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Zhakula-Kostadinova N, Taylor AM. Patterns of Aneuploidy and Signaling Consequences in Cancer. Cancer Res 2024; 84:2575-2587. [PMID: 38924459 PMCID: PMC11325152 DOI: 10.1158/0008-5472.can-24-0169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 03/29/2024] [Accepted: 06/20/2024] [Indexed: 06/28/2024]
Abstract
Aneuploidy, or a change in the number of whole chromosomes or chromosome arms, is a near-universal feature of cancer. Chromosomes affected by aneuploidy are not random, with observed cancer-specific and tissue-specific patterns. Recent advances in genome engineering methods have allowed the creation of models with targeted aneuploidy events. These models can be used to uncover the downstream effects of individual aneuploidies on cancer phenotypes including proliferation, apoptosis, metabolism, and immune signaling. Here, we review the current state of research into the patterns of aneuploidy in cancer and their impact on signaling pathways and biological processes.
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Affiliation(s)
- Nadja Zhakula-Kostadinova
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, New York
- Department of Genetics and Development, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York
| | - Alison M Taylor
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, New York
- Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York
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2
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Mohapatra B, Pakala SB. Emerging roles of the chromatin remodeler MORC2 in cancer metabolism. Med Oncol 2024; 41:221. [PMID: 39117768 DOI: 10.1007/s12032-024-02464-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2024] [Accepted: 07/26/2024] [Indexed: 08/10/2024]
Abstract
Cancer is characterized by metabolic reprogramming in cancer cells, which is crucial for tumorigenesis. The highly deregulated chromatin remodeler MORC2 contributes to cell proliferation, invasion, migration, DNA repair, and chemoresistance. MORC2 also plays a key role in metabolic reprogramming, including lipogenesis, glucose, and glutamine metabolism. A recent study showed that MORC2-regulated glucose metabolism affects the expression of E-cadherin, a crucial protein in the epithelial-to-mesenchymal transition. This review discusses recent developments in MORC2 regulated cancer cell metabolism and its role in cancer progression.
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Affiliation(s)
- Bibhukalyan Mohapatra
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, 500 046, India
| | - Suresh B Pakala
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, 500 046, India.
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3
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Shahrouzi P, Forouz F, Mathelier A, Kristensen VN, Duijf PHG. Copy number alterations: a catastrophic orchestration of the breast cancer genome. Trends Mol Med 2024; 30:750-764. [PMID: 38772764 DOI: 10.1016/j.molmed.2024.04.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 04/12/2024] [Accepted: 04/26/2024] [Indexed: 05/23/2024]
Abstract
Breast cancer (BCa) is a prevalent malignancy that predominantly affects women around the world. Somatic copy number alterations (CNAs) are tumor-specific amplifications or deletions of DNA segments that often drive BCa development and therapy resistance. Hence, the complex patterns of CNAs complement BCa classification systems. In addition, understanding the precise contributions of CNAs is essential for tailoring personalized treatment approaches. This review highlights how tumor evolution drives the acquisition of CNAs, which in turn shape the genomic landscapes of BCas. It also discusses advanced methodologies for identifying recurrent CNAs, studying CNAs in BCa and their clinical impact.
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Affiliation(s)
- Parastoo Shahrouzi
- Department of Medical Genetics, Institute of Basic Medical Science, Faculty of Medicine, University of Oslo and Oslo University Hospital, Oslo, Norway.
| | - Farzaneh Forouz
- School of Pharmacy, University of Queensland, Woolloongabba, Brisbane, Australia
| | - Anthony Mathelier
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, 0318 Oslo, Norway; Center for Bioinformatics, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway; Department of Medical Genetics, Institute of Clinical Medicine, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Vessela N Kristensen
- Department of Medical Genetics, Institute of Clinical Medicine, University of Oslo and Oslo University Hospital, Oslo, Norway; Division of Medicine, Department of Clinical Molecular Biology and Laboratory Science (EpiGen), Akershus University Hospital, Lørenskog, Norway; Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Pascal H G Duijf
- Department of Medical Genetics, Institute of Clinical Medicine, University of Oslo and Oslo University Hospital, Oslo, Norway; Centre for Cancer Biology, UniSA Clinical and Health Sciences, University of South Australia and SA Pathology, Adelaide, Australia.
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4
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Chen X, Agustinus AS, Li J, DiBona M, Bakhoum SF. Chromosomal instability as a driver of cancer progression. Nat Rev Genet 2024:10.1038/s41576-024-00761-7. [PMID: 39075192 DOI: 10.1038/s41576-024-00761-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/25/2024] [Indexed: 07/31/2024]
Abstract
Chromosomal instability (CIN) refers to an increased propensity of cells to acquire structural and numerical chromosomal abnormalities during cell division, which contributes to tumour genetic heterogeneity. CIN has long been recognized as a hallmark of cancer, and evidence over the past decade has strongly linked CIN to tumour evolution, metastasis, immune evasion and treatment resistance. Until recently, the mechanisms by which CIN propels cancer progression have remained elusive. Beyond the generation of genomic copy number heterogeneity, recent work has unveiled additional tumour-promoting consequences of abnormal chromosome segregation. These mechanisms include complex chromosomal rearrangements, epigenetic reprogramming and the induction of cancer cell-intrinsic inflammation, emphasizing the multifaceted role of CIN in cancer.
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Affiliation(s)
- Xuelan Chen
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Albert S Agustinus
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Pharmacology Graduate Program, Weill Cornell Medicine, New York, NY, USA
| | - Jun Li
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Melody DiBona
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Samuel F Bakhoum
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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5
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Sanjaya A, Ratnawati H, Adhika OA, Rahmatilah FR. The heterogeneity of breast cancer metastasis: a bioinformatics analysis utilizing single-cell RNA sequencing data. Breast Cancer Res Treat 2024:10.1007/s10549-024-07428-1. [PMID: 38992286 DOI: 10.1007/s10549-024-07428-1] [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: 04/07/2024] [Accepted: 07/02/2024] [Indexed: 07/13/2024]
Abstract
PURPOSE Breast cancer is a common malignancy in women, and its metastasis is a leading cause of cancer-related deaths. Single-cell RNA sequencing (scRNA-seq) can distinguish the molecular characteristics of metastasis and identify predictor genes for patient prognosis. This article explores gene expression in primary breast cancer tumor tissue against metastatic cells in the lymph node and liver using scRNA-seq. METHODS Breast cancer scRNA-seq data from the Gene Expression Omnibus were used. The data were processed using R and the Seurat package. The cells were clustered and identified using Metascape. InferCNV is used to analyze the variation in copy number. Differential expression analysis was conducted for the cancer cells using Seurat and was enriched using Metascape. RESULTS We identified 18 distinct cell clusters, 6 of which were epithelial. CNV analysis identified significant alterations with duplication of chromosomes 1, 8, and 19. Differential gene analysis resulted in 17 upregulated and 171 downregulated genes for the primary tumor in the primary tumor vs. liver metastasis comparison and 43 upregulated and 4 downregulated genes in the primary tumor in the primary tumor vs lymph node metastasis comparison. Several enriched terms include Ribosome biogenesis, NTP synthesis, Epithelial dedifferentiation, Autophagy, and genes associated with epithelial-to-mesenchymal transitions. CONCLUSION No single gene or pathway can clearly explain the mechanisms behind tumor metastasis. Several mechanisms contribute to lymph node and liver metastasis, such as the loss of differentiation, epithelial-to-mesenchymal transition, and autophagy. These findings necessitate further study of metastatic tissue for effective drug development.
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Affiliation(s)
- Ardo Sanjaya
- Department of Anatomy, Faculty of Medicine, Maranatha Christian University, Jl. Surya Sumantri No. 65, Bandung, 40164, West Java, Indonesia.
- Biomedical Research Laboratory, Faculty of Medicine, Maranatha Christian University, Bandung, 40164, West Java, Indonesia.
| | - Hana Ratnawati
- Biomedical Research Laboratory, Faculty of Medicine, Maranatha Christian University, Bandung, 40164, West Java, Indonesia
- Department of Histology, Faculty of Medicine, Maranatha Christian University, Bandung, 40164, West Java, Indonesia
| | - Oeij Anindita Adhika
- Department of Anatomy, Faculty of Medicine, Maranatha Christian University, Jl. Surya Sumantri No. 65, Bandung, 40164, West Java, Indonesia
| | - Faiz Rizqy Rahmatilah
- Undergraduate Program in Medicine, Faculty of Medicine, Maranatha Christian University, Bandung, 40164, West Java, Indonesia
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6
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Carey-Smith SL, Kotecha RS, Cheung LC, Malinge S. Insights into the Clinical, Biological and Therapeutic Impact of Copy Number Alteration in Cancer. Int J Mol Sci 2024; 25:6815. [PMID: 38999925 PMCID: PMC11241182 DOI: 10.3390/ijms25136815] [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: 05/21/2024] [Revised: 06/15/2024] [Accepted: 06/17/2024] [Indexed: 07/14/2024] Open
Abstract
Copy number alterations (CNAs), resulting from the gain or loss of genetic material from as little as 50 base pairs or as big as entire chromosome(s), have been associated with many congenital diseases, de novo syndromes and cancer. It is established that CNAs disturb the dosage of genomic regions including enhancers/promoters, long non-coding RNA and gene(s) among others, ultimately leading to an altered balance of key cellular functions. In cancer, CNAs have been associated with almost all steps of the disease: predisposition, initiation, development, maintenance, response to treatment, resistance, and relapse. Therefore, understanding how specific CNAs contribute to tumourigenesis may provide prognostic insight and ultimately lead to the development of new therapeutic approaches to improve patient outcomes. In this review, we provide a snapshot of what is currently known about CNAs and cancer, incorporating topics regarding their detection, clinical impact, origin, and nature, and discuss the integration of innovative genetic engineering strategies, to highlight the potential for targeting CNAs using novel, dosage-sensitive and less toxic therapies for CNA-driven cancer.
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Affiliation(s)
- Shannon L. Carey-Smith
- Telethon Kids Cancer Centre, Telethon Kids Institute, Perth, WA 6009, Australia; (S.L.C.-S.); (R.S.K.); (L.C.C.)
- Curtin Medical School, Curtin University, Perth, WA 6102, Australia
| | - Rishi S. Kotecha
- Telethon Kids Cancer Centre, Telethon Kids Institute, Perth, WA 6009, Australia; (S.L.C.-S.); (R.S.K.); (L.C.C.)
- Curtin Medical School, Curtin University, Perth, WA 6102, Australia
- Department of Clinical Haematology, Oncology, Blood and Marrow Transplantation, Perth Children’s Hospital, Perth, WA 6009, Australia
- UWA Medical School, University of Western Australia, Perth, WA 6009, Australia
| | - Laurence C. Cheung
- Telethon Kids Cancer Centre, Telethon Kids Institute, Perth, WA 6009, Australia; (S.L.C.-S.); (R.S.K.); (L.C.C.)
- Curtin Medical School, Curtin University, Perth, WA 6102, Australia
- Curtin Health Innovation Research Institute, Curtin University, Perth, WA 6102, Australia
| | - Sébastien Malinge
- Telethon Kids Cancer Centre, Telethon Kids Institute, Perth, WA 6009, Australia; (S.L.C.-S.); (R.S.K.); (L.C.C.)
- Curtin Medical School, Curtin University, Perth, WA 6102, Australia
- UWA Medical School, University of Western Australia, Perth, WA 6009, Australia
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7
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Liang W, Yang X, Li X, Wang P, Zhu Z, Liu S, Xu D, Zhi X, Xue J. Investigating gene signatures associated with immunity in colon adenocarcinoma to predict the immunotherapy effectiveness using NFM and WGCNA algorithms. Aging (Albany NY) 2024; 16:7596-7621. [PMID: 38742936 PMCID: PMC11131999 DOI: 10.18632/aging.205763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 03/26/2024] [Indexed: 05/16/2024]
Abstract
Colon adenocarcinoma (COAD), a frequently encountered and highly lethal malignancy of the digestive system, has been the focus of intensive research regarding its prognosis. The intricate immune microenvironment plays a pivotal role in the pathological progression of COAD; nevertheless, the underlying molecular mechanisms remain incompletely understood. This study aims to explore the immune gene expression patterns in COAD, construct a robust prognostic model, and delve into the molecular mechanisms and potential therapeutic targets for COAD liver metastasis, thereby providing critical support for individualized treatment strategies and prognostic evaluation. Initially, we curated a comprehensive dataset by screening 2600 immune-related genes (IRGs) from the ImmPort and InnateDB databases, successfully obtaining a rich data resource. Subsequently, the COAD patient cohort was classified using the non-negative matrix factorization (NMF) algorithm, enabling accurate categorization. Continuing on, utilizing the weighted gene co-expression network analysis (WGCNA) method, we analyzed the top 5000 genes with the smallest p-values among the differentially expressed genes (DEGs) between immune subtypes. Through this rigorous screening process, we identified the gene modules with the strongest correlation to the COAD subpopulation, and the intersection of genes in these modules with DEGs (COAD vs COAD vs Normal colon tissue) is referred to as Differentially Expressed Immune Genes Associated with COAD (DEIGRC). Employing diverse bioinformatics methodologies, we successfully developed a prognostic model (DPM) consisting of six genes derived from the DEIGRC, which was further validated across multiple independent datasets. Not only does this predictive model accurately forecast the prognosis of COAD patients, but it also provides valuable insights for formulating personalized treatment regimens. Within the constructed DPM, we observed a downregulation of CALB2 expression levels in COAD tissues, whereas NOXA1, KDF1, LARS2, GSR, and TIMP1 exhibited upregulated expression levels. These genes likely play indispensable roles in the initiation and progression of COAD and thus represent potential therapeutic targets for patient management. Furthermore, our investigation into the molecular mechanisms and therapeutic targets for COAD liver metastasis revealed associations with relevant processes such as fat digestion and absorption, cancer gene protein polysaccharides, and nitrogen metabolism. Consequently, genes including CAV1, ANXA1, CPS1, EDNRA, and GC emerge as promising candidates as therapeutic targets for COAD liver metastasis, thereby providing crucial insights for future clinical practices and drug development. In summary, this study uncovers the immune gene expression patterns in COAD, establishes a robust prognostic model, and elucidates the molecular mechanisms and potential therapeutic targets for COAD liver metastasis, thereby possessing significant theoretical and clinical implications. These findings are anticipated to offer substantial support for both the treatment and prognosis management of COAD patients.
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Affiliation(s)
- Weizheng Liang
- Central Laboratory, The First Affiliated Hospital of Hebei North University, Zhangjiakou 075000, Hebei, China
- Department of General Surgery, The First Affiliated Hospital of Hebei North University, Zhangjiakou 075000, Hebei, China
| | - Xiangyu Yang
- Department of Gastroenterology and Hepatology, The Second Affiliated Hospital of Chongqing Medical University, Yuzhong 400010, Chongqing, China
| | - Xiushen Li
- Department of Obstetrics and Gynecology, Shenzhen University General Hospital, Shenzhen 518055, Guangdong, China
| | - Peng Wang
- Department of General Surgery, The First Affiliated Hospital of Hebei North University, Zhangjiakou 075000, Hebei, China
| | - Zhenpeng Zhu
- Department of General Surgery, The First Affiliated Hospital of Hebei North University, Zhangjiakou 075000, Hebei, China
| | - Shan Liu
- Bioimaging Core of Shenzhen Bay Laboratory Shenzhen, Shenzhen 518132, Guangdong, China
| | - Dandan Xu
- Central Laboratory, The First Affiliated Hospital of Hebei North University, Zhangjiakou 075000, Hebei, China
| | - Xuejun Zhi
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Hebei North University, Zhangjiakou 075000, Hebei, China
| | - Jun Xue
- Department of General Surgery, The First Affiliated Hospital of Hebei North University, Zhangjiakou 075000, Hebei, China
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8
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Barriga FM, Lowe SW. Engineering megabase-sized genomic deletions with MACHETE (Molecular Alteration of Chromosomes with Engineered Tandem Elements). Nat Protoc 2024; 19:1381-1399. [PMID: 38326496 DOI: 10.1038/s41596-024-00953-9] [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: 06/01/2023] [Accepted: 11/21/2023] [Indexed: 02/09/2024]
Abstract
The elimination of large genomic regions has been enabled by the advent of site-specific nucleases. However, as the intended deletions get larger, the efficiency of successful engineering decreases to a point where it is not feasible to retrieve edited cells due to the rarity of on-target events. To address this issue, we developed a system called molecular alteration of chromosomes with engineered tandem elements (MACHETE). MACHETE is a CRISPR-Cas9-based system involving two stages: the initial insertion of a bicistronic positive/negative selection cassette to the locus of interest. This is followed by the introduction of single-guide RNAs flanking the knockin cassette to engineer the intended deletion, where only cells that have lost the locus survive the negative selection. In contrast to other approaches optimizing the activity of sequence-specific nucleases, MACHETE selects for the deletion event itself, thus greatly enriching for cells with the engineered alteration. The procedure routinely takes 4-6 weeks from design to selection of polyclonal populations bearing the deletion of interest. We have successfully deployed MACHETE to engineer deletions of up to 45 Mb, as well as the rapid creation of allelic series to map the relevant activities within a locus. This protocol details the design and step-by-step procedure to engineer megabase-sized deletions in cells of interest, with potential application for cancer genetics, transcriptional regulation, genome architecture and beyond.
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Affiliation(s)
- Francisco M Barriga
- Systems Oncology Program, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain.
| | - Scott W Lowe
- Cancer Biology and Genetics Program and Howard Hughes Medical Institute, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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Kuzmin E, Baker TM, Lesluyes T, Monlong J, Abe KT, Coelho PP, Schwartz M, Del Corpo J, Zou D, Morin G, Pacis A, Yang Y, Martinez C, Barber J, Kuasne H, Li R, Bourgey M, Fortier AM, Davison PG, Omeroglu A, Guiot MC, Morris Q, Kleinman CL, Huang S, Gingras AC, Ragoussis J, Bourque G, Van Loo P, Park M. Evolution of chromosome-arm aberrations in breast cancer through genetic network rewiring. Cell Rep 2024; 43:113988. [PMID: 38517886 PMCID: PMC11063629 DOI: 10.1016/j.celrep.2024.113988] [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: 09/01/2023] [Revised: 02/02/2024] [Accepted: 03/07/2024] [Indexed: 03/24/2024] Open
Abstract
The basal breast cancer subtype is enriched for triple-negative breast cancer (TNBC) and displays consistent large chromosomal deletions. Here, we characterize evolution and maintenance of chromosome 4p (chr4p) loss in basal breast cancer. Analysis of The Cancer Genome Atlas data shows recurrent deletion of chr4p in basal breast cancer. Phylogenetic analysis of a panel of 23 primary tumor/patient-derived xenograft basal breast cancers reveals early evolution of chr4p deletion. Mechanistically we show that chr4p loss is associated with enhanced proliferation. Gene function studies identify an unknown gene, C4orf19, within chr4p, which suppresses proliferation when overexpressed-a member of the PDCD10-GCKIII kinase module we name PGCKA1. Genome-wide pooled overexpression screens using a barcoded library of human open reading frames identify chromosomal regions, including chr4p, that suppress proliferation when overexpressed in a context-dependent manner, implicating network interactions. Together, these results shed light on the early emergence of complex aneuploid karyotypes involving chr4p and adaptive landscapes shaping breast cancer genomes.
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Affiliation(s)
- Elena Kuzmin
- Rosalind and Morris Goodman Cancer Institute, Montreal, QC H3A 1A3, Canada; Department of Biochemistry, McGill University, Montreal, QC H3G 1Y6, Canada.
| | | | | | - Jean Monlong
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada; McGill Genome Centre, Montreal, QC H3A 0G1, Canada
| | - Kento T Abe
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health, Toronto, ON M5G 1X5, Canada
| | - Paula P Coelho
- Rosalind and Morris Goodman Cancer Institute, Montreal, QC H3A 1A3, Canada; Department of Biochemistry, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Michael Schwartz
- Rosalind and Morris Goodman Cancer Institute, Montreal, QC H3A 1A3, Canada; Department of Biochemistry, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Joseph Del Corpo
- Department of Biology, Concordia University, Montreal, QC H4B 1R6, Canada
| | - Dongmei Zou
- Rosalind and Morris Goodman Cancer Institute, Montreal, QC H3A 1A3, Canada
| | - Genevieve Morin
- Rosalind and Morris Goodman Cancer Institute, Montreal, QC H3A 1A3, Canada; Department of Biochemistry, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Alain Pacis
- McGill Genome Centre, Montreal, QC H3A 0G1, Canada; Canadian Centre for Computational Genomics (C3G), McGill University, Montreal, QC H3A 0G1, Canada
| | - Yang Yang
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada
| | - Constanza Martinez
- Rosalind and Morris Goodman Cancer Institute, Montreal, QC H3A 1A3, Canada; Department of Pathology, McGill University, Montreal, QC H3A 2B4, Canada; Gerald Bronfman Department of Oncology, McGill University, Montreal, QC H4A 3T2, Canada
| | - Jarrett Barber
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Vector Institute, Toronto, ON M5G 1M1, Canada; Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada; Computational and Systems Biology, Sloan Kettering Institute, New York City, NY 10065, USA
| | - Hellen Kuasne
- Rosalind and Morris Goodman Cancer Institute, Montreal, QC H3A 1A3, Canada
| | - Rui Li
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada; McGill Genome Centre, Montreal, QC H3A 0G1, Canada
| | - Mathieu Bourgey
- McGill Genome Centre, Montreal, QC H3A 0G1, Canada; Canadian Centre for Computational Genomics (C3G), McGill University, Montreal, QC H3A 0G1, Canada
| | - Anne-Marie Fortier
- Rosalind and Morris Goodman Cancer Institute, Montreal, QC H3A 1A3, Canada
| | - Peter G Davison
- Department of Surgery, McGill University, Montreal, QC H3G 1A4, Canada; McGill University Health Centre, Montreal, QC H4A 3J1, Canada
| | - Atilla Omeroglu
- Department of Pathology, McGill University, Montreal, QC H3A 2B4, Canada
| | | | - Quaid Morris
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Vector Institute, Toronto, ON M5G 1M1, Canada; Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada; Computational and Systems Biology, Sloan Kettering Institute, New York City, NY 10065, USA; Gerstner Sloan Kettering Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Claudia L Kleinman
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada; Lady Davis Institute for Medical Research, Montreal, QC H3T 1E2, Canada
| | - Sidong Huang
- Rosalind and Morris Goodman Cancer Institute, Montreal, QC H3A 1A3, Canada; Department of Biochemistry, McGill University, Montreal, QC H3G 1Y6, Canada; Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada
| | - Anne-Claude Gingras
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health, Toronto, ON M5G 1X5, Canada
| | - Jiannis Ragoussis
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada; McGill Genome Centre, Montreal, QC H3A 0G1, Canada
| | - Guillaume Bourque
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada; McGill Genome Centre, Montreal, QC H3A 0G1, Canada; Canadian Centre for Computational Genomics (C3G), McGill University, Montreal, QC H3A 0G1, Canada
| | - Peter Van Loo
- The Francis Crick Institute, NW1 1AT London, UK; Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Morag Park
- Rosalind and Morris Goodman Cancer Institute, Montreal, QC H3A 1A3, Canada; Department of Biochemistry, McGill University, Montreal, QC H3G 1Y6, Canada; Gerald Bronfman Department of Oncology, McGill University, Montreal, QC H4A 3T2, Canada.
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10
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Jubran J, Slutsky R, Rozenblum N, Rokach L, Ben-David U, Yeger-Lotem E. Machine-learning analysis reveals an important role for negative selection in shaping cancer aneuploidy landscapes. Genome Biol 2024; 25:95. [PMID: 38622679 PMCID: PMC11020441 DOI: 10.1186/s13059-024-03225-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 03/26/2024] [Indexed: 04/17/2024] Open
Abstract
BACKGROUND Aneuploidy, an abnormal number of chromosomes within a cell, is a hallmark of cancer. Patterns of aneuploidy differ across cancers, yet are similar in cancers affecting closely related tissues. The selection pressures underlying aneuploidy patterns are not fully understood, hindering our understanding of cancer development and progression. RESULTS Here, we apply interpretable machine learning methods to study tissue-selective aneuploidy patterns. We define 20 types of features corresponding to genomic attributes of chromosome-arms, normal tissues, primary tumors, and cancer cell lines (CCLs), and use them to model gains and losses of chromosome arms in 24 cancer types. To reveal the factors that shape the tissue-specific cancer aneuploidy landscapes, we interpret the machine learning models by estimating the relative contribution of each feature to the models. While confirming known drivers of positive selection, our quantitative analysis highlights the importance of negative selection for shaping aneuploidy landscapes. This is exemplified by tumor suppressor gene density being a better predictor of gain patterns than oncogene density, and vice versa for loss patterns. We also identify the importance of tissue-selective features and demonstrate them experimentally, revealing KLF5 as an important driver for chr13q gain in colon cancer. Further supporting an important role for negative selection in shaping the aneuploidy landscapes, we find compensation by paralogs to be among the top predictors of chromosome arm loss prevalence and demonstrate this relationship for one paralog interaction. Similar factors shape aneuploidy patterns in human CCLs, demonstrating their relevance for aneuploidy research. CONCLUSIONS Our quantitative, interpretable machine learning models improve the understanding of the genomic properties that shape cancer aneuploidy landscapes.
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Affiliation(s)
- Juman Jubran
- Department of Clinical Biochemistry and Pharmacology, Ben-Gurion University of the Negev, 84105, Beer Sheva, Israel
| | - Rachel Slutsky
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Nir Rozenblum
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Lior Rokach
- Department of Software & Information Systems Engineering, Ben-Gurion University of the Negev, 84105, Beer Sheva, Israel
| | - Uri Ben-David
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.
| | - Esti Yeger-Lotem
- Department of Clinical Biochemistry and Pharmacology, Ben-Gurion University of the Negev, 84105, Beer Sheva, Israel.
- The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, 84105, Beer Sheva, Israel.
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11
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Hosea R, Hillary S, Naqvi S, Wu S, Kasim V. The two sides of chromosomal instability: drivers and brakes in cancer. Signal Transduct Target Ther 2024; 9:75. [PMID: 38553459 PMCID: PMC10980778 DOI: 10.1038/s41392-024-01767-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 01/18/2024] [Accepted: 02/06/2024] [Indexed: 04/02/2024] Open
Abstract
Chromosomal instability (CIN) is a hallmark of cancer and is associated with tumor cell malignancy. CIN triggers a chain reaction in cells leading to chromosomal abnormalities, including deviations from the normal chromosome number or structural changes in chromosomes. CIN arises from errors in DNA replication and chromosome segregation during cell division, leading to the formation of cells with abnormal number and/or structure of chromosomes. Errors in DNA replication result from abnormal replication licensing as well as replication stress, such as double-strand breaks and stalled replication forks; meanwhile, errors in chromosome segregation stem from defects in chromosome segregation machinery, including centrosome amplification, erroneous microtubule-kinetochore attachments, spindle assembly checkpoint, or defective sister chromatids cohesion. In normal cells, CIN is deleterious and is associated with DNA damage, proteotoxic stress, metabolic alteration, cell cycle arrest, and senescence. Paradoxically, despite these negative consequences, CIN is one of the hallmarks of cancer found in over 90% of solid tumors and in blood cancers. Furthermore, CIN could endow tumors with enhanced adaptation capabilities due to increased intratumor heterogeneity, thereby facilitating adaptive resistance to therapies; however, excessive CIN could induce tumor cells death, leading to the "just-right" model for CIN in tumors. Elucidating the complex nature of CIN is crucial for understanding the dynamics of tumorigenesis and for developing effective anti-tumor treatments. This review provides an overview of causes and consequences of CIN, as well as the paradox of CIN, a phenomenon that continues to perplex researchers. Finally, this review explores the potential of CIN-based anti-tumor therapy.
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Affiliation(s)
- Rendy Hosea
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400045, China
- The 111 Project Laboratory of Biomechanics and Tissue Repair, College of Bioengineering, Chongqing University, Chongqing, 400044, China
| | - Sharon Hillary
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400045, China
- The 111 Project Laboratory of Biomechanics and Tissue Repair, College of Bioengineering, Chongqing University, Chongqing, 400044, China
| | - Sumera Naqvi
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400045, China
- The 111 Project Laboratory of Biomechanics and Tissue Repair, College of Bioengineering, Chongqing University, Chongqing, 400044, China
| | - Shourong Wu
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400045, China.
- The 111 Project Laboratory of Biomechanics and Tissue Repair, College of Bioengineering, Chongqing University, Chongqing, 400044, China.
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, Chongqing University, Chongqing, 400030, China.
| | - Vivi Kasim
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400045, China.
- The 111 Project Laboratory of Biomechanics and Tissue Repair, College of Bioengineering, Chongqing University, Chongqing, 400044, China.
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, Chongqing University, Chongqing, 400030, China.
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12
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Bhatia S, Khanna KK, Duijf PHG. Targeting chromosomal instability and aneuploidy in cancer. Trends Pharmacol Sci 2024; 45:210-224. [PMID: 38355324 DOI: 10.1016/j.tips.2024.01.009] [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: 12/21/2023] [Revised: 01/18/2024] [Accepted: 01/19/2024] [Indexed: 02/16/2024]
Abstract
Cancer development and therapy resistance are driven by chromosomal instability (CIN), which causes chromosome gains and losses (i.e., aneuploidy) and structural chromosomal alterations. Technical limitations and knowledge gaps have delayed therapeutic targeting of CIN and aneuploidy in cancers. However, our toolbox for creating and studying aneuploidy in cell models has greatly expanded recently. Moreover, accumulating evidence suggests that seven conventional antimitotic chemotherapeutic drugs achieve clinical response by inducing CIN instead of mitotic arrest, although additional anticancer activities may also contribute in vivo. In this review, we discuss these recent developments. We also highlight new discoveries, which together show that 25 chromosome arm aneuploidies (CAAs) may be targetable by 36 drugs across 14 types of cancer. Collectively, these advances offer many new opportunities to improve cancer treatment.
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Affiliation(s)
- Sugandha Bhatia
- Queensland University of Technology (QUT), School of Biomedical Sciences, Centre for Genomics and Personalised Health and Centre for Biomedical Technologies at the Translational Research Institute, Woolloongabba, QLD 4102, Australia.
| | - Kum Kum Khanna
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, QLD 4006, Australia; Mater Research Institute, The University of Queensland, Translational Research Institute, Woolloongabba, QLD 4102, Australia
| | - Pascal H G Duijf
- Queensland University of Technology (QUT), School of Biomedical Sciences, Centre for Genomics and Personalised Health and Centre for Biomedical Technologies at the Translational Research Institute, Woolloongabba, QLD 4102, Australia; Centre for Cancer Biology, Clinical and Health Sciences, University of South Australia and SA Pathology, Adelaide, SA 5001, Australia; Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway; Department of Medical Genetics, Oslo University Hospital, Oslo, Norway.
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13
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Hattori T, Fundora KA, Hamamoto K, Opozda DM, Liang X, Liu X, Zhang J, Uzun Y, Takahashi Y, Wang HG. ER stress elicits non-canonical CASP8 (caspase 8) activation on autophagosomal membranes to induce apoptosis. Autophagy 2024; 20:349-364. [PMID: 37733908 PMCID: PMC10813646 DOI: 10.1080/15548627.2023.2258701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 09/07/2023] [Indexed: 09/23/2023] Open
Abstract
The VPS37A gene encodes a subunit of the endosomal sorting complex required for transport (ESCRT)-I complex that is frequently lost in a wide variety of human solid cancers. We have previously demonstrated the role of VPS37A in directing the ESCRT membrane scission machinery to seal the phagophore for autophagosome completion. Here, we report that VPS37A-deficient cells exhibit an accumulation of the apoptotic initiator CASP8 (caspase 8) on the phagophore and are primed to undergo rapid apoptosis through the intracellular death-inducing signaling complex (iDISC)-mediated CASP8 activation upon exposure to endoplasmic reticulum (ER) stress. Using CRISPR-Cas9 gene editing and comparative transcriptome analysis, we identified the ATF4-mediated stress response pathway as a crucial mediator to elicit iDISC-mediated apoptosis following the inhibition of autophagosome closure. Notably, ATF4-mediated iDISC activation occurred independently of the death receptor TNFRSF10B/DR5 upregulation but required the pro-apoptotic transcriptional factor DDIT3/CHOP to enhance the mitochondrial amplification pathway for full-activation of CASP8 in VPS37A-deficient cells stimulated with ER stress inducers. Our analysis also revealed the upregulation of NFKB/NF-kB signaling as a potential mechanism responsible for restraining iDISC activation and promoting cell survival upon VPS37A depletion. These findings have important implications for the future development of new strategies to treat human cancers, especially those with VPS37A loss.Abbreviations: ATG: autophagy related; BMS: BMS-345541; CASP: caspase; CHMP: charged multivesicular body protein; DKO: double knockout; Dox: doxycycline; ER: endoplasmic reticulum; ESCRT: endosomal sorting complex required for transport; gRNA: guide RNA; GSEA: gene set enrichment analysis; GSK157: GSK2656157; iDISC: intracellular death-inducing signaling complex; IKK: inhibitor of NFKB kinase; IPA: ingenuity pathway analysis; KO: knockout; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; NFKB/NF-kB: nuclear factor kappa B; OZ: 5Z-7-oxozeaenol; RNA-seq: RNA sequencing; UPR: unfolded protein response; TFT: transcription factor target; THG: thapsigargin; TUN: tunicamycin; VPS: vacuolar protein sorting.
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Affiliation(s)
- Tatsuya Hattori
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, The Pennsylvania State University College of Medicine, Hershey, PA, USA
- Department of Pharmacology, The Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Kevin A. Fundora
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, The Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Kouta Hamamoto
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, The Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - David M. Opozda
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, The Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Xinwen Liang
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, The Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Xiaoming Liu
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, The Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Jiawen Zhang
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, The Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Yasin Uzun
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, The Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Yoshinori Takahashi
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, The Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Hong-Gang Wang
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, The Pennsylvania State University College of Medicine, Hershey, PA, USA
- Department of Pharmacology, The Pennsylvania State University College of Medicine, Hershey, PA, USA
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14
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Huth T, Dreher EC, Lemke S, Fritzsche S, Sugiyanto RN, Castven D, Ibberson D, Sticht C, Eiteneuer E, Jauch A, Pusch S, Albrecht T, Goeppert B, Candia J, Wang XW, Ji J, Marquardt JU, Nahnsen S, Schirmacher P, Roessler S. Chromosome 8p engineering reveals increased metastatic potential targetable by patient-specific synthetic lethality in liver cancer. SCIENCE ADVANCES 2023; 9:eadh1442. [PMID: 38134284 PMCID: PMC10745716 DOI: 10.1126/sciadv.adh1442] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 11/22/2023] [Indexed: 12/24/2023]
Abstract
Large-scale chromosomal aberrations are prevalent in human cancer, but their function remains poorly understood. We established chromosome-engineered hepatocellular carcinoma cell lines using CRISPR-Cas9 genome editing. A 33-mega-base pair region on chromosome 8p (chr8p) was heterozygously deleted, mimicking a frequently observed chromosomal deletion. Using this isogenic model system, we delineated the functional consequences of chr8p loss and its impact on metastatic behavior and patient survival. We found that metastasis-associated genes on chr8p act in concert to induce an aggressive and invasive phenotype characteristic for chr8p-deleted tumors. Genome-wide CRISPR-Cas9 viability screening in isogenic chr8p-deleted cells served as a powerful tool to find previously unidentified synthetic lethal targets and vulnerabilities accompanying patient-specific chromosomal alterations. Using this target identification strategy, we showed that chr8p deletion sensitizes tumor cells to targeting of the reactive oxygen sanitizing enzyme Nudix hydrolase 17. Thus, chromosomal engineering allowed for the identification of novel synthetic lethalities specific to chr8p loss of heterozygosity.
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Affiliation(s)
- Thorben Huth
- Heidelberg University, Medical Faculty, Institute of Pathology, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Emely C. Dreher
- Heidelberg University, Medical Faculty, Institute of Pathology, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Steffen Lemke
- Quantitative Biology Center (QBiC), University of Tübingen, 72076 Tübingen, Germany
- Department of Peptide-based Immunotherapy, University and University Hospital Tübingen, 72076 Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, 72076 Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, 72076 Tübingen, Germany
| | - Sarah Fritzsche
- Heidelberg University, Medical Faculty, Institute of Pathology, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Raisatun N. Sugiyanto
- Heidelberg University, Medical Faculty, Institute of Pathology, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Darko Castven
- Department of Medicine I, University Medical Center Schleswig Holstein, 23538 Lübeck, Germany
| | - David Ibberson
- Deep Sequencing Core Facility, CellNetworks Excellence Cluster, Heidelberg University, 69120 Heidelberg, Germany
| | - Carsten Sticht
- NGS Core Facility, Medical Faculty Mannheim, Heidelberg University, 68167 Mannheim, Germany
| | - Eva Eiteneuer
- Heidelberg University, Medical Faculty, Institute of Pathology, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Anna Jauch
- Institute of Human Genetics, Heidelberg University, 69120 Heidelberg, Germany
| | - Stefan Pusch
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, 69120 Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Thomas Albrecht
- Heidelberg University, Medical Faculty, Institute of Pathology, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Benjamin Goeppert
- Heidelberg University, Medical Faculty, Institute of Pathology, University Hospital Heidelberg, 69120 Heidelberg, Germany
- Institute of Tissue Medicine and Pathology, University of Bern, 3008 Bern, Switzerland
- Institute of Pathology and Neuropathology, RKH Klinikum Ludwigsburg, 71640 Ludwigsburg, Germany
| | - Julián Candia
- Longitudinal Studies Section, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Xin Wei Wang
- Laboratory of Human Carcinogenesis and Liver Cancer Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Junfang Ji
- The MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Jens U. Marquardt
- Department of Medicine I, University Medical Center Schleswig Holstein, 23538 Lübeck, Germany
| | - Sven Nahnsen
- Quantitative Biology Center (QBiC), University of Tübingen, 72076 Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, 72076 Tübingen, Germany
- Biomedical Data Science, Department of Computer Science, University of Tübingen, 72076 Tübingen, Germany
- The M3 Research Center, University of Tübingen, 72076 Tübingen, Germany
| | - Peter Schirmacher
- Heidelberg University, Medical Faculty, Institute of Pathology, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Stephanie Roessler
- Heidelberg University, Medical Faculty, Institute of Pathology, University Hospital Heidelberg, 69120 Heidelberg, Germany
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15
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Lakhani AA, Thompson SL, Sheltzer JM. Aneuploidy in human cancer: new tools and perspectives. Trends Genet 2023; 39:968-980. [PMID: 37778926 PMCID: PMC10715718 DOI: 10.1016/j.tig.2023.09.002] [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: 05/25/2023] [Revised: 09/04/2023] [Accepted: 09/07/2023] [Indexed: 10/03/2023]
Abstract
Chromosome copy number imbalances, otherwise known as aneuploidies, are a common but poorly understood feature of cancer. Here, we describe recent advances in both detecting and manipulating aneuploidies that have greatly advanced our ability to study their role in tumorigenesis. In particular, new clustered regularly interspaced short palindromic repeats (CRISPR)-based techniques have been developed that allow the creation of isogenic cell lines with specific chromosomal changes, thereby facilitating experiments in genetically controlled backgrounds to uncover the consequences of aneuploidy. These approaches provide increasing evidence that aneuploidy is a key driver of cancer development and enable the identification of multiple dosage-sensitive genes encoded on aneuploid chromosomes. Consequently, measuring aneuploidy may inform clinical prognosis, while treatment strategies that target aneuploidy could represent a novel method to counter malignant growth.
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Affiliation(s)
- Asad A Lakhani
- Cold Spring Harbor Laboratory School of Biological Sciences, Cold Spring, Harbor, NY 11724, USA
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16
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Kumar BS. Recent Advances and Applications of Ambient Mass Spectrometry Imaging in Cancer Research: An Overview. Mass Spectrom (Tokyo) 2023; 12:A0129. [PMID: 37789912 PMCID: PMC10542858 DOI: 10.5702/massspectrometry.a0129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 08/25/2023] [Indexed: 10/05/2023] Open
Abstract
Cancer metabolic variability has a significant impact on both diagnosis and treatment outcomes. The discovery of novel biological indicators and metabolic dysregulation, can significantly rely on comprehension of the modified metabolism in cancer, is a research focus. Tissue histology is a critical feature in the diagnostic testing of many ailments, such as cancer. To assess the surgical margin of the tumour on patients, frozen section histology is a tedious, laborious, and typically arbitrary method. Concurrent monitoring of ion images in tissues facilitated by the latest advancements in mass spectrometry imaging (MSI) is far more efficient than optical tissue image analysis utilized in conventional histopathology examination. This article focuses on the "desorption electrospray ionization (DESI)-MSI" technique's most recent advancements and uses in cancer research. DESI-MSI can provide wealthy information based on the variances in metabolites and lipids in normal and cancerous tissues by acquiring ion images of the lipid and metabolite variances on biopsy samples. As opposed to a systematic review, this article offers a synopsis of the most widely employed cutting-edge DESI-MSI techniques in cancer research.
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Affiliation(s)
- Bharath S. Kumar
- Correspondence to: Bharath S. Kumar, 21, B2, 27th Street, Nanganallur, Chennai, India, e-mail:
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17
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Dehner CA, Bell RC, Cao Y, He K, Chrisinger JS, Armstrong AE, Yohe M, Shern J, Hirbe AC. Loss of Chromosome 3q Is a Prognostic Marker in Fusion-Negative Rhabdomyosarcoma. JCO Precis Oncol 2023; 7:e2300037. [PMID: 37738543 PMCID: PMC10861018 DOI: 10.1200/po.23.00037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 06/05/2023] [Accepted: 07/16/2023] [Indexed: 09/24/2023] Open
Abstract
PURPOSE Soft tissue sarcomas (STS) are rare mesenchymal neoplasms that frequently show complex chromosomal aberrations such as amplifications or deletions of DNA sequences or even whole chromosomes. We recently found that gain of chromosome (chr) 8 is associated with worse overall survival (OS) in STS as a group. We therefore aimed to investigate the overall copy number profile of rhabdomyosarcoma (RMS) to evaluate for prognostic signatures. METHODS Fluorescence in situ hybridization (FISH) testing was performed on a cohort of STS to assess for chr8 gain. Copy number variation (CNV) data from the National Cancer Institute were analyzed to assess for prognostically significant CNV aberrations in FOXO1 fusion-negative (FN)- versus fusion-positive (FP)-RMS. FISH testing was performed on a cohort of FN-RMS to assess for chr3q loss and correlate with outcomes. RESULTS Chr8 gain is a highly prevalent CNV in embryonal RMS and shows slightly improved prognosis. Meanwhile, loss of chr3q was associated with worse outcome in FN-RMS compared with FP-RMS. CONCLUSION The pathogenesis of STS including FN-RMS remains poorly understood, emphasizing the need for new therapeutic advances and adequate risk stratification. Our data demonstrate that loss of chr3q is associated with poor OS in FN-RMS, supporting it as an important tool for risk stratification.
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Affiliation(s)
- Carina A. Dehner
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO
- Department of Pathology/Dermatopathology, Indiana University, Indianapolis, IN
| | - Robert C. Bell
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO
- Department of Pathology, University of Michigan, Ann Arbor, MI
| | - Yang Cao
- Division of Oncology, Washington University School of Medicine, St Louis, MO
| | - Kevin He
- Division of Oncology, Washington University School of Medicine, St Louis, MO
| | - John S.A. Chrisinger
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO
| | - Amy E. Armstrong
- Division of Pediatric Hematology/Oncology, Washington University School of Medicine, St Louis, MO
| | - Marielle Yohe
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Jack Shern
- Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | - Angela C. Hirbe
- Division of Oncology, Washington University School of Medicine, St Louis, MO
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18
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Wang R, Hu Q, Wu Y, Guan N, Han X, Guan X. Intratumoral lipid metabolic reprogramming as a pro-tumoral regulator in the tumor milieu. Biochim Biophys Acta Rev Cancer 2023; 1878:188962. [PMID: 37541532 DOI: 10.1016/j.bbcan.2023.188962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Revised: 07/28/2023] [Accepted: 07/29/2023] [Indexed: 08/06/2023]
Abstract
Reprogramming of the tumor microenvironment (TME) is a hallmark of cancer. Metabolic reprogramming is a vital approach to sustaining the energy supply in the TME. This alteration exists in both cancer cells and TME cells, collectively establishing an immunotolerant niche to facilitate tumor progression. Limited resources lead to metabolic competition and hinder the biological functions of anti-tumoral immunity. Reprogramming of lipid metabolism and tumor progression is closely related to each other. Due to the complexity of fatty acid (FA) types and the lack of an effective approach for detection, the mechanisms and effects of FA metabolic reprogramming have been unclear. Herein, we review FA metabolism in the tumor milieu, summarize how FA metabolic reprogramming influences antitumor immune response, suggest the mechanisms by which FAs affect immunotherapy against cancer, and discuss the potential of FA metabolism-based drugs in cancer treatment.
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Affiliation(s)
- Runtian Wang
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Qin Hu
- Department of Cardiothoracic Surgery, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong 226001, China
| | - Yueyao Wu
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Nan Guan
- College of Literature, Science, and the Arts, University of Michigan, Ann Arbor, MI 48109, USA
| | - Xin Han
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China.
| | - Xiaoxiang Guan
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China; Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Personalized Cancer Medicine, Nanjing Medical University, Nanjing 211166, China.
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19
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Truong MA, Cané-Gasull P, Lens SMA. Modeling specific aneuploidies: from karyotype manipulations to biological insights. Chromosome Res 2023; 31:25. [PMID: 37640903 PMCID: PMC10462580 DOI: 10.1007/s10577-023-09735-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 07/11/2023] [Accepted: 08/09/2023] [Indexed: 08/31/2023]
Abstract
An abnormal chromosome number, or aneuploidy, underlies developmental disorders and is a common feature of cancer, with different cancer types exhibiting distinct patterns of chromosomal gains and losses. To understand how specific aneuploidies emerge in certain tissues and how they contribute to disease development, various methods have been developed to alter the karyotype of mammalian cells and mice. In this review, we provide an overview of both classic and novel strategies for inducing or selecting specific chromosomal gains and losses in human and murine cell systems. We highlight how these customized aneuploidy models helped expanding our knowledge of the consequences of specific aneuploidies to (cancer) cell physiology.
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Affiliation(s)
- My Anh Truong
- Oncode Institute and Center for Molecular Medicine, University Medical Center Utrecht, Universiteitsweg 100, 3584, CG, Utrecht, The Netherlands
| | - Paula Cané-Gasull
- Oncode Institute and Center for Molecular Medicine, University Medical Center Utrecht, Universiteitsweg 100, 3584, CG, Utrecht, The Netherlands
| | - Susanne M A Lens
- Oncode Institute and Center for Molecular Medicine, University Medical Center Utrecht, Universiteitsweg 100, 3584, CG, Utrecht, The Netherlands.
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20
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Cheng YJ, Fan F, Zhang Z, Zhang HJ. Lipid metabolism in malignant tumor brain metastasis: reprogramming and therapeutic potential. Expert Opin Ther Targets 2023; 27:861-878. [PMID: 37668244 DOI: 10.1080/14728222.2023.2255377] [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: 10/30/2022] [Revised: 07/19/2023] [Accepted: 08/31/2023] [Indexed: 09/06/2023]
Abstract
INTRODUCTION Brain metastasis is a highly traumatic event in the progression of malignant tumors, often symbolizing higher mortality. Metabolic alterations are hallmarks of cancer, and the mask of lipid metabolic program rearrangement in cancer progression is gradually being unraveled. AREAS COVERED In this work, we reviewed clinical and fundamental studies related to lipid expression and activity changes in brain metastases originating from lung, breast, and cutaneous melanomas, respectively. Novel roles of lipid metabolic reprogramming in the development of brain metastasis from malignant tumors were identified and its potential as a therapeutic target was evaluated. Published literature and clinical studies in databases consisting of PubMed, Embase, Scopus and www.ClinicalTrials.gov from 1990 to 2022 were searched. EXPERT OPINION Lipid metabolic reprogramming in brain metastasis is involved in de novo lipid synthesis within low lipid availability environments, regulation of lipid uptake and storage, metabolic interactions between brain tumors and the brain microenvironment, and membrane lipid remodeling, in addition to being a second messenger for signal transduction. Although some lipid metabolism modulators work efficiently in preclinical models, there is still a long way to go from laboratory to clinic. This area of research holds assurance for the organ-targeted treatment of brain metastases through drug-regulated metabolic targets and dietary interventions.
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Affiliation(s)
- Yan-Jie Cheng
- Department of Oncology, Zhongda Hospital, Medical School of Southeast University, Nanjing, Jiangsu, People's Republic of China
- Department of Oncology, Shanghai Fengxian District Central Hospital, Shanghai, China
| | - Fan Fan
- Department of Oncology, Zhongda Hospital, Medical School of Southeast University, Nanjing, Jiangsu, People's Republic of China
| | - Zhong Zhang
- Department of Oncology, Zhongda Hospital, Medical School of Southeast University, Nanjing, Jiangsu, People's Republic of China
| | - Hai-Jun Zhang
- Department of Oncology, Zhongda Hospital, Medical School of Southeast University, Nanjing, Jiangsu, People's Republic of China
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21
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Shih J, Sarmashghi S, Zhakula-Kostadinova N, Zhang S, Georgis Y, Hoyt SH, Cuoco MS, Gao GF, Spurr LF, Berger AC, Ha G, Rendo V, Shen H, Meyerson M, Cherniack AD, Taylor AM, Beroukhim R. Cancer aneuploidies are shaped primarily by effects on tumour fitness. Nature 2023; 619:793-800. [PMID: 37380777 PMCID: PMC10529820 DOI: 10.1038/s41586-023-06266-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 05/26/2023] [Indexed: 06/30/2023]
Abstract
Aneuploidies-whole-chromosome or whole-arm imbalances-are the most prevalent alteration in cancer genomes1,2. However, it is still debated whether their prevalence is due to selection or ease of generation as passenger events1,2. Here we developed a method, BISCUT, that identifies loci subject to fitness advantages or disadvantages by interrogating length distributions of telomere- or centromere-bounded copy-number events. These loci were significantly enriched for known cancer driver genes, including genes not detected through analysis of focal copy-number events, and were often lineage specific. BISCUT identified the helicase-encoding gene WRN as a haploinsufficient tumour-suppressor gene on chromosome 8p, which is supported by several lines of evidence. We also formally quantified the role of selection and mechanical biases in driving aneuploidy, finding that rates of arm-level copy-number alterations are most highly correlated with their effects on cellular fitness1,2. These results provide insight into the driving forces behind aneuploidy and its contribution to tumorigenesis.
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Affiliation(s)
- Juliann Shih
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Tufts University School of Medicine, Boston, MA, USA
- Department of Internal Medicine, Kirk Kerkorian School of Medicine at the University of Nevada, Las Vegas, NV, USA
| | - Shahab Sarmashghi
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Nadja Zhakula-Kostadinova
- Department of Pathology and Cell Biology, Herbert Irving Comprehensive Cancer Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Department of Genetics and Development, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Shu Zhang
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Yohanna Georgis
- Department of Pathology and Cell Biology, Herbert Irving Comprehensive Cancer Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Stephanie H Hoyt
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Michael S Cuoco
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Galen F Gao
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Liam F Spurr
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Ashton C Berger
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Gavin Ha
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Veronica Rendo
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Hui Shen
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
| | - Matthew Meyerson
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Andrew D Cherniack
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Alison M Taylor
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Department of Pathology and Cell Biology, Herbert Irving Comprehensive Cancer Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA.
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
| | - Rameen Beroukhim
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Medicine, Harvard Medical School, Boston, MA, USA.
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
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22
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Oza PP, Kashfi K. The evolving landscape of PCSK9 inhibition in cancer. Eur J Pharmacol 2023; 949:175721. [PMID: 37059376 PMCID: PMC10229316 DOI: 10.1016/j.ejphar.2023.175721] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 03/23/2023] [Accepted: 04/11/2023] [Indexed: 04/16/2023]
Abstract
Cancer is a disease with a significant global burden in terms of premature mortality, loss of productivity, healthcare expenditures, and impact on mental health. Recent decades have seen numerous advances in cancer research and treatment options. Recently, a new role of cholesterol-lowering PCSK9 inhibitor therapy has come to light in the context of cancer. PCSK9 is an enzyme that induces the degradation of low-density lipoprotein receptors (LDLRs), which are responsible for clearing cholesterol from the serum. Thus, PCSK9 inhibition is currently used to treat hypercholesterolemia, as it can upregulate LDLRs and enable cholesterol reduction through these receptors. The cholesterol-lowering effects of PCSK9 inhibitors have been suggested as a potential mechanism to combat cancer, as cancer cells have been found to increasingly rely on cholesterol for their growth needs. Additionally, PCSK9 inhibition has demonstrated the potential to induce cancer cell apoptosis through several pathways, increase the efficacy of a class of existing anticancer therapies, and boost the host immune response to cancer. A role in managing cancer- or cancer treatment-related development of dyslipidemia and life-threatening sepsis has also been suggested. This review examines the current evidence regarding the effects of PCSK9 inhibition in the context of different cancers and cancer-associated complications.
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Affiliation(s)
- Palak P Oza
- Department of Molecular, Cellular and Biomedical Sciences, Sophie Davis School of Biomedical Education, City University of New York School of Medicine, New York, NY, 10031, USA
| | - Khosrow Kashfi
- Department of Molecular, Cellular and Biomedical Sciences, Sophie Davis School of Biomedical Education, City University of New York School of Medicine, New York, NY, 10031, USA; Graduate Program in Biology, City University of New York Graduate Center, New York, 10091, USA.
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23
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Kuna RS, Kumar A, Wessendorf-Rodriguez KA, Galvez H, Green CR, McGregor GH, Cordes T, Shaw RJ, Svensson RU, Metallo CM. Inter-organelle cross-talk supports acetyl-coenzyme A homeostasis and lipogenesis under metabolic stress. SCIENCE ADVANCES 2023; 9:eadf0138. [PMID: 37134162 PMCID: PMC10156121 DOI: 10.1126/sciadv.adf0138] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 04/03/2023] [Indexed: 05/05/2023]
Abstract
Proliferating cells rely on acetyl-CoA to support membrane biogenesis and acetylation. Several organelle-specific pathways are available for provision of acetyl-CoA as nutrient availability fluctuates, so understanding how cells maintain acetyl-CoA homeostasis under such stresses is critically important. To this end, we applied 13C isotope tracing cell lines deficient in these mitochondrial [ATP-citrate lyase (ACLY)]-, cytosolic [acetyl-CoA synthetase (ACSS2)]-, and peroxisomal [peroxisomal biogenesis factor 5 (PEX5)]-dependent pathways. ACLY knockout in multiple cell lines reduced fatty acid synthesis and increased reliance on extracellular lipids or acetate. Knockout of both ACLY and ACSS2 (DKO) severely stunted but did not entirely block proliferation, suggesting that alternate pathways can support acetyl-CoA homeostasis. Metabolic tracing and PEX5 knockout studies link peroxisomal oxidation of exogenous lipids as a major source of acetyl-CoA for lipogenesis and histone acetylation in cells lacking ACLY, highlighting a role for inter-organelle cross-talk in supporting cell survival in response to nutrient fluctuations.
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Affiliation(s)
- Ramya S. Kuna
- Department of Molecular and Cell Biology, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Avi Kumar
- Department of Molecular and Cell Biology, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Karl A. Wessendorf-Rodriguez
- Department of Molecular and Cell Biology, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Hector Galvez
- Department of Molecular and Cell Biology, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Courtney R. Green
- Department of Molecular and Cell Biology, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Grace H. McGregor
- Department of Molecular and Cell Biology, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Thekla Cordes
- Department of Molecular and Cell Biology, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
- Department of Bioinformatics and Biochemistry, Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig 38106, Germany
| | - Reuben J. Shaw
- Department of Molecular and Cell Biology, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | | | - Christian M. Metallo
- Department of Molecular and Cell Biology, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
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24
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Shi S, Zhong J, Peng W, Yin H, Zhong D, Cui H, Sun X. System analysis based on the migration- and invasion-related gene sets identifies the infiltration-related genes of glioma. Front Oncol 2023; 13:1075716. [PMID: 37091145 PMCID: PMC10117932 DOI: 10.3389/fonc.2023.1075716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 03/23/2023] [Indexed: 04/09/2023] Open
Abstract
The current database has no information on the infiltration of glioma samples. Here, we assessed the glioma samples' infiltration in The Cancer Gene Atlas (TCGA) through the single-sample Gene Set Enrichment Analysis (ssGSEA) with migration and invasion gene sets. The Weighted Gene Co-expression Network Analysis (WGCNA) and the differentially expressed genes (DEGs) were used to identify the genes most associated with infiltration. Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) were used to analyze the major biological processes and pathways. Protein-protein interaction (PPI) network analysis and the least absolute shrinkage and selection operator (LASSO) were used to screen the key genes. Furthermore, the nomograms and receiver operating characteristic (ROC) curve were used to evaluate the prognostic and predictive accuracy of this clinical model in patients in TCGA and the Chinese Glioma Genome Atlas (CGGA). The results showed that turquoise was selected as the hub module, and with the intersection of DEGs, we screened 104 common genes. Through LASSO regression, TIMP1, EMP3, IGFBP2, and the other nine genes were screened mostly in correlation with infiltration and prognosis. EMP3 was selected to be verified in vitro. These findings could help researchers better understand the infiltration of gliomas and provide novel therapeutic targets for the treatment of gliomas.
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Affiliation(s)
- Shuang Shi
- Department of Neurosurgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Jiacheng Zhong
- Department of Neurosurgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Wen Peng
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
- Cancer Center, Medical Research Institute, Southwest University, Chongqing, China
| | - Haoyang Yin
- Department of Neurosurgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Dong Zhong
- Department of Neurosurgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Hongjuan Cui
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
- Cancer Center, Medical Research Institute, Southwest University, Chongqing, China
| | - Xiaochuan Sun
- Department of Neurosurgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
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25
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Han L, Zhang C, Wang D, Zhang J, Tang Q, Li MJ, Sack MN, Wang L, Zhu L. Retrograde regulation of mitochondrial fission and epithelial to mesenchymal transition in hepatocellular carcinoma by GCN5L1. Oncogene 2023; 42:1024-1037. [PMID: 36759571 DOI: 10.1038/s41388-023-02621-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 01/29/2023] [Accepted: 01/31/2023] [Indexed: 02/11/2023]
Abstract
Metabolic reprogram is crucial to support cancer cell growth and movement as well as determine cell fate. Mitochondrial protein acetylation regulates mitochondrial metabolism, which is relevant to cancer cell migration and invasion. The functional role of mitochondrial protein acetylation on cancer cell migration remains unclear. General control of amino acid synthesis 5 like-1(GCN5L1), as the regulator of mitochondrial protein acetylation, functions on metabolic reprogramming in mouse livers. In this study, we find that GCN5L1 expression is significantly decreased in metastatic HCC tissues. Loss of GCN5L1 promotes reactive oxygen species (ROS) generation through enhanced fatty acid oxidation (FAO), followed by activation of cellular ERK and DRP1 to promote mitochondrial fission and epithelia to mesenchymal transition (EMT) to boost cell migration. Moreover, palmitate and carnitine-stimulated FAO promotes mitochondrial fission and EMT gene expression to activate HCC cell migration. On the other hand, increased cellular acetyl-CoA level, the product of FAO, enhances HCC cell migration. Taken together, our finding uncovers the metastasis suppressor role as well as the underlying mechanism of GCN5L1 in HCC and also provides evidence of FAO retrograde control of HCC metastasis.
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Affiliation(s)
- Linmeng Han
- Department of Pharmacology, Tianjin Key Laboratory of Inflammatory Biology, The province and ministry co-sponsored collaborative innovation center for medical epigenetics, NHC Key Laboratory of Hormones and Development, Chu Hsien-I Memorial Hospital and Tianjin Institute of Endocrinology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Chunyu Zhang
- Department of Pharmacology, Tianjin Key Laboratory of Inflammatory Biology, The province and ministry co-sponsored collaborative innovation center for medical epigenetics, NHC Key Laboratory of Hormones and Development, Chu Hsien-I Memorial Hospital and Tianjin Institute of Endocrinology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Danni Wang
- Department of Pharmacology, Tianjin Key Laboratory of Inflammatory Biology, The province and ministry co-sponsored collaborative innovation center for medical epigenetics, NHC Key Laboratory of Hormones and Development, Chu Hsien-I Memorial Hospital and Tianjin Institute of Endocrinology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Jiaqi Zhang
- Department of Physiology and Pathophysiology, Tianjin Key Laboratory of Cell Homeostasis and Major Diseases, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Qiqi Tang
- Department of Pharmacology, Tianjin Key Laboratory of Inflammatory Biology, The province and ministry co-sponsored collaborative innovation center for medical epigenetics, NHC Key Laboratory of Hormones and Development, Chu Hsien-I Memorial Hospital and Tianjin Institute of Endocrinology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Mulin Jun Li
- Department of Bioinformatics, Tianjin Key Laboratory of Inflammation Biology, School of Basic Medical Sciences, Tianjin, China
| | - Michael N Sack
- Laboratory of Mitochondrial Biology and Metabolism, NHLBI, National Institutes of Health, Bethesda, MD, USA
| | - Lingdi Wang
- Department of Physiology and Pathophysiology, Tianjin Key Laboratory of Cell Homeostasis and Major Diseases, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China.
| | - Lu Zhu
- Department of Pharmacology, Tianjin Key Laboratory of Inflammatory Biology, The province and ministry co-sponsored collaborative innovation center for medical epigenetics, NHC Key Laboratory of Hormones and Development, Chu Hsien-I Memorial Hospital and Tianjin Institute of Endocrinology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China.
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26
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Lee SHT, Kim JY, Kim P, Dong Z, Su CY, Ahn EH. Changes of Mutations and Copy-Number and Enhanced Cell Migration during Breast Tumorigenesis. Adv Biol (Weinh) 2023; 7:e2200072. [PMID: 36449747 PMCID: PMC10836759 DOI: 10.1002/adbi.202200072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 11/14/2022] [Indexed: 12/02/2022]
Abstract
Although cancer stem cells (CSCs) play a major role in tumorigenesis and metastasis, the role of genetic alterations in invasiveness of CSCs is still unclear. Tumor microenvironment signals, such as extracellular matrix (ECM) composition, significantly influence cell behaviors. Unfortunately, these signals are often lost in in vitro cell culture. This study determines putative CSC populations, examines genetic changes during tumorigenesis of human breast epithelial stem cells, and investigates single-cell migration properties on ECM-mimetic platforms. Whole exome sequencing data indicate that tumorigenic cells have a higher somatic mutation burden than non-tumorigenic cells, and that mutations exclusive to tumorigenic cells exhibit higher predictive deleterious scores. Tumorigenic cells exhibit distinct somatic copy number variations (CNVs) including gain of duplications in chromosomes 5 and 8. ECM-mimetic topography selectively enhances migration speed of tumorigenic cells, but not of non-tumorigenic cells, and results in a wide distribution of tumorigenic single-cell migration speeds, suggesting heterogeneity in cellular sensing of contact guidance cues. This study identifies mutations and CNVs acquired during breast tumorigenesis, which can be associated with enhanced migration of breast tumorigenic cells, and demonstrates that a nanotopographically-defined platform can be applied to recapitulate an ECM structure for investigating cellular migration in the simulated tumor microenvironment.
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Affiliation(s)
- Seung Hyuk T. Lee
- Department of Pathology, University of Washington, Seattle,
WA 98195, USA
| | - Joon Yup Kim
- Department of Pathology, University of Washington, Seattle,
WA 98195, USA
| | - Peter Kim
- Department of Bioengineering, University of Washington,
Seattle, WA 98195, USA
| | - Zhipeng Dong
- Department of Biomedical Engineering, Johns Hopkins
University, Baltimore, MD 21205, USA
| | - Chia-Yi Su
- Department of Biomedical Engineering, Johns Hopkins
University, Baltimore, MD 21205, USA
| | - Eun Hyun Ahn
- Department of Biomedical Engineering, Johns Hopkins
University, Baltimore, MD 21205, USA
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27
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Tsujino T, Takai T, Hinohara K, Gui F, Tsutsumi T, Bai X, Miao C, Feng C, Gui B, Sztupinszki Z, Simoneau A, Xie N, Fazli L, Dong X, Azuma H, Choudhury AD, Mouw KW, Szallasi Z, Zou L, Kibel AS, Jia L. CRISPR screens reveal genetic determinants of PARP inhibitor sensitivity and resistance in prostate cancer. Nat Commun 2023; 14:252. [PMID: 36650183 PMCID: PMC9845315 DOI: 10.1038/s41467-023-35880-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Accepted: 01/05/2023] [Indexed: 01/18/2023] Open
Abstract
Prostate cancer harboring BRCA1/2 mutations are often exceptionally sensitive to PARP inhibitors. However, genomic alterations in other DNA damage response genes have not been consistently predictive of clinical response to PARP inhibition. Here, we perform genome-wide CRISPR-Cas9 knockout screens in BRCA1/2-proficient prostate cancer cells and identify previously unknown genes whose loss has a profound impact on PARP inhibitor response. Specifically, MMS22L deletion, frequently observed (up to 14%) in prostate cancer, renders cells hypersensitive to PARP inhibitors by disrupting RAD51 loading required for homologous recombination repair, although this response is TP53-dependent. Unexpectedly, loss of CHEK2 confers resistance rather than sensitivity to PARP inhibition through increased expression of BRCA2, a target of CHEK2-TP53-E2F7-mediated transcriptional repression. Combined PARP and ATR inhibition overcomes PARP inhibitor resistance caused by CHEK2 loss. Our findings may inform the use of PARP inhibitors beyond BRCA1/2-deficient tumors and support reevaluation of current biomarkers for PARP inhibition in prostate cancer.
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Affiliation(s)
- Takuya Tsujino
- Division of Urology, Department of Surgery, Brigham and Women's Hospital & Harvard Medical School, Boston, MA, USA
- Department of Urology, Osaka Medical and Pharmaceutical University, Osaka, Japan
| | - Tomoaki Takai
- Division of Urology, Department of Surgery, Brigham and Women's Hospital & Harvard Medical School, Boston, MA, USA
- Department of Urology, Osaka Medical and Pharmaceutical University, Osaka, Japan
| | - Kunihiko Hinohara
- Department of Medical Oncology, Dana-Farber Cancer Institute & Harvard Medical School, Boston, MA, USA
- Department of Immunology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Fu Gui
- Division of Urology, Department of Surgery, Brigham and Women's Hospital & Harvard Medical School, Boston, MA, USA
| | - Takeshi Tsutsumi
- Division of Urology, Department of Surgery, Brigham and Women's Hospital & Harvard Medical School, Boston, MA, USA
- Department of Urology, Osaka Medical and Pharmaceutical University, Osaka, Japan
| | - Xiao Bai
- Division of Urology, Department of Surgery, Brigham and Women's Hospital & Harvard Medical School, Boston, MA, USA
| | - Chenkui Miao
- Division of Urology, Department of Surgery, Brigham and Women's Hospital & Harvard Medical School, Boston, MA, USA
| | - Chao Feng
- Division of Urology, Department of Surgery, Brigham and Women's Hospital & Harvard Medical School, Boston, MA, USA
| | - Bin Gui
- Division of Urology, Department of Surgery, Brigham and Women's Hospital & Harvard Medical School, Boston, MA, USA
| | - Zsofia Sztupinszki
- Computational Health Informatics Program, Boston Children's Hospital, Boston, MA, USA
- Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Antoine Simoneau
- Department of Pathology, Massachusetts General Hospital & Harvard Medical School, Boston, MA, USA
| | - Ning Xie
- Vancouver Prostate Centre, Vancouver General Hospital, Vancouver, British Columbia, Canada
| | - Ladan Fazli
- Vancouver Prostate Centre, Vancouver General Hospital, Vancouver, British Columbia, Canada
| | - Xuesen Dong
- Vancouver Prostate Centre, Vancouver General Hospital, Vancouver, British Columbia, Canada
- Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Haruhito Azuma
- Department of Urology, Osaka Medical and Pharmaceutical University, Osaka, Japan
| | - Atish D Choudhury
- Department of Medical Oncology, Dana-Farber Cancer Institute & Harvard Medical School, Boston, MA, USA
| | - Kent W Mouw
- Department of Radiation Oncology, Dana-Farber Cancer Institute & Brigham and Women's Hospital & Harvard Medical School, Boston, MA, USA
| | - Zoltan Szallasi
- Computational Health Informatics Program, Boston Children's Hospital, Boston, MA, USA
- Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Lee Zou
- Department of Pathology, Massachusetts General Hospital & Harvard Medical School, Boston, MA, USA
| | - Adam S Kibel
- Division of Urology, Department of Surgery, Brigham and Women's Hospital & Harvard Medical School, Boston, MA, USA
| | - Li Jia
- Division of Urology, Department of Surgery, Brigham and Women's Hospital & Harvard Medical School, Boston, MA, USA.
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28
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Copy Number Variations as Determinants of Colorectal Tumor Progression in Liquid Biopsies. Int J Mol Sci 2023; 24:ijms24021738. [PMID: 36675253 PMCID: PMC9866722 DOI: 10.3390/ijms24021738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/09/2023] [Accepted: 01/12/2023] [Indexed: 01/18/2023] Open
Abstract
Over the years, increasing evidence has shown that copy number variations (CNVs) play an important role in the pathogenesis and prognosis of Colorectal Cancer (CRC). Colorectal adenomas are highly prevalent lesions, but only 5% of these adenomas ever progress to carcinoma. This review summarizes the different CNVs associated with adenoma-carcinoma CRC progression and with CRC staging. Characterization of CNVs in circulating free-RNA and in blood-derived exosomes augers well with the potential of using such assays for patient management and early detection of metastasis. To overcome the limitations related to tissue biopsies and tumor heterogeneity, using CNVs to characterize tumor-derived materials in biofluids provides less invasive sampling methods and a sample that collectively represents multiple tumor sites in heterogeneous samples. Liquid biopsies provide a source of circulating tumor DNA (ctDNA), circulating tumor cells (CTCs), tumor-derived exosomes (TDE), circulating free RNA, and non-coding RNA. This review provides an overview of the current diagnostic and predictive models from liquid biopsies.
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29
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Wang ZH, Li W, Dong H, Han F. Current state of NK cell-mediated immunotherapy in chronic lymphocytic leukemia. Front Oncol 2023; 12:1077436. [PMID: 37078002 PMCID: PMC10107371 DOI: 10.3389/fonc.2022.1077436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Accepted: 12/13/2022] [Indexed: 01/06/2023] Open
Abstract
Chronic lymphocytic leukemia (CLL) has become one of the most common hematological diseases in western countries, with an annual incidence of 42/100,000. Conventional chemotherapy and targeted therapeutic drugs showed limitations in prognosis or in efficiency in high-risk patients. Immunotherapy represented is one of the most effective therapeutic approaches with the potential of better effect and prognosis. Natural killer (NK) cells are good options for immunotherapy as they can effectively mediate anti-tumor activity of immune system by expressing activating and inhibiting receptors and recognizing specific ligands on various tumor cells. NK cells are critical in the immunotherapy of CLL by enhancing self-mediated antibody-dependent cytotoxicity (ADCC), allogeneic NK cell therapy and chimeric antigen receptor-natural killer (CAR-NK) cell therapy. In this article, we reviewed the features, working mechanisms, and receptors of NK cells, and the available evidence of the advantages and disadvantages of NK cell-based immunotherapies, and put forward future study directions in this field.
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Affiliation(s)
- Zong-Han Wang
- Cancer Center, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Wei Li
- Department of General Surgery, Second Affiliated Hospital of Jilin University, Changchun, Jilin, China
| | - Hao Dong
- Department of Gastrointestinal Nutrition and Surgical Surgery, The Second Affiliated Hospital of Jilin University, Changchun, Jilin, China
- *Correspondence: Hao Dong, ; Fujun Han,
| | - Fujun Han
- Cancer Center, The First Hospital of Jilin University, Changchun, Jilin, China
- *Correspondence: Hao Dong, ; Fujun Han,
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30
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Liao YY, Cao WM. The progress in our understanding of CIN in breast cancer research. Front Oncol 2023; 13:1067735. [PMID: 36874134 PMCID: PMC9978327 DOI: 10.3389/fonc.2023.1067735] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 01/02/2023] [Indexed: 02/18/2023] Open
Abstract
Chromosomal instability (CIN) is an important marker of cancer, which is closely related to tumorigenesis, disease progression, treatment efficacy, and patient prognosis. However, due to the limitations of the currently available detection methods, its exact clinical significance remains unknown. Previous studies have demonstrated that 89% of invasive breast cancer cases possess CIN, suggesting that it has potential application in breast cancer diagnosis and treatment. In this review, we describe the two main types of CIN and discuss the associated detection methods. Subsequently, we highlight the impact of CIN in breast cancer development and progression and describe how it can influence treatment and prognosis. The goal of this review is to provide a reference on its mechanism for researchers and clinicians.
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Affiliation(s)
- Yu-Yang Liao
- Wenzhou Medical University, Wenzhou, China.,Department of Breast Medical Oncology, Zhejiang Cancer Hospital, Hangzhou, China
| | - Wen-Ming Cao
- Department of Breast Medical Oncology, Zhejiang Cancer Hospital, Hangzhou, China
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Qian L, Liu YF, Lu SM, Yang JJ, Miao HJ, He X, Huang H, Zhang JG. Construction of a fatty acid metabolism-related gene signature for predicting prognosis and immune response in breast cancer. Front Genet 2023; 14:1002157. [PMID: 36936412 PMCID: PMC10014556 DOI: 10.3389/fgene.2023.1002157] [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: 07/24/2022] [Accepted: 02/20/2023] [Indexed: 03/05/2023] Open
Abstract
Background: Breast cancer has the highest incidence among malignant tumors in women, and its prevalence ranks first in global cancer morbidity. Aim: This study aimed to explore the feasibility of a prognostic model for patients with breast cancer based on the differential expression of genes related to fatty acid metabolism. Methods: The mRNA expression matrix of breast cancer and paracancer tissues was downloaded from The Cancer Genome Atlas database. The differentially expressed genes related to fatty acid metabolism were screened in R language. The TRRUST database was used to predict transcriptional regulators related to hub genes and construct an mRNA-transcription factor interaction network. A consensus clustering approach was used to identify different fatty acid regulatory patterns. In combination with patient survival data, Lasso and multivariate Cox proportional risk regression models were used to establish polygenic prognostic models based on fatty acid metabolism. The median risk score was used to categorize patients into high- and low-risk groups. Kaplan-Meier survival curves were used to analyze the survival differences between both groups. The Cox regression analysis included risk score and clinicopathological factors to determine whether risk score was an independent risk factor. Models based on genes associated with fatty acid metabolism were evaluated using receiver operating characteristic curves. A comparison was made between risk score levels and the fatty acid metabolism-associated genes in different subtypes of breast cancer. The differential gene sets of the Kyoto Encyclopedia of Genes and Genomes for screening high- and low-risk populations were compared using a gene set enrichment analysis. Furthermore, we utilized CIBERSORT to examine the abundance of immune cells in breast cancer in different clustering models. Results: High expression levels of ALDH1A1 and UBE2L6 prevented breast cancer, whereas high RDH16 expression levels increased its risk. Our comprehensive assessment of the association between prognostic risk scoring models and tumor microenvironment characteristics showed significant differences in the abundance of various immune cells between high- and low-risk breast cancer patients. Conclusions: By assessing fatty acid metabolism patterns, we gained a better understanding of the infiltration characteristics of the tumor microenvironment. Our findings are valuable for prognosis prediction and treatment of patients with breast cancer based on their clinicopathological characteristics.
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Affiliation(s)
- Li Qian
- Department of Pathology, Affiliated Hospital of Nantong University, Nantong, China
| | - Yi-Fei Liu
- Department of Pathology, Affiliated Hospital of Nantong University, Nantong, China
| | - Shu-Min Lu
- Department of Oncology, Shanghai Jiaotong University School of Medicine Xinhua Hospital, Shanghai, China
| | - Juan-Juan Yang
- Department of Pathology, Affiliated Hospital of Nantong University, Nantong, China
| | - Hua-Jie Miao
- Department of Pathology, Affiliated Hospital of Nantong University, Nantong, China
| | - Xin He
- Department of Pathology, Affiliated Hospital of Nantong University, Nantong, China
| | - Hua Huang
- Department of Pathology, Affiliated Hospital of Nantong University, Nantong, China
- *Correspondence: Hua Huang, ; Jian-Guo Zhang,
| | - Jian-Guo Zhang
- Department of Pathology, Affiliated Hospital of Nantong University, Nantong, China
- *Correspondence: Hua Huang, ; Jian-Guo Zhang,
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32
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Barriga FM, Tsanov KM, Ho YJ, Sohail N, Zhang A, Baslan T, Wuest AN, Del Priore I, Meškauskaitė B, Livshits G, Alonso-Curbelo D, Simon J, Chaves-Perez A, Bar-Sagi D, Iacobuzio-Donahue CA, Notta F, Chaligne R, Sharma R, Pe'er D, Lowe SW. MACHETE identifies interferon-encompassing chromosome 9p21.3 deletions as mediators of immune evasion and metastasis. NATURE CANCER 2022; 3:1367-1385. [PMID: 36344707 PMCID: PMC9701143 DOI: 10.1038/s43018-022-00443-5] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 09/13/2022] [Indexed: 11/09/2022]
Abstract
The most prominent homozygous deletions in cancer affect chromosome 9p21.3 and eliminate CDKN2A/B tumor suppressors, disabling a cell-intrinsic barrier to tumorigenesis. Half of 9p21.3 deletions, however, also encompass a type I interferon (IFN) gene cluster; the consequences of this co-deletion remain unexplored. To functionally dissect 9p21.3 and other large genomic deletions, we developed a flexible deletion engineering strategy, MACHETE (molecular alteration of chromosomes with engineered tandem elements). Applying MACHETE to a syngeneic mouse model of pancreatic cancer, we found that co-deletion of the IFN cluster promoted immune evasion, metastasis and immunotherapy resistance. Mechanistically, IFN co-deletion disrupted type I IFN signaling in the tumor microenvironment, leading to marked changes in infiltrating immune cells and escape from CD8+ T-cell surveillance, effects largely driven by the poorly understood interferon epsilon. These results reveal a chromosomal deletion that disables both cell-intrinsic and cell-extrinsic tumor suppression and provide a framework for interrogating large deletions in cancer and beyond.
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Affiliation(s)
- Francisco M Barriga
- Cancer Biology & Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kaloyan M Tsanov
- Cancer Biology & Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yu-Jui Ho
- Cancer Biology & Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Noor Sohail
- Program for Computational and Systems Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Amy Zhang
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Timour Baslan
- Cancer Biology & Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alexandra N Wuest
- Cancer Biology & Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Isabella Del Priore
- Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, New York, NY, USA
| | - Brigita Meškauskaitė
- Program for Computational and Systems Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Geulah Livshits
- Cancer Biology & Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Direna Alonso-Curbelo
- Cancer Biology & Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Janelle Simon
- Cancer Biology & Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Almudena Chaves-Perez
- Cancer Biology & Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Dafna Bar-Sagi
- Department of Biochemistry, New York University School of Medicine, New York, NY, USA
| | - Christine A Iacobuzio-Donahue
- David M. Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Faiyaz Notta
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Division of Research, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Ronan Chaligne
- Program for Computational and Systems Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Roshan Sharma
- Program for Computational and Systems Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Dana Pe'er
- Program for Computational and Systems Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Scott W Lowe
- Cancer Biology & Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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Kanu GA, Parambath JBM, Abu Odeh RO, Mohamed AA. Gold Nanoparticle-Mediated Gene Therapy. Cancers (Basel) 2022; 14:5366. [PMID: 36358785 PMCID: PMC9653658 DOI: 10.3390/cancers14215366] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 10/27/2022] [Accepted: 10/28/2022] [Indexed: 07/30/2023] Open
Abstract
Gold nanoparticles (AuNPs) have gained increasing attention as novel drug-delivery nanostructures for the treatment of cancers, infections, inflammations, and other diseases and disorders. They are versatile in design, synthesis, modification, and functionalization. This has many advantages in terms of gene editing and gene silencing, and their application in genetic illnesses. The development of several techniques such as CRISPR/Cas9, TALEN, and ZFNs has raised hopes for the treatment of genetic abnormalities, although more focused experimentation is still needed. AuNPs, however, have been much more effective in trending research on this subject. In this review, we highlight recently well-developed advancements that are relevant to cutting-edge gene therapies, namely gene editing and gene silencing in diseases caused by a single gene in humans by taking an edge of the unique properties of the AuNPs, which will be an important outlook for future research.
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Affiliation(s)
- Gayathri A. Kanu
- Department of Medical Laboratory Sciences, College of Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Javad B. M. Parambath
- Department of Chemistry, College of Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates
- Center for Advanced Materials Research, Research Institute of Sciences and Engineering, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Raed O. Abu Odeh
- Department of Medical Laboratory Sciences, College of Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Ahmed A. Mohamed
- Department of Chemistry, College of Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates
- Center for Advanced Materials Research, Research Institute of Sciences and Engineering, University of Sharjah, Sharjah 27272, United Arab Emirates
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Shen Y, Singh J, Sah B, Chen Z, Ha W, Henzler C, Su T, Xie L, Deng Y, Li G, Guo H, Hibshoosh H, Liu L. The Histone Demethylase HR Suppresses Breast Cancer Development through Enhanced CELF2 Tumor Suppressor Activity. Cancers (Basel) 2022; 14:4648. [PMID: 36230572 PMCID: PMC9564370 DOI: 10.3390/cancers14194648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 09/21/2022] [Accepted: 09/22/2022] [Indexed: 11/17/2022] Open
Abstract
The hairless (HR) gene encodes a transcription factor with histone demethylase activity that is essential for development and tissue homeostasis. Previous studies suggest that mutational inactivation of HR promotes tumorigenesis. To investigate HR mutations in breast cancer, we performed targeted next-generation sequencing using DNA isolated from primary breast cancer tissues. We identified HR somatic mutations in approximately 15% of the patient cohort (n = 85), compared with 23% for BRCA2, 13% for GATA3, 7% for BRCA1, and 3% for PTEN in the same patient cohort. We also found an average 23% HR copy number loss in breast cancers. In support of HR's antitumor functions, HR reconstitution in HR-deficient human breast cancer cells significantly suppressed tumor growth in orthotopic xenograft mouse models. We further demonstrated that HR's antitumor activity was at least partly mediated by transcriptional activation of CELF2, a tumor suppressor with RNA-binding activity. Consistent with HR's histone demethylase activity, pharmacologic inhibition of histone methylation suppressed HR-deficient breast cancer cell proliferation, migration and tumor growth. Taken together, we identified HR as a novel tumor suppressor that is frequently mutated in breast cancer. We also showed that pharmacologic inhibition of histone methylation is effective in suppressing HR-deficient breast tumor growth and progression.
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Affiliation(s)
- Yao Shen
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Jasvinder Singh
- The Hormel Institute, University of Minnesota, Austin, MN 55912, USA
| | - Bindeshwar Sah
- The Hormel Institute, University of Minnesota, Austin, MN 55912, USA
| | - Zhongming Chen
- The Hormel Institute, University of Minnesota, Austin, MN 55912, USA
| | - Wootae Ha
- The Hormel Institute, University of Minnesota, Austin, MN 55912, USA
| | - Christine Henzler
- Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN 55455, USA
| | - Tao Su
- Department of Pathology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Lillian Xie
- The Hormel Institute, University of Minnesota, Austin, MN 55912, USA
| | - Yibin Deng
- Department of Urology, University of Minnesota Medical School, Minneapolis, MN 55455, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Gen Li
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Hua Guo
- Department of Pathology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Hanina Hibshoosh
- Department of Pathology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Liang Liu
- The Hormel Institute, University of Minnesota, Austin, MN 55912, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
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35
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Suelmann BBM, Rademaker A, van Dooijeweert C, van der Wall E, van Diest PJ, Moelans CB. Genomic copy number alterations as biomarkers for triple negative pregnancy-associated breast cancer. Cell Oncol (Dordr) 2022; 45:591-600. [PMID: 35792986 PMCID: PMC9424154 DOI: 10.1007/s13402-022-00685-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/02/2022] [Indexed: 11/28/2022] Open
Abstract
Abstract
Background
PABC, commonly defined as breast cancer diagnosed during or ≤ 1 year after pregnancy, accounts for 7% of all breast cancers in women ≤ 45 years. Compared to age-matched non-PABC patients, PABC is characterized by a particularly aggressive histopathologic profile with poorly differentiated and estrogen- and progesterone receptor negative tumors and associated high mortality rates. This study assessed the genomic background of triple-negative PABC tumors by detection of copy number alterations (CNAs).
Methods
MLPA was used to compare CNAs in breast cancer-associated chromosomal loci between triple-negative PABC- and subtype-matched non-PABC patients. Both CNA patterns were evaluated by cluster analysis; associations between individual gene CNAs, pathological characteristics and survival were explored.
Results
Triple-negative PABC tumors exhibited unique CNAs compared to non-PABC tumors, including enrichment for TOP2A copy number loss, an independent predictor of worse overall survival (HR 8.96, p = 0.020). Cluster analysis based on CNA profiles identified a triple-negative PABC-subgroup with a particularly poor prognosis, characterized by chromosome 8p copy number loss. Individual gene CNAs analysis revealed that FGFR1 copy number loss on chromosome 8p11.23 was an independent predictor of poor outcome in multivariate analysis (HR 3.59, p = 0.053) and predicted the development of distant metastases (p = 0.048).
Conclusion
This study provides novel insights into the biology of triple-negative PABC tumors suggesting that CNAs, particularly 8p loss and TOP2A loss, are involved in the development of breast cancer during pregnancy. FGFR1 loss and TOP2A loss seem to be promising new biomarkers that independently identify subgroups of PABC patients with poor prognosis. These genomic biomarkers may provide clues for personalized therapy.
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Affiliation(s)
- B B M Suelmann
- Department of Medical Oncology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - A Rademaker
- Department of Pathology, University Medical Center Utrecht, PO Box 85500, Utrecht, 3508 GA, The Netherlands
| | - C van Dooijeweert
- Department of Pathology, University Medical Center Utrecht, PO Box 85500, Utrecht, 3508 GA, The Netherlands
| | - E van der Wall
- Department of Medical Oncology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - P J van Diest
- Department of Pathology, University Medical Center Utrecht, PO Box 85500, Utrecht, 3508 GA, The Netherlands
| | - C B Moelans
- Department of Pathology, University Medical Center Utrecht, PO Box 85500, Utrecht, 3508 GA, The Netherlands.
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36
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Kostecka A, Nowikiewicz T, Olszewski P, Koczkowska M, Horbacz M, Heinzl M, Andreou M, Salazar R, Mair T, Madanecki P, Gucwa M, Davies H, Skokowski J, Buckley PG, Pęksa R, Śrutek E, Szylberg Ł, Hartman J, Jankowski M, Zegarski W, Tiemann-Boege I, Dumanski JP, Piotrowski A. High prevalence of somatic PIK3CA and TP53 pathogenic variants in the normal mammary gland tissue of sporadic breast cancer patients revealed by duplex sequencing. NPJ Breast Cancer 2022; 8:76. [PMID: 35768433 PMCID: PMC9243094 DOI: 10.1038/s41523-022-00443-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 06/10/2022] [Indexed: 11/08/2022] Open
Abstract
The mammary gland undergoes hormonally stimulated cycles of proliferation, lactation, and involution. We hypothesized that these factors increase the mutational burden in glandular tissue and may explain high cancer incidence rate in the general population, and recurrent disease. Hence, we investigated the DNA sequence variants in the normal mammary gland, tumor, and peripheral blood from 52 reportedly sporadic breast cancer patients. Targeted resequencing of 542 cancer-associated genes revealed subclonal somatic pathogenic variants of: PIK3CA, TP53, AKT1, MAP3K1, CDH1, RB1, NCOR1, MED12, CBFB, TBX3, and TSHR in the normal mammary gland at considerable allelic frequencies (9 × 10-2- 5.2 × 10-1), indicating clonal expansion. Further evaluation of the frequently damaged PIK3CA and TP53 genes by ultra-sensitive duplex sequencing demonstrated a diversified picture of multiple low-level subclonal (in 10-2-10-4 alleles) hotspot pathogenic variants. Our results raise a question about the oncogenic potential in non-tumorous mammary gland tissue of breast-conserving surgery patients.
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Affiliation(s)
- Anna Kostecka
- Faculty of Pharmacy, Medical University of Gdansk, Gdansk, Poland.
- 3P Medicine Lab, Medical University of Gdansk, Gdansk, Poland.
| | - Tomasz Nowikiewicz
- Department of Surgical Oncology, Ludwik Rydygier's Collegium Medicum UMK, Bydgoszcz, Poland.
- Department of Breast Cancer and Reconstructive Surgery, Prof. F. Lukaszczyk Oncology Center, Bydgoszcz, Poland.
| | - Paweł Olszewski
- 3P Medicine Lab, Medical University of Gdansk, Gdansk, Poland
| | - Magdalena Koczkowska
- Faculty of Pharmacy, Medical University of Gdansk, Gdansk, Poland
- 3P Medicine Lab, Medical University of Gdansk, Gdansk, Poland
| | - Monika Horbacz
- 3P Medicine Lab, Medical University of Gdansk, Gdansk, Poland
| | - Monika Heinzl
- Institute of Biophysics, Johannes Kepler University, Linz, Austria
| | - Maria Andreou
- 3P Medicine Lab, Medical University of Gdansk, Gdansk, Poland
| | - Renato Salazar
- Institute of Biophysics, Johannes Kepler University, Linz, Austria
| | - Theresa Mair
- Institute of Biophysics, Johannes Kepler University, Linz, Austria
| | - Piotr Madanecki
- Faculty of Pharmacy, Medical University of Gdansk, Gdansk, Poland
| | - Magdalena Gucwa
- Faculty of Pharmacy, Medical University of Gdansk, Gdansk, Poland
| | - Hanna Davies
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Jarosław Skokowski
- Department of Surgical Oncology, Medical University of Gdansk, Gdansk, Poland
| | | | - Rafał Pęksa
- Department of Patomorphology, Medical University of Gdansk, Gdansk, Poland
| | - Ewa Śrutek
- Department of Surgical Oncology, Ludwik Rydygier's Collegium Medicum UMK, Bydgoszcz, Poland
| | - Łukasz Szylberg
- Department of Tumor Pathology, Prof. F. Lukaszczyk Oncology Center, Bydgoszcz, Poland
- Department of Perinatology, Gynaecology and Gynaecologic, Oncology, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Torun, Bydgoszcz, Poland
| | - Johan Hartman
- Department of Oncology and Pathology, Karolinska Institutet, Stockholm, Sweden
- Department of Pathology, Karolinska University Hospital, Stockholm, Sweden
- MedTech Labs, Bioclinicum, Karolinska University Hospital, Stockholm, Sweden
| | - Michał Jankowski
- Department of Surgical Oncology, Ludwik Rydygier's Collegium Medicum UMK, Bydgoszcz, Poland
| | - Wojciech Zegarski
- Department of Surgical Oncology, Ludwik Rydygier's Collegium Medicum UMK, Bydgoszcz, Poland
| | | | - Jan P Dumanski
- 3P Medicine Lab, Medical University of Gdansk, Gdansk, Poland
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Arkadiusz Piotrowski
- Faculty of Pharmacy, Medical University of Gdansk, Gdansk, Poland.
- 3P Medicine Lab, Medical University of Gdansk, Gdansk, Poland.
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Robustness of the Autophagy Pathway to Somatic Copy Number Losses. Cells 2022; 11:cells11111762. [PMID: 35681458 PMCID: PMC9179279 DOI: 10.3390/cells11111762] [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: 04/29/2022] [Revised: 05/23/2022] [Accepted: 05/25/2022] [Indexed: 02/04/2023] Open
Abstract
Autophagy allows cells to temporarily tolerate energy stress by replenishing critical metabolites through self-digestion, thereby attenuating the cytotoxic effects of anticancer drugs that target tumor metabolism. Autophagy defects could therefore mark a metabolically vulnerable cancer state and open a therapeutic window. While mutations of autophagy genes (ATGs) are notably rare in cancer, haploinsufficiency network analyses across many cancers have shown that the autophagy pathway is frequently hit by somatic copy number losses of ATGs such as MAP1LC3B/ATG8F (LC3), BECN1/ATG6 (Beclin-1), and ATG10. Here, we used CRISPR/Cas9 technology to delete increasing numbers of copies of one or more of these ATGs in non-small cell lung cancer cells and examined the effects on sensitivity to compounds targeting aerobic glycolysis, a hallmark of cancer metabolism. Whereas the complete knockout of one ATG blocked autophagy and led to profound metabolic vulnerability, this was not the case for combinations of different nonhomozygous deletions. In cancer patients, the effect of ATG copy number loss was blunted at the protein level and did not lead to the accumulation of p62 as a sign of reduced autophagic flux. Thus, the autophagy pathway is shown to be markedly robust and resilient, even with the concomitant copy number loss of key autophagy genes.
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38
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Menendez JA, Lupu R. Fatty acid synthase: A druggable driver of breast cancer brain metastasis. Expert Opin Ther Targets 2022; 26:427-444. [PMID: 35545806 DOI: 10.1080/14728222.2022.2077189] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
INTRODUCTION Brain metastasis (BrM) is a key contributor to morbidity and mortality in breast cancer patients, especially among high-risk epidermal growth factor receptor 2-positive (HER2+) and triple-negative/basal-like molecular subtypes. Optimal management of BrM is focused on characterizing a "BrM dependency map" to prioritize targetable therapeutic vulnerabilities. AREAS COVERED We review recent studies addressing the targeting of BrM in the lipid-deprived brain environment, which selects for brain-tropic breast cancer cells capable of cell-autonomously generating fatty acids by upregulating de novo lipogenesis via fatty acid synthase (FASN). Disruption of FASN activity impairs breast cancer growth in the brain, but not extracranially, and mapping of the molecular causes of organ-specific patterns of metastasis has uncovered an enrichment of lipid metabolism signatures in brain metastasizing cells. Targeting SREBP1-the master regulator of lipogenic gene transcription-curtails the ability of breast cancer cells to survive in the brain microenvironment. EXPERT OPINION Targeting FASN represents a new therapeutic opportunity for patients with breast cancer and BrM. Delivery of brain-permeable FASN inhibitors and identifying strategies to target metabolic plasticity that might compensate for impaired brain FASN activity are two potential roadblocks that may hinder FASN-centered strategies against BrM.
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Affiliation(s)
- Javier A Menendez
- Metabolism and Cancer Group, Program Against Cancer Therapeutic Resistance (ProCURE), Catalan Institute of Oncology, 17007 Girona, Spain.,Girona Biomedical Research Institute (IDIBGI), 17190 Girona, Spain
| | - Ruth Lupu
- Department of Laboratory Medicine and Pathology, Division of Experimental Pathology, Mayo Clinic, Rochester, MN 55905, USA.,Department of Biochemistry and Molecular Biology Laboratory, Mayo Clinic Minnesota, Rochester, MN 55905, USA.,Mayo Clinic Cancer Center, Rochester, MN 55905, USA
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Petersson A, Andersson N, Hau SO, Eberhard J, Karlsson J, Chattopadhyay S, Valind A, Elebro J, Nodin B, Leandersson K, Gisselsson D, Jirström K. Branching Copy-Number Evolution and Parallel Immune Profiles across the Regional Tumor Space of Resected Pancreatic Cancer. Mol Cancer Res 2022; 20:749-761. [PMID: 35149544 PMCID: PMC9381114 DOI: 10.1158/1541-7786.mcr-21-0986] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 01/05/2022] [Accepted: 02/04/2022] [Indexed: 01/07/2023]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) remains a highly lethal disease. The only option for curative treatment is resection of the tumor followed by standard adjuvant chemotherapy. Yet, early relapse due to chemoresistance is almost inevitable. Herein, we delineated the genetic intratumor heterogeneity in resected PDAC, with the aim to identify evolutionary patterns that may be associated with overall survival (OS) following treatment with curative intent. Potential relationships with the adjacent immune microenvironment were also examined. The genetic and immune landscapes of the regional tumor space were analyzed in nine patients with resected PDAC. Targeted deep sequencing and genome wide SNP array were followed by clonal deconvolution and phylogenetic analysis. A mathematical complexity score was developed to calculate the network extent of each phylogeny. Spatial variation in abundancy and tumor nest infiltration of immune cells was analyzed by double IHC staining. Copy-number heterogeneity was denoted as the major contributing factor to the branching architectures of the produced phylogenetic trees. Increased tree complexity was significantly inversely associated with OS, and larger regional maximum aberrations (higher treetops) were associated with increased PD-L1 expression on tumor cells. Contrastingly, an FREM1 gene amplification, found in one patient, coincided with a particularly vigorous immune response. Findings from this limited case series suggest that complex evolutionary patterns may be associated with a shorter survival in surgically treated patients with PDAC. Some hypothesis-generating associations with the surrounding immune microenvironment were also detected. IMPLICATIONS Evolutionary copy-number patterns may be associated with survival in patients with resected PDAC.
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Affiliation(s)
- Alexandra Petersson
- Division of Oncology and Therapeutic Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Natalie Andersson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Sofie Olsson Hau
- Division of Oncology and Therapeutic Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Jakob Eberhard
- Division of Oncology and Therapeutic Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Jenny Karlsson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Subhayan Chattopadhyay
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Anders Valind
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
- Department of Pediatrics, Skåne University Hospital, Lund, Sweden
| | - Jacob Elebro
- Division of Oncology and Therapeutic Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Björn Nodin
- Division of Oncology and Therapeutic Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Karin Leandersson
- Cancer Immunology, Department of Translational Medicine, Lund University, Malmö, Sweden
| | - David Gisselsson
- Division of Oncology and Therapeutic Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Karin Jirström
- Division of Oncology and Therapeutic Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
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40
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Consequences of Chromosome Loss: Why Do Cells Need Each Chromosome Twice? Cells 2022; 11:cells11091530. [PMID: 35563836 PMCID: PMC9101035 DOI: 10.3390/cells11091530] [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: 03/24/2022] [Revised: 04/25/2022] [Accepted: 04/28/2022] [Indexed: 12/26/2022] Open
Abstract
Aneuploidy is a cellular state with an unbalanced chromosome number that deviates from the usual euploid status. During evolution, elaborate cellular mechanisms have evolved to maintain the correct chromosome content over generations. The rare errors often lead to cell death, cell cycle arrest, or impaired proliferation. At the same time, aneuploidy can provide a growth advantage under selective conditions in a stressful, frequently changing environment. This is likely why aneuploidy is commonly found in cancer cells, where it correlates with malignancy, drug resistance, and poor prognosis. To understand this “aneuploidy paradox”, model systems have been established and analyzed to investigate the consequences of aneuploidy. Most of the evidence to date has been based on models with chromosomes gains, but chromosome losses and recurrent monosomies can also be found in cancer. We summarize the current models of chromosome loss and our understanding of its consequences, particularly in comparison to chromosome gains.
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41
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Tan ES, Knepper TC, Wang X, Permuth JB, Wang L, Fleming JB, Xie H. Copy Number Alterations as Novel Biomarkers and Therapeutic Targets in Colorectal Cancer. Cancers (Basel) 2022; 14:2223. [PMID: 35565354 PMCID: PMC9101426 DOI: 10.3390/cancers14092223] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 04/21/2022] [Accepted: 04/24/2022] [Indexed: 12/10/2022] Open
Abstract
In colorectal cancer, somatic mutations have played an important role as prognostic and predictive biomarkers, with some also functioning as therapeutic targets. Another genetic aberration that has shown significance in colorectal cancer is copy number alterations (CNAs). CNAs occur when a change to the DNA structure propagates gain/amplification or loss/deletion in sections of DNA, which can often lead to changes in protein expression. Multiple techniques have been developed to detect CNAs, including comparative genomic hybridization with microarray, low pass whole genome sequencing, and digital droplet PCR. In this review, we summarize key findings in the literature regarding the role of CNAs in the pathogenesis of colorectal cancer, from adenoma to carcinoma to distant metastasis, and discuss the roles of CNAs as prognostic and predictive biomarkers in colorectal cancer.
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Affiliation(s)
- Elaine S. Tan
- Department of Gastrointestinal Oncology, H. Lee Moffitt Cancer Center and Research Institute, 12902 USF Magnolia Drive Tampa, Tampa, FL 33612, USA; (E.S.T.); (J.B.P.); (J.B.F.)
| | - Todd C. Knepper
- Department of Individualized Cancer Management, H. Lee Moffitt Cancer Center and Research Institute, 12902 USF Magnolia Drive Tampa, Tampa, FL 33612, USA;
| | - Xuefeng Wang
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, 12902 USF Magnolia Drive Tampa, Tampa, FL 33612, USA;
| | - Jennifer B. Permuth
- Department of Gastrointestinal Oncology, H. Lee Moffitt Cancer Center and Research Institute, 12902 USF Magnolia Drive Tampa, Tampa, FL 33612, USA; (E.S.T.); (J.B.P.); (J.B.F.)
| | - Liang Wang
- Department of Tumor Biology, H. Lee Moffitt Cancer Center and Research Institute, 12901 USF Magnolia Drive Tampa, Tampa, FL 33612, USA;
| | - Jason B. Fleming
- Department of Gastrointestinal Oncology, H. Lee Moffitt Cancer Center and Research Institute, 12902 USF Magnolia Drive Tampa, Tampa, FL 33612, USA; (E.S.T.); (J.B.P.); (J.B.F.)
| | - Hao Xie
- Department of Gastrointestinal Oncology, H. Lee Moffitt Cancer Center and Research Institute, 12902 USF Magnolia Drive Tampa, Tampa, FL 33612, USA; (E.S.T.); (J.B.P.); (J.B.F.)
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Bowers RR, Jones CM, Paz EA, Barrows JK, Armeson K, Long D, Delaney J. SWAN pathway-network identification of common aneuploidy-based oncogenic drivers. Nucleic Acids Res 2022; 50:3673-3692. [PMID: 35380699 PMCID: PMC9023287 DOI: 10.1093/nar/gkac200] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 02/26/2022] [Accepted: 03/14/2022] [Indexed: 02/07/2023] Open
Abstract
Haploinsufficiency drives Darwinian evolution. Siblings, while alike in many aspects, differ due to monoallelic differences inherited from each parent. In cancer, solid tumors exhibit aneuploid genetics resulting in hundreds to thousands of monoallelic gene-level copy-number alterations (CNAs) in each tumor. Aneuploidy patterns are heterogeneous, posing a challenge to identify drivers in this high-noise genetic environment. Here, we developed Shifted Weighted Annotation Network (SWAN) analysis to assess biology impacted by cumulative monoallelic changes. SWAN enables an integrated pathway-network analysis of CNAs, RNA expression, and mutations via a simple web platform. SWAN is optimized to best prioritize known and novel tumor suppressors and oncogenes, thereby identifying drivers and potential druggable vulnerabilities within cancer CNAs. Protein homeostasis, phospholipid dephosphorylation, and ion transport pathways are commonly suppressed. An atlas of CNA pathways altered in each cancer type is released. These CNA network shifts highlight new, attractive targets to exploit in solid tumors.
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Affiliation(s)
- Robert R Bowers
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC, USA
| | - Christian M Jones
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC, USA
| | - Edwin A Paz
- Departments of Neurology, Neurobiology, and Cell Biology, and the Duke Center for Neurodegeneration & Neurotherapeutics, Duke University School of Medicine, Durham, NC, USA
| | - John K Barrows
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC, USA
| | - Kent E Armeson
- Department of Public Health Sciences, Medical University of South Carolina, Charleston, SC, USA
| | - David T Long
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC, USA
| | - Joe R Delaney
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC, USA
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Mesenchymal and stem-like prostate cancer linked to therapy-induced lineage plasticity and metastasis. Cell Rep 2022; 39:110595. [PMID: 35385726 PMCID: PMC9414743 DOI: 10.1016/j.celrep.2022.110595] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 09/18/2021] [Accepted: 03/09/2022] [Indexed: 12/13/2022] Open
Abstract
Bioinformatic analysis of 94 patient-derived xenografts (PDXs), cell lines, and organoids (PCOs) identifies three intrinsic transcriptional subtypes of metastatic castration-resistant prostate cancer: androgen receptor (AR) pathway + prostate cancer (PC) (ARPC), mesenchymal and stem-like PC (MSPC), and neuroendocrine PC (NEPC). A sizable proportion of castration-resistant and metastatic stage PC (M-CRPC) cases are admixtures of ARPC and MSPC. Analysis of clinical datasets and mechanistic studies indicates that MSPC arises from ARPC as a consequence of therapy-induced lineage plasticity. AR blockade with enzalutamide induces (1) transcriptional silencing of TP53 and hence dedifferentiation to a hybrid epithelial and mesenchymal and stem-like state and (2) inhibition of BMP signaling, which promotes resistance to AR inhibition. Enzalutamide-tolerant LNCaP cells re-enter the cell cycle in response to neuregulin and generate metastasis in mice. Combined inhibition of HER2/3 and AR or mTORC1 exhibits efficacy in models of ARPC and MSPC or MSPC, respectively. These results define MSPC, trace its origin to therapy-induced lineage plasticity, and reveal its sensitivity to HER2/3 inhibition.
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Hong W, Li A, Liu Y, Xiao X, Christiani DC, Hung RJ, McKay J, Field J, Amos CI, Cheng C. Clonal Hematopoiesis Mutations in Patients with Lung Cancer Are Associated with Lung Cancer Risk Factors. Cancer Res 2022; 82:199-209. [PMID: 34815255 PMCID: PMC8815061 DOI: 10.1158/0008-5472.can-21-1903] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 08/23/2021] [Accepted: 11/15/2021] [Indexed: 01/12/2023]
Abstract
Clonal hematopoiesis (CH) is a phenomenon caused by expansion of white blood cells descended from a single hematopoietic stem cell. While CH can be associated with leukemia and some solid tumors, the relationship between CH and lung cancer remains largely unknown. To help clarify this relationship, we analyzed whole-exome sequencing (WES) data from 1,958 lung cancer cases and controls. Potential CH mutations were identified by a set of hierarchical filtering criteria in different exonic regions, and the associations between the number of CH mutations and clinical traits were investigated. Family history of lung cancer (FHLC) may exert diverse influences on the accumulation of CH mutations in different age groups. In younger subjects, FHLC was the strongest risk factor for CH mutations. Association analysis of genome-wide genetic variants identified dozens of genetic loci associated with CH mutations, including a candidate SNP rs2298110, which may promote CH by increasing expression of a potential leukemia promoter gene OTUD3. Hundreds of potentially novel CH mutations were identified, and smoking was found to potentially shape the CH mutational signature. Genetic variants and lung cancer risk factors, especially FHLC, correlated with CH. These analyses improve our understanding of the relationship between lung cancer and CH, and future experimental studies will be necessary to corroborate the uncovered correlations. SIGNIFICANCE: Analysis of whole-exome sequencing data uncovers correlations between clonal hematopoiesis and lung cancer risk factors, identifies genetic variants correlated with clonal hematopoiesis, and highlights hundreds of potential novel clonal hematopoiesis mutations.
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Affiliation(s)
- Wei Hong
- Department of Medicine, Baylor College of Medicine, Houston, Texas
| | - Ang Li
- Department of Medicine, Baylor College of Medicine, Houston, Texas
| | - Yanhong Liu
- Department of Medicine, Baylor College of Medicine, Houston, Texas
| | - Xiangjun Xiao
- Department of Medicine, Baylor College of Medicine, Houston, Texas
| | | | - Rayjean J Hung
- Mount Sinai Hospital Lunenfeld-Tanenbaum Research Institute, Toronto, Ontario, Canada
| | - James McKay
- World Health Organization International Agency for Research on Cancer, Lyon CEDEX, France
| | - John Field
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | | | - Chao Cheng
- Department of Medicine, Baylor College of Medicine, Houston, Texas.
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Nachmanson D, Officer A, Mori H, Gordon J, Evans MF, Steward J, Yao H, O'Keefe T, Hasteh F, Stein GS, Jepsen K, Weaver DL, Hirst GL, Sprague BL, Esserman LJ, Borowsky AD, Stein JL, Harismendy O. The breast pre-cancer atlas illustrates the molecular and micro-environmental diversity of ductal carcinoma in situ. NPJ Breast Cancer 2022; 8:6. [PMID: 35027560 PMCID: PMC8758681 DOI: 10.1038/s41523-021-00365-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Accepted: 12/06/2021] [Indexed: 12/15/2022] Open
Abstract
Microenvironmental and molecular factors mediating the progression of Breast Ductal Carcinoma In Situ (DCIS) are not well understood, impeding the development of prevention strategies and the safe testing of treatment de-escalation. We addressed methodological barriers and characterized the mutational, transcriptional, histological, and microenvironmental landscape across 85 multiple microdissected regions from 39 cases. Most somatic alterations, including whole-genome duplications, were clonal, but genetic divergence increased with physical distance. Phenotypic and subtype heterogeneity was frequently associated with underlying genetic heterogeneity and regions with low-risk features preceded those with high-risk features according to the inferred phylogeny. B- and T-lymphocytes spatial analysis identified three immune states, including an epithelial excluded state located preferentially at DCIS regions, and characterized by histological and molecular features of immune escape, independently from molecular subtypes. Such breast pre-cancer atlas with uniquely integrated observations will help scope future expansion studies and build finer models of outcomes and progression risk.
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Affiliation(s)
- Daniela Nachmanson
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, 9500 Gilman Drive, San Diego, CA, 92093, USA
| | - Adam Officer
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, 9500 Gilman Drive, San Diego, CA, 92093, USA
- Division of Biomedical Informatics, Department of Medicine, University of California San Diego, 9500 Gilman Drive, San Diego, CA, 92093, USA
| | - Hidetoshi Mori
- Department of Pathology and Laboratory Medicine, Center for Immunology and Infectious Diseases, School of Medicine, University of California Davis, 2315 Stockton Blvd, Sacramento, CA, 95817, USA
| | - Jonathan Gordon
- University of Vermont Cancer Center, 111 Colchester Avenue Main Campus, Main Pavillion, Level, 2, Burlington, VT, 05401, USA
- Department of Biochemistry, University of Vermont, Burlington, VT, 05405, USA
| | - Mark F Evans
- University of Vermont Cancer Center, 111 Colchester Avenue Main Campus, Main Pavillion, Level, 2, Burlington, VT, 05401, USA
- Department of Pathology and Laboratory Medicine, University of Vermont, Burlington, VT, 05405, USA
| | - Joseph Steward
- Moores Cancer Center, University of California San Diego, 3855 Health Science Drive, San Diego, CA, 92093, USA
| | - Huazhen Yao
- Institute for Genomic Medicine, University of California San Diego, 9500 Gilman Drive, San Diego, CA, 92093, USA
| | - Thomas O'Keefe
- Department of Surgery, University of California San Diego, 9500 Gilman Drive, San Diego, CA, 92093, USA
| | - Farnaz Hasteh
- Moores Cancer Center, University of California San Diego, 3855 Health Science Drive, San Diego, CA, 92093, USA
- Department of Pathology, University of California San Diego, 9500 Gilman Drive, San Diego, CA, 92093, USA
| | - Gary S Stein
- University of Vermont Cancer Center, 111 Colchester Avenue Main Campus, Main Pavillion, Level, 2, Burlington, VT, 05401, USA
- Department of Biochemistry, University of Vermont, Burlington, VT, 05405, USA
| | - Kristen Jepsen
- Institute for Genomic Medicine, University of California San Diego, 9500 Gilman Drive, San Diego, CA, 92093, USA
| | - Donald L Weaver
- University of Vermont Cancer Center, 111 Colchester Avenue Main Campus, Main Pavillion, Level, 2, Burlington, VT, 05401, USA
- Department of Pathology and Laboratory Medicine, University of Vermont, Burlington, VT, 05405, USA
| | - Gillian L Hirst
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, 1450 3rd St, San Francisco, CA, 94158, USA
| | - Brian L Sprague
- University of Vermont Cancer Center, 111 Colchester Avenue Main Campus, Main Pavillion, Level, 2, Burlington, VT, 05401, USA
- Department of Surgery, University of Vermont, Burlington, VT, 05405, USA
| | - Laura J Esserman
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, 1450 3rd St, San Francisco, CA, 94158, USA
| | - Alexander D Borowsky
- Department of Pathology and Laboratory Medicine, Center for Immunology and Infectious Diseases, School of Medicine, University of California Davis, 2315 Stockton Blvd, Sacramento, CA, 95817, USA
| | - Janet L Stein
- University of Vermont Cancer Center, 111 Colchester Avenue Main Campus, Main Pavillion, Level, 2, Burlington, VT, 05401, USA
- Department of Biochemistry, University of Vermont, Burlington, VT, 05405, USA
| | - Olivier Harismendy
- Division of Biomedical Informatics, Department of Medicine, University of California San Diego, 9500 Gilman Drive, San Diego, CA, 92093, USA.
- Moores Cancer Center, University of California San Diego, 3855 Health Science Drive, San Diego, CA, 92093, USA.
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Matsumoto T, Okayama H, Nakajima S, Saito K, Ito M, Kaneta A, Kanke Y, Onozawa H, Hayase S, Fujita S, Sakamoto W, Saito M, Seze Z, Momma T, Mimura K, Kono K. SH2D4A downregulation due to loss of chromosome 8p is associated with poor prognosis and low T cell infiltration in colorectal cancer. Br J Cancer 2021; 126:917-926. [PMID: 34893760 DOI: 10.1038/s41416-021-01660-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 11/21/2021] [Accepted: 11/30/2021] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND Colorectal cancer (CRC) develops through chromosomal instability (CIN) or microsatellite instability (MSI) due to deficient mismatch-repair (dMMR). We aimed to characterise novel cancer-associated genes that are downregulated upon malignant transformation in microsatellite stable (MSS) CRCs, which typically exhibit CIN with proficient mismatch-repair (pMMR). METHODS Comprehensive screening was conducted on adenomas, MSI/MSS CRCs and cell lines, followed by copy number analysis, and their genetic and prognostic relevance was confirmed in microarray and RNA-seq cohorts (n = 3262, in total). Immunohistochemistry for SH2D4A was performed in 524 specimens of adenoma, carcinoma in situ and dMMR/pMMR CRC. The functional role of SH2D4A was investigated using CRC cell lines. RESULTS A set of 11 genes, including SH2D4A, was downregulated during the adenoma-carcinoma sequence in MSS/CIN CRCs, mainly due to chromosome 8p deletions, and their negative prognostic impact was validated in independent cohorts. All adenomas were SH2D4A positive, but a subset of CRCs (5.3%) lacked SH2D4A immunohistochemical staining, correlating with poor prognosis and scarce T cell infiltration. SH2D4A depletion did not affect cell proliferation or IL-6-induced STAT3 phosphorylation. CONCLUSIONS Our findings suggest that downregulation of multiple genes on chromosome 8p, including SH2D4A, cooperatively contribute to tumorigenesis, resulting in the immune cold tumour microenvironment and poor prognosis.
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Affiliation(s)
- Takuro Matsumoto
- Department of Gastrointestinal Tract Surgery, Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Hirokazu Okayama
- Department of Gastrointestinal Tract Surgery, Fukushima Medical University School of Medicine, Fukushima, Japan.
| | - Shotaro Nakajima
- Department of Gastrointestinal Tract Surgery, Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Katsuharu Saito
- Department of Gastrointestinal Tract Surgery, Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Misato Ito
- Department of Gastrointestinal Tract Surgery, Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Akinao Kaneta
- Department of Gastrointestinal Tract Surgery, Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Yasuyuki Kanke
- Department of Gastrointestinal Tract Surgery, Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Hisashi Onozawa
- Department of Gastrointestinal Tract Surgery, Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Suguru Hayase
- Department of Gastrointestinal Tract Surgery, Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Shotaro Fujita
- Department of Gastrointestinal Tract Surgery, Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Wataru Sakamoto
- Department of Gastrointestinal Tract Surgery, Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Motonobu Saito
- Department of Gastrointestinal Tract Surgery, Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Zenichiro Seze
- Department of Gastrointestinal Tract Surgery, Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Tomoyuki Momma
- Department of Gastrointestinal Tract Surgery, Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Kosaku Mimura
- Department of Gastrointestinal Tract Surgery, Fukushima Medical University School of Medicine, Fukushima, Japan.,Department of Blood Transfusion and Transplantation Immunology, Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Koji Kono
- Department of Gastrointestinal Tract Surgery, Fukushima Medical University School of Medicine, Fukushima, Japan
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Kues WA, Kumar D, Selokar NL, Talluri TR. Applications of genome editing tools in stem cells towards regenerative medicine: An update. Curr Stem Cell Res Ther 2021; 17:267-279. [PMID: 34819011 DOI: 10.2174/1574888x16666211124095527] [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: 02/10/2021] [Revised: 09/14/2021] [Accepted: 09/25/2021] [Indexed: 11/22/2022]
Abstract
Precise and site specific genome editing through application of emerging and modern gene engineering techniques, namely zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs) and clustered regularly interspaced short palindromic repeats (CRISPR/Cas9) have swiftly progressed the application and use of the stem cell technology in the sphere of in-vitro disease modelling and regenerative medicine. Genome editing tools facilitate the manipulating of any gene in various types of cells with target specific nucleases. These tools aid in elucidating the genetics and etiology behind different diseases and have immense promise as novel therapeutics for correcting the genetic mutations, make alterations and cure diseases permanently that are not responding and resistant to traditional therapies. These genome engineering tools have evolved in the field of biomedical research and have also shown to have a significant improvement in clinical trials. However, their widespread use in research revealed potential safety issues, which need to be addressed before implementing such techniques in clinical purposes. Significant and valiant attempts are being made in order to surpass those hurdles. The current review outlines the advancements of several genome engineering tools and describes suitable strategies for their application towards regenerative medicine.
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Affiliation(s)
- Wilfried A Kues
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Department of Biotechnology, Stem Cell Physiology, Höltystr 10, 31535 Neustadt. Germany
| | - Dharmendra Kumar
- Animal Physiology and Reproduction Division, ICAR-Central Institute for Research on Buffaloes, Hisar-125001, Haryana. India
| | - Naresh L Selokar
- Animal Physiology and Reproduction Division, ICAR-Central Institute for Research on Buffaloes, Hisar-125001, Haryana. India
| | - Thirumala Rao Talluri
- Equine Production Campus, ICAR- National Research Centre on Equines, Bikaner-334001, Rajasthan. India
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48
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Zerdes I, Simonetti M, Matikas A, Harbers L, Acs B, Boyaci C, Zhang N, Salgkamis D, Agartz S, Moreno-Ruiz P, Bai Y, Rimm DL, Hartman J, Mezheyeuski A, Bergh J, Crosetto N, Foukakis T. Interplay between copy number alterations and immune profiles in the early breast cancer Scandinavian Breast Group 2004-1 randomized phase II trial: results from a feasibility study. NPJ Breast Cancer 2021; 7:144. [PMID: 34799582 PMCID: PMC8604966 DOI: 10.1038/s41523-021-00352-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 10/21/2021] [Indexed: 12/12/2022] Open
Abstract
Emerging data indicate that genomic alterations can shape immune cell composition in early breast cancer. However, there is a need for complementary imaging and sequencing methods for the quantitative assessment of combined somatic copy number alteration (SCNA) and immune profiling in pathological samples. Here, we tested the feasibility of three approaches-CUTseq, for high-throughput low-input SCNA profiling, multiplexed fluorescent immunohistochemistry (mfIHC) and digital-image analysis (DIA) for quantitative immuno-profiling- in archival formalin-fixed paraffin-embedded (FFPE) tissue samples from patients enrolled in the randomized SBG-2004-1 phase II trial. CUTseq was able to reproducibly identify amplification and deletion events with a resolution of 100 kb using only 6 ng of DNA extracted from FFPE tissue and pooling together 77 samples into the same sequencing library. In the same samples, mfIHC revealed that CD4 + T-cells and CD68 + macrophages were the most abundant immune cells and they mostly expressed PD-L1 and PD-1. Combined analysis showed that the SCNA burden was inversely associated with lymphocytic infiltration. Our results set the basis for further applications of CUTseq, mfIHC and DIA to larger cohorts of early breast cancer patients.
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Affiliation(s)
- Ioannis Zerdes
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
- Breast Center, Theme Cancer, Karolinska University Hospital, Stockholm, Sweden
| | - Michele Simonetti
- Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Science for Life Laboratory, Stockholm, Sweden
| | - Alexios Matikas
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
- Breast Center, Theme Cancer, Karolinska University Hospital, Stockholm, Sweden
| | - Luuk Harbers
- Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Science for Life Laboratory, Stockholm, Sweden
| | - Balazs Acs
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
- Department of Pathology and Cytology, Karolinska University Hospital, Stockholm, Sweden
| | - Ceren Boyaci
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
- Department of Pathology and Cytology, Karolinska University Hospital, Stockholm, Sweden
| | - Ning Zhang
- Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Science for Life Laboratory, Stockholm, Sweden
| | | | - Susanne Agartz
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Pablo Moreno-Ruiz
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Yalai Bai
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - David L Rimm
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - Johan Hartman
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
- Department of Pathology and Cytology, Karolinska University Hospital, Stockholm, Sweden
| | - Artur Mezheyeuski
- Department of Immunology, Genetics, and Pathology, Uppsala University, Uppsala, Sweden
| | - Jonas Bergh
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden.
- Breast Center, Theme Cancer, Karolinska University Hospital, Stockholm, Sweden.
| | - Nicola Crosetto
- Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.
- Science for Life Laboratory, Stockholm, Sweden.
| | - Theodoros Foukakis
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden.
- Breast Center, Theme Cancer, Karolinska University Hospital, Stockholm, Sweden.
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Fu Y, Zou T, Shen X, Nelson PJ, Li J, Wu C, Yang J, Zheng Y, Bruns C, Zhao Y, Qin L, Dong Q. Lipid metabolism in cancer progression and therapeutic strategies. MedComm (Beijing) 2021; 2:27-59. [PMID: 34766135 PMCID: PMC8491217 DOI: 10.1002/mco2.27] [Citation(s) in RCA: 113] [Impact Index Per Article: 37.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 07/17/2020] [Accepted: 07/23/2020] [Indexed: 12/24/2022] Open
Abstract
Dysregulated lipid metabolism represents an important metabolic alteration in cancer. Fatty acids, cholesterol, and phospholipid are the three most prevalent lipids that act as energy producers, signaling molecules, and source material for the biogenesis of cell membranes. The enhanced synthesis, storage, and uptake of lipids contribute to cancer progression. The rewiring of lipid metabolism in cancer has been linked to the activation of oncogenic signaling pathways and cross talk with the tumor microenvironment. The resulting activity favors the survival and proliferation of tumor cells in the harsh conditions within the tumor. Lipid metabolism also plays a vital role in tumor immunogenicity via effects on the function of the noncancer cells within the tumor microenvironment, especially immune‐associated cells. Targeting altered lipid metabolism pathways has shown potential as a promising anticancer therapy. Here, we review recent evidence implicating the contribution of lipid metabolic reprogramming in cancer to cancer progression, and discuss the molecular mechanisms underlying lipid metabolism rewiring in cancer, and potential therapeutic strategies directed toward lipid metabolism in cancer. This review sheds new light to fully understanding of the role of lipid metabolic reprogramming in the context of cancer and provides valuable clues on therapeutic strategies targeting lipid metabolism in cancer.
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Affiliation(s)
- Yan Fu
- Department of General Surgery, Huashan Hospital & Cancer Metastasis Institute & Institutes of Biomedical Sciences Fudan University Shanghai China
| | - Tiantian Zou
- Department of General Surgery, Huashan Hospital & Cancer Metastasis Institute & Institutes of Biomedical Sciences Fudan University Shanghai China
| | - Xiaotian Shen
- Department of General Surgery, Huashan Hospital & Cancer Metastasis Institute & Institutes of Biomedical Sciences Fudan University Shanghai China
| | - Peter J Nelson
- Medical Clinic and Policlinic IV Ludwig-Maximilian-University (LMU) Munich Germany
| | - Jiahui Li
- General, Visceral and Cancer Surgery University Hospital of Cologne Cologne Germany
| | - Chao Wu
- Department of General Surgery, Ruijin Hospital Shanghai Jiao Tong University School of Medicine Shanghai China
| | - Jimeng Yang
- Department of General Surgery, Huashan Hospital & Cancer Metastasis Institute & Institutes of Biomedical Sciences Fudan University Shanghai China
| | - Yan Zheng
- Department of General Surgery, Huashan Hospital & Cancer Metastasis Institute & Institutes of Biomedical Sciences Fudan University Shanghai China
| | - Christiane Bruns
- General, Visceral and Cancer Surgery University Hospital of Cologne Cologne Germany
| | - Yue Zhao
- General, Visceral and Cancer Surgery University Hospital of Cologne Cologne Germany
| | - Lunxiu Qin
- Department of General Surgery, Huashan Hospital & Cancer Metastasis Institute & Institutes of Biomedical Sciences Fudan University Shanghai China
| | - Qiongzhu Dong
- Department of General Surgery, Huashan Hospital & Cancer Metastasis Institute & Institutes of Biomedical Sciences Fudan University Shanghai China
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Bang S, Jee S, Son H, Wi YC, Kim H, Park H, Myung J, Shin SJ, Paik SS. Loss of DUSP4 Expression as a Prognostic Biomarker in Clear Cell Renal Cell Carcinoma. Diagnostics (Basel) 2021; 11:diagnostics11101939. [PMID: 34679636 PMCID: PMC8534388 DOI: 10.3390/diagnostics11101939] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 10/14/2021] [Accepted: 10/16/2021] [Indexed: 11/16/2022] Open
Abstract
Dual-specificity protein phosphatase 4 (DUSP4) is a negative regulator of mitogen-activated protein kinases. The prognostic impact of DUSP4 expression in renal cell carcinoma is not well studied. Therefore, we evaluated the clinicopathological implications of DUSP4 expression in clear cell renal cell carcinoma by performing immunohistochemistry (IHC). The clinical outcome according to DUSP4 expression was evaluated through survival analyses, and the association between mRNA expression and prognosis was confirmed by online analysis (Kaplan-Meier plotter). Loss of DUSP4 expression was noted in most histological subtypes of renal cell carcinoma. Loss of DUSP4 expression in clear cell renal cell carcinoma was significantly correlated with old age (p = 0.033), high histologic grade (p < 0.001), tumor necrosis (p < 0.001), and high pT category (p < 0.001). In survival analysis, loss of DUSP4 expression was associated with poor clinical outcomes in cancer-specific survival and recurrence-free survival (p = 0.010 and p = 0.007, respectively). Upon TCGA data analysis, patients with low DUSP4 mRNA expression showed a shorter overall survival (p = 0.023). These results suggest that loss of DUSP4 expression can be used as a potential biomarker for predicting clinical outcomes in clear cell renal cell carcinoma patients.
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Affiliation(s)
- Seongsik Bang
- Department of Pathology, Hanyang University Seoul Hospital, Hanyang University College of Medicine, Seoul 04763, Korea; (S.B.); (S.J.); (H.S.); (H.K.); (H.P.); (J.M.)
| | - Seungyun Jee
- Department of Pathology, Hanyang University Seoul Hospital, Hanyang University College of Medicine, Seoul 04763, Korea; (S.B.); (S.J.); (H.S.); (H.K.); (H.P.); (J.M.)
| | - Hwangkyu Son
- Department of Pathology, Hanyang University Seoul Hospital, Hanyang University College of Medicine, Seoul 04763, Korea; (S.B.); (S.J.); (H.S.); (H.K.); (H.P.); (J.M.)
| | - Young Chan Wi
- Department of Pathology, Eunpyeong St. Mary’s Hospital, The Catholic University of Korea, Seoul 03312, Korea;
| | - Hyunsung Kim
- Department of Pathology, Hanyang University Seoul Hospital, Hanyang University College of Medicine, Seoul 04763, Korea; (S.B.); (S.J.); (H.S.); (H.K.); (H.P.); (J.M.)
| | - Hosub Park
- Department of Pathology, Hanyang University Seoul Hospital, Hanyang University College of Medicine, Seoul 04763, Korea; (S.B.); (S.J.); (H.S.); (H.K.); (H.P.); (J.M.)
| | - Jaekyung Myung
- Department of Pathology, Hanyang University Seoul Hospital, Hanyang University College of Medicine, Seoul 04763, Korea; (S.B.); (S.J.); (H.S.); (H.K.); (H.P.); (J.M.)
| | - Su-Jin Shin
- Department of Pathology, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul 06273, Korea;
| | - Seung Sam Paik
- Department of Pathology, Hanyang University Seoul Hospital, Hanyang University College of Medicine, Seoul 04763, Korea; (S.B.); (S.J.); (H.S.); (H.K.); (H.P.); (J.M.)
- Correspondence: ; Tel.: +82-02-2220-8960
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