy of Medical Sciences and Medical Research Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University
| | - Min Zhang
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yan-Sen University
| | - Jian Shi
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-Sen University
| | - Yue Zhu
- Department of Breast Surgery at Harbin Medical University Cancer Hospital and the Medical Research Institute of Guangdong Provincial People's Hospital
| | - Xin Wang
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yan-Sen University
| | - Shaojun Zhang
- Medical Research Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University
| | - Fang Wang
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yan-Sen University
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11
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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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12
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Zhu X, Zhao W, Zhou Z, Gu X. Unraveling the Drivers of Tumorigenesis in the Context of Evolution: Theoretical Models and Bioinformatics Tools. J Mol Evol 2023:10.1007/s00239-023-10117-0. [PMID: 37246992 DOI: 10.1007/s00239-023-10117-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 05/09/2023] [Indexed: 05/30/2023]
Abstract
Cancer originates from somatic cells that have accumulated mutations. These mutations alter the phenotype of the cells, allowing them to escape homeostatic regulation that maintains normal cell numbers. The emergence of malignancies is an evolutionary process in which the random accumulation of somatic mutations and sequential selection of dominant clones cause cancer cells to proliferate. The development of technologies such as high-throughput sequencing has provided a powerful means to measure subclonal evolutionary dynamics across space and time. Here, we review the patterns that may be observed in cancer evolution and the methods available for quantifying the evolutionary dynamics of cancer. An improved understanding of the evolutionary trajectories of cancer will enable us to explore the molecular mechanism of tumorigenesis and to design tailored treatment strategies.
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Affiliation(s)
- Xunuo Zhu
- Innovation Institute for Artificial Intelligence in Medicine, Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Wenyi Zhao
- Innovation Institute for Artificial Intelligence in Medicine, Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Zhan Zhou
- Innovation Institute for Artificial Intelligence in Medicine, Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China.
- The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, 322000, China.
- Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou, 310058, China.
| | - Xun Gu
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, 50011, USA.
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13
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Razia S, Nakayama K, Yamashita H, Ishibashi T, Ishikawa M, Kanno K, Sato S, Kyo S. Histological and Genetic Diversity in Ovarian Mucinous Carcinomas: A Pilot Study. Curr Oncol 2023; 30:4052-4059. [PMID: 37185420 PMCID: PMC10137024 DOI: 10.3390/curroncol30040307] [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: 02/10/2023] [Revised: 03/31/2023] [Accepted: 04/01/2023] [Indexed: 05/17/2023] Open
Abstract
Tumor heterogeneity remains an ongoing challenge in the field of cancer therapy. Intratumor heterogeneity significantly complicates the diagnosis of cancer and presents challenging clinical problems due to resistance to drug therapy. This study aimed to elucidate the genetic changes histologically (mucinous cystadenoma (MCA), mucinous borderline tumor (MBT), and mucinous ovarian carcinoma (MOC)) in a portion of mucinous ovarian tumors within the same sample. Seven tumor samples obtained from different patients were used to evaluate the genetic mutations in each component. Intratumor genetic heterogeneity was observed in all patients; among them, BRAF (V600E) and p53 (T118I, P142S, T150I, and T170M) point mutations were observed in the MBT component, while KRAS (G12D and G13D) and PIK3CA (E545K) mutations were found in the MOC component. The current findings suggest that diverse genetic alterations occur in mucinous tumors, according to tumor histology. Tumor heterogeneity and genetic diversity in mucinous ovarian tumors might be the cause of treatment failure. Knowledge of intertumor heterogeneity may lead to an increased understanding of the tumor response to treatment.
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Affiliation(s)
- Sultana Razia
- Department of Obstetrics and Gynecology, Shimane University School of Medicine, Izumo 6938501, Japan
| | - Kentaro Nakayama
- Department of Obstetrics and Gynecology, Shimane University School of Medicine, Izumo 6938501, Japan
| | - Hitomi Yamashita
- Department of Obstetrics and Gynecology, Shimane University School of Medicine, Izumo 6938501, Japan
| | - Tomoka Ishibashi
- Department of Obstetrics and Gynecology, Shimane University School of Medicine, Izumo 6938501, Japan
| | - Masako Ishikawa
- Department of Obstetrics and Gynecology, Shimane University School of Medicine, Izumo 6938501, Japan
| | - Kosuke Kanno
- Department of Obstetrics and Gynecology, Shimane University School of Medicine, Izumo 6938501, Japan
| | - Seiya Sato
- Department of Obstetrics and Gynecology, Shimane University School of Medicine, Izumo 6938501, Japan
| | - Satoru Kyo
- Department of Obstetrics and Gynecology, Shimane University School of Medicine, Izumo 6938501, Japan
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14
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Moravec JC, Lanfear R, Spector DL, Diermeier SD, Gavryushkin A. Testing for Phylogenetic Signal in Single-Cell RNA-Seq Data. J Comput Biol 2023; 30:518-537. [PMID: 36475926 PMCID: PMC10125402 DOI: 10.1089/cmb.2022.0357] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Phylogenetic methods are emerging as a useful tool to understand cancer evolutionary dynamics, including tumor structure, heterogeneity, and progression. Most currently used approaches utilize either bulk whole genome sequencing or single-cell DNA sequencing and are based on calling copy number alterations and single nucleotide variants (SNVs). Single-cell RNA sequencing (scRNA-seq) is commonly applied to explore differential gene expression of cancer cells throughout tumor progression. The method exacerbates the single-cell sequencing problem of low yield per cell with uneven expression levels. This accounts for low and uneven sequencing coverage and makes SNV detection and phylogenetic analysis challenging. In this article, we demonstrate for the first time that scRNA-seq data contain sufficient evolutionary signal and can also be utilized in phylogenetic analyses. We explore and compare results of such analyses based on both expression levels and SNVs called from scRNA-seq data. Both techniques are shown to be useful for reconstructing phylogenetic relationships between cells, reflecting the clonal composition of a tumor. Both standardized expression values and SNVs appear to be equally capable of reconstructing a similar pattern of phylogenetic relationship. This pattern is stable even when phylogenetic uncertainty is taken in account. Our results open up a new direction of somatic phylogenetics based on scRNA-seq data. Further research is required to refine and improve these approaches to capture the full picture of somatic evolutionary dynamics in cancer.
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Affiliation(s)
- Jiří C. Moravec
- Department of Computer Science, University of Otago, Dunedin, New Zealand
- School of Mathematics and Statistics, University of Canterbury, Christchurch, New Zealand
| | - Robert Lanfear
- Division of Ecology and Evolution, Research School of Biology, Australian National University, Canberra, Australia
| | | | | | - Alex Gavryushkin
- School of Mathematics and Statistics, University of Canterbury, Christchurch, New Zealand
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15
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Huss R, Raffler J, Märkl B. Artificial intelligence and digital biomarker in precision pathology guiding immune therapy selection and precision oncology. Cancer Rep (Hoboken) 2023:e1796. [PMID: 36813293 PMCID: PMC10363837 DOI: 10.1002/cnr2.1796] [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: 08/29/2022] [Revised: 01/15/2023] [Accepted: 02/09/2023] [Indexed: 02/24/2023] Open
Abstract
BACKGROUND The currently available immunotherapies already changed the strategy how many cancers are treated from first to last line. Understanding even the most complex heterogeneity in tumor tissue and mapping the spatial cartography of the tumor immunity allows the best and optimized selection of immune modulating agents to (re-)activate the patient's immune system and direct it against the individual cancer in the most effective way. RECENT FINDINGS Primary cancer and metastases maintain a high degree of plasticity to escape any immune surveillance and continue to evolve depending on many intrinsic and extrinsic factors In the field of immune-oncology (IO) immune modulating agents are recognized as practice changing therapeutic modalities. Recent studies have shown that an optimal and lasting efficacy of IO therapeutics depends on the understanding of the spatial communication network and functional context of immune and cancer cells within the tumor microenvironment. Artificial intelligence (AI) provides an insight into the immune-cancer-network through the visualization of very complex tumor and immune interactions in cancer tissue specimens and allows the computer-assisted development and clinical validation of such digital biomarker. CONCLUSIONS The successful implementation of AI-supported digital biomarker solutions guides the clinical selection of effective immune therapeutics based on the retrieval and visualization of spatial and contextual information from cancer tissue images and standardized data. As such, computational pathology (CP) turns into "precision pathology" delivering individual therapy response prediction. Precision Pathology does not only include digital and computational solutions but also high levels of standardized processes in the routine histopathology workflow and the use of mathematical tools to support clinical and diagnostic decisions as the basic principle of a "precision oncology".
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Affiliation(s)
- Ralf Huss
- Medical Faculty University Augsburg, Augsburg, Germany
- Institute for Digital Medicine, University Hospital Augsburg, Augsburg, Germany
| | - Johannes Raffler
- Institute for Digital Medicine, University Hospital Augsburg, Augsburg, Germany
| | - Bruno Märkl
- Medical Faculty University Augsburg, Augsburg, Germany
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16
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Cabral LKD, Giraudi PJ, Giannelli G, Dituri F, Negro R, Tiribelli C, Sukowati CHC. Network Analysis for the Discovery of Common Oncogenic Biomarkers in Liver Cancer Experimental Models. Biomedicines 2023; 11:342. [PMID: 36830879 PMCID: PMC9953082 DOI: 10.3390/biomedicines11020342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 01/12/2023] [Accepted: 01/20/2023] [Indexed: 01/27/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is a malignancy marked by heterogeneity. This study aimed to discover target molecules for potential therapeutic efficacy that may encompass HCC heterogeneity. In silico analysis using published datasets identified 16 proto-oncogenes as potential pharmacological targets. We used an immortalized hepatocyte (IHH) and five HCC cell lines under two subtypes: S1/TGFβ-Wnt-activated (HLE, HLF, and JHH6) and the S2/progenitor subtype (HepG2 and Huh7). Three treatment modalities, 5 µM 5-Azacytidine, 50 µM Sorafenib, and 20 nM PD-L1 gene silencing, were evaluated in vitro. The effect of treatments on the proto-oncogene targets was assessed by gene expression and Western blot analysis. Our results showed that 10/16 targets were upregulated in HCC cells, where cells belonging to the S2/progenitor subtype had more upregulated targets compared to the S1/TGFβ-Wnt-activated subtype (81% vs. 62%, respectively). Among the targets, FGR was consistently down-regulated in the cell lines following the three different treatments. Sorafenib was effective to down-regulate targets in S2/progenitor subtype while PD-L1 silencing was able to decrease targets in all HCC subtypes, suggesting that this treatment strategy may comprise cellular heterogeneity. This study strengthens the relevance of liver cancer cellular heterogeneity in response to cancer therapies.
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Affiliation(s)
- Loraine Kay D. Cabral
- Fondazione Italiana Fegato ONLUS, AREA Science Park, Campus Basovizza, 34149 Trieste, Italy; (L.K.D.C.); (P.J.G.); (C.T.)
- Doctoral School in Molecular Biomedicine, University of Trieste, 34127 Trieste, Italy
| | - Pablo J. Giraudi
- Fondazione Italiana Fegato ONLUS, AREA Science Park, Campus Basovizza, 34149 Trieste, Italy; (L.K.D.C.); (P.J.G.); (C.T.)
| | - Gianluigi Giannelli
- National Institute of Gastroenterology IRCCS “S. De Bellis” Research Hospital, 70013 Bari, Italy; (G.G.); (F.D.); (R.N.)
| | - Francesco Dituri
- National Institute of Gastroenterology IRCCS “S. De Bellis” Research Hospital, 70013 Bari, Italy; (G.G.); (F.D.); (R.N.)
| | - Roberto Negro
- National Institute of Gastroenterology IRCCS “S. De Bellis” Research Hospital, 70013 Bari, Italy; (G.G.); (F.D.); (R.N.)
| | - Claudio Tiribelli
- Fondazione Italiana Fegato ONLUS, AREA Science Park, Campus Basovizza, 34149 Trieste, Italy; (L.K.D.C.); (P.J.G.); (C.T.)
| | - Caecilia H. C. Sukowati
- Fondazione Italiana Fegato ONLUS, AREA Science Park, Campus Basovizza, 34149 Trieste, Italy; (L.K.D.C.); (P.J.G.); (C.T.)
- Eijkman Research Center for Molecular Biology, National Research and Innovation Agency of Indonesia (BRIN), Jakarta Pusat 10340, Indonesia
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CFNC, a neocryptolepine derivative, inhibited the growth of gastric cancer AGS cells by inhibiting PI3K/AKT signaling pathway. Eur J Pharmacol 2022; 938:175408. [PMID: 36442620 DOI: 10.1016/j.ejphar.2022.175408] [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: 10/20/2022] [Revised: 11/17/2022] [Accepted: 11/21/2022] [Indexed: 11/26/2022]
Abstract
Gastric cancer is highly heterogeneous and there is still a lack of efficient, low-toxicity small molecule compounds for the treatment of gastric cancer. Natural products are important sources for the development of antitumor compounds. Therefore, it is promising strategy to find the lead compound of anti-gastric cancer agents by structural modification of natural products. The aim of this study was to synthesize a novel neocryptolepine derivative CFNC and explore its potential anti-gastric cancer effect and molecular mechanism. The MTT assay showed that the IC50 of CFNC on AGS cells reached 148 nM. CFNC arrested AGS cells in the G2/M phase of the cell cycle. Furthermore, CFNC inhibited cell proliferation and migration, leading to the loss of membrane potential by causing mitochondrial dysfunction, which induced the apoptosis of AGS cells. Western blot assay suggested that CFNC could inhibit the expression of important proteins in the PI3K/AKT/mTOR signaling pathway. These results showed that CFNC exhibited strong cytotoxic activity in gastric cancer cell lines by regulating the PI3K/AKT/mTOR signaling pathway. Taken together, CFNC could be a promising lead compound for the clinical treatment of gastric cancer.
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18
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Cheng H, Guo Z, Zhang X, Wang XJ, Li Z, Huo WW, Zhong HC, Li XJ, Wu XW, Li WH, Chen ZW, Wu TC, Gan XF, Zhong BL, Lyubetsky VA, Rusin LY, Yang J, Zhao Q, Cao QD, Yang JR. Lack of evolutionary convergence in multiple primary lung cancer suggests insufficient specificity of personalized therapy. J Genet Genomics 2022; 50:330-340. [PMID: 36414223 DOI: 10.1016/j.jgg.2022.11.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 11/11/2022] [Indexed: 11/20/2022]
Abstract
Multiple primary lung cancer (MPLC) is an increasingly prevalent subtype of lung cancer. According to recent genomic studies, the different lesions of a single MPLC patient exhibit functional similarities that may reflect evolutionary convergence. We performed whole-exome sequencing for a unique cohort of MPLC patients with multiple samples from each lesion found. Using our own and other relevant public data, evolutionary tree reconstruction revealed that cancer driver gene mutations occurred at the early trunk, indicating evolutionary contingency rather than adaptive convergence. Additionally, tumors from the same MPLC patient are as genetically diverse as those from different patients, while within-tumor genetic heterogeneity is significantly lower. Furthermore, the aberrant molecular functions enriched in mutated genes for a sample show a strong overlap with other samples from the same tumor, but not with samples from other tumors or other patients. Overall, there is no evidence of adaptive convergence during the evolution of MPLC. Most importantly, the similar between-tumor diversity and between-patient diversity suggest that personalized therapies may not adequately account for the genetic diversity among different tumors in an MPLC patient. To fully exploit the strategic value of precision medicine, targeted therapies should be designed and delivered on a per-lesion basis.
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Affiliation(s)
- Hua Cheng
- Department of Thoracic Surgery, The Fifth Affiliated Hospital, Sun Yat-Sen University, Zhuhai, Guangdong 519000, China
| | - Ziyan Guo
- Department of Genetics and Biomedical Informatics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - Xiaoyu Zhang
- Department of Genetics and Biomedical Informatics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - Xiao-Jin Wang
- Department of Thoracic Surgery, The Fifth Affiliated Hospital, Sun Yat-Sen University, Zhuhai, Guangdong 519000, China; Program in Cancer Research, Zhongshan School of Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - Zizhang Li
- Department of Genetics and Biomedical Informatics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - Wen-Wen Huo
- Department of Thoracic Surgery, The Fifth Affiliated Hospital, Sun Yat-Sen University, Zhuhai, Guangdong 519000, China; Program in Cancer Research, Zhongshan School of Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - Hong-Cheng Zhong
- Department of Thoracic Surgery, The Fifth Affiliated Hospital, Sun Yat-Sen University, Zhuhai, Guangdong 519000, China
| | - Xiao-Jian Li
- Department of Thoracic Surgery, The Fifth Affiliated Hospital, Sun Yat-Sen University, Zhuhai, Guangdong 519000, China
| | - Xiang-Wen Wu
- Department of Thoracic Surgery, The Fifth Affiliated Hospital, Sun Yat-Sen University, Zhuhai, Guangdong 519000, China
| | - Wen-Hao Li
- Department of Thoracic Surgery, The Fifth Affiliated Hospital, Sun Yat-Sen University, Zhuhai, Guangdong 519000, China
| | - Zhuo-Wen Chen
- Department of Thoracic Surgery, The Fifth Affiliated Hospital, Sun Yat-Sen University, Zhuhai, Guangdong 519000, China
| | - Tian-Chi Wu
- Department of Thoracic Surgery, The Fifth Affiliated Hospital, Sun Yat-Sen University, Zhuhai, Guangdong 519000, China
| | - Xiang-Feng Gan
- Department of Thoracic Surgery, The Fifth Affiliated Hospital, Sun Yat-Sen University, Zhuhai, Guangdong 519000, China
| | - Bei-Long Zhong
- Department of Thoracic Surgery, The Fifth Affiliated Hospital, Sun Yat-Sen University, Zhuhai, Guangdong 519000, China
| | - Vassily A Lyubetsky
- Kharkevich Institute for Information Transmission Problems Russian Academy Sciences, Moscow 127051, Russia; Department of Mathematical Logic and Theory of Algorithms, Faculty of Mechanics and Mathematics, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Leonid Yu Rusin
- Kharkevich Institute for Information Transmission Problems Russian Academy Sciences, Moscow 127051, Russia
| | - Junnan Yang
- Department of Genetics and Biomedical Informatics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - Qiyi Zhao
- Department of Infectious Diseases, Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong 510630, China; Guangdong Provincial Key Laboratory of Liver Disease Research the Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510630, China
| | - Qing-Dong Cao
- Department of Thoracic Surgery, The Fifth Affiliated Hospital, Sun Yat-Sen University, Zhuhai, Guangdong 519000, China.
| | - Jian-Rong Yang
- Department of Genetics and Biomedical Informatics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China; Program in Cancer Research, Zhongshan School of Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510080, China; Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-sen University, Guangzhou, Guangdong 510080, China.
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19
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Chen B, Wu X, Ruan Y, Zhang Y, Cai Q, Zapata L, Wu CI, Lan P, Wen H. Very large hidden genetic diversity in one single tumor: evidence for tumors-in-tumor. Natl Sci Rev 2022; 9:nwac250. [PMID: 36694802 PMCID: PMC9869076 DOI: 10.1093/nsr/nwac250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 10/12/2022] [Accepted: 10/20/2022] [Indexed: 11/13/2022] Open
Abstract
Despite the concern of within-tumor genetic diversity, this diversity is in fact limited by the kinship among cells in the tumor. Indeed, genomic studies have amply supported the 'Nowell dogma' whereby cells of the same tumor descend from a single progenitor cell. In parallel, genomic data also suggest that the diversity could be >10-fold larger if tumor cells are of multiple origins. We develop an evolutionary hypothesis that a single tumor may often harbor multiple cell clones of independent origins, but only one would be large enough to be detected. To test the hypothesis, we search for independent tumors within a larger one (or tumors-in-tumor). Very high density sampling was done on two cases of colon tumors. Case 1 indeed has 13 independent clones of disparate sizes, many having heavy mutation burdens and potentially highly tumorigenic. In Case 2, despite a very intensive search, only two small independent clones could be found. The two cases show very similar movements and metastasis of the dominant clone. Cells initially move actively in the expanding tumor but become nearly immobile in late stages. In conclusion, tumors-in-tumor are plausible but could be very demanding to find. Despite their small sizes, they can enhance the within-tumor diversity by orders of magnitude. Such increases may contribute to the missing genetic diversity associated with the resistance to cancer therapy.
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Affiliation(s)
| | | | - Yongsen Ruan
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou510275, China
| | - Yulin Zhang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou510275, China
| | - Qichun Cai
- Cancer Center, Clifford Hospital, Jinan University, Guangzhou 511495, China
| | - Luis Zapata
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London SW7 3RP, UK
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20
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van den Bosch T, Derks S, Miedema DM. Chromosomal Instability, Selection and Competition: Factors That Shape the Level of Karyotype Intra-Tumor Heterogeneity. Cancers (Basel) 2022; 14:cancers14204986. [PMID: 36291770 PMCID: PMC9600040 DOI: 10.3390/cancers14204986] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 10/07/2022] [Accepted: 10/09/2022] [Indexed: 12/03/2022] Open
Abstract
Simple Summary Each cancer consists of billions of cells. These cells are far from identical; hence, the population of cells that constitute a tumor is heterogeneous. A salient property that varies between cells in a tumor is their karyotype, the number and configuration of the chromosomes. The level of karyotype heterogeneity can be used to predict the survival of a patient. In this review, we describe the processes that shape the level of karyotype heterogeneity in a cancer. Abstract Intra-tumor heterogeneity (ITH) is a pan-cancer predictor of survival, with high ITH being correlated to a dismal prognosis. The level of ITH is, hence, a clinically relevant characteristic of a malignancy. ITH of karyotypes is driven by chromosomal instability (CIN). However, not all new karyotypes generated by CIN are viable or competitive, which limits the amount of ITH. Here, we review the cellular processes and ecological properties that determine karyotype ITH. We propose a framework to understand karyotype ITH, in which cells with new karyotypes emerge through CIN, are selected by cell intrinsic and cell extrinsic selective pressures, and propagate through a cancer in competition with other malignant cells. We further discuss how CIN modulates the cell phenotype and immune microenvironment, and the implications this has for the subsequent selection of karyotypes. Together, we aim to provide a comprehensive overview of the biological processes that shape the level of karyotype heterogeneity.
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Affiliation(s)
- Tom van den Bosch
- Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Cancer Center Amsterdam and Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam University Medical Centers—Location AMC, 1105 AZ Amsterdam, The Netherlands
- Oncode Institute, 1105 AZ Amsterdam, The Netherlands
| | - Sarah Derks
- Oncode Institute, 1105 AZ Amsterdam, The Netherlands
- Department of Medical Oncology, Amsterdam University Medical Centers—Location VUmc, 1081 HV Amsterdam, The Netherlands
- Correspondence: (S.D.); (D.M.M.)
| | - Daniël M. Miedema
- Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Cancer Center Amsterdam and Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam University Medical Centers—Location AMC, 1105 AZ Amsterdam, The Netherlands
- Oncode Institute, 1105 AZ Amsterdam, The Netherlands
- Correspondence: (S.D.); (D.M.M.)
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21
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Manini C, López JI. Ecology and games in cancer: new insights into the disease. Pathologica 2022; 114:347-351. [PMID: 36305020 PMCID: PMC9614302 DOI: 10.32074/1591-951x-798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Accepted: 08/14/2022] [Indexed: 06/16/2023] Open
Affiliation(s)
- Claudia Manini
- Department of Pathology, San Giovanni Bosco Hospital, Turin, Italy
- Department of Sciences of Public Health and Pediatrics, University of Turin, Turin, Italy
| | - José I. López
- Biomarkers in Cancer Unit, Biocruces-Bizkaia Health Research Institute, Barakaldo, Spain
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22
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Li Y, Wu X, Yang P, Jiang G, Luo Y. Machine Learning for Lung Cancer Diagnosis, Treatment, and Prognosis. GENOMICS, PROTEOMICS & BIOINFORMATICS 2022; 20:850-866. [PMID: 36462630 PMCID: PMC10025752 DOI: 10.1016/j.gpb.2022.11.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 10/03/2022] [Accepted: 11/17/2022] [Indexed: 12/03/2022]
Abstract
The recent development of imaging and sequencing technologies enables systematic advances in the clinical study of lung cancer. Meanwhile, the human mind is limited in effectively handling and fully utilizing the accumulation of such enormous amounts of data. Machine learning-based approaches play a critical role in integrating and analyzing these large and complex datasets, which have extensively characterized lung cancer through the use of different perspectives from these accrued data. In this review, we provide an overview of machine learning-based approaches that strengthen the varying aspects of lung cancer diagnosis and therapy, including early detection, auxiliary diagnosis, prognosis prediction, and immunotherapy practice. Moreover, we highlight the challenges and opportunities for future applications of machine learning in lung cancer.
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Affiliation(s)
- Yawei Li
- Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Xin Wu
- Department of Medicine, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Ping Yang
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN 55905 / Scottsdale, AZ 85259, USA
| | - Guoqian Jiang
- Department of Artificial Intelligence and Informatics, Mayo Clinic, Rochester, MN 55905, USA
| | - Yuan Luo
- Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA.
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23
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Ní Leathlobhair M, Lenski RE. Population genetics of clonally transmissible cancers. Nat Ecol Evol 2022; 6:1077-1089. [PMID: 35879542 DOI: 10.1038/s41559-022-01790-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 05/12/2022] [Indexed: 11/08/2022]
Abstract
Populations of cancer cells are subject to the same core evolutionary processes as asexually reproducing, unicellular organisms. Transmissible cancers are particularly striking examples of these processes. These unusual cancers are clonal lineages that can spread through populations via physical transfer of living cancer cells from one host individual to another, and they have achieved long-term success in the colonization of at least eight different host species. Population genetic theory provides a useful framework for understanding the shift from a multicellular sexual animal into a unicellular asexual clone and its long-term effects on the genomes of these cancers. In this Review, we consider recent findings from transmissible cancer research with the goals of developing an evolutionarily informed perspective on transmissible cancers, examining possible implications for their long-term fate and identifying areas for future research on these exceptional lineages.
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Affiliation(s)
- Máire Ní Leathlobhair
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK.
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
- Department of Microbiology, Moyne Institute of Preventive Medicine, School of Genetics and Microbiology, Trinity College Dublin, Dublin, Ireland.
| | - Richard E Lenski
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
- Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, MI, USA
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24
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Kurpas MK, Kimmel M. Modes of Selection in Tumors as Reflected by Two Mathematical Models and Site Frequency Spectra. Front Ecol Evol 2022; 10:889438. [PMID: 37333691 PMCID: PMC10275603 DOI: 10.3389/fevo.2022.889438] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/28/2024] Open
Abstract
The tug-of-war model was developed in a series of papers of McFarland and co-authors to account for existence of mutually counteracting rare advantageous driver mutations and more frequent slightly deleterious passenger mutations in cancer. In its original version, it was a state-dependent branching process. Because of its formulation, the tug-of-war model is of importance for tackling the problem as to whether evolution of cancerous tumors is "Darwinian" or "non-Darwinian." We define two Time-Continuous Markov Chain versions of the model, including identical mutation processes but adopting different drift and selection components. In Model A, drift and selection process preserves expected fitness whereas in Model B it leads to non-decreasing expected fitness. We investigate these properties using mathematical analysis and extensive simulations, which detect the effect of the so-called drift barrier in Model B but not in Model A. These effects are reflected in different structure of clone genealogies in the two models. Our work is related to the past theoretical work in the field of evolutionary genetics, concerning the interplay among mutation, drift and selection, in absence of recombination (asexual reproduction), where epistasis plays a major role. Finally, we use the statistics of mutation frequencies known as the Site Frequency Spectra (SFS), to compare the variant frequencies in DNA of sequenced HER2+ breast cancers, to those based on Model A and B simulations. The tumor-based SFS are better reproduced by Model A, pointing out a possible selection pattern of HER2+ tumor evolution. To put our models in context, we carried out an exploratory study of how publicly accessible data from breast, prostate, skin and ovarian cancers fit a range of models found in the literature.
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Affiliation(s)
- Monika K. Kurpas
- Department of Systems Biology and Engineering, Silesian University of Technology, Gliwice, Poland
| | - Marek Kimmel
- Department of Systems Biology and Engineering, Silesian University of Technology, Gliwice, Poland
- Department of Statistics and Bioengineering, Rice University, Houston, TX, United States
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25
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Chan SL, Wong N, Lam WKJ, Kuang M. Personalized treatment for hepatocellular carcinoma: Current status and future perspectives. J Gastroenterol Hepatol 2022; 37:1197-1206. [PMID: 35570200 DOI: 10.1111/jgh.15889] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 05/08/2022] [Indexed: 12/24/2022]
Abstract
Systemic treatment for hepatocellular carcinoma (HCC) has been advancing rapidly over the last decade. More novel agents, including both targeted agents and immune checkpoint inhibitors, are available for physicians to use sequentially or concurrently for patients with advanced HCC. Despite more options, only a proportion of patients benefit from each regimen. Therefore, clinicians are facing challenges on how to choose the right regimen for the right patient with HCC, which raises the importance of personalized treatment approach. To advance personalized treatment for HCC, one approach relies on the acquisition of biomarker data from clinical trials to evaluate clinical parameters or genotypes in association with outcomes of selected drugs. This approach has led to finding of high baseline alpha-fetoprotein levels in association with benefits of ramucirumab. Cumulative findings from multiple clinical trials and translational studies also suggest that selected etiology and/or genotype of HCC could predict resistance to immune checkpoint inhibitors. The second approach is to decipher the tumor heterogeneity of HCC with an aim to identify clinically relevant patterns to guide clinical decisions. Tumor heterogeneity could exist within a single tumor (intra-tumoral heterogeneity), among different tumors in the same patient (inter-tumoral heterogeneity) or between primary and recurrent tumors (temporal tumor heterogeneity). The analyses of tumor heterogeneity have also been powered by coverage of tumor immune environment and incorporation of circulating tumor nucleic acid technology. Emerging publications have been reported above tumor heterogeneity exist in HCC, which is potentially clinically impactful.
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Affiliation(s)
- Stephen L Chan
- Department of Clinical Oncology, Sir Y.K. Pao Centre for Cancer, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China.,State Key Laboratory of Translational Oncology, The Chinese University of Hong Kong, Hong Kong, China
| | - Nathalie Wong
- State Key Laboratory of Translational Oncology, The Chinese University of Hong Kong, Hong Kong, China.,Department of Surgery at Sir Y.K. Pao Center for Cancer, The Chinese University of Hong Kong, Hong Kong, China
| | - W K Jacky Lam
- Li Ka Shing Institute of Health Sciences, Department of Chemical Pathology, The Chinese University of Hong Kong, Hong Kong, China.,Department of Chemical Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
| | - Ming Kuang
- Center of Hepatopancreatobiliary Surgery, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China.,Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
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26
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van den Bosch T, Vermeulen L, Miedema DM. Quantitative models for the inference of intratumor heterogeneity. COMPUTATIONAL AND SYSTEMS ONCOLOGY 2022. [DOI: 10.1002/cso2.1034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Tom van den Bosch
- Laboratory for Experimental Oncology and Radiobiology Center for Experimental and Molecular Medicine Cancer Center Amsterdam and Amsterdam Gastroenterology and Metabolism Amsterdam University Medical Centers Amsterdam The Netherlands
- Oncode Institute Amsterdam The Netherlands
| | - Louis Vermeulen
- Laboratory for Experimental Oncology and Radiobiology Center for Experimental and Molecular Medicine Cancer Center Amsterdam and Amsterdam Gastroenterology and Metabolism Amsterdam University Medical Centers Amsterdam The Netherlands
- Oncode Institute Amsterdam The Netherlands
| | - Daniël M. Miedema
- Laboratory for Experimental Oncology and Radiobiology Center for Experimental and Molecular Medicine Cancer Center Amsterdam and Amsterdam Gastroenterology and Metabolism Amsterdam University Medical Centers Amsterdam The Netherlands
- Oncode Institute Amsterdam The Netherlands
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27
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Wu L, Shi S, Sun H, Zhang H. Tumor Size Is an Independent Prognostic Factor for Stage I Ovarian Clear Cell Carcinoma: A Large Retrospective Cohort Study of 1,000 Patients. Front Oncol 2022; 12:862944. [PMID: 35651798 PMCID: PMC9149085 DOI: 10.3389/fonc.2022.862944] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 04/11/2022] [Indexed: 11/13/2022] Open
Abstract
Objective The aim of this study was to investigate the prognostic value and stratification cutoff point for tumor size in stage I ovarian clear cell carcinoma (OCCC). Methods This was a retrospective cohort study using the Surveillance, Epidemiology, and End Results database (version: SEER 8.3.9). Patients diagnosed with stage I OCCC from 1988 to 2018 were included for further analysis. X-Tile software was used to identify the potential cutoff point for tumor size. Stratification analysis, propensity score matching, and inverse probability weighting analysis were used to balance the potential confounding factors. Results A total of 1,000 stage I OCCC patients were included. Of these 1,000 patients, median follow-up was 106 months (95% confidence interval [CI]: 89-112 months). Multivariate analysis showed that tumor size, age at diagnosis, and stage IC were significantly associated with stage I OCCC patients. Eight centimeters is a promising cutoff point that can divide stage I OCCC patients into a good or a poor prognosis group. After controlling potential confounding factors with propensity score matching and inverse probability weighting, we demonstrated that stage I OCCC patients with tumor size ≤ 8 cm enjoyed a significantly better 5-year overall survival (OS, 89.8% vs. 81%, p < 0.0001). Tumor size ≤ 8 cm was an independent prognostic factor of stage I OCCC patients (hazard ratio [HR] 0.5608, 95% CI: 0.4126-0.7622, p = 0.0002). Conclusions Tumor size is an independent prognostic factor for stage I OCCC, and 8 cm is a promising cutoff point for tumor size for risk stratification. However, using tumor size in the stratification management of stage I OCCC patients warrants further investigation.
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Affiliation(s)
| | | | - Hong Sun
- Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
| | - Haiyan Zhang
- Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
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28
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Gutierrez C, Vilas CK, Wu CJ, Al'Khafaji AM. Functionalized Lineage Tracing Can Enable the Development of Homogenization-Based Therapeutic Strategies in Cancer. Front Immunol 2022; 13:859032. [PMID: 35603167 PMCID: PMC9120583 DOI: 10.3389/fimmu.2022.859032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 03/22/2022] [Indexed: 11/13/2022] Open
Abstract
The therapeutic landscape across many cancers has dramatically improved since the introduction of potent targeted agents and immunotherapy. Nonetheless, success of these approaches is too often challenged by the emergence of therapeutic resistance, fueled by intratumoral heterogeneity and the immense evolutionary capacity inherent to cancers. To date, therapeutic strategies have attempted to outpace the evolutionary tempo of cancer but frequently fail, resulting in lack of tumor response and/or relapse. This realization motivates the development of novel therapeutic approaches which constrain evolutionary capacity by reducing the degree of intratumoral heterogeneity prior to treatment. Systematic development of such approaches first requires the ability to comprehensively characterize heterogeneous populations over the course of a perturbation, such as cancer treatment. Within this context, recent advances in functionalized lineage tracing approaches now afford the opportunity to efficiently measure multimodal features of clones within a tumor at single cell resolution, enabling the linkage of these features to clonal fitness over the course of tumor progression and treatment. Collectively, these measurements provide insights into the dynamic and heterogeneous nature of tumors and can thus guide the design of homogenization strategies which aim to funnel heterogeneous cancer cells into known, targetable phenotypic states. We anticipate the development of homogenization therapeutic strategies to better allow for cancer eradication and improved clinical outcomes.
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Affiliation(s)
- Catherine Gutierrez
- Department of Medicine, Harvard Medical School, Boston, MA, United States
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, United States
| | - Caroline K Vilas
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, United States
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, TX, United States
| | - Catherine J Wu
- Department of Medicine, Harvard Medical School, Boston, MA, United States
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, United States
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, United States
- Broad Institute of MIT and Harvard, Cambridge, MA, United States
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29
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Emerging Role for 7T MRI and Metabolic Imaging for Pancreatic and Liver Cancer. Metabolites 2022; 12:metabo12050409. [PMID: 35629913 PMCID: PMC9145477 DOI: 10.3390/metabo12050409] [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: 03/25/2022] [Revised: 04/25/2022] [Accepted: 04/27/2022] [Indexed: 11/16/2022] Open
Abstract
Advances in magnet technologies have led to next generation 7T magnetic resonance scanners which can fit in the footprint and price point of conventional hospital scanners (1.5−3T). It is therefore worth asking if there is a role for 7T magnetic resonance imaging and spectroscopy for the treatment of solid tumor cancers. Herein, we survey the medical literature to evaluate the unmet clinical needs for patients with pancreatic and hepatic cancer, and the potential of ultra-high field proton imaging and phosphorus spectroscopy to fulfil those needs. We draw on clinical literature, preclinical data, nuclear magnetic resonance spectroscopic data of human derived samples, and the efforts to date with 7T imaging and phosphorus spectroscopy. At 7T, the imaging capabilities approach histological resolution. The spectral and spatial resolution enhancements at high field for phospholipid spectroscopy have the potential to reduce the number of exploratory surgeries due to tumor boundaries undefined at conventional field strengths. Phosphorus metabolic imaging at 7T magnetic field strength, is already a mainstay in preclinical models for molecular phenotyping, energetic status evaluation, dosimetry, and assessing treatment response for both pancreatic and liver cancers. Metabolic imaging of primary tumors and lymph nodes may provide powerful metrics to aid staging and treatment response. As tumor tissues contain extreme levels of phospholipid metabolites compared to the background signal, even spectroscopic volumes containing less than 50% tumor can be detected and/or monitored. Phosphorus spectroscopy allows non-invasive pH measurements, indicating hypoxia, as a predictor of patients likely to recur. We conclude that 7T multiparametric approaches that include metabolic imaging with phosphorus spectroscopy have the potential to meet the unmet needs of non-invasive location-specific treatment monitoring, lymph node staging, and the reduction in unnecessary surgeries for patients undergoing resections for pancreatic cancer. There is also potential for the use of 7T phosphorous spectra for the phenotyping of tumor subtypes and even early diagnosis (<2 mL). Whether or not 7T can be used for all patients within the next decade, the technology is likely to speed up the translation of new therapeutics.
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Distinguishing excess mutations and increased cell death based on variant allele frequencies. PLoS Comput Biol 2022; 18:e1010048. [PMID: 35468135 PMCID: PMC9071171 DOI: 10.1371/journal.pcbi.1010048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 05/05/2022] [Accepted: 03/22/2022] [Indexed: 12/03/2022] Open
Abstract
Tumors often harbor orders of magnitude more mutations than healthy tissues. The increased number of mutations may be due to an elevated mutation rate or frequent cell death and correspondingly rapid cell turnover, or a combination of the two. It is difficult to disentangle these two mechanisms based on widely available bulk sequencing data, where sequences from individual cells are intermixed and, thus, the cell lineage tree of the tumor cannot be resolved. Here we present a method that can simultaneously estimate the cell turnover rate and the rate of mutations from bulk sequencing data. Our method works by simulating tumor growth and finding the parameters with which the observed data can be reproduced with maximum likelihood. Applying this method to a real tumor sample, we find that both the mutation rate and the frequency of death may be high. Tumors frequently harbor an elevated number of mutations, compared to healthy tissue. These extra mutations may be generated either by an increased mutation rate or the presence of cell death resulting in increased cellular turnover and additional cell divisions for tumor growth. Separating the effects of these two factors is a nontrivial problem. Here we present a method which can simultaneously estimate cell turnover rate and genomic mutation rate from bulk sequencing data. Our method is based on the estimation of the parameters of a generative model of tumor growth and mutations. Applying our method to a human hepatocellular carcinoma sample reveals an elevated per cell division mutation rate and high cell turnover.
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Analysis of the Heterogeneity of the Tumor Microenvironment and the Prognosis and Immunotherapy Response of Different Immune Subtypes in Hepatocellular Carcinoma. JOURNAL OF ONCOLOGY 2022; 2022:1087399. [PMID: 35401750 PMCID: PMC8984740 DOI: 10.1155/2022/1087399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 03/04/2022] [Indexed: 11/17/2022]
Abstract
Purpose The current clinical classification of hepatocellular carcinoma (HCC) cannot well predict the patient's possible response to the treatment plan, nor can it predict the patient's prognosis. We use the gene expression patterns of patients with hepatocellular carcinoma to reveal the heterogeneity of hepatocellular carcinoma and analyze the differences in prognosis and immunotherapy response of different immune subtypes. Methods Firstly, using the hepatocellular carcinoma expression profile data of TCGA, combined with the single sample gene set enrichment analysis (ssGSEA) algorithm, the immune enrichment of the patient's tumor microenvironment was analyzed. Subsequently, the spectral clustering algorithm was used to extract different classifications, and the cohort of hepatocellular carcinoma was divided into 3 subtypes, and the correlation between immune subtypes and clinical characteristics and survival prognosis was established. The patient's risk index is obtained through the prognostic prediction model, suggesting the correlation between the risk index and various types of immune cells. Results We can divide the liver cancer cohort into three subtypes: stromal cell activated immune-enriched type (A-IS), general immune-enriched type (N-IS), and non-immune-enriched type (non-IS). The 3-year survival rate of TCGA's A-IS is higher than that of N-IS and non-IS, and the three components are significantly different (p = 0.017). The 3-year survival rates of ICGC's A-IS and N-IS groups were higher than those of the non-IS group. The analysis of the correlation between the risk index and immune cells showed that the patient's disease risk was significantly positively correlated with cancer-associated fibroblast (CAF) stimulated cell, activated stroma cell, and anti-PD-1 resistant cell. Conclusion The tumor gene expression characteristics of patients with hepatocellular carcinoma can be used as a basis for clinical patient classification. Different immune subtypes are closely related to survival prognosis. Different immune cell states of patients may lead to different disease risk levels. All these provide important references for the clinical identification and prognosis prediction of hepatocellular carcinoma.
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Deciphering Tumour Heterogeneity: From Tissue to Liquid Biopsy. Cancers (Basel) 2022; 14:cancers14061384. [PMID: 35326534 PMCID: PMC8946040 DOI: 10.3390/cancers14061384] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 03/04/2022] [Accepted: 03/05/2022] [Indexed: 12/12/2022] Open
Abstract
Simple Summary Most malignant tumours are highly heterogeneous at molecular and phenotypic levels. Tumour variability poses challenges for the management of patients, as it arises between patients and even evolves in space and time within a single patient. Currently, treatment-decision making usually relies on the molecular characteristics of a limited tumour tissue sample at the time of diagnosis or disease progression but does not take into account the complexity of the bulk tumours and their constant evolution over time. In this review, we explore the extent of tumour heterogeneity and report the mechanisms that promote and sustain this diversity in cancers. We summarise the clinical strikes of tumour diversity in the management of patients with cancer. Finally, we discuss the current material and technological approaches that are relevant to adequately appreciate tumour heterogeneity. Abstract Human solid malignancies harbour a heterogeneous set of cells with distinct genotypes and phenotypes. This heterogeneity is installed at multiple levels. A biological diversity is commonly observed between tumours from different patients (inter-tumour heterogeneity) and cannot be fully captured by the current consensus molecular classifications for specific cancers. To extend the complexity in cancer, there are substantial differences from cell to cell within an individual tumour (intra-tumour heterogeneity, ITH) and the features of cancer cells evolve in space and time. Currently, treatment-decision making usually relies on the molecular characteristics of a limited tumour tissue sample at the time of diagnosis or disease progression but does not take into account the complexity of the bulk tumours and their constant evolution over time. In this review, we explore the extent of tumour heterogeneity with an emphasis on ITH and report the mechanisms that promote and sustain this diversity in cancers. We summarise the clinical strikes of ITH in the management of patients with cancer. Finally, we discuss the current material and technological approaches that are relevant to adequately appreciate ITH.
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Tez M. Chronic mechanical irritation and oral squamous cell carcinoma: Let’s look from evolutionary perspective. Oral Oncol 2022; 125:105727. [DOI: 10.1016/j.oraloncology.2022.105727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 01/12/2022] [Indexed: 10/19/2022]
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Aliya S, Lee H, Alhammadi M, Umapathi R, Huh YS. An Overview on Single-Cell Technology for Hepatocellular Carcinoma Diagnosis. Int J Mol Sci 2022; 23:1402. [PMID: 35163329 PMCID: PMC8835749 DOI: 10.3390/ijms23031402] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 01/22/2022] [Accepted: 01/22/2022] [Indexed: 02/05/2023] Open
Abstract
Hepatocellular carcinoma is a primary liver cancer caused by the accumulation of genetic mutation patterns associated with epidemiological conditions. This lethal malignancy exhibits tumor heterogeneity, which is considered as one of the main reasons for drug resistance development and failure of clinical trials. Recently, single-cell technology (SCT), a new advanced sequencing technique that analyzes every single cell in a tumor tissue specimen, aids complete insight into the genetic heterogeneity of cancer. This helps in identifying and assessing rare cell populations by analyzing the difference in gene expression pattern between individual cells of single biopsy tissue which normally cannot be identified from pooled cell gene expression pattern (traditional sequencing technique). Thus, SCT improves the clinical diagnosis, treatment, and prognosis of hepatocellular carcinoma as the limitations of other techniques impede this cancer research progression. Application of SCT at the genomic, transcriptomic, and epigenomic levels to promote individualized hepatocellular carcinoma diagnosis and therapy. The current review has been divided into ten sections. Herein we deliberated on the SCT, hepatocellular carcinoma diagnosis, tumor microenvironment analysis, single-cell genomic sequencing, single-cell transcriptomics, single-cell omics sequencing for biomarker development, identification of hepatocellular carcinoma origination and evolution, limitations, challenges, conclusions, and future perspectives.
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Affiliation(s)
| | | | | | | | - Yun Suk Huh
- Department of Biological Sciences and Bioengineering, NanoBio High-Tech Materials Research Center, Inha University, Inha-ro 100, Incheon 22212, Korea; (S.A.); (H.L.); (M.A.); (R.U.)
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35
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Noble R, Burri D, Le Sueur C, Lemant J, Viossat Y, Kather JN, Beerenwinkel N. Spatial structure governs the mode of tumour evolution. Nat Ecol Evol 2022; 6:207-217. [PMID: 34949822 PMCID: PMC8825284 DOI: 10.1038/s41559-021-01615-9] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 11/10/2021] [Indexed: 12/12/2022]
Abstract
Characterizing the mode-the way, manner or pattern-of evolution in tumours is important for clinical forecasting and optimizing cancer treatment. Sequencing studies have inferred various modes, including branching, punctuated and neutral evolution, but it is unclear why a particular pattern predominates in any given tumour. Here we propose that tumour architecture is key to explaining the variety of observed genetic patterns. We examine this hypothesis using spatially explicit population genetics models and demonstrate that, within biologically relevant parameter ranges, different spatial structures can generate four tumour evolutionary modes: rapid clonal expansion, progressive diversification, branching evolution and effectively almost neutral evolution. Quantitative indices for describing and classifying these evolutionary modes are presented. Using these indices, we show that our model predictions are consistent with empirical observations for cancer types with corresponding spatial structures. The manner of cell dispersal and the range of cell-cell interactions are found to be essential factors in accurately characterizing, forecasting and controlling tumour evolution.
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Affiliation(s)
- Robert Noble
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland. .,SIB Swiss Institute of Bioinformatics, Basel, Switzerland. .,Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland. .,Department of Mathematics, City, University of London, London, UK.
| | - Dominik Burri
- grid.5801.c0000 0001 2156 2780Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland ,grid.6612.30000 0004 1937 0642Biozentrum, University of Basel, Basel, Switzerland
| | - Cécile Le Sueur
- grid.5801.c0000 0001 2156 2780Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Jeanne Lemant
- grid.5801.c0000 0001 2156 2780Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Yannick Viossat
- grid.11024.360000000120977052Ceremade, Université Paris Dauphine-PSL, Paris, France
| | - Jakob Nikolas Kather
- grid.7497.d0000 0004 0492 0584German Cancer Consortium (DKTK), Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584Applied Tumor Immunity, German Cancer Research Center (DKFZ), Heidelberg, Germany ,grid.412301.50000 0000 8653 1507Internal Medicine III, University Hospital RWTH Aachen, Aachen, Germany
| | - Niko Beerenwinkel
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland. .,SIB Swiss Institute of Bioinformatics, Basel, Switzerland.
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36
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Tez M. Comments on "Bridging Tumorigenesis and Therapy Resistance With a Non-Darwinian and Non-Lamarckian Mechanism of Adaptive Evolution". Front Oncol 2021; 11:775723. [PMID: 34966681 PMCID: PMC8710497 DOI: 10.3389/fonc.2021.775723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 11/16/2021] [Indexed: 11/18/2022] Open
Affiliation(s)
- Mesut Tez
- Department of Surgery, Ankara Numune Hospital, Ankara, Turkey
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37
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Ao H, Xin Z, Jian Z. Liquid biopsy to identify biomarkers for immunotherapy in hepatocellular carcinoma. Biomark Res 2021; 9:91. [PMID: 34930486 PMCID: PMC8686238 DOI: 10.1186/s40364-021-00348-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 11/03/2021] [Indexed: 12/12/2022] Open
Abstract
The past years have witnessed the vigorous development of immunotherapy, mainly immune checkpoint inhibitors (ICIs) targeting the programmed cell death-1 (PD-1) protein and its ligand, PD-L1, and cytotoxic T-lymphocyte-associated antigen-4 (CTLA-4). Indeed, ICIs have largely revolutionized the management and improved the prognosis of patients with intermediate and advanced hepatocellular carcinoma (HCC). However, biomarker-based stratification of HCC patients for optimal response to ICI treatment is still of unmet need and again, there exists the necessity to dynamically monitor treatment effect in real-time manner. The role of conventional biomarkers in immunotherapy surveillance is largely limited by spatial and temporal tumor heterogeneity whereas liquid biopsy seems to be promising to circumvent tumor heterogeneity to identify candidate patients who may response to immunotherapy, to dynamically monitor treatment effect and to unveil resistance mechanism. Herein, we provide a thorough review about the potential utility of liquid biopsy in immunotherapy for HCC and discuss its future perspectives.
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Affiliation(s)
- Huang Ao
- Department of Liver Surgery and Transplantation, Zhongshan Hospital, Fudan University; Key Laboratory of Carcinogenesis and Cancer Invasion (Fudan University), Ministry of Education; Shanghai Key Laboratory of Organ Transplantation, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Zhang Xin
- Department of Liver Surgery and Transplantation, Zhongshan Hospital, Fudan University; Key Laboratory of Carcinogenesis and Cancer Invasion (Fudan University), Ministry of Education; Shanghai Key Laboratory of Organ Transplantation, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Zhou Jian
- Department of Liver Surgery and Transplantation, Zhongshan Hospital, Fudan University; Key Laboratory of Carcinogenesis and Cancer Invasion (Fudan University), Ministry of Education; Shanghai Key Laboratory of Organ Transplantation, Zhongshan Hospital, Fudan University, Shanghai, 200032, China.
- Institute of Biomedical Sciences, Fudan University, Shanghai, 200032, China.
- State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China.
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, 136 Yi Xue Yuan Road, Shanghai, 200032, China.
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Li G, Yang Z, Wu D, Liu S, Li X, Li T, Li Y, Liang L, Zou W, Wu CI, Wang HY, Lu X. Evolution under spatially heterogeneous selection in solid tumors. Mol Biol Evol 2021; 39:6440067. [PMID: 34850073 PMCID: PMC8788224 DOI: 10.1093/molbev/msab335] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Spatial genetic and phenotypic diversity within solid tumors has been well documented. Nevertheless, how this heterogeneity affects temporal dynamics of tumorigenesis has not been rigorously examined because solid tumors do not evolve as the standard population genetic model due to the spatial constraint. We therefore, propose a neutral spatial (NS) model whereby the mutation accumulation increases toward the periphery; the genealogical relationship is spatially determined and the selection efficacy is blunted (due to kin competition). In this model, neutral mutations are accrued and spatially distributed in manners different from those of advantageous mutations. Importantly, the distinctions could be blurred in the conventional model. To test the NS model, we performed a three-dimensional multiple microsampling of two hepatocellular carcinomas. Whole-genome sequencing (WGS) revealed a 2-fold increase in mutations going from the center to the periphery. The operation of natural selection can then be tested by examining the spatially determined clonal relationships and the clonal sizes. Due to limited migration, only the expansion of highly advantageous clones can sweep through a large part of the tumor to reveal the selective advantages. Hence, even multiregional sampling can only reveal a fraction of fitness differences in solid tumors. Our results suggest that the NS patterns are crucial for testing the influence of natural selection during tumorigenesis, especially for small solid tumors.
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Affiliation(s)
- Guanghao Li
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,China National Center for Bioinformation, Beijing, 100101, China.,CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zuyu Yang
- China National Center for Bioinformation, Beijing, 100101, China.,CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China.,Institute of Environmental Science and Research, Porirua, New Zealand
| | - Dafei Wu
- China National Center for Bioinformation, Beijing, 100101, China.,CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China.,Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Sixue Liu
- China National Center for Bioinformation, Beijing, 100101, China.,CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xuening Li
- China National Center for Bioinformation, Beijing, 100101, China.,CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Tao Li
- China National Center for Bioinformation, Beijing, 100101, China.,CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yawei Li
- China National Center for Bioinformation, Beijing, 100101, China.,CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Liji Liang
- China National Center for Bioinformation, Beijing, 100101, China.,CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Weilong Zou
- Surgery of Liver Transplant, The Third Medical Center of Chinese PLA General Hospital, Beijing, 100039, China.,Surgery of Hepatopancreatobiliary, Peking University Shougang Hospital, Beijing, 100144, China
| | - Chung-I Wu
- China National Center for Bioinformation, Beijing, 100101, China.,CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China.,State Key Laboratory of Biocontrol, College of Ecology and Evolution, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Hurng-Yi Wang
- Graduate Institute of Clinical Medicine, National Taiwan University, Taipei, 11031, Taiwan.,Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei, 106, Taiwan
| | - Xuemei Lu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,China National Center for Bioinformation, Beijing, 100101, China.,CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
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Blomain ES, Moding EJ. Liquid Biopsies for Molecular Biology-Based Radiotherapy. Int J Mol Sci 2021; 22:11267. [PMID: 34681925 PMCID: PMC8538046 DOI: 10.3390/ijms222011267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 10/13/2021] [Accepted: 10/15/2021] [Indexed: 11/29/2022] Open
Abstract
Molecular alterations drive cancer initiation and evolution during development and in response to therapy. Radiotherapy is one of the most commonly employed cancer treatment modalities, but radiobiologic approaches for personalizing therapy based on tumor biology and individual risks remain to be defined. In recent years, analysis of circulating nucleic acids has emerged as a non-invasive approach to leverage tumor molecular abnormalities as biomarkers of prognosis and treatment response. Here, we evaluate the roles of circulating tumor DNA and related analyses as powerful tools for precision radiotherapy. We highlight emerging work advancing liquid biopsies beyond biomarker studies into translational research investigating tumor clonal evolution and acquired resistance.
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Affiliation(s)
- Erik S. Blomain
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA;
| | - Everett J. Moding
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA;
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
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40
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Personalization of medical treatments in oncology: time for rethinking the disease concept to improve individual outcomes. EPMA J 2021; 12:545-558. [PMID: 34642594 PMCID: PMC8495186 DOI: 10.1007/s13167-021-00254-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 09/01/2021] [Indexed: 12/12/2022]
Abstract
The agenda of pharmacology discovery in the field of personalized oncology was dictated by the search of molecular targets assumed to deterministically drive tumor development. In this perspective, genes play a fundamental "causal" role while cells simply act as causal proxies, i.e., an intermediate between the molecular input and the organismal output. However, the ceaseless genomic change occurring across time within the same primary and metastatic tumor has broken the hope of a personalized treatment based only upon genomic fingerprint. Indeed, current models are unable in capturing the unfathomable complexity behind the outbreak of a disease, as they discard the contribution of non-genetic factors, environment constraints, and the interplay among different tiers of organization. Herein, we posit that a comprehensive personalized model should view at the disease as a "historical" process, in which different spatially and timely distributed factors interact with each other across multiple levels of organization, which collectively interact with a dynamic gene-expression pattern. Given that a disease is a dynamic, non-linear process - and not a static-stable condition - treatments should be tailored according to the "timing-frame" of each condition. This approach can help in detecting those critical transitions through which the system can access different attractors leading ultimately to diverse outcomes - from a pre-disease state to an overt illness or, alternatively, to recovery. Identification of such tipping points can substantiate the predictive and the preventive ambition of the Predictive, Preventive and Personalized Medicine (PPPM/3PM). However, an unusual effort is required to conjugate multi-omics approaches, data collection, and network analysis reconstruction (eventually involving innovative Artificial Intelligent tools) to recognize the critical phases and the relevant targets, which could help in patient stratification and therapy personalization.
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41
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Gunnarsson EB, Leder K, Foo J. Exact site frequency spectra of neutrally evolving tumors: A transition between power laws reveals a signature of cell viability. Theor Popul Biol 2021; 142:67-90. [PMID: 34560155 DOI: 10.1016/j.tpb.2021.09.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 08/24/2021] [Accepted: 09/11/2021] [Indexed: 11/28/2022]
Abstract
The site frequency spectrum (SFS) is a popular summary statistic of genomic data. While the SFS of a constant-sized population undergoing neutral mutations has been extensively studied in population genetics, the rapidly growing amount of cancer genomic data has attracted interest in the spectrum of an exponentially growing population. Recent theoretical results have generally dealt with special or limiting cases, such as considering only cells with an infinite line of descent, assuming deterministic tumor growth, or taking large-time or large-population limits. In this work, we derive exact expressions for the expected SFS of a cell population that evolves according to a stochastic branching process, first for cells with an infinite line of descent and then for the total population, evaluated either at a fixed time (fixed-time spectrum) or at the stochastic time at which the population reaches a certain size (fixed-size spectrum). We find that while the rate of mutation scales the SFS of the total population linearly, the rates of cell birth and cell death change the shape of the spectrum at the small-frequency end, inducing a transition between a 1/j2 power-law spectrum and a 1/j spectrum as cell viability decreases. We show that this insight can in principle be used to estimate the ratio between the rate of cell death and cell birth, as well as the mutation rate, using the site frequency spectrum alone. Although the discussion is framed in terms of tumor dynamics, our results apply to any exponentially growing population of individuals undergoing neutral mutations.
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Affiliation(s)
- Einar Bjarki Gunnarsson
- Department of Industrial and Systems Engineering, University of Minnesota, Twin Cities, MN 55455, USA.
| | - Kevin Leder
- Department of Industrial and Systems Engineering, University of Minnesota, Twin Cities, MN 55455, USA.
| | - Jasmine Foo
- School of Mathematics, University of Minnesota, Twin Cities, MN 55455, USA.
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Vendramin R, Litchfield K, Swanton C. Cancer evolution: Darwin and beyond. EMBO J 2021; 40:e108389. [PMID: 34459009 PMCID: PMC8441388 DOI: 10.15252/embj.2021108389] [Citation(s) in RCA: 108] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 06/04/2021] [Accepted: 06/25/2021] [Indexed: 12/16/2022] Open
Abstract
Clinical and laboratory studies over recent decades have established branched evolution as a feature of cancer. However, while grounded in somatic selection, several lines of evidence suggest a Darwinian model alone is insufficient to fully explain cancer evolution. First, the role of macroevolutionary events in tumour initiation and progression contradicts Darwin's central thesis of gradualism. Whole-genome doubling, chromosomal chromoplexy and chromothripsis represent examples of single catastrophic events which can drive tumour evolution. Second, neutral evolution can play a role in some tumours, indicating that selection is not always driving evolution. Third, increasing appreciation of the role of the ageing soma has led to recent generalised theories of age-dependent carcinogenesis. Here, we review these concepts and others, which collectively argue for a model of cancer evolution which extends beyond Darwin. We also highlight clinical opportunities which can be grasped through targeting cancer vulnerabilities arising from non-Darwinian patterns of evolution.
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Affiliation(s)
- Roberto Vendramin
- Cancer Research UK Lung Cancer Centre of ExcellenceUniversity College London Cancer InstituteLondonUK
| | - Kevin Litchfield
- Cancer Research UK Lung Cancer Centre of ExcellenceUniversity College London Cancer InstituteLondonUK
| | - Charles Swanton
- Cancer Research UK Lung Cancer Centre of ExcellenceUniversity College London Cancer InstituteLondonUK
- Cancer Evolution and Genome Instability LaboratoryThe Francis Crick InstituteLondonUK
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Qin Y, Zhou J, Fan Z, Gu J, Li X, Lin D, Deng D, Wei W. Evaluation of the Impact of Intratumoral Heterogeneity of Esophageal Cancer on Pathological Diagnosis and P16 Methylation and the Representativity of Endoscopic Biopsy. Front Oncol 2021; 11:683876. [PMID: 34485122 PMCID: PMC8416173 DOI: 10.3389/fonc.2021.683876] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 07/27/2021] [Indexed: 01/22/2023] Open
Abstract
Background P16 methylation is expected to be potential diagnostic and therapeutic targets for esophageal cancer (EC). The intratumoral heterogeneity (ITH) of EC has been mentioned but has not been quantitatively measured yet. We aimed to clarify the impact of ITH on pathological diagnosis and P16 methylation, and the concordance between endoscopic biopsy and the corresponding surgically resected tissue. Methods We designed a systematic sampling method (SSM) compared with a general sampling method (GSM) to obtain EC tumor tissue, tumor biopsy, and normal squamous epithelium biopsy. MethyLight assay was utilized to test P16 methylation. All specimens obtained by the SSM were pathologically diagnosed. Results A total of 81 cases were collected by the GSM, and 91.4% and 8.6% of them were esophageal squamous cell carcinomas (ESCCs) and esophageal adenocarcinomas (EADs), respectively. Nine SSM cases were 100.0% ESCCs. The positive rates of P16 methylation of the GSM tumor and normal tissues were 63.0% (51/81) and 32.1% (26/81), respectively. For SSM samples, tumor tissues were 100.0% (40/40) EC and 85.0% (34/40) P16 methylated; tumor biopsy was 64.4% (29/45) diagnosed of EC and 68.9% P16 methylated; the corresponding normal biopsies were 15.7% (8/51) dysplasia and 54.9% (28/51) P16 methylated. The concordance of pathological diagnosis and P16 methylation between tumor biopsy and the corresponding tumor tissue was 75.0% and 62.5%, respectively. Conclusion The SSM we designed was efficient in measuring the ITH of EC. We found inadequate concordance between tumor biopsy and tissue in pathological diagnosis and P16 methylation.
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Affiliation(s)
- Yu Qin
- National Cancer Registry Office, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jing Zhou
- Key Laboratory of Carcinogenesis and Translational Research, Peking University Cancer Hospital, Beijing, China
| | - Zhiyuan Fan
- National Cancer Registry Office, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jianhua Gu
- National Cancer Registry Office, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xinqing Li
- National Cancer Registry Office, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Dongmei Lin
- Department of Pathology, Peking University Cancer Hospital, Beijing, China
| | - Dajun Deng
- Key Laboratory of Carcinogenesis and Translational Research, Peking University Cancer Hospital, Beijing, China
| | - Wenqiang Wei
- National Cancer Registry Office, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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Niida A, Mimori K, Shibata T, Miyano S. Modeling colorectal cancer evolution. J Hum Genet 2021; 66:869-878. [PMID: 33986478 PMCID: PMC8384629 DOI: 10.1038/s10038-021-00930-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 04/09/2021] [Accepted: 04/13/2021] [Indexed: 11/27/2022]
Abstract
Understanding cancer evolution provides a clue to tackle therapeutic difficulties in colorectal cancer. In this review, together with related works, we will introduce a series of our studies, in which we constructed an evolutionary model of colorectal cancer by combining genomic analysis and mathematical modeling. In our model, multiple subclones were generated by driver mutation acquisition and subsequent clonal expansion in early-stage tumors. Among the subclones, the one obtaining driver copy number alterations is endowed with malignant potentials to constitute a late-stage tumor in which extensive intratumor heterogeneity is generated by the accumulation of neutral mutations. We will also discuss how to translate our understanding of cancer evolution to a solution to the problem related to therapeutic resistance: mathematical modeling suggests that relapse caused by acquired resistance could be suppressed by utilizing clonal competition between sensitive and resistant clones. Considering the current rate of technological development, modeling cancer evolution by combining genomic analysis and mathematical modeling will be an increasingly important approach for understanding and overcoming cancer.
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Affiliation(s)
- Atsushi Niida
- Laboratory of Molecular Medicine, Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
| | - Koshi Mimori
- Department of Surgery, Kyushu University Beppu Hospital, Beppu, Japan
| | - Tatsuhiro Shibata
- Laboratory of Molecular Medicine, Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Satoru Miyano
- M&D Data Science Center, Tokyo Medical and Dental University, Tokyo, Japan
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45
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Parker TM, Gupta K, Palma AM, Yekelchyk M, Fisher PB, Grossman SR, Won KJ, Madan E, Moreno E, Gogna R. Cell competition in intratumoral and tumor microenvironment interactions. EMBO J 2021; 40:e107271. [PMID: 34368984 DOI: 10.15252/embj.2020107271] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 06/14/2021] [Accepted: 06/16/2021] [Indexed: 12/18/2022] Open
Abstract
Tumors are complex cellular and acellular environments within which cancer clones are under continuous selection pressures. Cancer cells are in a permanent mode of interaction and competition with each other as well as with the immediate microenvironment. In the course of these competitive interactions, cells share information regarding their general state of fitness, with less-fit cells being typically eliminated via apoptosis at the hands of those cells with greater cellular fitness. Competitive interactions involving exchange of cell fitness information have implications for tumor growth, metastasis, and therapy outcomes. Recent research has highlighted sophisticated pathways such as Flower, Hippo, Myc, and p53 signaling, which are employed by cancer cells and the surrounding microenvironment cells to achieve their evolutionary goals by means of cell competition mechanisms. In this review, we discuss these recent findings and explain their importance and role in evolution, growth, and treatment of cancer. We further consider potential physiological conditions, such as hypoxia and chemotherapy, that can function as selective pressures under which cell competition mechanisms may evolve differently or synergistically to confer oncogenic advantages to cancer.
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Affiliation(s)
- Taylor M Parker
- Department of Biochemistry, West Virginia University School of Medicine, Morgantown, WV, USA
| | - Kartik Gupta
- Department of Surgery, School of Medicine and Public Health, University of Wisconsin, Madison, WI, USA
| | | | - Michail Yekelchyk
- Department of Cardiac Development and Remodelling, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Paul B Fisher
- Department of Human and Molecular Genetics, School of Medicine, Virginia Commonwealth University, Richmond, VA, USA.,VCU Massey Cancer Center, School of Medicine, Virginia Commonwealth University, Richmond, VA, USA.,VCU Institute of Molecular Medicine, Virginia Commonwealth University, School of Medicine, Richmond, VA, USA
| | - Steven R Grossman
- Department of Medicine, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Kyoung Jae Won
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen North, Denmark.,Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, University of Copenhagen, Copenhagen North, Denmark
| | - Esha Madan
- Champalimaud Centre for the Unknown, Lisbon, Portugal
| | | | - Rajan Gogna
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen North, Denmark.,Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, University of Copenhagen, Copenhagen North, Denmark
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46
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Yao N, Schmitz RJ, Johannes F. Epimutations Define a Fast-Ticking Molecular Clock in Plants. Trends Genet 2021; 37:699-710. [PMID: 34016450 PMCID: PMC8282728 DOI: 10.1016/j.tig.2021.04.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 04/15/2021] [Accepted: 04/16/2021] [Indexed: 12/16/2022]
Abstract
Stochastic gains and losses of DNA methylation at CG dinucleotides are a frequent occurrence in plants. These spontaneous 'epimutations' occur at a rate that is 100 000 times higher than the genetic mutation rate, are effectively neutral at the genome-wide scale, and are stably inherited across mitotic and meiotic cell divisions. Mathematical models have been extraordinarily successful at describing how epimutations accumulate in plant genomes over time, making this process one of the most predictable epigenetic phenomena to date. Here, we propose that their high rate and effective neutrality make epimutations a powerful new molecular clock for timing evolutionary events of the recent past and for age dating of long-lived perennials such as trees.
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Affiliation(s)
- Nan Yao
- Department of Genetics, University of Georgia, Athens, GA, USA
| | - Robert J Schmitz
- Department of Genetics, University of Georgia, Athens, GA, USA; Institute for Advanced Study, Technical University of Munich, Garching, Germany
| | - Frank Johannes
- Institute for Advanced Study, Technical University of Munich, Garching, Germany; Population Epigenetics and Epigenomics, Technical University of Munich, Freising, Germany.
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47
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Lu Z, Nie B, Zhai W, Hu Z. Delineating the longitudinal tumor evolution using organoid models. J Genet Genomics 2021; 48:560-570. [PMID: 34366272 DOI: 10.1016/j.jgg.2021.06.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 06/11/2021] [Accepted: 06/16/2021] [Indexed: 02/07/2023]
Abstract
Cancer is an evolutionary process fueled by genetic or epigenetic alterations in the genome. Understanding the evolutionary dynamics that are operative at different stages of tumor progression might inform effective strategies in early detection, diagnosis, and treatment of cancer. However, our understanding on the dynamics of tumor evolution through time is very limited since it is usually impossible to sample patient tumors repeatedly. The recent advances in in vitro 3D organoid culture technologies have opened new avenues for the development of more realistic human cancer models that mimic many in vivo biological characteristics in human tumors. Here, we review recent progresses and challenges in cancer genomic evolution studies and advantages of using tumor organoids to study cancer evolution. We propose to establish an experimental evolution model based on continuous passages of patient-derived organoids and longitudinal sampling to study clonal dynamics and evolutionary patterns over time. Development and integration of population genetic theories and computational models into time-course genomic data in tumor organoids will help to pinpoint the key cellular mechanisms underlying cancer evolutionary dynamics, thus providing novel insights on therapeutic strategies for highly dynamic and heterogeneous tumors.
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Affiliation(s)
- Zhaolian Lu
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Beina Nie
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Weiwei Zhai
- CAS Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
| | - Zheng Hu
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.
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48
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scDPN for High-throughput Single-cell CNV Detection to Uncover Clonal Evolution During HCC Recurrence. GENOMICS PROTEOMICS & BIOINFORMATICS 2021; 19:346-357. [PMID: 34280548 PMCID: PMC8864190 DOI: 10.1016/j.gpb.2021.03.008] [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: 01/24/2021] [Revised: 12/10/2020] [Accepted: 03/06/2021] [Indexed: 11/28/2022]
Abstract
Single-cell genomics provides substantial resources for dissecting cellular heterogeneity and cancer evolution. Unfortunately, classical DNA amplification-based methods have low throughput and introduce coverage bias during sample preamplification. We developed a single-cell DNA library preparation method without preamplification in nanolitre scale (scDPN) to address these issues. The method achieved a throughput of up to 1800 cells per run for copy number variation (CNV) detection. Also, our approach demonstrated a lower level of amplification bias and noise than the multiple displacement amplification (MDA) method and showed high sensitivity and accuracy for cell line and tumor tissue evaluation. We used this approach to profile the tumor clones in paired primary and relapsed tumor samples of hepatocellular carcinoma (HCC). We identified three clonal subpopulations with a multitude of aneuploid alterations across the genome. Furthermore, we observed that a minor clone of the primary tumor containing additional alterations in chromosomes 1q, 10q, and 14q developed into the dominant clone in the recurrent tumor, indicating clonal selection during recurrence in HCC. Overall, this approach provides a comprehensive and scalable solution to understand genome heterogeneity and evolution
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Chan DKH, Buczacki SJA. Tumour heterogeneity and evolutionary dynamics in colorectal cancer. Oncogenesis 2021; 10:53. [PMID: 34272358 PMCID: PMC8285471 DOI: 10.1038/s41389-021-00342-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 06/21/2021] [Accepted: 06/28/2021] [Indexed: 12/25/2022] Open
Abstract
Colorectal cancer (CRC) has a global burden of disease. Our current understanding of CRC has progressed from initial discoveries which focused on the stepwise accumulation of key driver mutations, as encapsulated in the Vogelstein model, to one in which marked heterogeneity leads to a complex interplay between clonal populations. Current evidence suggests that an initial explosion, or “Big Bang”, of genetic diversity is followed by a period of neutral dynamics. A thorough understanding of this interplay between clonal populations during neutral evolution gives insights into the roles in which driver genes may participate in the progress from normal colonic epithelium to adenoma and carcinoma. Recent advances have focused not only on genetics, transcriptomics, and proteomics but have also investigated the ecological and evolutionary processes which transform normal cells into cancer. This review first describes the role which driver mutations play in the Vogelstein model and subsequently demonstrates the evidence which supports a more complex model. This article also aims to underscore the significance of tumour heterogeneity and diverse clonal populations in cancer progression.
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Affiliation(s)
- Dedrick Kok Hong Chan
- Nuffield Department of Surgical Sciences, Medical Sciences Division, University of Oxford, Oxford, UK
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50
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Mitochondrial Heteroplasmy Shifting as a Potential Biomarker of Cancer Progression. Int J Mol Sci 2021; 22:ijms22147369. [PMID: 34298989 PMCID: PMC8304746 DOI: 10.3390/ijms22147369] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 06/25/2021] [Accepted: 06/28/2021] [Indexed: 02/07/2023] Open
Abstract
Cancer is a serious health problem with a high mortality rate worldwide. Given the relevance of mitochondria in numerous physiological and pathological mechanisms, such as adenosine triphosphate (ATP) synthesis, apoptosis, metabolism, cancer progression and drug resistance, mitochondrial genome (mtDNA) analysis has become of great interest in the study of human diseases, including cancer. To date, a high number of variants and mutations have been identified in different types of tumors, which coexist with normal alleles, a phenomenon named heteroplasmy. This mechanism is considered an intermediate state between the fixation or elimination of the acquired mutations. It is suggested that mutations, which confer adaptive advantages to tumor growth and invasion, are enriched in malignant cells. Notably, many recent studies have reported a heteroplasmy-shifting phenomenon as a potential shaper in tumor progression and treatment response, and we suggest that each cancer type also has a unique mitochondrial heteroplasmy-shifting profile. So far, a plethora of data evidencing correlations among heteroplasmy and cancer-related phenotypes are available, but still, not authentic demonstrations, and whether the heteroplasmy or the variation in mtDNA copy number (mtCNV) in cancer are cause or consequence remained unknown. Further studies are needed to support these findings and decipher their clinical implications and impact in the field of drug discovery aimed at treating human cancer.
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