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Ma W, Tang W, Kwok JS, Tong AH, Lo CW, Chu AT, Chung BH. A review on trends in development and translation of omics signatures in cancer. Comput Struct Biotechnol J 2024; 23:954-971. [PMID: 38385061 PMCID: PMC10879706 DOI: 10.1016/j.csbj.2024.01.024] [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: 10/27/2023] [Revised: 01/31/2024] [Accepted: 01/31/2024] [Indexed: 02/23/2024] Open
Abstract
The field of cancer genomics and transcriptomics has evolved from targeted profiling to swift sequencing of individual tumor genome and transcriptome. The steady growth in genome, epigenome, and transcriptome datasets on a genome-wide scale has significantly increased our capability in capturing signatures that represent both the intrinsic and extrinsic biological features of tumors. These biological differences can help in precise molecular subtyping of cancer, predicting tumor progression, metastatic potential, and resistance to therapeutic agents. In this review, we summarized the current development of genomic, methylomic, transcriptomic, proteomic and metabolic signatures in the field of cancer research and highlighted their potentials in clinical applications to improve diagnosis, prognosis, and treatment decision in cancer patients.
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Affiliation(s)
- Wei Ma
- Hong Kong Genome Institute, Hong Kong, China
| | - Wenshu Tang
- Hong Kong Genome Institute, Hong Kong, China
| | | | | | | | | | - Brian H.Y. Chung
- Hong Kong Genome Institute, Hong Kong, China
- Department of Pediatrics and Adolescent Medicine, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Hong Kong Genome Project
- Hong Kong Genome Institute, Hong Kong, China
- Department of Pediatrics and Adolescent Medicine, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
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2
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Deyell RJ, Shen Y, Titmuss E, Dixon K, Williamson LM, Pleasance E, Nelson JMT, Abbasi S, Krzywinski M, Armstrong L, Bonakdar M, Ch'ng C, Chuah E, Dunham C, Fok A, Jones M, Lee AF, Ma Y, Moore RA, Mungall AJ, Mungall KL, Rogers PC, Schrader KA, Virani A, Wee K, Young SS, Zhao Y, Jones SJM, Laskin J, Marra MA, Rassekh SR. Whole genome and transcriptome integrated analyses guide clinical care of pediatric poor prognosis cancers. Nat Commun 2024; 15:4165. [PMID: 38755180 PMCID: PMC11099106 DOI: 10.1038/s41467-024-48363-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 04/29/2024] [Indexed: 05/18/2024] Open
Abstract
The role for routine whole genome and transcriptome analysis (WGTA) for poor prognosis pediatric cancers remains undetermined. Here, we characterize somatic mutations, structural rearrangements, copy number variants, gene expression, immuno-profiles and germline cancer predisposition variants in children and adolescents with relapsed, refractory or poor prognosis malignancies who underwent somatic WGTA and matched germline sequencing. Seventy-nine participants with a median age at enrollment of 8.8 y (range 6 months to 21.2 y) are included. Germline pathogenic/likely pathogenic variants are identified in 12% of participants, of which 60% were not known prior. Therapeutically actionable variants are identified by targeted gene report and whole genome in 32% and 62% of participants, respectively, and increase to 96% after integrating transcriptome analyses. Thirty-two molecularly informed therapies are pursued in 28 participants with 54% achieving a clinical benefit rate; objective response or stable disease ≥6 months. Integrated WGTA identifies therapeutically actionable variants in almost all tumors and are directly translatable to clinical care of children with poor prognosis cancers.
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Affiliation(s)
- Rebecca J Deyell
- Department of Pediatrics, BC Children's Hospital and Research Institute, Vancouver, BC, Canada.
| | - Yaoqing Shen
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Emma Titmuss
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Katherine Dixon
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Laura M Williamson
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Erin Pleasance
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Jessica M T Nelson
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Sanna Abbasi
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Martin Krzywinski
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Linlea Armstrong
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Melika Bonakdar
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Carolyn Ch'ng
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Eric Chuah
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Chris Dunham
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Alexandra Fok
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Martin Jones
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Anna F Lee
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Yussanne Ma
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Richard A Moore
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Andrew J Mungall
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Karen L Mungall
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Paul C Rogers
- Department of Pediatrics, BC Children's Hospital and Research Institute, Vancouver, BC, Canada
| | - Kasmintan A Schrader
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Alice Virani
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Kathleen Wee
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Sean S Young
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
- Cancer Genetics and Genomics Laboratory, Department of Pathology and Laboratory Medicine, BC Cancer, Vancouver, Canada
| | - Yongjun Zhao
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Steven J M Jones
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Janessa Laskin
- Department of Medical Oncology, BC Cancer, Vancouver, BC, Canada
| | - Marco A Marra
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Shahrad R Rassekh
- Department of Pediatrics, BC Children's Hospital and Research Institute, Vancouver, BC, Canada.
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3
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Speer RM, Nandi SP, Cooper KL, Zhou X, Yu H, Guo Y, Hudson LG, Alexandrov LB, Liu KJ. Arsenic is a potent co-mutagen of ultraviolet light. Commun Biol 2023; 6:1273. [PMID: 38104187 PMCID: PMC10725444 DOI: 10.1038/s42003-023-05659-4] [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: 02/22/2023] [Accepted: 12/01/2023] [Indexed: 12/19/2023] Open
Abstract
Arsenic enhances the carcinogenicity of ultraviolet radiation (UVR). However, the mechanisms of arsenic-driven oncogenesis are not well understood. Here, we utilize experimental systems to investigate the carcinogenic and mutagenic properties of co-exposure to arsenic and UVR. In vitro and in vivo exposures indicate that, by itself, arsenic is not mutagenic. However, in combination with UVR, arsenic exposure has a synergistic effect leading to an accelerated mouse skin carcinogenesis and to more than 2-fold enrichment of UVR mutational burden. Notably, mutational signature ID13, previously found only in UVR-associated human skin cancers, is observed exclusively in mouse skin tumors and cell lines jointly exposed to arsenic and UVR. This signature was not observed in any model system exposed purely to arsenic or purely to UVR, making ID13, to the best of our knowledge, the first co-exposure signature to be reported using controlled experimental conditions. Analysis of existing skin cancer genomics data reveals that only a subset of cancers harbor ID13 and these exhibit an elevated UVR mutagenesis. Our results report a unique mutational signature caused by a co-exposure to two environmental carcinogens and provide comprehensive evidence that arsenic is a potent co-mutagen and co-carcinogen of UVR.
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Affiliation(s)
- Rachel M Speer
- Department of Pharmaceutical Sciences, College of Pharmacy, University of New Mexico, Albuquerque, NM, 87106, USA
| | - Shuvro P Nandi
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, 92093, USA
- Moores Cancer Center, UC San Diego, La Jolla, CA, 92037, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA, 92093, USA
| | - Karen L Cooper
- Department of Pharmaceutical Sciences, College of Pharmacy, University of New Mexico, Albuquerque, NM, 87106, USA
| | - Xixi Zhou
- Department of Pharmaceutical Sciences, College of Pharmacy, University of New Mexico, Albuquerque, NM, 87106, USA
| | - Hui Yu
- Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, 33136, USA
| | - Yan Guo
- Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, 33136, USA
| | - Laurie G Hudson
- Department of Pharmaceutical Sciences, College of Pharmacy, University of New Mexico, Albuquerque, NM, 87106, USA
| | - Ludmil B Alexandrov
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, 92093, USA.
- Moores Cancer Center, UC San Diego, La Jolla, CA, 92037, USA.
- Department of Bioengineering, UC San Diego, La Jolla, CA, 92093, USA.
| | - Ke Jian Liu
- Department of Pharmaceutical Sciences, College of Pharmacy, University of New Mexico, Albuquerque, NM, 87106, USA.
- Stony Brook Cancer Center, Stony Brook University, Stony Brook, NY, 11794, USA.
- Department of Pathology, Stony Brook University School of Medicine, Stony Brook, NY, 11794, USA.
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Sangiorgi E, Giannuzzi F, Molinario C, Rapari G, Riccio M, Cuffaro G, Castri F, Benvenuto R, Genuardi M, Massi D, Savino G. Base-Excision Repair Mutational Signature in Two Sebaceous Carcinomas of the Eyelid. Genes (Basel) 2023; 14:2055. [PMID: 38002998 PMCID: PMC10671510 DOI: 10.3390/genes14112055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 11/03/2023] [Accepted: 11/07/2023] [Indexed: 11/26/2023] Open
Abstract
Personalized medicine aims to develop tailored treatments for individual patients based on specific mutations present in the affected organ. This approach has proven paramount in cancer treatment, as each tumor carries distinct driver mutations that respond to targeted drugs and, in some cases, may confer resistance to other therapies. Particularly for rare conditions, personalized medicine has the potential to revolutionize treatment strategies. Rare cancers often lack extensive datasets of molecular and pathological information, large-scale trials for novel therapies, and established treatment guidelines. Consequently, surgery is frequently the only viable option for many rare tumors, when feasible, as traditional multimodal approaches employed for more common cancers often play a limited role. Sebaceous carcinoma of the eyelid is an exceptionally rare cancer affecting the eye's adnexal tissues, most frequently reported in Asia, but whose prevalence is significantly increasing even in Europe and the US. The sole established curative treatment is surgical excision, which can lead to significant disfigurement. In cases of metastatic sebaceous carcinoma, validated drug options are currently lacking. In this project, we set out to characterize the mutational landscape of two sebaceous carcinomas of the eyelid following surgical excision. Utilizing available bioinformatics tools, we demonstrated our ability to identify common features promptly and accurately in both tumors. These features included a Base-Excision Repair mutational signature, a notably high tumor mutational burden, and key driver mutations in somatic tissues. These findings had not been previously reported in similar studies. This report underscores how, in the case of rare tumors, it is possible to comprehensively characterize the mutational landscape of each individual case, potentially opening doors to targeted therapeutic options.
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Affiliation(s)
- Eugenio Sangiorgi
- Sezione di Medicina Genomica, Dipartimento di Scienze della Vita e Sanità Pubblica, Università Cattolica del Sacro Cuore, 00168 Roma, Italy; (G.R.); (M.R.); (M.G.)
| | - Federico Giannuzzi
- Ocular Oncology Unit, Fondazione Policlinico Universitario A. Gemelli-IRCCS, Università Cattolica del Sacro Cuore, 00168 Roma, Italy; (F.G.); (G.C.); (G.S.)
| | - Clelia Molinario
- Division of Anatomic Pathology and Histology, Fondazione Policlinico Universitario A. Gemelli-IRCCS, Università Cattolica del Sacro Cuore, 00168 Roma, Italy; (C.M.); (F.C.); (R.B.)
| | - Giulia Rapari
- Sezione di Medicina Genomica, Dipartimento di Scienze della Vita e Sanità Pubblica, Università Cattolica del Sacro Cuore, 00168 Roma, Italy; (G.R.); (M.R.); (M.G.)
| | - Melania Riccio
- Sezione di Medicina Genomica, Dipartimento di Scienze della Vita e Sanità Pubblica, Università Cattolica del Sacro Cuore, 00168 Roma, Italy; (G.R.); (M.R.); (M.G.)
| | - Giovanni Cuffaro
- Ocular Oncology Unit, Fondazione Policlinico Universitario A. Gemelli-IRCCS, Università Cattolica del Sacro Cuore, 00168 Roma, Italy; (F.G.); (G.C.); (G.S.)
| | - Federica Castri
- Division of Anatomic Pathology and Histology, Fondazione Policlinico Universitario A. Gemelli-IRCCS, Università Cattolica del Sacro Cuore, 00168 Roma, Italy; (C.M.); (F.C.); (R.B.)
| | - Roberta Benvenuto
- Division of Anatomic Pathology and Histology, Fondazione Policlinico Universitario A. Gemelli-IRCCS, Università Cattolica del Sacro Cuore, 00168 Roma, Italy; (C.M.); (F.C.); (R.B.)
| | - Maurizio Genuardi
- Sezione di Medicina Genomica, Dipartimento di Scienze della Vita e Sanità Pubblica, Università Cattolica del Sacro Cuore, 00168 Roma, Italy; (G.R.); (M.R.); (M.G.)
- UOC Genetica Medica, Fondazione Policlinico Universitario A. Gemelli-IRCCS, 00168 Roma, Italy
| | - Daniela Massi
- Section of Pathology, Department of Health Sciences, University of Florence, 50121 Florence, Italy;
| | - Gustavo Savino
- Ocular Oncology Unit, Fondazione Policlinico Universitario A. Gemelli-IRCCS, Università Cattolica del Sacro Cuore, 00168 Roma, Italy; (F.G.); (G.C.); (G.S.)
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