1
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Ma W, Tang W, Kwok JS, Tong AH, Lo CW, Chu AT, Chung BH. A review on trends in development and translation of omics signatures in cancer. Comput Struct Biotechnol J 2024; 23:954-971. [PMID: 38385061 PMCID: PMC10879706 DOI: 10.1016/j.csbj.2024.01.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 01/31/2024] [Accepted: 01/31/2024] [Indexed: 02/23/2024] Open
Abstract
The field of cancer genomics and transcriptomics has evolved from targeted profiling to swift sequencing of individual tumor genome and transcriptome. The steady growth in genome, epigenome, and transcriptome datasets on a genome-wide scale has significantly increased our capability in capturing signatures that represent both the intrinsic and extrinsic biological features of tumors. These biological differences can help in precise molecular subtyping of cancer, predicting tumor progression, metastatic potential, and resistance to therapeutic agents. In this review, we summarized the current development of genomic, methylomic, transcriptomic, proteomic and metabolic signatures in the field of cancer research and highlighted their potentials in clinical applications to improve diagnosis, prognosis, and treatment decision in cancer patients.
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Affiliation(s)
- Wei Ma
- Hong Kong Genome Institute, Hong Kong, China
| | - Wenshu Tang
- Hong Kong Genome Institute, Hong Kong, China
| | | | | | | | | | - Brian H.Y. Chung
- Hong Kong Genome Institute, Hong Kong, China
- Department of Pediatrics and Adolescent Medicine, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Hong Kong Genome Project
- Hong Kong Genome Institute, Hong Kong, China
- Department of Pediatrics and Adolescent Medicine, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
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2
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Niavarani A. The role of distinct APOBEC/ADAR mRNA levels in mutational signatures linked to aging and ultraviolet radiation. Sci Rep 2024; 14:15395. [PMID: 38965255 PMCID: PMC11224270 DOI: 10.1038/s41598-024-64986-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 06/14/2024] [Indexed: 07/06/2024] Open
Abstract
The APOBEC/AID family is known for its mutator activity, and recent evidence also supports the potential impact of ADARs. Furthermore, the mutator impacts of APOBEC/ADAR mutations have not yet been investigated. Assessment of pancancer TCGA exomes identified enriched somatic variants among exomes with nonsynonymous APOBEC1, APOBEC3B, APOBEC3C, ADAR, and ADARB1 mutations, compared to exomes with synonymous ones. Principal component (PC) analysis reduced the number of potential players to eight in cancer exomes/genomes, and to five in cancer types. Multivariate regression analysis was used to assess the impact of the PCs on each COSMIC mutational signature among pancancer exomes/genomes and particular cancers, identifying several novel links, including SBS17b, SBS18, and ID7 mainly determined by APOBEC1 mRNA levels; SBS40, ID1, and ID2 by age; SBS3 and SBS16 by APOBEC3A/APOBEC3B mRNA levels; ID5 and DBS9 by DNA repair/replication (DRR) defects; and SBS7a-d, SBS38, ID4, ID8, ID13, and DBS1 by ultraviolet (UV) radiation/ADARB1 mRNA levels. APOBEC/ADAR mutations appeared to potentiate the impact of DRR defects on several mutational signatures, and some factors seemed to inversely affect certain signatures. These findings potentially implicate certain APOBEC/ADAR mutations/mRNA levels in distinct mutational signatures, particularly APOBEC1 mRNA levels in aging-related signatures and ADARB1 mRNA levels in UV radiation-related signatures.
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Affiliation(s)
- Ahmadreza Niavarani
- Digestive Oncology Research Center, Digestive Disease Research Institute, Tehran University of Medical Sciences, Tehran, Iran.
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3
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Franco I, Supek F. Genomics reveal unknown mutation-promoting agents at global sites. Nature 2024; 629:767-768. [PMID: 38773293 DOI: 10.1038/d41586-024-01190-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2024]
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4
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Takamatsu S, Murakami K, Matsumura N. Homologous Recombination Deficiency Unrelated to Platinum and PARP Inhibitor Response in Cell Line Libraries. Sci Data 2024; 11:171. [PMID: 38321018 PMCID: PMC10847511 DOI: 10.1038/s41597-024-03018-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 01/29/2024] [Indexed: 02/08/2024] Open
Abstract
While large publicly available cancer cell line databases are invaluable for preclinical drug discovery and biomarker development, the association between homologous recombination deficiency (HRD) and drug sensitivity in these resources remains unclear. In this study, we comprehensively analyzed molecular profiles and drug screening data from the Cancer Cell Line Encyclopedia. Unexpectedly, gene alterations in BRCA1/2 or homologous recombination-related genes, HRD scores, or mutational signature 3 were not positively correlated with sensitivity to platinum agents or PARP inhibitors. Rather, higher HRD scores and mutational signature 3 were significantly associated with resistance to these agents in multiple assays. These findings were consistent when analyzing exclusively breast and ovarian cancer cell lines and when using data from the COSMIC Cell Line Project. Collectively, the existing data from established cancer cell lines do not reflect the expected association between HRD status and drug response to platinum agents and PARP inhibitors in clinical tumors. This discrepancy may extend to other tumor characteristics, highlighting the importance of recognizing potential limitations in cell line data for researchers.
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Affiliation(s)
- Shiro Takamatsu
- Department of Gynecology and Obstetrics, Kyoto University Graduate School of Medicine, Kyoto, Kyoto, Japan
- Department of Genomic Medicine, the University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Kosuke Murakami
- Department of Obstetrics and Gynecology, Kindai University Faculty of Medicine, Osaka-Sayama, Osaka, Japan
- The Bloomberg~Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University, Baltimore, Maryland, USA
| | - Noriomi Matsumura
- Department of Obstetrics and Gynecology, Kindai University Faculty of Medicine, Osaka-Sayama, Osaka, Japan.
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5
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Salu P, Reindl KM. Advancements in Preclinical Models of Pancreatic Cancer. Pancreas 2024; 53:e205-e220. [PMID: 38206758 PMCID: PMC10842038 DOI: 10.1097/mpa.0000000000002277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/13/2024]
Abstract
ABSTRACT Pancreatic cancer remains one of the deadliest of all cancer types with a 5-year overall survival rate of just 12%. Preclinical models available for understanding the disease pathophysiology have evolved significantly in recent years. Traditionally, commercially available 2-dimensional cell lines were developed to investigate mechanisms underlying tumorigenesis, metastasis, and drug resistance. However, these cells grow as monolayer cultures that lack heterogeneity and do not effectively represent tumor biology. Developing patient-derived xenografts and genetically engineered mouse models led to increased cellular heterogeneity, molecular diversity, and tissues that histologically represent the original patient tumors. However, these models are relatively expensive and very timing consuming. More recently, the advancement of fast and inexpensive in vitro models that better mimic disease conditions in vivo are on the rise. Three-dimensional cultures like organoids and spheroids have gained popularity and are considered to recapitulate complex disease characteristics. In addition, computational genomics, transcriptomics, and metabolomic models are being developed to simulate pancreatic cancer progression and predict better treatment strategies. Herein, we review the challenges associated with pancreatic cancer research and available analytical models. We suggest that an integrated approach toward using these models may allow for developing new strategies for pancreatic cancer precision medicine.
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Affiliation(s)
- Philip Salu
- From the Department of Biological Sciences, North Dakota State University, Fargo, ND
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6
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Drummond RD, Defelicibus A, Meyenberg M, Valieris R, Dias-Neto E, Rosales RA, da Silva IT. Relating mutational signature exposures to clinical data in cancers via signeR 2.0. BMC Bioinformatics 2023; 24:439. [PMID: 37990302 PMCID: PMC10664385 DOI: 10.1186/s12859-023-05550-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 10/27/2023] [Indexed: 11/23/2023] Open
Abstract
BACKGROUND Cancer is a collection of diseases caused by the deregulation of cell processes, which is triggered by somatic mutations. The search for patterns in somatic mutations, known as mutational signatures, is a growing field of study that has already become a useful tool in oncology. Several algorithms have been proposed to perform one or both the following two tasks: (1) de novo estimation of signatures and their exposures, (2) estimation of the exposures of each one of a set of pre-defined signatures. RESULTS Our group developed signeR, a Bayesian approach to both of these tasks. Here we present a new version of the software, signeR 2.0, which extends the possibilities of previous analyses to explore the relation of signature exposures to other data of clinical relevance. signeR 2.0 includes a user-friendly interface developed using the R-Shiny framework and improvements in performance. This version allows the analysis of submitted data or public TCGA data, which is embedded in the package for easy access. CONCLUSION signeR 2.0 is a valuable tool to generate and explore exposure data, both from de novo or fitting analyses and is an open-source R package available through the Bioconductor project at ( https://doi.org/10.18129/B9.bioc.signeR ).
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Affiliation(s)
- Rodrigo D Drummond
- Laboratory of Computational Biology and Bioinformatics, CIPE/A.C.Camargo Cancer Center, São Paulo, São Paulo, 01508-010, Brazil
| | - Alexandre Defelicibus
- Laboratory of Computational Biology and Bioinformatics, CIPE/A.C.Camargo Cancer Center, São Paulo, São Paulo, 01508-010, Brazil
| | - Mathilde Meyenberg
- CeMM Research Center for Molecular Medicine, Austrian Academy of Sciences, Vienna, Austria
| | - Renan Valieris
- Laboratory of Computational Biology and Bioinformatics, CIPE/A.C.Camargo Cancer Center, São Paulo, São Paulo, 01508-010, Brazil
| | - Emmanuel Dias-Neto
- Laboratory of Computational Biology and Bioinformatics, CIPE/A.C.Camargo Cancer Center, São Paulo, São Paulo, 01508-010, Brazil
| | - Rafael A Rosales
- Departamento de Computação e Matemática, Universidade de São Paulo, Ribeirão Preto, São Paulo, 14040-901, Brazil.
| | - Israel Tojal da Silva
- Laboratory of Computational Biology and Bioinformatics, CIPE/A.C.Camargo Cancer Center, São Paulo, São Paulo, 01508-010, Brazil.
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7
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Wang P, Sun S, Lam S, Lockwood WW. New insights into the biology and development of lung cancer in never smokers-implications for early detection and treatment. J Transl Med 2023; 21:585. [PMID: 37653450 PMCID: PMC10472682 DOI: 10.1186/s12967-023-04430-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 08/10/2023] [Indexed: 09/02/2023] Open
Abstract
Lung cancer is the leading cause of cancer deaths worldwide. Despite never smokers comprising between 10 and 25% of all cases, lung cancer in never smokers (LCNS) is relatively under characterized from an etiological and biological perspective. The application of multi-omics techniques on large patient cohorts has significantly advanced the current understanding of LCNS tumor biology. By synthesizing the findings of multi-omics studies on LCNS from a clinical perspective, we can directly translate knowledge regarding tumor biology into implications for patient care. Primarily focused on never smokers with lung adenocarcinoma, this review details the predominance of driver mutations, particularly in East Asian patients, as well as the frequency and importance of germline variants in LCNS. The mutational patterns present in LCNS tumors are thoroughly explored, highlighting the high abundance of the APOBEC signature. Moreover, this review recognizes the spectrum of immune profiles present in LCNS tumors and posits how it can be translated to treatment selection. The recurring and novel insights from multi-omics studies on LCNS tumor biology have a wide range of clinical implications. Risk factors such as exposure to outdoor air pollution, second hand smoke, and potentially diet have a genomic imprint in LCNS at varying degrees, and although they do not encompass all LCNS cases, they can be leveraged to stratify risk. Germline variants similarly contribute to a notable proportion of LCNS, which warrants detailed documentation of family history of lung cancer among never smokers and demonstrates value in developing testing for pathogenic variants in never smokers for early detection in the future. Molecular driver subtypes and specific co-mutations and mutational signatures have prognostic value in LCNS and can guide treatment selection. LCNS tumors with no known driver alterations tend to be stem-like and genes contributing to this state may serve as potential therapeutic targets. Overall, the comprehensive findings of multi-omics studies exert a wide influence on clinical management and future research directions in the realm of LCNS.
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Affiliation(s)
- Peiyao Wang
- Department of Integrative Oncology, British Columbia Cancer Research Institute, Vancouver, BC, Canada
- Interdisciplinary Oncology Program, University of British Columbia, Vancouver, BC, Canada
| | - Sophie Sun
- Department of Medical Oncology, British Columbia Cancer Agency Vancouver, Vancouver, BC, Canada
| | - Stephen Lam
- Department of Integrative Oncology, British Columbia Cancer Research Institute, Vancouver, BC, Canada
| | - William W Lockwood
- Department of Integrative Oncology, British Columbia Cancer Research Institute, Vancouver, BC, Canada.
- Interdisciplinary Oncology Program, University of British Columbia, Vancouver, BC, Canada.
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada.
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8
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Hamida R, Ali MA, Mugren N, Al-Zaban MI, Bin-Meferij MM, Redhwan A. Planophila laetevirens-Mediated Synthesis of Silver Nanoparticles: Optimization, Characterization, and Anticancer and Antibacterial Potentials. ACS OMEGA 2023; 8:29169-29188. [PMID: 37599946 PMCID: PMC10433340 DOI: 10.1021/acsomega.3c02368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 07/17/2023] [Indexed: 08/22/2023]
Abstract
Algal-mediated synthesis of nanoparticles (NPs) opens the horizon for green and sustainable synthesis of NPs that can be used in many fields, such as medicine and industry. We extracellularly synthesized silver NPs (Ag-NPs) using the novel microalgae Planophila laetevirens under optimized conditions. The isolate was collected from freshwater/soil, purified, morphologically identified, and genetically identified using light, inverted light, scanning electron microscopy, and 18S rRNA sequencing. The phytochemicals in the algal extract were detected by GC-MS. Aqueous biomass extracts and cell-free media were used to reduce silver nitrate to Ag-NPs. To get small, uniformly shaped, and stable Ag-NPs, various abiotic parameters, including precursor concentration, the ratio between the reductant and precursor, temperature, time of temperature exposure, pH, illumination, and incubation time, were controlled during the synthesis of Ag-NPs. B-P@Ag-NPs and S-P@Ag-NPs (Ag-NPs synthesized using biomass and cell-free medium, respectively) were characterized using UV-vis spectroscopy, transmission electron microscopy, scanning electron microscopy, energy-dispersive X-ray analysis (EDX) and mapping, Fourier transform infrared (FTIR) spectroscopy, and a zeta sizer. S-P@Ag-NPs had a smaller size (10.8 ± 0.3 nm) than B-P@Ag-NPs (19.0 ± 0.6 nm), while their shapes were uniform quasispherical (S-P@Ag-NPs) and spherical to oval (B-P@Ag-NPs). EDX and mapping analyses demonstrated that Ag was the dominant element in the B-P@Ag-NP and S-P@Ag-NP samples, while FTIR revealed the presence of O-H, C-H, N-H, and C-O groups, indicating that polysaccharides and proteins acted as reductants, while polysaccharides/fatty acids acted as stabilizers during the synthesis of NPs. The hydrodynamic diameters of B-P@Ag-NPs and S-P@Ag-NPs were 37.7 and 28.3 nm, respectively, with negative charges on their surfaces, suggesting their colloidal stability. Anticancer activities against colon cancer (Sw620 and HT-29 cells), breast cancer (MDA-MB231 and MCF-7 cells), and normal human fibroblasts (HFs) were screened using the MTT assay. B-P@Ag-NPs and S-P@Ag-NPs had a greater antiproliferative effect against colon cancer than against breast cancer, with biocompatibility against HFs. The biocidal effects of the B-P@Ag-NPs and S-P@Ag-NPs were evaluated against Escherichia coli, Bacillus cereus, and Bacillus subtilis using agar well diffusion and resazurin dye assays. B-P@Ag-NPs and S-P@Ag-NPs caused higher growth inhibition of Gram-negative bacteria than of Gram-positive bacteria. B-P@Ag-NPs and S-P@Ag-NPs synthesized by P. laetevirens are promising antitumor and biocidal agents.
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Affiliation(s)
| | - Mohamed Abdelaal Ali
- Plant
Production Department, Arid Lands Cultivation
Research Institute, City of Scientific Research and Technological
Applications (SRTA-CITY) New Borg El-Arab, Alexandria 21934, Egypt
| | - Njoud Mugren
- Graduated
Student, Department of Chemistry, College of Science, Princess Nourah bint Abdulrahman University, Riyadh 11671, Saudi Arabia
| | - Mayasar Ibrahim Al-Zaban
- Department
of Biology, College of Science, Princess
Nourah bint Abdulrahman University, Riyadh 11671, Saudi Arabia
| | - Mashael Mohammed Bin-Meferij
- Department
of Biology, College of Science, Princess
Nourah bint Abdulrahman University, Riyadh 11671, Saudi Arabia
| | - Alya Redhwan
- Department
of Heath, College of Health, and Rehabilitation Sciences, Princess Nourah bint Abdulrahman University, Riyadh 11671, Saudi Arabia
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9
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Díaz-Gay M, Vangara R, Barnes M, Wang X, Islam SMA, Vermes I, Narasimman NB, Yang T, Jiang Z, Moody S, Senkin S, Brennan P, Stratton MR, Alexandrov LB. Assigning mutational signatures to individual samples and individual somatic mutations with SigProfilerAssignment. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.10.548264. [PMID: 37502962 PMCID: PMC10369904 DOI: 10.1101/2023.07.10.548264] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Analysis of mutational signatures is a powerful approach for understanding the mutagenic processes that have shaped the evolution of a cancer genome. Here we present SigProfilerAssignment, a desktop and an online computational framework for assigning all types of mutational signatures to individual samples. SigProfilerAssignment is the first tool that allows both analysis of copy-number signatures and probabilistic assignment of signatures to individual somatic mutations. As its computational engine, the tool uses a custom implementation of the forward stagewise algorithm for sparse regression and nonnegative least squares for numerical optimization. Analysis of 2,700 synthetic cancer genomes with and without noise demonstrates that SigProfilerAssignment outperforms four commonly used approaches for assigning mutational signatures. SigProfilerAssignment is freely available at https://github.com/AlexandrovLab/SigProfilerAssignment with a web implementation at https://cancer.sanger.ac.uk/signatures/assignment/.
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Affiliation(s)
- Marcos Díaz-Gay
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, 92093, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA, 92093, US
- Moores Cancer Center, UC San Diego, La Jolla, CA, 92037, USA
| | - Raviteja Vangara
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, 92093, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA, 92093, US
- Moores Cancer Center, UC San Diego, La Jolla, CA, 92037, USA
| | - Mark Barnes
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, 92093, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA, 92093, US
- Moores Cancer Center, UC San Diego, La Jolla, CA, 92037, USA
| | - Xi Wang
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, 92093, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA, 92093, US
- Moores Cancer Center, UC San Diego, La Jolla, CA, 92037, USA
| | - S M Ashiqul Islam
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, 92093, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA, 92093, US
- Moores Cancer Center, UC San Diego, La Jolla, CA, 92037, USA
| | - Ian Vermes
- COSMIC, Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Nithish Bharadhwaj Narasimman
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, 92093, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA, 92093, US
- Moores Cancer Center, UC San Diego, La Jolla, CA, 92037, USA
| | - Ting Yang
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, 92093, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA, 92093, US
- Moores Cancer Center, UC San Diego, La Jolla, CA, 92037, USA
| | - Zichen Jiang
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, 92093, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA, 92093, US
- Moores Cancer Center, UC San Diego, La Jolla, CA, 92037, USA
| | - Sarah Moody
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
| | - Sergey Senkin
- Genomic Epidemiology Branch, International Agency for Research on Cancer, 69366 Lyon CEDEX 07, France
| | - Paul Brennan
- Genomic Epidemiology Branch, International Agency for Research on Cancer, 69366 Lyon CEDEX 07, France
| | - Michael R Stratton
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
| | - Ludmil B Alexandrov
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, 92093, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA, 92093, US
- Moores Cancer Center, UC San Diego, La Jolla, CA, 92037, USA
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10
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Liu Y, Zheng H, Gu AM, Li Y, Wang T, Li C, Gu Y, Lin J, Ding X. Identification and Validation of a Metabolism-Related Prognostic Signature Associated with M2 Macrophage Infiltration in Gastric Cancer. Int J Mol Sci 2023; 24:10625. [PMID: 37445803 DOI: 10.3390/ijms241310625] [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: 04/21/2023] [Revised: 06/12/2023] [Accepted: 06/16/2023] [Indexed: 07/15/2023] Open
Abstract
High levels of M2 macrophage infiltration invariably contribute to poor cancer prognosis and can be manipulated by metabolic reprogramming in the tumor microenvironment. However, the metabolism-related genes (MRGs) affecting M2 macrophage infiltration and their clinical implications are not fully understood. In this study, we identified 173 MRGs associated with M2 macrophage infiltration in cases of gastric cancer (GC) using the TCGA and GEO databases. Twelve MRGs were eventually adopted as the prognostic signature to develop a risk model. In the high-risk group, the patients showed poorer survival outcomes than patients in the low-risk group. Additionally, the patients in the high-risk group were less sensitive to certain drugs, such as 5-Fluorouracil, Oxaliplatin, and Cisplatin. Risk scores were positively correlated with the infiltration of multiple immune cells, including CD8+ T cells and M2 macrophages. Furthermore, a difference was observed in the expression and distribution between the 12 signature genes in the tumor microenvironment through single-cell sequencing analysis. In vitro experiments proved that the M2 polarization of macrophages was suppressed by Sorcin-knockdown GC cells, thereby hindering the proliferation and migration of GC cells. These findings provide a valuable prognostic signature for evaluating clinical outcomes and corresponding treatment options and identifying potential targets for GC treatment.
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Affiliation(s)
- Yunze Liu
- The First Clinical Medical College, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Haocheng Zheng
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Anna Meilin Gu
- Biology Department: Physiology, University of Washington, Seattle, WA 98105, USA
| | - Yuan Li
- National Institute of TCM Constitution and Preventive Medicine, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Tieshan Wang
- Beijing Research Institute of Chinese Medicine, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Chengze Li
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Yixiao Gu
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Jie Lin
- National Institute of TCM Constitution and Preventive Medicine, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Xia Ding
- The First Clinical Medical College, Beijing University of Chinese Medicine, Beijing 100029, China
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing 100029, China
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11
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Udalov A, Kumar L, Gaudette AN, Zhang R, Salomao J, Saigal S, Nosrati M, McAllister SD, Desprez PY. Automated Dashboards for the Identification of Pathogenic Circulating Tumor DNA Mutations in Longitudinal Blood Draws of Cancer Patients. Methods Protoc 2023; 6:mps6030046. [PMID: 37218906 DOI: 10.3390/mps6030046] [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: 02/16/2023] [Revised: 04/16/2023] [Accepted: 04/19/2023] [Indexed: 05/24/2023] Open
Abstract
The longitudinal monitoring of patient circulating tumor DNA (ctDNA) provides a powerful method for tracking the progression, remission, and recurrence of several types of cancer. Often, clinical and research approaches involve the manual review of individual liquid biopsy reports after sampling and genomic testing. Here, we describe a process developed to integrate techniques utilized in data science within a cancer research framework. Using data collection, an analysis that classifies genetic cancer mutations as pathogenic, and a patient matching methodology that identifies the same donor within all liquid biopsy reports, the manual work for research personnel is drastically reduced. Automated dashboards provide longitudinal views of patient data for research studies to investigate tumor progression and treatment efficacy via the identification of ctDNA variant allele frequencies over time.
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Affiliation(s)
- Aleksandr Udalov
- Graduate School of Management, UC Davis, 1 Shields Ave., Davis, CA 95616, USA
| | - Lexman Kumar
- Graduate School of Management, UC Davis, 1 Shields Ave., Davis, CA 95616, USA
| | - Anna N Gaudette
- Graduate School of Management, UC Davis, 1 Shields Ave., Davis, CA 95616, USA
| | - Ran Zhang
- Graduate School of Management, UC Davis, 1 Shields Ave., Davis, CA 95616, USA
| | - Joao Salomao
- Graduate School of Management, UC Davis, 1 Shields Ave., Davis, CA 95616, USA
| | - Sanjay Saigal
- Graduate School of Management, UC Davis, 1 Shields Ave., Davis, CA 95616, USA
| | - Mehdi Nosrati
- California Pacific Medical Center, Research Institute, 475 Brannan St., San Francisco, CA 94107, USA
| | - Sean D McAllister
- California Pacific Medical Center, Research Institute, 475 Brannan St., San Francisco, CA 94107, USA
| | - Pierre-Yves Desprez
- California Pacific Medical Center, Research Institute, 475 Brannan St., San Francisco, CA 94107, USA
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12
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Fito-Lopez B, Salvadores M, Alvarez MM, Supek F. Prevalence, causes and impact of TP53-loss phenocopying events in human tumors. BMC Biol 2023; 21:92. [PMID: 37095494 PMCID: PMC10127307 DOI: 10.1186/s12915-023-01595-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 04/12/2023] [Indexed: 04/26/2023] Open
Abstract
BACKGROUND TP53 is a master tumor suppressor gene, mutated in approximately half of all human cancers. Given the many regulatory roles of the corresponding p53 protein, it is possible to infer loss of p53 activity - which may occur due to alterations in trans - from gene expression patterns. Several such alterations that phenocopy p53 loss are known, however additional ones may exist, but their identity and prevalence among human tumors are not well characterized. RESULTS We perform a large-scale statistical analysis on transcriptomes of ~ 7,000 tumors and ~ 1,000 cell lines, estimating that 12% and 8% of tumors and cancer cell lines, respectively, phenocopy TP53 loss: they are likely deficient in the activity of the p53 pathway, while not bearing obvious TP53 inactivating mutations. While some of these cases are explained by amplifications in the known phenocopying genes MDM2, MDM4 and PPM1D, many are not. An association analysis of cancer genomic scores jointly with CRISPR/RNAi genetic screening data identified an additional common TP53-loss phenocopying gene, USP28. Deletions in USP28 are associated with a TP53 functional impairment in 2.9-7.6% of breast, bladder, lung, liver and stomach tumors, and have comparable effect size to MDM4 amplifications. Additionally, in the known copy number alteration (CNA) segment harboring MDM2, we identify an additional co-amplified gene (CNOT2) that may cooperatively boost the TP53 functional inactivation effect of MDM2. An analysis of cancer cell line drug screens using phenocopy scores suggests that TP53 (in)activity commonly modulates associations between anticancer drug effects and various genetic markers, such as PIK3CA and PTEN mutations, and should thus be considered as a drug activity modifying factor in precision medicine. As a resource, we provide the drug-genetic marker associations that differ depending on TP53 functional status. CONCLUSIONS Human tumors that do not bear obvious TP53 genetic alterations but that phenocopy p53 activity loss are common, and the USP28 gene deletions are one likely cause.
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Affiliation(s)
- Bruno Fito-Lopez
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute for Science and Technology (BIST), Barcelona, Spain
| | - Marina Salvadores
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute for Science and Technology (BIST), Barcelona, Spain
| | - Miguel-Martin Alvarez
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute for Science and Technology (BIST), Barcelona, Spain
| | - Fran Supek
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute for Science and Technology (BIST), Barcelona, Spain.
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain.
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13
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Ostroverkhova D, Przytycka TM, Panchenko AR. Cancer driver mutations: predictions and reality. Trends Mol Med 2023:S1471-4914(23)00067-9. [PMID: 37076339 DOI: 10.1016/j.molmed.2023.03.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 03/17/2023] [Accepted: 03/23/2023] [Indexed: 04/21/2023]
Abstract
Cancer cells accumulate many genetic alterations throughout their lifetime, but only a few of them drive cancer progression, termed driver mutations. Driver mutations may vary between cancer types and patients, can remain latent for a long time and become drivers at particular cancer stages, or may drive oncogenesis only in conjunction with other mutations. The high mutational, biochemical, and histological tumor heterogeneity makes driver mutation identification very challenging. In this review we summarize recent efforts to identify driver mutations in cancer and annotate their effects. We underline the success of computational methods to predict driver mutations in finding novel cancer biomarkers, including in circulating tumor DNA (ctDNA). We also report on the boundaries of their applicability in clinical research.
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Affiliation(s)
- Daria Ostroverkhova
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, ON, Canada
| | - Teresa M Przytycka
- National Library of Medicine, National Institutes of Health (NIH), Bethesda, MD, USA.
| | - Anna R Panchenko
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, ON, Canada; Department of Biology and Molecular Sciences, Queen's University, Kingston, ON, Canada; School of Computing, Queen's University, Kingston, ON, Canada; Ontario Institute of Cancer Research, Toronto, ON, Canada.
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14
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El Harane S, Zidi B, El Harane N, Krause KH, Matthes T, Preynat-Seauve O. Cancer Spheroids and Organoids as Novel Tools for Research and Therapy: State of the Art and Challenges to Guide Precision Medicine. Cells 2023; 12:cells12071001. [PMID: 37048073 PMCID: PMC10093533 DOI: 10.3390/cells12071001] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 03/14/2023] [Accepted: 03/20/2023] [Indexed: 04/14/2023] Open
Abstract
Spheroids and organoids are important novel players in medical and life science research. They are gradually replacing two-dimensional (2D) cell cultures. Indeed, three-dimensional (3D) cultures are closer to the in vivo reality and open promising perspectives for academic research, drug screening, and personalized medicine. A large variety of cells and tissues, including tumor cells, can be the starting material for the generation of 3D cultures, including primary tissues, stem cells, or cell lines. A panoply of methods has been developed to generate 3D structures, including spontaneous or forced cell aggregation, air-liquid interface conditions, low cell attachment supports, magnetic levitation, and scaffold-based technologies. The choice of the most appropriate method depends on (i) the origin of the tissue, (ii) the presence or absence of a disease, and (iii) the intended application. This review summarizes methods and approaches for the generation of cancer spheroids and organoids, including their advantages and limitations. We also highlight some of the challenges and unresolved issues in the field of cancer spheroids and organoids, and discuss possible therapeutic applications.
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Affiliation(s)
- Sanae El Harane
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, 1206 Geneva, Switzerland
| | - Bochra Zidi
- Department of Medicine, Faculty of Medicine, University of Geneva, 1206 Geneva, Switzerland
| | - Nadia El Harane
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, 1206 Geneva, Switzerland
| | - Karl-Heinz Krause
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, 1206 Geneva, Switzerland
| | - Thomas Matthes
- Department of Medicine, Faculty of Medicine, University of Geneva, 1206 Geneva, Switzerland
| | - Olivier Preynat-Seauve
- Department of Medicine, Faculty of Medicine, University of Geneva, 1206 Geneva, Switzerland
- Laboratory of Experimental Cell Therapy, Department of Diagnostics, Geneva University Hospitals, 1206 Geneva, Switzerland
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15
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Wang M, Yao X, Bo Z, Zheng J, Yu H, Xie X, Lin Z, Wang Y, Chen G, Wu L. Synergistic Effect of Lenvatinib and Chemotherapy in Hepatocellular Carcinoma Using Preclinical Models. J Hepatocell Carcinoma 2023; 10:483-495. [PMID: 37007211 PMCID: PMC10065123 DOI: 10.2147/jhc.s395474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 03/11/2023] [Indexed: 03/29/2023] Open
Abstract
Purpose The current study aimed to evaluate the synergistic efficacy of lenvatinib and FOLFOX (infusional fluorouracil (FU), folinic acid, and oxaliplatin) in hepatocellular carcinoma (HCC) using patient-derived xenograft (PDX) and PDX-derived organotypic spheroid (XDOTS) models in vivo and in vitro. Methods PDX and matched XDOTS models originating from three patients with HCC were established. All models were divided into four groups and treated with drugs alone or in combination. Tumor growth in the PDX models was measured and recorded, and angiogenesis and phosphorylation of the vascular endothelial growth factor receptor (VEGFR2), rearranged during transfection (RET), and extracellular signal-regulated kinase (ERK) were detected using immunohistochemistry and Western blot assays. The proliferative ability of XDOTS was evaluated through active staining and immunofluorescence staining, and the effect of the combined medication was evaluated using the Celltiter-Glo luminescent cell viability assay. Results Three PDX models with genetic characteristics similar to those of the original tumors were successfully established. Combining lenvatinib with FOLFOX led to a higher tumor growth inhibition rate than individual therapies (P < 0.01). Immunohistochemical analysis demonstrated that the combined treatment significantly inhibited the proliferation and angiogenesis of PDX tissues (P < 0.05), and Western blot analysis showed that the combined treatment significantly inhibited the phosphorylation of VEGFR2, RET, and ERK compared with single-agent treatment. Additionally, all three matched XDOTS models were successfully cultured with satisfactory activity and proliferation, and the combined therapies led to better suppression of XDOTS growth compared with individual therapy (P < 0.05). Conclusion Lenvatinib combined with FOLFOX had a synergistic antitumor effect in HCC PDX and XDOTS models by inhibiting the phosphorylation of VEGFR, RET, and ERK.
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Affiliation(s)
- Mingxun Wang
- Department of Ultrasonography, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, People’s Republic of China
| | - Xinfei Yao
- The First Clinical College, Wenzhou Medical University, Wenzhou, People’s Republic of China
| | - Zhiyuan Bo
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, People’s Republic of China
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, People’s Republic of China
| | - Jiuyi Zheng
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, People’s Republic of China
| | - Haitao Yu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, People’s Republic of China
| | - Xiaozai Xie
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, People’s Republic of China
| | - Zixia Lin
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, People’s Republic of China
| | - Yi Wang
- Department of Epidemiology and Biostatistics, School of Public Health and Management, Wenzhou Medical University, Wenzhou, People’s Republic of China
| | - Gang Chen
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, People’s Republic of China
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, People’s Republic of China
| | - Lijun Wu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, People’s Republic of China
- Correspondence: Lijun Wu; Gang Chen, Department of Hepatobiliary Surgery, The First Affiliated Hospital of Wenzhou Medical University, Fuxue Road, Wenzhou, Zhejiang, 325035, People’s Republic of China, Tel +86 577 55579-453, Fax +86 577 55579-555, Email ;
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16
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Zhivagui M, Hoda A, Valenzuela N, Yeh YY, Dai J, He Y, Nandi SP, Otlu B, Van Houten B, Alexandrov LB. DNA damage and somatic mutations in mammalian cells after irradiation with a nail polish dryer. Nat Commun 2023; 14:276. [PMID: 36650165 PMCID: PMC9845303 DOI: 10.1038/s41467-023-35876-8] [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: 02/07/2021] [Accepted: 01/05/2023] [Indexed: 01/19/2023] Open
Abstract
Ultraviolet A light is commonly emitted by UV-nail polish dryers with recent reports suggesting that long-term use may increase the risk for developing skin cancer. However, no experimental evaluation has been conducted to reveal the effect of radiation emitted by UV-nail polish dryers on mammalian cells. Here, we show that irradiation by a UV-nail polish dryer causes high levels of reactive oxygen species, consistent with 8-oxo-7,8-dihydroguanine damage and mitochondrial dysfunction. Analysis of somatic mutations reveals a dose-dependent increase of C:G>A:T substitutions in irradiated samples with mutagenic patterns similar to mutational signatures previously attributed to reactive oxygen species. In summary, this study demonstrates that radiation emitted by UV-nail polish dryers can both damage DNA and permanently engrave mutations on the genomes of primary mouse embryonic fibroblasts, human foreskin fibroblasts, and human epidermal keratinocytes.
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Affiliation(s)
- Maria Zhivagui
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, 92093, USA.,Department of Bioengineering, UC San Diego, La Jolla, CA, 92093, USA.,Moores Cancer Center, UC San Diego, La Jolla, CA, 92037, USA
| | - Areebah Hoda
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, 92093, USA
| | | | - Yi-Yu Yeh
- Department of Bioengineering, UC San Diego, La Jolla, CA, 92093, USA
| | - Jason Dai
- Department of Bioengineering, UC San Diego, La Jolla, CA, 92093, USA
| | - Yudou He
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, 92093, USA.,Department of Bioengineering, UC San Diego, La Jolla, CA, 92093, USA.,Moores Cancer Center, UC San Diego, La Jolla, CA, 92037, USA
| | - Shuvro P Nandi
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, 92093, USA.,Department of Bioengineering, UC San Diego, La Jolla, CA, 92093, USA.,Moores Cancer Center, UC San Diego, La Jolla, CA, 92037, USA
| | - Burcak Otlu
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, 92093, USA.,Department of Bioengineering, UC San Diego, La Jolla, CA, 92093, USA.,Moores Cancer Center, UC San Diego, La Jolla, CA, 92037, USA
| | - Bennett Van Houten
- UPMC-Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, 15213, USA
| | - Ludmil B Alexandrov
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, 92093, USA. .,Department of Bioengineering, UC San Diego, La Jolla, CA, 92093, USA. .,Moores Cancer Center, UC San Diego, La Jolla, CA, 92037, USA.
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17
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The Involvement of Natural Polyphenols in Molecular Mechanisms Inducing Apoptosis in Tumor Cells: A Promising Adjuvant in Cancer Therapy. Int J Mol Sci 2023; 24:ijms24021680. [PMID: 36675194 PMCID: PMC9863215 DOI: 10.3390/ijms24021680] [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: 12/12/2022] [Revised: 01/09/2023] [Accepted: 01/11/2023] [Indexed: 01/18/2023] Open
Abstract
Various literature data show how a diet rich in vegetables could reduce the incidence of several cancers due to the contribution of the natural polyphenols contained in them. Polyphenols are attributed multiple pharmacological actions such as anti-inflammatory, anti-oxidant, antibiotic, antiseptic, anti-allergic, cardioprotective and even anti-tumor properties. The multiple mechanisms involved in their anti-tumor action include signaling pathways modulation associated with cell proliferation, differentiation, migration, angiogenesis, metastasis and cell death. Since the dysregulation of death processes is involved in cancer etiopathology, the natural compounds able to kill cancer cells could be used as new anticancer agents. Apoptosis, a programmed form of cell death, is the most potent defense against cancer and the main mechanism used by both chemotherapy agents and polyphenols. The aim of this review is to provide an update of literature data on the apoptotic molecular mechanisms induced by some representative polyphenol family members in cancer cells. This aspect is particularly important because it may be useful in the design of new therapeutic strategies against cancer involving the polyphenols as adjuvants.
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18
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The Analysis of Trends in Survival for Patients with Melanoma Brain Metastases with Introduction of Novel Therapeutic Options before the Era of Combined Immunotherapy-Multicenter Italian-Polish Report. Cancers (Basel) 2022; 14:cancers14235763. [PMID: 36497248 PMCID: PMC9737166 DOI: 10.3390/cancers14235763] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 11/17/2022] [Accepted: 11/21/2022] [Indexed: 11/25/2022] Open
Abstract
Stage IV melanoma patients develop melanoma brain metastases (MBM) in 50% of cases. Their prognosis is improving, and its understanding outside the context of clinical trials is relevant. We have retrospectively analyzed the clinical data, course of treatment, and outcomes of 531 subsequent stage IV melanoma patients with BM treated in five reference Italian and Polish melanoma centers between 2014 and 2021. Patients with MBM after 2017 had a better prognosis, with a significantly improved median of overall survival (OS) after 2017 in the worst mol-GPA prognostic groups (mol-GPA ≤ 2): a median OS >6 months and HR 0.76 vs. those treated before 2017 (CI: 0.60−0.97, p = 0.027). In our prognostic model, mol-GPA was highly predictive for survival, and symptoms without steroid use did not have prognostic significance. Local therapy significantly improved survival regardless of the year of diagnosis (treated before or after 2017), with median survival >12 months. Systemic therapy improved outcomes when it was combined with local therapy. Local surgery was associated with improved OS regardless of the timing related to treatment start (i.e., before or after 30 days from MBM diagnosis). Local and systemic treatment significantly prolong survival for the poorest mol-GPA prognosis. Use of modern treatment modalities is justified in all mol-GPA prognostic groups.
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TP53-dependent toxicity of CRISPR/Cas9 cuts is differential across genomic loci and can confound genetic screening. Nat Commun 2022; 13:4520. [PMID: 35927263 PMCID: PMC9352712 DOI: 10.1038/s41467-022-32285-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 07/26/2022] [Indexed: 12/14/2022] Open
Abstract
CRISPR/Cas9 gene editing can inactivate genes in a precise manner. This process involves DNA double-strand breaks (DSB), which may incur a loss of cell fitness. We hypothesize that DSB toxicity may be variable depending on the chromatin environment in the targeted locus. Here, by analyzing isogenic cell line pair CRISPR experiments jointly with previous screening data from across ~900 cell lines, we show that TP53-associated break toxicity is higher in genomic regions that harbor active chromatin, such as gene regulatory elements or transcription elongation histone marks. DSB repair pathway choice and DNA sequence context also associate with toxicity. We also show that, due to noise introduced by differential toxicity of sgRNA-targeted sites, the power of genetic screens to detect conditional essentiality is reduced in TP53 wild-type cells. Understanding the determinants of Cas9 cut toxicity will help improve design of CRISPR reagents to avoid incidental selection of TP53-deficient and/or DNA repair deficient cells. Toxicity of CRISPR/Cas9 induced DNA breaks depends on their repair mechanism, and on the chromatin environment at the cut site. Here the authors show that edits in active genes or regulatory elements can incur a higher toxicity via a TP53-dependent mechanism.
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Vali-Pour M, Park S, Espinosa-Carrasco J, Ortiz-Martínez D, Lehner B, Supek F. The impact of rare germline variants on human somatic mutation processes. Nat Commun 2022; 13:3724. [PMID: 35764656 PMCID: PMC9240060 DOI: 10.1038/s41467-022-31483-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 06/17/2022] [Indexed: 02/07/2023] Open
Abstract
Somatic mutations are an inevitable component of ageing and the most important cause of cancer. The rates and types of somatic mutation vary across individuals, but relatively few inherited influences on mutation processes are known. We perform a gene-based rare variant association study with diverse mutational processes, using human cancer genomes from over 11,000 individuals of European ancestry. By combining burden and variance tests, we identify 207 associations involving 15 somatic mutational phenotypes and 42 genes that replicated in an independent data set at a false discovery rate of 1%. We associate rare inherited deleterious variants in genes such as MSH3, EXO1, SETD2, and MTOR with two phenotypically different forms of DNA mismatch repair deficiency, and variants in genes such as EXO1, PAXIP1, RIF1, and WRN with deficiency in homologous recombination repair. In addition, we identify associations with other mutational processes, such as APEX1 with APOBEC-signature mutagenesis. Many of the genes interact with each other and with known mutator genes within cellular sub-networks. Considered collectively, damaging variants in the identified genes are prevalent in the population. We suggest that rare germline variation in diverse genes commonly impacts mutational processes in somatic cells.
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Affiliation(s)
- Mischan Vali-Pour
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Solip Park
- Centro Nacional de Investigaciones Oncológicas (CNIO), Madrid, Spain
| | - Jose Espinosa-Carrasco
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Daniel Ortiz-Martínez
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Ben Lehner
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.
- Universitat Pompeu Fabra (UPF), Barcelona, Spain.
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain.
| | - Fran Supek
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain.
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