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Vinceti A, Iannuzzi RM, Boyle I, Trastulla L, Campbell CD, Vazquez F, Dempster JM, Iorio F. A benchmark of computational methods for correcting biases of established and unknown origin in CRISPR-Cas9 screening data. Genome Biol 2024; 25:192. [PMID: 39030569 PMCID: PMC11264729 DOI: 10.1186/s13059-024-03336-1] [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: 01/12/2024] [Accepted: 07/10/2024] [Indexed: 07/21/2024] Open
Abstract
BACKGROUND CRISPR-Cas9 dropout screens are formidable tools for investigating biology with unprecedented precision and scale. However, biases in data lead to potential confounding effects on interpretation and compromise overall quality. The activity of Cas9 is influenced by structural features of the target site, including copy number amplifications (CN bias). More worryingly, proximal targeted loci tend to generate similar gene-independent responses to CRISPR-Cas9 targeting (proximity bias), possibly due to Cas9-induced whole chromosome-arm truncations or other genomic structural features and different chromatin accessibility levels. RESULTS We benchmarked eight computational methods, rigorously evaluating their ability to reduce both CN and proximity bias in the two largest publicly available cell-line-based CRISPR-Cas9 screens to date. We also evaluated the capability of each method to preserve data quality and heterogeneity by assessing the extent to which the processed data allows accurate detection of true positive essential genes, established oncogenetic addictions, and known/novel biomarkers of cancer dependency. Our analysis sheds light on the ability of each method to correct biases under different scenarios. AC-Chronos outperforms other methods in correcting both CN and proximity biases when jointly processing multiple screens of models with available CN information, whereas CRISPRcleanR is the top performing method for individual screens or when CN information is not available. In addition, Chronos and AC-Chronos yield a final dataset better able to recapitulate known sets of essential and non-essential genes. CONCLUSIONS Overall, our investigation provides guidance for the selection of the most appropriate bias-correction method, based on its strengths, weaknesses and experimental settings.
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Affiliation(s)
| | | | | | - Lucia Trastulla
- Computational Biology Research Centre, Human Technopole, Milan, Italy
| | | | | | | | - Francesco Iorio
- Computational Biology Research Centre, Human Technopole, Milan, Italy.
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Dietzen M, Zhai H, Lucas O, Pich O, Barrington C, Lu WT, Ward S, Guo Y, Hynds RE, Zaccaria S, Swanton C, McGranahan N, Kanu N. Replication timing alterations are associated with mutation acquisition during breast and lung cancer evolution. Nat Commun 2024; 15:6039. [PMID: 39019871 PMCID: PMC11255325 DOI: 10.1038/s41467-024-50107-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Accepted: 07/01/2024] [Indexed: 07/19/2024] Open
Abstract
During each cell cycle, the process of DNA replication timing is tightly regulated to ensure the accurate duplication of the genome. The extent and significance of alterations in this process during malignant transformation have not been extensively explored. Here, we assess the impact of altered replication timing (ART) on cancer evolution by analysing replication-timing sequencing of cancer and normal cell lines and 952 whole-genome sequenced lung and breast tumours. We find that 6%-18% of the cancer genome exhibits ART, with regions with a change from early to late replication displaying an increased mutation rate and distinct mutational signatures. Whereas regions changing from late to early replication contain genes with increased expression and present a preponderance of APOBEC3-mediated mutation clusters and associated driver mutations. We demonstrate that ART occurs relatively early during cancer evolution and that ART may have a stronger correlation with mutation acquisition than alterations in chromatin structure.
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Affiliation(s)
- Michelle Dietzen
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Haoran Zhai
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Olivia Lucas
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Computational Cancer Genomics Research Group, University College London Cancer Institute, London, UK
- Department of Oncology, University College London Hospitals, London, UK
| | - Oriol Pich
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Christopher Barrington
- Bioinformatics and Biostatistics Science Technology Platform, The Francis Crick Institute, London, UK
| | - Wei-Ting Lu
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Sophia Ward
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Advanced Sequencing Facility, The Francis Crick Institute, London, UK
| | - Yanping Guo
- CRUK Flow Cytometry Translational Technology Platform, UCL Cancer Institute, London, UK
| | - Robert E Hynds
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Simone Zaccaria
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Computational Cancer Genomics Research Group, University College London Cancer Institute, London, UK
| | - Charles Swanton
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Department of Oncology, University College London Hospitals, London, UK
| | - Nicholas McGranahan
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
| | - Nnennaya Kanu
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK.
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3
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Weber SE, Chawla HS, Ehrig L, Hickey LT, Frisch M, Snowdon RJ. Accurate prediction of quantitative traits with failed SNP calls in canola and maize. FRONTIERS IN PLANT SCIENCE 2023; 14:1221750. [PMID: 37936929 PMCID: PMC10627008 DOI: 10.3389/fpls.2023.1221750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 10/05/2023] [Indexed: 11/09/2023]
Abstract
In modern plant breeding, genomic selection is becoming the gold standard to select superior genotypes in large breeding populations that are only partially phenotyped. Many breeding programs commonly rely on single-nucleotide polymorphism (SNP) markers to capture genome-wide data for selection candidates. For this purpose, SNP arrays with moderate to high marker density represent a robust and cost-effective tool to generate reproducible, easy-to-handle, high-throughput genotype data from large-scale breeding populations. However, SNP arrays are prone to technical errors that lead to failed allele calls. To overcome this problem, failed calls are often imputed, based on the assumption that failed SNP calls are purely technical. However, this ignores the biological causes for failed calls-for example: deletions-and there is increasing evidence that gene presence-absence and other kinds of genome structural variants can play a role in phenotypic expression. Because deletions are frequently not in linkage disequilibrium with their flanking SNPs, permutation of missing SNP calls can potentially obscure valuable marker-trait associations. In this study, we analyze published datasets for canola and maize using four parametric and two machine learning models and demonstrate that failed allele calls in genomic prediction are highly predictive for important agronomic traits. We present two statistical pipelines, based on population structure and linkage disequilibrium, that enable the filtering of failed SNP calls that are likely caused by biological reasons. For the population and trait examined, prediction accuracy based on these filtered failed allele calls was competitive to standard SNP-based prediction, underlying the potential value of missing data in genomic prediction approaches. The combination of SNPs with all failed allele calls or the filtered allele calls did not outperform predictions with only SNP-based prediction due to redundancy in genomic relationship estimates.
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Affiliation(s)
- Sven E. Weber
- Department of Plant Breeding, Justus Liebig University, Giessen, Germany
| | | | - Lennard Ehrig
- Department of Plant Breeding, Justus Liebig University, Giessen, Germany
| | - Lee T. Hickey
- Centre for Crop Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia
| | - Matthias Frisch
- Department of Biometry and Population Genetics, Justus Liebig University, Giessen, Germany
| | - Rod J. Snowdon
- Department of Plant Breeding, Justus Liebig University, Giessen, Germany
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4
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Ruohan W, Yuwei Z, Mengbo W, Xikang F, Jianping W, Shuai Cheng L. Resolving single-cell copy number profiling for large datasets. Brief Bioinform 2022; 23:6633647. [PMID: 35801503 DOI: 10.1093/bib/bbac264] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 05/29/2022] [Accepted: 06/06/2022] [Indexed: 11/14/2022] Open
Abstract
The advances of single-cell DNA sequencing (scDNA-seq) enable us to characterize the genetic heterogeneity of cancer cells. However, the high noise and low coverage of scDNA-seq impede the estimation of copy number variations (CNVs). In addition, existing tools suffer from intensive execution time and often fail on large datasets. Here, we propose SeCNV, an efficient method that leverages structural entropy, to profile the copy numbers. SeCNV adopts a local Gaussian kernel to construct a matrix, depth congruent map (DCM), capturing the similarities between any two bins along the genome. Then, SeCNV partitions the genome into segments by minimizing the structural entropy from the DCM. With the partition, SeCNV estimates the copy numbers within each segment for cells. We simulate nine datasets with various breakpoint distributions and amplitudes of noise to benchmark SeCNV. SeCNV achieves a robust performance, i.e. the F1-scores are higher than 0.95 for breakpoint detections, significantly outperforming state-of-the-art methods. SeCNV successfully processes large datasets (>50 000 cells) within 4 min, while other tools fail to finish within the time limit, i.e. 120 h. We apply SeCNV to single-nucleus sequencing datasets from two breast cancer patients and acoustic cell tagmentation sequencing datasets from eight breast cancer patients. SeCNV successfully reproduces the distinct subclones and infers tumor heterogeneity. SeCNV is available at https://github.com/deepomicslab/SeCNV.
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Affiliation(s)
- Wang Ruohan
- Department of Computer Science at City University of Hong Kong
| | - Zhang Yuwei
- Department of Computer Science at City University of Hong Kong
| | - Wang Mengbo
- Department of Computer Science at City University of Hong Kong
| | - Feng Xikang
- School of Software, Northwestern Polytechnical University
| | - Wang Jianping
- Department of Computer Science at City University of Hong Kong
| | - Li Shuai Cheng
- Department of Computer Science at City University of Hong Kong
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5
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Köferle A, Schlattl A, Hörmann A, Thatikonda V, Popa A, Spreitzer F, Ravichandran MC, Supper V, Oberndorfer S, Puchner T, Wieshofer C, Corcokovic M, Reiser C, Wöhrle S, Popow J, Pearson M, Martinez J, Weitzer S, Mair B, Neumüller RA. Interrogation of cancer gene dependencies reveals paralog interactions of autosome and sex chromosome-encoded genes. Cell Rep 2022; 39:110636. [PMID: 35417719 DOI: 10.1016/j.celrep.2022.110636] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 12/22/2021] [Accepted: 03/16/2022] [Indexed: 02/07/2023] Open
Abstract
Genetic networks are characterized by extensive buffering. During tumor evolution, disruption of functional redundancies can create de novo vulnerabilities that are specific to cancer cells. Here, we systematically search for cancer-relevant paralog interactions using CRISPR screens and publicly available loss-of-function datasets. Our analysis reveals >2,000 candidate dependencies, several of which we validate experimentally, including CSTF2-CSTF2T, DNAJC15-DNAJC19, FAM50A-FAM50B, and RPP25-RPP25L. We provide evidence that RPP25L can physically and functionally compensate for the absence of RPP25 as a member of the RNase P/MRP complexes in tRNA processing. Our analysis also reveals unexpected redundancies between sex chromosome genes. We show that chrX- and chrY-encoded paralogs, such as ZFX-ZFY, DDX3X-DDX3Y, and EIF1AX-EIF1AY, are functionally linked. Tumor cell lines from male patients with loss of chromosome Y become dependent on the chrX-encoded gene. We propose targeting of chrX-encoded paralogs as a general therapeutic strategy for human tumors that have lost the Y chromosome.
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Affiliation(s)
- Anna Köferle
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Andreas Schlattl
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Alexandra Hörmann
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Venu Thatikonda
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Alexandra Popa
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Fiona Spreitzer
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | | | - Verena Supper
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Sarah Oberndorfer
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Teresa Puchner
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Corinna Wieshofer
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Maja Corcokovic
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Christoph Reiser
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Simon Wöhrle
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Johannes Popow
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Mark Pearson
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Javier Martinez
- Max Perutz Labs, Medical University of Vienna, Vienna BioCenter (VBC), Dr. Bohr-Gasse 9/2, 1030 Vienna, Austria
| | - Stefan Weitzer
- Max Perutz Labs, Medical University of Vienna, Vienna BioCenter (VBC), Dr. Bohr-Gasse 9/2, 1030 Vienna, Austria
| | - Barbara Mair
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria.
| | - Ralph A Neumüller
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria.
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6
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Chen S, Wu Y, Wang S, Wu J, Wu X, Zheng Z. A risk model of gene signatures for predicting platinum response and survival in ovarian cancer. J Ovarian Res 2022; 15:39. [PMID: 35361267 PMCID: PMC8973612 DOI: 10.1186/s13048-022-00969-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Accepted: 03/08/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Ovarian cancer (OC) is the deadliest tumor in the female reproductive tract. And increased resistance to platinum-based chemotherapy represents the major obstacle in the treatment of OC currently. Robust and accurate gene expression models are crucial tools in distinguishing platinum therapy response and evaluating the prognosis of OC patients. METHODS In this study, 230 samples from The Cancer Genome Atlas (TCGA) OV dataset were subjected to mRNA expression profiling, single nucleotide polymorphism (SNP), and copy number variation (CNV) analysis comprehensively to screen out the differentially expressed genes (DEGs). An SVM classifier and a prognostic model were constructed using the Random Forest algorithm and LASSO Cox regression model respectively via R. The Gene Expression Omnibus (GEO) database was applied as the validation set. RESULTS Forty-eight differentially expressed genes (DEGs) were figured out through integrated analysis of gene expression, single nucleotide polymorphism (SNP), and copy number variation (CNV) data. A 10-gene classifier was constructed which could discriminate platinum-sensitive samples precisely with an AUC of 0.971 in the training set and of 0.926 in the GEO dataset (GSE638855). In addition, 8 optimal genes were further selected to construct the prognostic risk model whose predictions were consistent with the actual survival outcomes in the training cohort (p = 9.613e-05) and validated in GSE638855 (p = 0.04862). PNLDC1, SLC5A1, and SYNM were then identified as hub genes that were associated with both platinum response status and prognosis, which was further validated by the Fudan University Shanghai cancer center (FUSCC) cohort. CONCLUSION These findings reveal a specific risk model that could serve as effective biomarkers to identify patients' platinum response status and predict survival outcomes for OC patients. PNLDC1, SLC5A1, and SYNM are the hub genes that may serve as potential biomarkers in OC treatment.
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Affiliation(s)
- Siyu Chen
- Department of Gynecologic Oncology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yong Wu
- Department of Gynecologic Oncology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Simin Wang
- Department of Gynecologic Oncology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jiangchun Wu
- Department of Gynecologic Oncology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xiaohua Wu
- Department of Gynecologic Oncology, Fudan University Shanghai Cancer Center, Shanghai, China.
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
| | - Zhong Zheng
- Department of Gynecologic Oncology, Fudan University Shanghai Cancer Center, Shanghai, China.
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
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7
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Elevated MACC1 Expression in Colorectal Cancer Is Driven by Chromosomal Instability and Is Associated with Molecular Subtype and Worse Patient Survival. Cancers (Basel) 2022; 14:cancers14071749. [PMID: 35406521 PMCID: PMC8997143 DOI: 10.3390/cancers14071749] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 03/21/2022] [Accepted: 03/28/2022] [Indexed: 12/19/2022] Open
Abstract
Metastasis-Associated in Colon Cancer 1 (MACC1) is a strong prognostic biomarker inducing proliferation, migration, invasiveness, and metastasis of cancer cells. The context of MACC1 dysregulation in cancers is, however, still poorly understood. Here, we investigated whether chromosomal instability and somatic copy number alterations (SCNA) frequently occurring in CRC contribute to MACC1 dysregulation, with prognostic and predictive impacts. Using the Oncotrack and Charité CRC cohorts of CRC patients, we showed that elevated MACC1 mRNA expression was tightly dependent on increased MACC1 gene SCNA and was associated with metastasis and shorter metastasis free survival. Deep analysis of the COAD-READ TCGA cohort revealed elevated MACC1 expression due to SCNA for advanced tumors exhibiting high chromosomal instability (CIN), and predominantly classified as CMS2 and CMS4 transcriptomic subtypes. For that cohort, we validated that elevated MACC1 mRNA expression correlated with reduced disease-free and overall survival. In conclusion, this study gives insights into the context of MACC1 expression in CRC. Increased MACC1 expression is largely driven by CIN, SCNA gains, and molecular subtypes, potentially determining the molecular risk for metastasis that might serve as a basis for patient-tailored treatment decisions.
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8
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Balagué-Dobón L, Cáceres A, González JR. Fully exploiting SNP arrays: a systematic review on the tools to extract underlying genomic structure. Brief Bioinform 2022; 23:bbac043. [PMID: 35211719 PMCID: PMC8921734 DOI: 10.1093/bib/bbac043] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 01/25/2022] [Accepted: 01/28/2022] [Indexed: 12/12/2022] Open
Abstract
Single nucleotide polymorphisms (SNPs) are the most abundant type of genomic variation and the most accessible to genotype in large cohorts. However, they individually explain a small proportion of phenotypic differences between individuals. Ancestry, collective SNP effects, structural variants, somatic mutations or even differences in historic recombination can potentially explain a high percentage of genomic divergence. These genetic differences can be infrequent or laborious to characterize; however, many of them leave distinctive marks on the SNPs across the genome allowing their study in large population samples. Consequently, several methods have been developed over the last decade to detect and analyze different genomic structures using SNP arrays, to complement genome-wide association studies and determine the contribution of these structures to explain the phenotypic differences between individuals. We present an up-to-date collection of available bioinformatics tools that can be used to extract relevant genomic information from SNP array data including population structure and ancestry; polygenic risk scores; identity-by-descent fragments; linkage disequilibrium; heritability and structural variants such as inversions, copy number variants, genetic mosaicisms and recombination histories. From a systematic review of recently published applications of the methods, we describe the main characteristics of R packages, command-line tools and desktop applications, both free and commercial, to help make the most of a large amount of publicly available SNP data.
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9
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Shao M, Jiang L, Meng Z, Xu J. Computational Drug Repurposing Based on a Recommendation System and Drug-Drug Functional Pathway Similarity. Molecules 2022; 27:1404. [PMID: 35209193 PMCID: PMC8878172 DOI: 10.3390/molecules27041404] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 02/13/2022] [Accepted: 02/16/2022] [Indexed: 02/05/2023] Open
Abstract
Drug repurposing identifies new clinical indications for existing drugs. It can be used to overcome common problems associated with cancers, such as heterogeneity and resistance to established therapies, by rapidly adapting known drugs for new treatment. In this study, we utilized a recommendation system learning model to prioritize candidate cancer drugs. We designed a drug-drug pathway functional similarity by integrating multiple genetic and epigenetic alterations such as gene expression, copy number variation (CNV), and DNA methylation. When compared with other similarities, such as SMILES chemical structures and drug targets based on the protein-protein interaction network, our approach provided better interpretable models capturing drug response mechanisms. Furthermore, our approach can achieve comparable accuracy when evaluated with other learning models based on large public datasets (CCLE and GDSC). A case study about the Erlotinib and OSI-906 (Linsitinib) indicated that they have a synergistic effect to reduce the growth rate of tumors, which is an alternative targeted therapy option for patients. Taken together, our computational method characterized drug response from the viewpoint of a multi-omics pathway and systematically predicted candidate cancer drugs with similar therapeutic effects.
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Affiliation(s)
- Mengting Shao
- Computational Systems Biology Laboratory, Department of Bioinformatics, Shantou University Medical College (SUMC), Shantou 515041, China
- Department of Computer Science, College of Computer Engineering and Applied Mathematics, Changsha University, Changsha 410005, China
| | - Leiming Jiang
- Computational Systems Biology Laboratory, Department of Bioinformatics, Shantou University Medical College (SUMC), Shantou 515041, China
| | - Zhigang Meng
- Department of Computer Science, College of Computer Engineering and Applied Mathematics, Changsha University, Changsha 410005, China
| | - Jianzhen Xu
- Computational Systems Biology Laboratory, Department of Bioinformatics, Shantou University Medical College (SUMC), Shantou 515041, China
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10
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Bao Y, Gabrielpillai J, Dietrich J, Zarbl R, Strieth S, Schröck F, Dietrich D. Fibroblast growth factor (FGF), FGF receptor (FGFR), and cyclin D1 (CCND1) DNA methylation in head and neck squamous cell carcinomas is associated with transcriptional activity, gene amplification, human papillomavirus (HPV) status, and sensitivity to tyrosine kinase inhibitors. Clin Epigenetics 2021; 13:228. [PMID: 34933671 PMCID: PMC8693503 DOI: 10.1186/s13148-021-01212-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 12/08/2021] [Indexed: 12/11/2022] Open
Abstract
Background Dysregulation of fibroblast growth factor receptor (FGFR) signaling pathway has been observed in head and neck squamous cell carcinoma (HNSCC) and is a promising therapeutic target for selective tyrosine kinase inhibitors (TKIs). Potential predictive biomarkers for response to FGFR-targeted therapies are urgently needed. Understanding the epigenetic regulation of FGF pathway related genes, i.e. FGFRs, FGFs, and CCND1, could enlighten the way towards biomarker-selected FGFR-targeted therapies. Methods We performed DNA methylation analysis of the encoding genes FGFR1, FGFR2, FGFR3, FGFR4, FGF1-14, FGF16-23, and CCND1 at single CpG site resolution (840 CpG sites) employing The Cancer Genome Research Atlas (TCGA) HNSCC cohort comprising N = 530 tumor tissue and N = 50 normal adjacent tissue samples. We correlated DNA methylation to mRNA expression with regard to human papilloma virus (HPV) and gene amplification status. Moreover, we investigated the correlation of methylation with sensitivity to the selective FGFR inhibitors PD 173074 and AZD4547 in N = 40 HPV(−) HNSCC cell lines. Results We found sequence-contextually nuanced CpG methylation patterns in concordance with epigenetically regulated genes. High methylation levels were predominantly found in the promoter flank and gene body region, while low methylation levels were present in the central promoter region for most of the analyzed CpG sites. FGFRs, FGFs, and CCND1 methylation differed significantly between tumor and normal adjacent tissue and was associated with HPV and gene amplification status. CCND1 promoter methylation correlated with CCND1 amplification. For most of the analyzed CpG sites, methylation levels correlated to mRNA expression in tumor tissue. Furthermore, we found significant correlations of DNA methylation of specific CpG sites with response to the FGFR1/3–selective inhibitors PD 173074 and AZD4547, predominantly within the transcription start site of CCND1. Conclusions Our results suggest an epigenetic regulation of CCND1, FGFRs, and FGFs via DNA methylation in HNSCC and warrants further investigation of DNA methylation as a potential predictive biomarker for response to selective FGFR inhibitors in clinical trials. Supplementary Information The online version contains supplementary material available at 10.1186/s13148-021-01212-4.
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Affiliation(s)
- Yilin Bao
- Department of Otorhinolaryngology, Head and Neck Surgery, University Medical Center Bonn (UKB), Sigmund-Freud-Str. 25, 53105, Bonn, Germany.,Department of Otolaryngology, Head and Neck Surgery, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Jennis Gabrielpillai
- Department of Otorhinolaryngology, Head and Neck Surgery, University Medical Center Bonn (UKB), Sigmund-Freud-Str. 25, 53105, Bonn, Germany
| | - Jörn Dietrich
- Department of Otorhinolaryngology, Head and Neck Surgery, University Medical Center Bonn (UKB), Sigmund-Freud-Str. 25, 53105, Bonn, Germany
| | - Romina Zarbl
- Department of Otorhinolaryngology, Head and Neck Surgery, University Medical Center Bonn (UKB), Sigmund-Freud-Str. 25, 53105, Bonn, Germany
| | - Sebastian Strieth
- Department of Otorhinolaryngology, Head and Neck Surgery, University Medical Center Bonn (UKB), Sigmund-Freud-Str. 25, 53105, Bonn, Germany
| | - Friederike Schröck
- Department of Psychiatry and Psychotherapy, University Hospital Bonn, Bonn, Germany
| | - Dimo Dietrich
- Department of Otorhinolaryngology, Head and Neck Surgery, University Medical Center Bonn (UKB), Sigmund-Freud-Str. 25, 53105, Bonn, Germany.
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11
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Vuaroqueaux V, Hendriks HR, Al-Hasani H, Peille AL, Das S, Fiebig HH. Pharmacogenomics characterization of the MDM2 inhibitor MI-773 reveals candidate tumours and predictive biomarkers. NPJ Precis Oncol 2021; 5:96. [PMID: 34711913 PMCID: PMC8553758 DOI: 10.1038/s41698-021-00235-7] [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: 08/28/2020] [Accepted: 10/04/2021] [Indexed: 11/25/2022] Open
Abstract
MI-773 is a recently developed small-molecule inhibitor of the mouse double minute 2 (MDM2) proto-oncogene. Preclinical data on the anti-tumour activity of MI-773 are limited and indicate that tumour cell lines (CLs) with mutated TP53 are more resistant to MI-773 than wild type TP53. Here, we explored the compound's therapeutic potential in vitro using a panel of 274 annotated CLs derived from a diversity of tumours. MI-773 exhibited a pronounced selectivity and moderate potency, with anti-tumour activity in the sub-micromolar range in about 15% of the CLs. The most sensitive tumour types were melanoma, sarcoma, renal and gastric cancers, leukaemia, and lymphoma. A COMPARE analysis showed that the profile of MI-773 was similar to that of Nutlin-3a, the first potent inhibitor of p53-MDM2 interactions, and, in addition, had a superior potency. In contrast, it poorly correlates with profiles of compounds targeting the p53 pathway with another mechanism of action. OMICS analyses confirmed that MI-773 was primarily active in CLs with wild type TP53. In silico biomarker investigations revealed that the TP53 mutation status plus the aggregated expression levels of 11 genes involved in the p53 signalling pathway predicted sensitivity or resistance of CLs to inhibitors of p53-MDM2 interactions reliably. The results obtained for MI-773 could help to refine the selection of cancer patients for therapy.
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Affiliation(s)
| | - Hans R Hendriks
- Hendriks Pharmaceutical Consulting, 1443 LR, Purmerend, The Netherlands
| | - Hoor Al-Hasani
- 4HF Biotec GmbH, Am Flughafen 14, 79108, Freiburg, Germany
| | | | - Samayita Das
- 4HF Biotec GmbH, Am Flughafen 14, 79108, Freiburg, Germany
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12
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Fedrizzi T, Ciani Y, Lorenzin F, Cantore T, Gasperini P, Demichelis F. Fast mutual exclusivity algorithm nominates potential synthetic lethal gene pairs through brute force matrix product computations. Comput Struct Biotechnol J 2021; 19:4394-4403. [PMID: 34429855 PMCID: PMC8369001 DOI: 10.1016/j.csbj.2021.08.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 08/02/2021] [Accepted: 08/03/2021] [Indexed: 12/12/2022] Open
Abstract
Mutual Exclusivity analysis of genomic aberrations contributes to the exploration of potential synthetic lethal (SL) relationships thus guiding the nomination of specific cancer cells vulnerabilities. When multiple classes of genomic aberrations and large cohorts of patients are interrogated, exhaustive genome-wide analyses are not computationally feasible with commonly used approaches. Here we present Fast Mutual Exclusivity (FaME), an algorithm based on matrix multiplication that employs a logarithm-based implementation of the Fisher's exact test to achieve fast computation of genome-wide mutual exclusivity tests; we show that brute force testing for mutual exclusivity of hundreds of millions of aberrations combinations can be performed in few minutes. We applied FaME to allele-specific data from whole exome experiments of 27 TCGA studies cohorts, detecting both mutual exclusivity of point mutations, as well as allele-specific copy number signals that span sets of contiguous cytobands. We next focused on a case study involving the loss of tumor suppressors and druggable genes while exploiting an integrated analysis of both public cell lines loss of function screens data and patients' transcriptomic profiles. FaME algorithm implementation as well as allele-specific analysis output are publicly available at https://github.com/demichelislab/FaME.
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Affiliation(s)
- Tarcisio Fedrizzi
- Department of Cellular, Computational and Integrative Biology, University of Trento, 38123 Trento, Italy
| | - Yari Ciani
- Department of Cellular, Computational and Integrative Biology, University of Trento, 38123 Trento, Italy
| | - Francesca Lorenzin
- Department of Cellular, Computational and Integrative Biology, University of Trento, 38123 Trento, Italy
| | - Thomas Cantore
- Department of Cellular, Computational and Integrative Biology, University of Trento, 38123 Trento, Italy
| | - Paola Gasperini
- Department of Cellular, Computational and Integrative Biology, University of Trento, 38123 Trento, Italy
| | - Francesca Demichelis
- Department of Cellular, Computational and Integrative Biology, University of Trento, 38123 Trento, Italy
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Al-Saud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10021, USA
- The Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10021, USA
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13
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Huang S, Hu P, Lakowski TM. Predicting breast cancer drug response using a multiple-layer cell line drug response network model. BMC Cancer 2021; 21:648. [PMID: 34059012 PMCID: PMC8166022 DOI: 10.1186/s12885-021-08359-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Accepted: 05/13/2021] [Indexed: 01/04/2023] Open
Abstract
Background Predicting patient drug response based on a patient’s molecular profile is one of the key goals of precision medicine in breast cancer (BC). Multiple drug response prediction models have been developed to address this problem. However, most of them were developed to make sensitivity predictions for multiple single drugs within cell lines from various cancer types instead of a single cancer type, do not take into account drug properties, and have not been validated in cancer patient-derived data. Among the multi-omics data, gene expression profiles have been shown to be the most informative data for drug response prediction. However, these models were often developed with individual genes. Therefore, this study aimed to develop a drug response prediction model for BC using multiple data types from both cell lines and drugs. Methods We first collected the baseline gene expression profiles of 49 BC cell lines along with IC50 values for 220 drugs tested in these cell lines from Genomics of Drug Sensitivity in Cancer (GDSC). Using these data, we developed a multiple-layer cell line-drug response network (ML-CDN2) by integrating a one-layer cell line similarity network based on the pathway activity profiles and a three-layer drug similarity network based on the drug structures, targets, and pan-cancer IC50 profiles. We further used ML-CDN2 to predict the drug response for new BC cell lines or patient-derived samples. Results ML-CDN2 demonstrated a good predictive performance, with the Pearson correlation coefficient between the observed and predicted IC50 values for all GDSC cell line-drug pairs of 0.873. Also, ML-CDN2 showed a good performance when used to predict drug response in new BC cell lines from the Cancer Cell Line Encyclopedia (CCLE), with a Pearson correlation coefficient of 0.718. Moreover, we found that the cell line-derived ML-CDN2 model could be applied to predict drug response in the BC patient-derived samples from The Cancer Genome Atlas (TCGA). Conclusions The ML-CDN2 model was built to predict BC drug response using comprehensive information from both cell lines and drugs. Compared with existing methods, it has the potential to predict the drug response for BC patient-derived samples. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-021-08359-6.
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Affiliation(s)
- Shujun Huang
- College of Pharmacy, University of Manitoba, Apotex Centre, 750 McDermot Avenue, Winnipeg, Manitoba, R3E 0T5, Canada
| | - Pingzhao Hu
- Department of Biochemistry and Medical Genetics, University of Manitoba, Room 308 - Basic Medical Sciences Building, 745 Bannatyne Avenue, Winnipeg, Manitoba, R3E 0J9, Canada. .,Cancer Care Manitoba Research Institute, 675 McDermot Avenue, Winnipeg, Manitoba, R3E 0V9, Canada.
| | - Ted M Lakowski
- College of Pharmacy, University of Manitoba, Apotex Centre, 750 McDermot Avenue, Winnipeg, Manitoba, R3E 0T5, Canada.
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14
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Jaiswal A, Gautam P, Pietilä EA, Timonen S, Nordström N, Akimov Y, Sipari N, Tanoli Z, Fleischer T, Lehti K, Wennerberg K, Aittokallio T. Multi-modal meta-analysis of cancer cell line omics profiles identifies ECHDC1 as a novel breast tumor suppressor. Mol Syst Biol 2021; 17:e9526. [PMID: 33750001 PMCID: PMC7983037 DOI: 10.15252/msb.20209526] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 02/17/2021] [Accepted: 02/19/2021] [Indexed: 12/12/2022] Open
Abstract
Molecular and functional profiling of cancer cell lines is subject to laboratory-specific experimental practices and data analysis protocols. The current challenge therefore is how to make an integrated use of the omics profiles of cancer cell lines for reliable biological discoveries. Here, we carried out a systematic analysis of nine types of data modalities using meta-analysis of 53 omics studies across 12 research laboratories for 2,018 cell lines. To account for a relatively low consistency observed for certain data modalities, we developed a robust data integration approach that identifies reproducible signals shared among multiple data modalities and studies. We demonstrated the power of the integrative analyses by identifying a novel driver gene, ECHDC1, with tumor suppressive role validated both in breast cancer cells and patient tumors. The multi-modal meta-analysis approach also identified synthetic lethal partners of cancer drivers, including a co-dependency of PTEN deficient endometrial cancer cells on RNA helicases.
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Affiliation(s)
- Alok Jaiswal
- Institute for Molecular Medicine Finland (FIMM)Helsinki Institute of Life Science (HiLIFE)University of HelsinkiHelsinkiFinland
- Present address:
The Broad Institute of MIT and HarvardCambridgeMAUSA
| | - Prson Gautam
- Institute for Molecular Medicine Finland (FIMM)Helsinki Institute of Life Science (HiLIFE)University of HelsinkiHelsinkiFinland
| | - Elina A Pietilä
- Individualized Drug Therapy, Research Programs UnitUniversity of HelsinkiHelsinkiFinland
| | - Sanna Timonen
- Institute for Molecular Medicine Finland (FIMM)Helsinki Institute of Life Science (HiLIFE)University of HelsinkiHelsinkiFinland
- Hematology Research Unit HelsinkiUniversity of Helsinki and Helsinki University Hospital Comprehensive Cancer CenterHelsinkiFinland
- Translational Immunology Research Program and Department of Clinical Chemistry and HematologyUniversity of HelsinkiHelsinkiFinland
| | - Nora Nordström
- Institute for Molecular Medicine Finland (FIMM)Helsinki Institute of Life Science (HiLIFE)University of HelsinkiHelsinkiFinland
| | - Yevhen Akimov
- Institute for Molecular Medicine Finland (FIMM)Helsinki Institute of Life Science (HiLIFE)University of HelsinkiHelsinkiFinland
| | - Nina Sipari
- Viikki Metabolomics UnitHelsinki Institute of Life Science (HiLIFE)University of HelsinkiHelsinkiFinland
| | - Ziaurrehman Tanoli
- Institute for Molecular Medicine Finland (FIMM)Helsinki Institute of Life Science (HiLIFE)University of HelsinkiHelsinkiFinland
| | - Thomas Fleischer
- Department of Cancer GeneticsInstitute for Cancer ResearchOslo University HospitalOsloNorway
| | - Kaisa Lehti
- Individualized Drug Therapy, Research Programs UnitUniversity of HelsinkiHelsinkiFinland
- Department of Microbiology, Tumor and Cell BiologyKarolinska InstitutetStockholmSweden
- Department of Biomedical Laboratory ScienceNorwegian University of Science and TechnologyTrondheimNorway
| | - Krister Wennerberg
- Institute for Molecular Medicine Finland (FIMM)Helsinki Institute of Life Science (HiLIFE)University of HelsinkiHelsinkiFinland
- Biotech Research & Innovation Centre (BRIC) and Novo Nordisk Foundation Center for Stem Cell Biology (DanStem)University of CopenhagenCopenhagenDenmark
| | - Tero Aittokallio
- Institute for Molecular Medicine Finland (FIMM)Helsinki Institute of Life Science (HiLIFE)University of HelsinkiHelsinkiFinland
- Department of Cancer GeneticsInstitute for Cancer ResearchOslo University HospitalOsloNorway
- Department of Mathematics and StatisticsUniversity of TurkuTurkuFinland
- Oslo Centre for Biostatistics and Epidemiology (OCBE)University of OsloOsloNorway
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15
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Lloyd JP, Soellner MB, Merajver SD, Li JZ. Impact of between-tissue differences on pan-cancer predictions of drug sensitivity. PLoS Comput Biol 2021; 17:e1008720. [PMID: 33630864 PMCID: PMC7906305 DOI: 10.1371/journal.pcbi.1008720] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 01/18/2021] [Indexed: 11/24/2022] Open
Abstract
Increased availability of drug response and genomics data for many tumor cell lines has accelerated the development of pan-cancer prediction models of drug response. However, it is unclear how much between-tissue differences in drug response and molecular characteristics may contribute to pan-cancer predictions. Also unknown is whether the performance of pan-cancer models could vary by cancer type. Here, we built a series of pan-cancer models using two datasets containing 346 and 504 cell lines, each with MEK inhibitor (MEKi) response and mRNA expression, point mutation, and copy number variation data, and found that, while the tissue-level drug responses are accurately predicted (between-tissue ρ = 0.88–0.98), only 5 of 10 cancer types showed successful within-tissue prediction performance (within-tissue ρ = 0.11–0.64). Between-tissue differences make substantial contributions to the performance of pan-cancer MEKi response predictions, as exclusion of between-tissue signals leads to a decrease in Spearman’s ρ from a range of 0.43–0.62 to 0.30–0.51. In practice, joint analysis of multiple cancer types usually has a larger sample size, hence greater power, than for one cancer type; and we observe that higher accuracy of pan-cancer prediction of MEKi response is almost entirely due to the sample size advantage. Success of pan-cancer prediction reveals how drug response in different cancers may invoke shared regulatory mechanisms despite tissue-specific routes of oncogenesis, yet predictions in different cancer types require flexible incorporation of between-cancer and within-cancer signals. As most datasets in genome sciences contain multiple levels of heterogeneity, careful parsing of group characteristics and within-group, individual variation is essential when making robust inference. One of the central goals for precision oncology is to tailor treatment of individual tumors by their molecular characteristics. While drug response predictions have traditionally been sought within each cancer type, it has long been hoped to develop more robust predictions by jointly considering diverse cancer types. While such pan-cancer approaches have improved in recent years, it remains unclear whether between-tissue differences are contributing to the reported pan-cancer prediction performance. This concern stems from the observation that, when cancer types differ in both molecular features and drug response, strong predictive information can come mainly from differences among tissue types. Our study finds that both between- and within-cancer type signals provide substantial contributions to pan-cancer drug response prediction models, and about half of the cancer types examined are poorly predicted despite strong overall performance across all cancer types. We also find that pan-cancer prediction models perform similarly or better than cancer type-specific models, and in many cases the advantage of pan-cancer models is due to the larger number of samples available for pan-cancer analysis. Our results highlight tissue-of-origin as a key consideration for pan-cancer drug response prediction models, and recommend cancer type-specific considerations when translating pan-cancer prediction models for clinical use.
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Affiliation(s)
- John P Lloyd
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, United States of America.,Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, United States of America.,Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Matthew B Soellner
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, United States of America.,Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Sofia D Merajver
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, United States of America.,Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Jun Z Li
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, United States of America.,Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan, United States of America
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16
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Zaccaria S, Raphael BJ. Characterizing allele- and haplotype-specific copy numbers in single cells with CHISEL. Nat Biotechnol 2021; 39:207-214. [PMID: 32879467 PMCID: PMC9876616 DOI: 10.1038/s41587-020-0661-6] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Accepted: 08/04/2020] [Indexed: 01/28/2023]
Abstract
Single-cell barcoding technologies enable genome sequencing of thousands of individual cells in parallel, but with extremely low sequencing coverage (<0.05×) per cell. While the total copy number of large multi-megabase segments can be derived from such data, important allele-specific mutations-such as copy-neutral loss of heterozygosity (LOH) in cancer-are missed. We introduce copy-number haplotype inference in single cells using evolutionary links (CHISEL), a method to infer allele- and haplotype-specific copy numbers in single cells and subpopulations of cells by aggregating sparse signal across hundreds or thousands of individual cells. We applied CHISEL to ten single-cell sequencing datasets of ~2,000 cells from two patients with breast cancer. We identified extensive allele-specific copy-number aberrations (CNAs) in these samples, including copy-neutral LOHs, whole-genome duplications (WGDs) and mirrored-subclonal CNAs. These allele-specific CNAs affect genomic regions containing well-known breast-cancer genes. We also refined the reconstruction of tumor evolution, timing allele-specific CNAs before and after WGDs, identifying low-frequency subpopulations distinguished by unique CNAs and uncovering evidence of convergent evolution.
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Affiliation(s)
- Simone Zaccaria
- Department of Computer Science, Princeton University, Princeton, NJ, USA
| | - Benjamin J Raphael
- Department of Computer Science, Princeton University, Princeton, NJ, USA.
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA.
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17
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In Silico Inference of Synthetic Cytotoxic Interactions from Paclitaxel Responses. Int J Mol Sci 2021; 22:ijms22031097. [PMID: 33499282 PMCID: PMC7865701 DOI: 10.3390/ijms22031097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 01/18/2021] [Accepted: 01/19/2021] [Indexed: 11/16/2022] Open
Abstract
To exploit negatively interacting pairs of cancer somatic mutations in chemotherapy responses or synthetic cytotoxicity (SC), we systematically determined mutational pairs that had significantly lower paclitaxel half maximal inhibitory concentration (IC50) values. We evaluated 407 cell lines with somatic mutation profiles and estimated their copy number and drug-inhibitory concentrations in Genomics of Drug Sensitivity in Cancer (GDSC) database. The SC effect of 142 mutated gene pairs on response to paclitaxel was successfully cross-validated using human cancer datasets for urogenital cancers available in The Cancer Genome Atlas (TCGA) database. We further analyzed the cumulative effect of increasing SC pair numbers on the TP53 tumor suppressor gene. Patients with TCGA bladder and urogenital cancer exhibited improved cancer survival rates as the number of disrupted SC partners (i.e., SYNE2, SON, and/or PRY) of TP53 increased. The prognostic effect of SC burden on response to paclitaxel treatment could be differentiated from response to other cytotoxic drugs. Thus, the concept of pairwise SC may aid the identification of novel therapeutic and prognostic targets.
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18
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Cinar O, Iyigun C, Ilk O. An evaluation of a novel approach for clustering genes with dissimilar replicates. COMMUN STAT-SIMUL C 2020. [DOI: 10.1080/03610918.2020.1839092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Ozan Cinar
- Department of Psychiatry and Neuropsychology, Maastricht University, Maastricht, The Netherlands
| | - Cem Iyigun
- Department of Industrial Engineering, Middle East Technical University, Ankara, Turkey
| | - Ozlem Ilk
- Department of Statistics, Middle East Technical University, Ankara, Turkey
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19
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Ayestaran I, Galhoz A, Spiegel E, Sidders B, Dry JR, Dondelinger F, Bender A, McDermott U, Iorio F, Menden MP. Identification of Intrinsic Drug Resistance and Its Biomarkers in High-Throughput Pharmacogenomic and CRISPR Screens. PATTERNS (NEW YORK, N.Y.) 2020; 1:100065. [PMID: 33205120 PMCID: PMC7660407 DOI: 10.1016/j.patter.2020.100065] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 05/14/2020] [Accepted: 06/08/2020] [Indexed: 12/15/2022]
Abstract
High-throughput drug screens in cancer cell lines test compounds at low concentrations, thereby enabling the identification of drug-sensitivity biomarkers, while resistance biomarkers remain underexplored. Dissecting meaningful drug responses at high concentrations is challenging due to cytotoxicity, i.e., off-target effects, thus limiting resistance biomarker discovery to frequently mutated cancer genes. To address this, we interrogate subpopulations carrying sensitivity biomarkers and consecutively investigate unexpectedly resistant (UNRES) cell lines for unique genetic alterations that may drive resistance. By analyzing the GDSC and CTRP datasets, we find 53 and 35 UNRES cases, respectively. For 24 and 28 of them, we highlight putative resistance biomarkers. We find clinically relevant cases such as EGFRT790M mutation in NCI-H1975 or PTEN loss in NCI-H1650 cells, in lung adenocarcinoma treated with EGFR inhibitors. Interrogating the underpinnings of drug resistance with publicly available CRISPR phenotypic assays assists in prioritizing resistance drivers, offering hypotheses for drug combinations.
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Affiliation(s)
- Iñigo Ayestaran
- Institute of Computational Biology, Helmholtz Zentrum München GmbH—German Research Center for Environmental Health, Neuherberg 85764, Germany
- CRUK Cambridge Centre Early Detection Programme, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Ana Galhoz
- Institute of Computational Biology, Helmholtz Zentrum München GmbH—German Research Center for Environmental Health, Neuherberg 85764, Germany
- Department of Biology, Ludwig-Maximilians University Munich, Martinsried 82152, Germany
| | - Elmar Spiegel
- Institute of Computational Biology, Helmholtz Zentrum München GmbH—German Research Center for Environmental Health, Neuherberg 85764, Germany
| | - Ben Sidders
- Research and Early Development, Oncology, AstraZeneca, Cambridge CB4 0WG, UK
| | - Jonathan R. Dry
- Research and Early Development, Oncology, AstraZeneca, Boston, MA 02451, USA
- Tempus Labs, Boston, MA, USA
| | - Frank Dondelinger
- Centre for Health Informatics, Computation and Statistics, Lancaster Medical School, Lancaster University, Lancaster LA1 4YW, UK
| | - Andreas Bender
- Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Ultan McDermott
- Research and Early Development, Oncology, AstraZeneca, Cambridge CB4 0WG, UK
| | - Francesco Iorio
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1RQ, UK
- Human Technopole, Palazzo Italia Via Cristina Belgioioso 171, Milano 20157, Italy
| | - Michael P. Menden
- Institute of Computational Biology, Helmholtz Zentrum München GmbH—German Research Center for Environmental Health, Neuherberg 85764, Germany
- Department of Biology, Ludwig-Maximilians University Munich, Martinsried 82152, Germany
- German Centre for Diabetes Research (DZD e.V.), Neuherberg 85764, Germany
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20
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Peille AL, Vuaroqueaux V, Wong SS, Ting J, Klingner K, Zeitouni B, Landesfeind M, Kim WH, Lee HJ, Kong SH, Wulur I, Bray S, Bronsert P, Zanella N, Donoho G, Yang HK, Fiebig HH, Reinhard C, Aggarwal A. Evaluation of molecular subtypes and clonal selection during establishment of patient-derived tumor xenografts from gastric adenocarcinoma. Commun Biol 2020; 3:367. [PMID: 32647357 PMCID: PMC7347869 DOI: 10.1038/s42003-020-1077-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 06/02/2020] [Indexed: 11/09/2022] Open
Abstract
Patient-derived xenografts (PDX) have emerged as an important translational research tool for understanding tumor biology and enabling drug efficacy testing. They are established by transfer of patient tumor into immune compromised mice with the intent of using them as Avatars; operating under the assumption that they closely resemble patient tumors. In this study, we established 27 PDX from 100 resected gastric cancers and studied their fidelity in histological and molecular subtypes. We show that the established PDX preserved histology and molecular subtypes of parental tumors. However, in depth investigation of the entire cohort revealed that not all histological and molecular subtypes are established. Also, for the established PDX models, genetic changes are selected at early passages and rare subclones can emerge in PDX. This study highlights the importance of considering the molecular and evolutionary characteristics of PDX for a proper use of such models, particularly for Avatar trials.
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Affiliation(s)
- Anne-Lise Peille
- Charles River Discovery Research Services Germany GmbH (formerly Oncotest GmbH), Am Flughafen 12-14, 79108, Freiburg, Germany
- 4HF Biotec GmbH, Am Flughafen 14, Freiburg, 79108, Germany
| | - Vincent Vuaroqueaux
- Charles River Discovery Research Services Germany GmbH (formerly Oncotest GmbH), Am Flughafen 12-14, 79108, Freiburg, Germany
- 4HF Biotec GmbH, Am Flughafen 14, Freiburg, 79108, Germany
| | - Swee-Seong Wong
- Lilly Research Labs, Eli Lilly and Company, Indianapolis, IN, 46285, USA
- LifeOmic, 351 W 10th St, Indianapolis, IN, USA
| | - Jason Ting
- Lilly Research Labs, Eli Lilly and Company, Indianapolis, IN, 46285, USA
| | - Kerstin Klingner
- Charles River Discovery Research Services Germany GmbH (formerly Oncotest GmbH), Am Flughafen 12-14, 79108, Freiburg, Germany
| | - Bruno Zeitouni
- Charles River Discovery Research Services Germany GmbH (formerly Oncotest GmbH), Am Flughafen 12-14, 79108, Freiburg, Germany
| | - Manuel Landesfeind
- Charles River Discovery Research Services Germany GmbH (formerly Oncotest GmbH), Am Flughafen 12-14, 79108, Freiburg, Germany
- Evotec International GmbH, Marie-Curie-Strasse, 37079, Göttingen, Germany
| | - Woo Ho Kim
- Department of Pathology, Seoul National University College of Medicine, 101 Daehak-ro, Jongno-gu, Seoul, Korea
| | - Hyuk-Joon Lee
- Department of Surgery and Cancer Research Institute, Seoul National University College of Medicine, 101 Daehak-ro, Jongno-gu, Seoul, Korea
| | - Seong-Ho Kong
- Department of Surgery, Seoul National University Hospital, 101 Daehak-ro, Jongno-gu, Seoul, Korea
| | - Isabella Wulur
- Lilly Research Labs, Eli Lilly and Company, Indianapolis, IN, 46285, USA
| | - Steven Bray
- Lilly Research Labs, Eli Lilly and Company, Indianapolis, IN, 46285, USA
- LifeOmic, 351 W 10th St, Indianapolis, IN, USA
| | - Peter Bronsert
- Institute for Surgical Pathology, Medical Center-University of Freiburg, Freiburg, Germany
- Comprehensive Cancer Center Freiburg, Medical Center-University of Freiburg, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Nina Zanella
- Charles River Discovery Research Services Germany GmbH (formerly Oncotest GmbH), Am Flughafen 12-14, 79108, Freiburg, Germany
| | - Greg Donoho
- Lilly Research Labs, Eli Lilly and Company, Indianapolis, IN, 46285, USA
| | - Han-Kwang Yang
- Department of Surgery and Cancer Research Institute, Seoul National University College of Medicine, 101 Daehak-ro, Jongno-gu, Seoul, Korea
| | - Heinz-Herbert Fiebig
- Charles River Discovery Research Services Germany GmbH (formerly Oncotest GmbH), Am Flughafen 12-14, 79108, Freiburg, Germany.
- 4HF Biotec GmbH, Am Flughafen 14, Freiburg, 79108, Germany.
| | - Christoph Reinhard
- Lilly Research Labs, Eli Lilly and Company, Indianapolis, IN, 46285, USA.
| | - Amit Aggarwal
- Lilly Research Labs, Eli Lilly and Company, Indianapolis, IN, 46285, USA.
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21
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Friedrich S, Barbulescu R, Helleday T, Sonnhammer ELL. MetaCNV - a consensus approach to infer accurate copy numbers from low coverage data. BMC Med Genomics 2020; 13:76. [PMID: 32487140 PMCID: PMC7268502 DOI: 10.1186/s12920-020-00731-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 05/20/2020] [Indexed: 12/23/2022] Open
Abstract
Background The majority of copy number callers requires high read coverage data that is often achieved with elevated material input, which increases the heterogeneity of tissue samples. However, to gain insights into smaller areas within a tissue sample, e.g. a cancerous area in a heterogeneous tissue sample, less material is used for sequencing, which results in lower read coverage. Therefore, more focus needs to be put on copy number calling that is sensitive enough for low coverage data. Results We present MetaCNV, a copy number caller that infers reliable copy numbers for human genomes with a consensus approach. MetaCNV specializes in low coverage data, but also performs well on normal and high coverage data. MetaCNV integrates the results of multiple copy number callers and infers absolute and unbiased copy numbers for the entire genome. MetaCNV is based on a meta-model that bypasses the weaknesses of current calling models while combining the strengths of existing approaches. Here we apply MetaCNV based on ReadDepth, SVDetect, and CNVnator to real and simulated datasets in order to demonstrate how the approach improves copy number calling. Conclusions MetaCNV, available at https://bitbucket.org/sonnhammergroup/metacnv, provides accurate copy number prediction on low coverage data and performs well on high coverage data.
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Affiliation(s)
- Stefanie Friedrich
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Box 1031, 17121, Solna, Sweden.
| | - Remus Barbulescu
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Box 1031, 17121, Solna, Sweden
| | - Thomas Helleday
- Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institutet, Solna, Sweden
| | - Erik L L Sonnhammer
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Box 1031, 17121, Solna, Sweden
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22
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Khalil AIS, Khyriem C, Chattopadhyay A, Sanyal A. Hierarchical discovery of large-scale and focal copy number alterations in low-coverage cancer genomes. BMC Bioinformatics 2020; 21:147. [PMID: 32299346 PMCID: PMC7160937 DOI: 10.1186/s12859-020-3480-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2019] [Accepted: 04/01/2020] [Indexed: 12/15/2022] Open
Abstract
Background Detection of DNA copy number alterations (CNAs) is critical to understand genetic diversity, genome evolution and pathological conditions such as cancer. Cancer genomes are plagued with widespread multi-level structural aberrations of chromosomes that pose challenges to discover CNAs of different length scales, and distinct biological origins and functions. Although several computational tools are available to identify CNAs using read depth (RD) signal, they fail to distinguish between large-scale and focal alterations due to inaccurate modeling of the RD signal of cancer genomes. Additionally, RD signal is affected by overdispersion-driven biases at low coverage, which significantly inflate false detection of CNA regions. Results We have developed CNAtra framework to hierarchically discover and classify ‘large-scale’ and ‘focal’ copy number gain/loss from a single whole-genome sequencing (WGS) sample. CNAtra first utilizes a multimodal-based distribution to estimate the copy number (CN) reference from the complex RD profile of the cancer genome. We implemented Savitzky-Golay smoothing filter and Modified Varri segmentation to capture the change points of the RD signal. We then developed a CN state-driven merging algorithm to identify the large segments with distinct copy numbers. Next, we identified focal alterations in each large segment using coverage-based thresholding to mitigate the adverse effects of signal variations. Using cancer cell lines and patient datasets, we confirmed CNAtra’s ability to detect and distinguish the segmental aneuploidies and focal alterations. We used realistic simulated data for benchmarking the performance of CNAtra against other single-sample detection tools, where we artificially introduced CNAs in the original cancer profiles. We found that CNAtra is superior in terms of precision, recall and f-measure. CNAtra shows the highest sensitivity of 93 and 97% for detecting large-scale and focal alterations respectively. Visual inspection of CNAs revealed that CNAtra is the most robust detection tool for low-coverage cancer data. Conclusions CNAtra is a single-sample CNA detection tool that provides an analytical and visualization framework for CNA profiling without relying on any reference control. It can detect chromosome-level segmental aneuploidies and high-confidence focal alterations, even from low-coverage data. CNAtra is an open-source software implemented in MATLAB®. It is freely available at https://github.com/AISKhalil/CNAtra.
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Affiliation(s)
- Ahmed Ibrahim Samir Khalil
- School of Computer Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore, 639798, Singapore
| | - Costerwell Khyriem
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Anupam Chattopadhyay
- School of Computer Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore, 639798, Singapore.
| | - Amartya Sanyal
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore.
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23
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Mazrouee S, Wang W. PolyCluster: Minimum Fragment Disagreement Clustering for Polyploid Phasing. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2020; 17:264-277. [PMID: 30040655 DOI: 10.1109/tcbb.2018.2858803] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Phasing is an emerging area in computational biology with important applications in clinical decision making and biomedical sciences. While machine learning techniques have shown tremendous potential in many biomedical applications, their utility in phasing has not yet been fully understood. In this paper, we investigate development of clustering-based techniques for phasing in polyploidy organisms where more than two copies of each chromosome exist in the cells of the organism under study. We develop a novel framework, called PolyCluster, based on the concept of correlation clustering followed by an effective cluster merging mechanism to minimize the amount of disagreement among short reads residing in each cluster. We first introduce a graph model to quantify the amount of similarity between each pair of DNA reads. We then present a combination of linear programming, rounding, region-growing, and cluster merging to group similar reads and reconstruct haplotypes. Our extensive analysis demonstrates the effectiveness of PolyCluster in accurate and scalable phasing. In particular, we show that PolyCluster reduces switching error of H-PoP, HapColor, and HapTree by 44.4, 51.2, and 48.3 percent, respectively. Also, the running time of PolyCluster is several orders-of-magnitude less than HapTree while it achieves a running time comparable to other algorithms.
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24
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Shao X, Lv N, Liao J, Long J, Xue R, Ai N, Xu D, Fan X. Copy number variation is highly correlated with differential gene expression: a pan-cancer study. BMC MEDICAL GENETICS 2019; 20:175. [PMID: 31706287 PMCID: PMC6842483 DOI: 10.1186/s12881-019-0909-5] [Citation(s) in RCA: 178] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 10/15/2019] [Indexed: 12/13/2022]
Abstract
BACKGROUND Cancer is a heterogeneous disease with many genetic variations. Lines of evidence have shown copy number variations (CNVs) of certain genes are involved in development and progression of many cancers through the alterations of their gene expression levels on individual or several cancer types. However, it is not quite clear whether the correlation will be a general phenomenon across multiple cancer types. METHODS In this study we applied a bioinformatics approach integrating CNV and differential gene expression mathematically across 1025 cell lines and 9159 patient samples to detect their potential relationship. RESULTS Our results showed there is a close correlation between CNV and differential gene expression and the copy number displayed a positive linear influence on gene expression for the majority of genes, indicating that genetic variation generated a direct effect on gene transcriptional level. Another independent dataset is utilized to revalidate the relationship between copy number and expression level. Further analysis show genes with general positive linear influence on gene expression are clustered in certain disease-related pathways, which suggests the involvement of CNV in pathophysiology of diseases. CONCLUSIONS This study shows the close correlation between CNV and differential gene expression revealing the qualitative relationship between genetic variation and its downstream effect, especially for oncogenes and tumor suppressor genes. It is of a critical importance to elucidate the relationship between copy number variation and gene expression for prevention, diagnosis and treatment of cancer.
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Affiliation(s)
- Xin Shao
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Ning Lv
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Jie Liao
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Jinbo Long
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Rui Xue
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Ni Ai
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Donghang Xu
- Department of Pharmacy, The 2nd Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310009, China.
| | - Xiaohui Fan
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China.
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25
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Bray SM, Lee J, Kim ST, Hur JY, Ebert PJ, Calley JN, Wulur IH, Gopalappa T, Wong SS, Qian HR, Ting JC, Liu J, Willard MD, Novosiadly RD, Park YS, Park JO, Lim HY, Kang WK, Aggarwal A, Kim HC, Reinhard C. Genomic characterization of intrinsic and acquired resistance to cetuximab in colorectal cancer patients. Sci Rep 2019; 9:15365. [PMID: 31653970 PMCID: PMC6814827 DOI: 10.1038/s41598-019-51981-5] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 10/08/2019] [Indexed: 12/15/2022] Open
Abstract
Anti-EGFR antibodies are effective in therapies for late-stage colorectal cancer (CRC); however, many tumours are unresponsive or develop resistance. We performed genomic analysis of intrinsic and acquired resistance to anti-EGFR therapy in prospectively collected tumour samples from 25 CRC patients receiving cetuximab (an EGFR inhibitor). Of 25 CRC patients, 13 displayed intrinsic resistance to cetuximab; 12 were intrinsically sensitive. We obtained six re-biopsy samples at acquired resistance from the intrinsically sensitive patients. NCOA4–RET and LMNA–NTRK1 fusions and NRG1 and GNAS amplifications were found in intrinsic-resistant patients. In cetuximab-sensitive patients, we found KRAS K117N and A146T mutations in addition to BRAF V600E, AKT1 E17K, PIK3CA E542K, and FGFR1 or ERBB2 amplifications. The comparison between baseline and acquired-resistant tumours revealed an extreme shift in variant allele frequency of somatic variants, suggesting that cetuximab exposure dramatically selected for rare resistant subclones that were initially undetectable. There was also an increase in epithelial-to-mesenchymal transition at acquired resistance, with a reduction in the immune infiltrate. Furthermore, characterization of an acquired-resistant, patient-derived cell line showed that PI3K/mTOR inhibition could rescue cetuximab resistance. Thus, we uncovered novel genomic alterations that elucidate the mechanisms of sensitivity and resistance to anti-EGFR therapy in metastatic CRC patients.
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Affiliation(s)
- Steven M Bray
- Eli Lilly and Company, Lilly Research Laboratories, Oncology Discovery Research, Indianapolis, IN, USA
| | - Jeeyun Lee
- Division of Hematology-Oncology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Seung Tae Kim
- Division of Hematology-Oncology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Joon Young Hur
- Division of Hematology-Oncology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Philip J Ebert
- Eli Lilly and Company, Lilly Research Laboratories, Oncology Discovery Research, Indianapolis, IN, USA
| | - John N Calley
- Eli Lilly and Company, Lilly Research Laboratories, Oncology Discovery Research, Indianapolis, IN, USA
| | - Isabella H Wulur
- Eli Lilly and Company, Lilly Research Laboratories, Oncology Discovery Research, Indianapolis, IN, USA
| | - Thejaswini Gopalappa
- Eli Lilly and Company, Lilly Research Laboratories, Oncology Discovery Research, Indianapolis, IN, USA
| | - Swee Seong Wong
- Eli Lilly and Company, Lilly Research Laboratories, Oncology Discovery Research, Indianapolis, IN, USA
| | - Hui-Rong Qian
- Eli Lilly and Company, Lilly Research Laboratories, Oncology Discovery Research, Indianapolis, IN, USA
| | - Jason C Ting
- Eli Lilly and Company, Lilly Research Laboratories, Oncology Discovery Research, Indianapolis, IN, USA
| | - Jiangang Liu
- Eli Lilly and Company, Lilly Research Laboratories, Oncology Discovery Research, Indianapolis, IN, USA
| | - Melinda D Willard
- Eli Lilly and Company, Lilly Research Laboratories, Oncology Discovery Research, Indianapolis, IN, USA
| | - Ruslan D Novosiadly
- Eli Lilly and Company, Lilly Research Laboratories, Oncology Discovery Research, Indianapolis, IN, USA
| | - Young Suk Park
- Division of Hematology-Oncology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Joon Oh Park
- Division of Hematology-Oncology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Ho Yeong Lim
- Division of Hematology-Oncology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Won Ki Kang
- Division of Hematology-Oncology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Amit Aggarwal
- Eli Lilly and Company, Lilly Research Laboratories, Oncology Discovery Research, Indianapolis, IN, USA
| | - Hee Cheol Kim
- Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea.
| | - Christoph Reinhard
- Eli Lilly and Company, Lilly Research Laboratories, Oncology Discovery Research, Indianapolis, IN, USA.
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26
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Zhang R, Ye J, Huang H, Du X. Mining featured biomarkers associated with vascular invasion in HCC by bioinformatics analysis with TCGA RNA sequencing data. Biomed Pharmacother 2019; 118:109274. [DOI: 10.1016/j.biopha.2019.109274] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2019] [Revised: 07/03/2019] [Accepted: 07/25/2019] [Indexed: 12/20/2022] Open
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27
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Jette NR, Radhamani S, Arthur G, Ye R, Goutam S, Bolyos A, Petersen LF, Bose P, Bebb DG, Lees-Miller SP. Combined poly-ADP ribose polymerase and ataxia-telangiectasia mutated/Rad3-related inhibition targets ataxia-telangiectasia mutated-deficient lung cancer cells. Br J Cancer 2019; 121:600-610. [PMID: 31481733 PMCID: PMC6889280 DOI: 10.1038/s41416-019-0565-8] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 06/19/2019] [Accepted: 06/21/2019] [Indexed: 12/15/2022] Open
Abstract
Background Up to 40% of lung adenocarcinoma have been reported to lack ataxia-telangiectasia mutated (ATM) protein expression. We asked whether ATM-deficient lung cancer cell lines are sensitive to poly-ADP ribose polymerase (PARP) inhibitors and determined the mechanism of action of olaparib in ATM-deficient A549 cells. Methods We analysed drug sensitivity data for olaparib and talazoparib in lung adenocarcinoma cell lines from the Genomics of Drug Sensitivity in Cancer (GDSC) project. We deleted ATM from A549 lung adenocarcinoma cells using CRISPR/Cas9 and determined the effects of olaparib and the ATM/Rad3-related (ATR) inhibitor VE-821 on cell viability. Results IC50 values for both olaparib and talazoparib positively correlated with ATM mRNA levels and gene amplification status in lung adenocarcinoma cell lines. ATM mutation was associated with a significant decrease in the IC50 for olaparib while a similar trend was observed for talazoparib. A549 cells with deletion of ATM were sensitive to ionising radiation and olaparib. Olaparib induced phosphorylation of DNA damage markers and reversible G2 arrest in ATM-deficient cells, while the combination of olaparib and VE-821 induced cell death. Conclusions Patients with tumours characterised by ATM-deficiency may benefit from treatment with a PARP inhibitor in combination with an ATR inhibitor.
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Affiliation(s)
- Nicholas R Jette
- Departments of Biochemistry and Molecular Biology, Robson DNA Science Centre and Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, 3330 Hospital Drive NW, Calgary, Alberta, T2N 1N4, Canada
| | - Suraj Radhamani
- Departments of Biochemistry and Molecular Biology, Robson DNA Science Centre and Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, 3330 Hospital Drive NW, Calgary, Alberta, T2N 1N4, Canada
| | - Greydon Arthur
- Departments of Biochemistry and Molecular Biology, Robson DNA Science Centre and Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, 3330 Hospital Drive NW, Calgary, Alberta, T2N 1N4, Canada
| | - Ruiqiong Ye
- Departments of Biochemistry and Molecular Biology, Robson DNA Science Centre and Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, 3330 Hospital Drive NW, Calgary, Alberta, T2N 1N4, Canada
| | - Siddhartha Goutam
- Departments of Biochemistry and Molecular Biology, Robson DNA Science Centre and Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, 3330 Hospital Drive NW, Calgary, Alberta, T2N 1N4, Canada
| | - Anthony Bolyos
- Departments of Biochemistry and Molecular Biology, Robson DNA Science Centre and Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, 3330 Hospital Drive NW, Calgary, Alberta, T2N 1N4, Canada
| | - Lars F Petersen
- Department Oncology, Robson DNA Science Centre and Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, 3330 Hospital Drive NW, Calgary, Alberta, T2N 1N4, Canada
| | - Pinaki Bose
- Departments of Biochemistry and Molecular Biology, Robson DNA Science Centre and Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, 3330 Hospital Drive NW, Calgary, Alberta, T2N 1N4, Canada.,Department Oncology, Robson DNA Science Centre and Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, 3330 Hospital Drive NW, Calgary, Alberta, T2N 1N4, Canada
| | - D Gwyn Bebb
- Department Oncology, Robson DNA Science Centre and Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, 3330 Hospital Drive NW, Calgary, Alberta, T2N 1N4, Canada
| | - Susan P Lees-Miller
- Departments of Biochemistry and Molecular Biology, Robson DNA Science Centre and Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, 3330 Hospital Drive NW, Calgary, Alberta, T2N 1N4, Canada. .,Department Oncology, Robson DNA Science Centre and Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, 3330 Hospital Drive NW, Calgary, Alberta, T2N 1N4, Canada.
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28
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Menden MP, Wang D, Mason MJ, Szalai B, Bulusu KC, Guan Y, Yu T, Kang J, Jeon M, Wolfinger R, Nguyen T, Zaslavskiy M, Jang IS, Ghazoui Z, Ahsen ME, Vogel R, Neto EC, Norman T, Tang EKY, Garnett MJ, Veroli GYD, Fawell S, Stolovitzky G, Guinney J, Dry JR, Saez-Rodriguez J. Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen. Nat Commun 2019; 10:2674. [PMID: 31209238 PMCID: PMC6572829 DOI: 10.1038/s41467-019-09799-2] [Citation(s) in RCA: 189] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 04/01/2019] [Indexed: 02/06/2023] Open
Abstract
The effectiveness of most cancer targeted therapies is short-lived. Tumors often develop resistance that might be overcome with drug combinations. However, the number of possible combinations is vast, necessitating data-driven approaches to find optimal patient-specific treatments. Here we report AstraZeneca's large drug combination dataset, consisting of 11,576 experiments from 910 combinations across 85 molecularly characterized cancer cell lines, and results of a DREAM Challenge to evaluate computational strategies for predicting synergistic drug pairs and biomarkers. 160 teams participated to provide a comprehensive methodological development and benchmarking. Winning methods incorporate prior knowledge of drug-target interactions. Synergy is predicted with an accuracy matching biological replicates for >60% of combinations. However, 20% of drug combinations are poorly predicted by all methods. Genomic rationale for synergy predictions are identified, including ADAM17 inhibitor antagonism when combined with PIK3CB/D inhibition contrasting to synergy when combined with other PI3K-pathway inhibitors in PIK3CA mutant cells.
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Affiliation(s)
- Michael P Menden
- Oncology, IMED Biotech Unit, AstraZeneca, Cambridge, SG8 6EH, UK
- European Bioinformatics Institute, European Molecular Biology Laboratory, Cambridge, CB10 1SD, UK
- Institute of Computational Biology, Helmholtz Zentrum München - German Research Center for Environmental Health, Munich, D-85764, Germany
| | - Dennis Wang
- Oncology, IMED Biotech Unit, AstraZeneca, Cambridge, SG8 6EH, UK
- Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield, S10 2TN, UK
| | | | - Bence Szalai
- Department of Physiology, Faculty of Medicine, Semmelweis University, Budapest, 1085, Hungary
- Laboratory of Molecular Physiology, Hungarian Academy of Sciences and Semmelweis University (MTA-SE), Budapest, 1085, Hungary
- RWTH Aachen University, Faculty of Medicine, Joint Research Center for Computational Biomedicine, Aachen, 52062, Germany
| | - Krishna C Bulusu
- Oncology, IMED Biotech Unit, AstraZeneca, Cambridge, SG8 6EH, UK
| | - Yuanfang Guan
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, 48109, USA
| | - Thomas Yu
- Sage Bionetworks, Seattle, WA, 98121, USA
| | - Jaewoo Kang
- Department of Computer Science and Engineering, Korea University, Seoul, 02841, Korea
| | - Minji Jeon
- Department of Computer Science and Engineering, Korea University, Seoul, 02841, Korea
| | | | - Tin Nguyen
- Department of Computer Science and Engineering, University of Nevada, Reno, 89557, USA
| | - Mikhail Zaslavskiy
- Independent Consultant in Computational Biology, Owkin, Inc., New York, NY, 10022, USA
| | | | - Zara Ghazoui
- Oncology, IMED Biotech Unit, AstraZeneca, Cambridge, SG8 6EH, UK
| | - Mehmet Eren Ahsen
- IBM Thomas J. Watson Research Center, Yorktown Heights, New York, 10598, USA
| | - Robert Vogel
- IBM Thomas J. Watson Research Center, Yorktown Heights, New York, 10598, USA
| | | | | | - Eric K Y Tang
- Oncology, IMED Biotech Unit, AstraZeneca, Cambridge, SG8 6EH, UK
| | | | - Giovanni Y Di Veroli
- Early Clinical Development, IMED Biotech Unit, AstraZeneca, Cambridge, SG8 6EH, UK
| | - Stephen Fawell
- Oncology, IMED Biotech Unit, AstraZeneca, R&D Boston, Waltham, MA, 02451, USA
| | - Gustavo Stolovitzky
- IBM Thomas J. Watson Research Center, Yorktown Heights, New York, 10598, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, 10029, USA
| | | | - Jonathan R Dry
- Oncology, IMED Biotech Unit, AstraZeneca, R&D Boston, Waltham, MA, 02451, USA.
| | - Julio Saez-Rodriguez
- European Bioinformatics Institute, European Molecular Biology Laboratory, Cambridge, CB10 1SD, UK.
- RWTH Aachen University, Faculty of Medicine, Joint Research Center for Computational Biomedicine, Aachen, 52062, Germany.
- Heidelberg University, Faculty of Medicine, Institute for Computational Biomedicine, Bioquant, 69120, Heidelberg, Germany.
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29
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Wang Q, Lu Z, Ma J, Zhang Q, Wang N, Qian L, Zhang J, Chen C, Lu B. Six-mRNA risk score system and nomogram constructed for patients with ovarian cancer. Oncol Lett 2019; 18:1235-1245. [PMID: 31423184 PMCID: PMC6607424 DOI: 10.3892/ol.2019.10404] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 03/01/2019] [Indexed: 12/11/2022] Open
Abstract
Platinum is a commonly used drug for the treatment of ovarian cancer (OC). The aim of the current study was to design and construct a risk score system for predicting the prognosis of patients with OC receiving platinum chemotherapy. The mRNA sequencing data and copy number variation (CNV) information (training set) of patients with OC were downloaded from The Cancer Genome Atlas database. A validation set, GSE63885, was obtained from Gene Expression Omnibus database. The differentially expressed genes (DEGs) and CNV genes (DECNs) between platinum-resistant and platinum-sensitive groups were identified using the limma package. The intersection between DEGs and DECNs were selected. Cox regression analysis was used to identify the genes and clinical factors associated with prognosis. Risk score system assessment and nomogram analysis were performed using the survival and rms packages in R. Gene Set Enrichment Analysis was used to identify the enriched pathways in high and low risk score groups. From 1,144 DEGs and 1,864 DECNs, 48 genes that occurred in the two datasets were selected. A total of six independent prognostic genes (T-box transcription factor T, synemin, tektin 5, growth differentiation factor 3, solute carrier family 22 member 3 and calcium voltage-gated channel subunit α1 C) and platinum response status were revealed to be associated with prognosis. Based on the six independent prognostic genes, a risk score system was constructed and assessed. Nomogram analysis revealed that the patients with the sensitive status and low risk scores had an improved prognosis. Furthermore, the current study revealed that the 574 DEGs identified were involved in eight pathways, including chemokine signaling pathway, toll-like receptor signaling pathway, cytokine-cytokine receptor interaction, RIG I like receptor signaling pathway, natural killer cell mediated cytotoxicity, apoptosis, T cell receptor signaling pathway and Fc ε receptor 1 signaling pathway. The six-mRNA risk score system designed in the present study may be used as prognosis predictor in patients with OC, whereas the nomogram may be valuable for identifying patients with OC who may benefit from platinum chemotherapy.
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Affiliation(s)
- Qianqian Wang
- Department of Obstetrics and Gynecology, Wuxi People's Hospital, Wuxi, Jiangsu 214023, P.R. China
| | - Zhuwu Lu
- Department of Obstetrics and Gynecology, Wuxi People's Hospital, Wuxi, Jiangsu 214023, P.R. China
| | - Jinqi Ma
- Department of Obstetrics and Gynecology, Wuxi People's Hospital, Wuxi, Jiangsu 214023, P.R. China
| | - Qingsong Zhang
- Department of Obstetrics and Gynecology, Wuxi People's Hospital, Wuxi, Jiangsu 214023, P.R. China
| | - Ni Wang
- Department of Obstetrics and Gynecology, Wuxi People's Hospital, Wuxi, Jiangsu 214023, P.R. China
| | - Li Qian
- Department of Obstetrics and Gynecology, Wuxi People's Hospital, Wuxi, Jiangsu 214023, P.R. China
| | - Jun Zhang
- Department of Obstetrics and Gynecology, Wuxi People's Hospital, Wuxi, Jiangsu 214023, P.R. China
| | - Chen Chen
- Department of Obstetrics and Gynecology, Wuxi People's Hospital, Wuxi, Jiangsu 214023, P.R. China
| | - Bei Lu
- Department of Obstetrics and Gynecology, Wuxi People's Hospital, Wuxi, Jiangsu 214023, P.R. China
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Hamid A, Petreaca B, Petreaca R. Frequent homozygous deletions of the CDKN2A locus in somatic cancer tissues. Mutat Res 2019; 815:30-40. [PMID: 31096160 DOI: 10.1016/j.mrfmmm.2019.04.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 04/09/2019] [Accepted: 04/10/2019] [Indexed: 02/07/2023]
Abstract
Here we present and describe data on homozygous deletions (HD) of human CDKN2 A and neighboring regions on the p arm of Chromosome 9 from cancer genome sequences deposited on the online Catalogue of Somatic Mutations in Cancer (COSMIC) database. Although CDKN2 A HDs have been previously described in many cancers, this is a pan-cancer report of these aberrations with the aim to map the distribution of the breakpoints. We find that HDs of this locus have a median range of 1,255,650bps. When the deletion breakpoints were mapped on both the telomere and centromere proximal sides of CDKN2A, most of the telomere proximal breakpoints concentrate to a narrow region of the chromosome which includes the gene MTAP.. The centromere proximal breakpoints of the deletions are distributed over a wider chromosomal region. Furthermore, gene expression analysis shows that the deletions that include the CDKN2A region also include the MTAP region and this observation is tissue independent. We propose a model that may explain the origin of the telomere proximal CDKN2A breakpoints Finally, we find that HD distributions for at least three other loci, RB1, SMAD4 and PTEN are also not random.
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Affiliation(s)
- Abdulaziz Hamid
- The Ohio State University, MSE110A, 1464 Mount Vernon Ave, Marion, OH 43302, United States
| | - Beniamin Petreaca
- The Ohio State University, MSE110A, 1464 Mount Vernon Ave, Marion, OH 43302, United States
| | - Ruben Petreaca
- The Ohio State University, MSE110A, 1464 Mount Vernon Ave, Marion, OH 43302, United States.
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Kessler MD, Bateman NW, Conrads TP, Maxwell GL, Dunning Hotopp JC, O’Connor TD. Ancestral characterization of 1018 cancer cell lines highlights disparities and reveals gene expression and mutational differences. Cancer 2019; 125:2076-2088. [PMID: 30865299 PMCID: PMC6541501 DOI: 10.1002/cncr.32020] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 01/15/2019] [Indexed: 12/11/2022]
Abstract
Background Although cell lines are an essential resource for studying cancer biology, many are of unknown ancestral origin, and their use may not be optimal for evaluating the biology of all patient populations. Methods An admixture analysis was performed using genome‐wide chip data from the Catalogue of Somatic Mutations in Cancer (COSMIC) Cell Lines Project to calculate genetic ancestry estimates for 1018 cancer cell lines. After stratifying the analyses by tissue and histology types, linear models were used to evaluate the influence of ancestry on gene expression and somatic mutation frequency. Results For the 701 cell lines with unreported ancestry, 215 were of East Asian origin, 30 were of African or African American origin, and 453 were of European origin. Notable imbalances were observed in ancestral representation across tissue type, with the majority of analyzed tissue types having few cell lines of African American ancestral origin, and with Hispanic and South Asian ancestry being almost entirely absent across all cell lines. In evaluating gene expression across these cell lines, expression levels of the genes neurobeachin line 1 (NBEAL1), solute carrier family 6 member 19 (SLC6A19), HEAT repeat containing 6 (HEATR6), and epithelial cell transforming 2 like (ECT2L) were associated with ancestry. Significant differences were also observed in the proportions of somatic mutation types across cell lines with varying ancestral proportions. Conclusions By estimating genetic ancestry for 1018 cancer cell lines, the authors have produced a resource that cancer researchers can use to ensure that their cell lines are ancestrally representative of the populations they intend to affect. Furthermore, the novel ancestry‐specific signal identified underscores the importance of ancestral awareness when studying cancer. Preclinical cancer cell line research is often conducted without an awareness of ancestral background, which results in incongruities between the genetic backgrounds of used cell lines and the patient populations they are intended to represent. By calculating genetic ancestry for 1018 common cancer cell lines and identifying ancestry‐specific expression and somatic mutation patterns, the importance of ancestral awareness is emphasized, and a resource is provided that can be used by cancer researchers to ensure that their cell lines are ancestrally representative of the populations they aim to impact.
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Affiliation(s)
- Michael D. Kessler
- Institute for Genome SciencesUniversity of Maryland School of MedicineBaltimoreMaryland
- Department of MedicineUniversity of Maryland School of MedicineBaltimoreMaryland
- Program in Personalized and Genomic MedicineUniversity of Maryland School of MedicineBaltimoreMaryland
- University of Maryland Marlene and Stewart Greenebaum Comprehensive Cancer CenterBaltimoreMaryland
| | - Nicholas W. Bateman
- Gynecologic Cancer Center of Excellence, Department of Obstetrics and Gynecology and the John P. Murtha Cancer CenterUniformed Services University of the Health Sciences and Walter Reed National Military Medical CenterBethesdaMaryland
- Inova Schar Cancer Institute, Inova Center for Personalized HealthFairfaxVirginia
| | - Thomas P. Conrads
- Gynecologic Cancer Center of Excellence, Department of Obstetrics and Gynecology and the John P. Murtha Cancer CenterUniformed Services University of the Health Sciences and Walter Reed National Military Medical CenterBethesdaMaryland
- Inova Schar Cancer Institute, Inova Center for Personalized HealthFairfaxVirginia
- Department of Obstetrics and GynecologyInova Fairfax Medical CampusFalls ChurchVirginia
| | - George L. Maxwell
- Gynecologic Cancer Center of Excellence, Department of Obstetrics and Gynecology and the John P. Murtha Cancer CenterUniformed Services University of the Health Sciences and Walter Reed National Military Medical CenterBethesdaMaryland
- Inova Schar Cancer Institute, Inova Center for Personalized HealthFairfaxVirginia
- Department of Obstetrics and GynecologyInova Fairfax Medical CampusFalls ChurchVirginia
| | - Julie C. Dunning Hotopp
- Institute for Genome SciencesUniversity of Maryland School of MedicineBaltimoreMaryland
- University of Maryland Marlene and Stewart Greenebaum Comprehensive Cancer CenterBaltimoreMaryland
- Department of Microbiology and ImmunologyUniversity of Maryland School of MedicineBaltimoreMaryland
| | - Timothy D. O’Connor
- Institute for Genome SciencesUniversity of Maryland School of MedicineBaltimoreMaryland
- Department of MedicineUniversity of Maryland School of MedicineBaltimoreMaryland
- Program in Personalized and Genomic MedicineUniversity of Maryland School of MedicineBaltimoreMaryland
- University of Maryland Marlene and Stewart Greenebaum Comprehensive Cancer CenterBaltimoreMaryland
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32
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Xia R, Lin Y, Zhou J, Geng T, Feng B, Tang J. Phylogenetic Reconstruction for Copy-Number Evolution Problems. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2019; 16:694-699. [PMID: 29993694 DOI: 10.1109/tcbb.2018.2829698] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Cancer is known for its heterogeneity and is regarded as an evolutionary process driven by somatic mutations and clonal expansions. This evolutionary process can be modeled by a phylogenetic tree and phylogenetic analysis of multiple subclones of cancer cells can facilitate the study of the tumor variants progression. Copy-number aberration occurs frequently in many types of tumors in terms of segmental amplifications and deletions. In this paper, we developed a distance-based method for reconstructing phylogenies from copy-number profiles of cancer cells. We demonstrate the importance of distance correction from the edit (minimum) distance to the estimated actual number of events. Experimental results show that our approaches provide accurate and scalable results in estimating the actual number of evolutionary events between copy number profiles and in reconstructing phylogenies.
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Seth S, Li CY, Ho IL, Corti D, Loponte S, Sapio L, Del Poggetto E, Yen EY, Robinson FS, Peoples M, Karpinets T, Deem AK, Kumar T, Song X, Jiang S, Kang Y, Fleming J, Kim M, Zhang J, Maitra A, Heffernan TP, Giuliani V, Genovese G, Futreal A, Draetta GF, Carugo A, Viale A. Pre-existing Functional Heterogeneity of Tumorigenic Compartment as the Origin of Chemoresistance in Pancreatic Tumors. Cell Rep 2019; 26:1518-1532.e9. [PMID: 30726735 DOI: 10.1016/j.celrep.2019.01.048] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 11/20/2018] [Accepted: 01/11/2019] [Indexed: 12/30/2022] Open
Abstract
Adaptive drug-resistance mechanisms allow human tumors to evade treatment through selection and expansion of treatment-resistant clones. Here, studying clonal evolution of tumor cells derived from human pancreatic tumors, we demonstrate that in vitro cultures and in vivo tumors are maintained by a common set of tumorigenic cells that can be used to establish clonal replica tumors (CRTs), large cohorts of animals bearing human tumors with identical clonal composition. Using CRTs to conduct quantitative assessments of adaptive responses to therapeutics, we uncovered a multitude of functionally heterogeneous subpopulations of cells with differential degrees of drug sensitivity. High-throughput isolation and deep characterization of unique clonal lineages showed genetic and transcriptomic diversity underlying functionally diverse subpopulations. Molecular annotation of gemcitabine-naive clonal lineages with distinct responses to treatment in the context of CRTs generated signatures that can predict the response to chemotherapy, representing a potential biomarker to stratify patients with pancreatic cancer.
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Affiliation(s)
- Sahil Seth
- Center for Co-Clinical Trials, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; UTHealth Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Chieh-Yuan Li
- UTHealth Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - I-Lin Ho
- UTHealth Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Denise Corti
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sara Loponte
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Luigi Sapio
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Edoardo Del Poggetto
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Er-Yen Yen
- UTHealth Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Frederick Scott Robinson
- Center for Co-Clinical Trials, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Michael Peoples
- Center for Co-Clinical Trials, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Tatiana Karpinets
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Angela Kay Deem
- Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Tapsi Kumar
- UTHealth Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Xingzhi Song
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Shan Jiang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ya'an Kang
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jason Fleming
- Department of Gastrointestinal Oncology, Moffitt Cancer Center, Tampa, FL, USA
| | - Michael Kim
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jianhua Zhang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Anirban Maitra
- Sheikh Ahmed Center for Pancreatic Cancer Research, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Timothy Paul Heffernan
- Center for Co-Clinical Trials, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Virginia Giuliani
- Center for Co-Clinical Trials, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Giannicola Genovese
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Andrew Futreal
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Giulio Francesco Draetta
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Alessandro Carugo
- Center for Co-Clinical Trials, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Andrea Viale
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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Gonçalves E, Behan FM, Louzada S, Arnol D, Stronach EA, Yang F, Yusa K, Stegle O, Iorio F, Garnett MJ. Structural rearrangements generate cell-specific, gene-independent CRISPR-Cas9 loss of fitness effects. Genome Biol 2019; 20:27. [PMID: 30722791 PMCID: PMC6362594 DOI: 10.1186/s13059-019-1637-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 01/22/2019] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND CRISPR-Cas9 genome editing is widely used to study gene function, from basic biology to biomedical research. Structural rearrangements are a ubiquitous feature of cancer cells and their impact on the functional consequences of CRISPR-Cas9 gene-editing has not yet been assessed. RESULTS Utilizing CRISPR-Cas9 knockout screens for 250 cancer cell lines, we demonstrate that targeting structurally rearranged regions, in particular tandem or interspersed amplifications, is highly detrimental to cellular fitness in a gene-independent manner. In contrast, amplifications caused by whole chromosomal duplication have little to no impact on fitness. This effect is cell line specific and dependent on the ploidy status. We devise a copy-number ratio metric that substantially improves the detection of gene-independent cell fitness effects in CRISPR-Cas9 screens. Furthermore, we develop a computational tool, called Crispy, to account for these effects on a single sample basis and provide corrected gene fitness effects. CONCLUSION Our analysis demonstrates the importance of structural rearrangements in mediating the effect of CRISPR-Cas9-induced DNA damage, with implications for the use of CRISPR-Cas9 gene-editing in cancer cells.
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Affiliation(s)
| | - Fiona M Behan
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Sandra Louzada
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Damien Arnol
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Euan A Stronach
- GSK, Medicines Research Center, Gunnels Wood Road, Stevenage, SG1 2NY, UK
| | - Fengtang Yang
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Kosuke Yusa
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Oliver Stegle
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Francesco Iorio
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
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35
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Ruan J, Liu Z, Sun M, Wang Y, Yue J, Yu G. DBS: a fast and informative segmentation algorithm for DNA copy number analysis. BMC Bioinformatics 2019; 20:1. [PMID: 30606105 PMCID: PMC6318921 DOI: 10.1186/s12859-018-2565-8] [Citation(s) in RCA: 115] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 12/07/2018] [Indexed: 12/02/2022] Open
Abstract
Background Genome-wide DNA copy number changes are the hallmark events in the initiation and progression of cancers. Quantitative analysis of somatic copy number alterations (CNAs) has broad applications in cancer research. With the increasing capacity of high-throughput sequencing technologies, fast and efficient segmentation algorithms are required when characterizing high density CNAs data. Results A fast and informative segmentation algorithm, DBS (Deviation Binary Segmentation), is developed and discussed. The DBS method is based on the least absolute error principles and is inspired by the segmentation method rooted in the circular binary segmentation procedure. DBS uses point-by-point model calculation to ensure the accuracy of segmentation and combines a binary search algorithm with heuristics derived from the Central Limit Theorem. The DBS algorithm is very efficient requiring a computational complexity of O(n*log n), and is faster than its predecessors. Moreover, DBS measures the change-point amplitude of mean values of two adjacent segments at a breakpoint, where the significant degree of change-point amplitude is determined by the weighted average deviation at breakpoints. Accordingly, using the constructed binary tree of significant degree, DBS informs whether the results of segmentation are over- or under-segmented. Conclusion DBS is implemented in a platform-independent and open-source Java application (ToolSeg), including a graphical user interface and simulation data generation, as well as various segmentation methods in the native Java language.
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Affiliation(s)
- Jun Ruan
- School of Information Engineering, Wuhan University of Technology, Wuhan, Hubei, 430070, China
| | - Zhen Liu
- School of Information Engineering, Wuhan University of Technology, Wuhan, Hubei, 430070, China
| | - Ming Sun
- School of Information Engineering, Wuhan University of Technology, Wuhan, Hubei, 430070, China
| | - Yue Wang
- Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, Arlington, VA, 22203, USA
| | - Junqiu Yue
- Department of Pathology, Hubei Cancer Hospital, Wuhan, Hubei, 430079, China
| | - Guoqiang Yu
- Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, Arlington, VA, 22203, USA.
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Iorio F, Behan FM, Gonçalves E, Bhosle SG, Chen E, Shepherd R, Beaver C, Ansari R, Pooley R, Wilkinson P, Harper S, Butler AP, Stronach EA, Saez-Rodriguez J, Yusa K, Garnett MJ. Unsupervised correction of gene-independent cell responses to CRISPR-Cas9 targeting. BMC Genomics 2018; 19:604. [PMID: 30103702 PMCID: PMC6088408 DOI: 10.1186/s12864-018-4989-y] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2018] [Accepted: 07/31/2018] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Genome editing by CRISPR-Cas9 technology allows large-scale screening of gene essentiality in cancer. A confounding factor when interpreting CRISPR-Cas9 screens is the high false-positive rate in detecting essential genes within copy number amplified regions of the genome. We have developed the computational tool CRISPRcleanR which is capable of identifying and correcting gene-independent responses to CRISPR-Cas9 targeting. CRISPRcleanR uses an unsupervised approach based on the segmentation of single-guide RNA fold change values across the genome, without making any assumption about the copy number status of the targeted genes. RESULTS Applying our method to existing and newly generated genome-wide essentiality profiles from 15 cancer cell lines, we demonstrate that CRISPRcleanR reduces false positives when calling essential genes, correcting biases within and outside of amplified regions, while maintaining true positive rates. Established cancer dependencies and essentiality signals of amplified cancer driver genes are detectable post-correction. CRISPRcleanR reports sgRNA fold changes and normalised read counts, is therefore compatible with downstream analysis tools, and works with multiple sgRNA libraries. CONCLUSIONS CRISPRcleanR is a versatile open-source tool for the analysis of CRISPR-Cas9 knockout screens to identify essential genes.
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Affiliation(s)
- Francesco Iorio
- European Molecular Biology Laboratory - European Bioinformatics Institute, Cambridge, UK. .,Wellcome Sanger Institute, Cambridge, UK. .,Open Targets, Cambridge, UK.
| | - Fiona M Behan
- Wellcome Sanger Institute, Cambridge, UK.,Open Targets, Cambridge, UK
| | | | | | | | | | | | | | | | | | | | | | | | - Julio Saez-Rodriguez
- European Molecular Biology Laboratory - European Bioinformatics Institute, Cambridge, UK.,Faculty of Medicine, Joint Research Center for Computational Biomedicine Aachen, RWTH Aachen University, Aachen, Germany.,Open Targets, Cambridge, UK.,Present address: Faculty of Medicine, Institute for Computational Biomedicine, Bioquant, Heidelberg University, Heidelberg, Germany
| | | | - Mathew J Garnett
- Wellcome Sanger Institute, Cambridge, UK. .,Open Targets, Cambridge, UK.
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Watkins TBK, Schwarz RF. Phylogenetic Quantification of Intratumor Heterogeneity. Cold Spring Harb Perspect Med 2018; 8:cshperspect.a028316. [PMID: 28710259 DOI: 10.1101/cshperspect.a028316] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
As sequencing efforts continue to reveal the extent of the intratumor heterogeneity (ITH) present in human cancers, the importance of evolutionary studies attempting to trace its etiology has increased. Sequencing multiple samples or tumor regions from the same patient has become affordable and is an effective way of tracing these evolutionary pathways, understanding selection, and detecting clonal expansions in ways impractical with single samples alone. In this article, we discuss and show the benefits of such multisample studies. We describe how multiple samples can guide tree inference through accurate phasing of germline variants and copy-number profiles. We show their relevance in detecting clonal expansions and deriving summary statistics quantifying the overall degree of ITH, and discuss how the relationship of metastatic clades might give us insight into the dominant mode of cancer progression. We further outline how multisample studies might help us better understand selective processes acting on cancer genomes and help to detect neutral evolution and mutator phenotypes.
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Affiliation(s)
| | - Roland F Schwarz
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany
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38
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Hilberg F, Tontsch-Grunt U, Baum A, Le AT, Doebele RC, Lieb S, Gianni D, Voss T, Garin-Chesa P, Haslinger C, Kraut N. Triple Angiokinase Inhibitor Nintedanib Directly Inhibits Tumor Cell Growth and Induces Tumor Shrinkage via Blocking Oncogenic Receptor Tyrosine Kinases. J Pharmacol Exp Ther 2018; 364:494-503. [PMID: 29263244 PMCID: PMC6040086 DOI: 10.1124/jpet.117.244129] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 12/11/2017] [Indexed: 12/11/2022] Open
Abstract
The triple-angiokinase inhibitor nintedanib is an orally available, potent, and selective inhibitor of tumor angiogenesis by blocking the tyrosine kinase activities of vascular endothelial growth factor receptor (VEGFR) 1-3, platelet-derived growth factor receptor (PDGFR)-α and -β, and fibroblast growth factor receptor (FGFR) 1-3. Nintedanib has received regulatory approval as second-line treatment of adenocarcinoma non-small cell lung cancer (NSCLC), in combination with docetaxel. In addition, nintedanib has been approved for the treatment of idiopathic lung fibrosis. Here we report the results from a broad kinase screen that identified additional kinases as targets for nintedanib in the low nanomolar range. Several of these kinases are known to be mutated or overexpressed and are involved in tumor development (discoidin domain receptor family, member 1 and 2, tropomyosin receptor kinase A (TRKA) and C, rearranged during transfection proto-oncogene [RET proto oncogene]), as well as in fibrotic diseases (e.g., DDRs). In tumor cell lines displaying molecular alterations in potential nintedanib targets, the inhibitor demonstrates direct antiproliferative effects: in the NSCLC cell line NCI-H1703 carrying a PDGFRα amplification (ampl.); the gastric cancer cell line KatoIII and the breast cancer cell line MFM223, both driven by a FGFR2 amplification; AN3CA (endometrial carcinoma) bearing a mutated FGFR2; the acute myeloid leukemia cell lines MOLM-13 and MV-4-11-B with FLT3 mutations; and the NSCLC adenocarcinoma LC-2/ad harboring a CCDC6-RET fusion. Potent kinase inhibition does not, however, strictly translate into antiproliferative activity, as demonstrated in the TRKA-dependent cell lines CUTO-3 and KM-12. Importantly, nintedanib treatment of NCI-H1703 tumor xenografts triggered effective tumor shrinkage, indicating a direct effect on the tumor cells in addition to the antiangiogenic effect on the tumor stroma. These findings will be instructive in guiding future genome-based clinical trials of nintedanib.
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Affiliation(s)
- Frank Hilberg
- Boehringer Ingelheim RCV GmbH Co KG, Vienna, Austria (F.H., U.T.-G., A.B., S.L., D.G., T.V., P.G.-C., C.H., N.K.); University of Colorado, School of Medicine, Division of Medical Oncology, Aurora, Colorado (A.T.L., R.C.D.); and AstraZeneca - Innovative Medicines and Early Development, Discovery Sciences, Cambridge Science Park, Milton, Cambridge (D.G.)
| | - Ulrike Tontsch-Grunt
- Boehringer Ingelheim RCV GmbH Co KG, Vienna, Austria (F.H., U.T.-G., A.B., S.L., D.G., T.V., P.G.-C., C.H., N.K.); University of Colorado, School of Medicine, Division of Medical Oncology, Aurora, Colorado (A.T.L., R.C.D.); and AstraZeneca - Innovative Medicines and Early Development, Discovery Sciences, Cambridge Science Park, Milton, Cambridge (D.G.)
| | - Anke Baum
- Boehringer Ingelheim RCV GmbH Co KG, Vienna, Austria (F.H., U.T.-G., A.B., S.L., D.G., T.V., P.G.-C., C.H., N.K.); University of Colorado, School of Medicine, Division of Medical Oncology, Aurora, Colorado (A.T.L., R.C.D.); and AstraZeneca - Innovative Medicines and Early Development, Discovery Sciences, Cambridge Science Park, Milton, Cambridge (D.G.)
| | - Anh T Le
- Boehringer Ingelheim RCV GmbH Co KG, Vienna, Austria (F.H., U.T.-G., A.B., S.L., D.G., T.V., P.G.-C., C.H., N.K.); University of Colorado, School of Medicine, Division of Medical Oncology, Aurora, Colorado (A.T.L., R.C.D.); and AstraZeneca - Innovative Medicines and Early Development, Discovery Sciences, Cambridge Science Park, Milton, Cambridge (D.G.)
| | - Robert C Doebele
- Boehringer Ingelheim RCV GmbH Co KG, Vienna, Austria (F.H., U.T.-G., A.B., S.L., D.G., T.V., P.G.-C., C.H., N.K.); University of Colorado, School of Medicine, Division of Medical Oncology, Aurora, Colorado (A.T.L., R.C.D.); and AstraZeneca - Innovative Medicines and Early Development, Discovery Sciences, Cambridge Science Park, Milton, Cambridge (D.G.)
| | - Simone Lieb
- Boehringer Ingelheim RCV GmbH Co KG, Vienna, Austria (F.H., U.T.-G., A.B., S.L., D.G., T.V., P.G.-C., C.H., N.K.); University of Colorado, School of Medicine, Division of Medical Oncology, Aurora, Colorado (A.T.L., R.C.D.); and AstraZeneca - Innovative Medicines and Early Development, Discovery Sciences, Cambridge Science Park, Milton, Cambridge (D.G.)
| | - Davide Gianni
- Boehringer Ingelheim RCV GmbH Co KG, Vienna, Austria (F.H., U.T.-G., A.B., S.L., D.G., T.V., P.G.-C., C.H., N.K.); University of Colorado, School of Medicine, Division of Medical Oncology, Aurora, Colorado (A.T.L., R.C.D.); and AstraZeneca - Innovative Medicines and Early Development, Discovery Sciences, Cambridge Science Park, Milton, Cambridge (D.G.)
| | - Tilman Voss
- Boehringer Ingelheim RCV GmbH Co KG, Vienna, Austria (F.H., U.T.-G., A.B., S.L., D.G., T.V., P.G.-C., C.H., N.K.); University of Colorado, School of Medicine, Division of Medical Oncology, Aurora, Colorado (A.T.L., R.C.D.); and AstraZeneca - Innovative Medicines and Early Development, Discovery Sciences, Cambridge Science Park, Milton, Cambridge (D.G.)
| | - Pilar Garin-Chesa
- Boehringer Ingelheim RCV GmbH Co KG, Vienna, Austria (F.H., U.T.-G., A.B., S.L., D.G., T.V., P.G.-C., C.H., N.K.); University of Colorado, School of Medicine, Division of Medical Oncology, Aurora, Colorado (A.T.L., R.C.D.); and AstraZeneca - Innovative Medicines and Early Development, Discovery Sciences, Cambridge Science Park, Milton, Cambridge (D.G.)
| | - Christian Haslinger
- Boehringer Ingelheim RCV GmbH Co KG, Vienna, Austria (F.H., U.T.-G., A.B., S.L., D.G., T.V., P.G.-C., C.H., N.K.); University of Colorado, School of Medicine, Division of Medical Oncology, Aurora, Colorado (A.T.L., R.C.D.); and AstraZeneca - Innovative Medicines and Early Development, Discovery Sciences, Cambridge Science Park, Milton, Cambridge (D.G.)
| | - Norbert Kraut
- Boehringer Ingelheim RCV GmbH Co KG, Vienna, Austria (F.H., U.T.-G., A.B., S.L., D.G., T.V., P.G.-C., C.H., N.K.); University of Colorado, School of Medicine, Division of Medical Oncology, Aurora, Colorado (A.T.L., R.C.D.); and AstraZeneca - Innovative Medicines and Early Development, Discovery Sciences, Cambridge Science Park, Milton, Cambridge (D.G.)
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39
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Kolluri KK, Alifrangis C, Kumar N, Ishii Y, Price S, Michaut M, Williams S, Barthorpe S, Lightfoot H, Busacca S, Sharkey A, Yuan Z, Sage EK, Vallath S, Le Quesne J, Tice DA, Alrifai D, von Karstedt S, Montinaro A, Guppy N, Waller DA, Nakas A, Good R, Holmes A, Walczak H, Fennell DA, Garnett M, Iorio F, Wessels L, McDermott U, Janes SM. Loss of functional BAP1 augments sensitivity to TRAIL in cancer cells. eLife 2018; 7:e30224. [PMID: 29345617 PMCID: PMC5773178 DOI: 10.7554/elife.30224] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 12/13/2017] [Indexed: 12/29/2022] Open
Abstract
Malignant mesothelioma (MM) is poorly responsive to systemic cytotoxic chemotherapy and invariably fatal. Here we describe a screen of 94 drugs in 15 exome-sequenced MM lines and the discovery of a subset defined by loss of function of the nuclear deubiquitinase BRCA associated protein-1 (BAP1) that demonstrate heightened sensitivity to TRAIL (tumour necrosis factor-related apoptosis-inducing ligand). This association is observed across human early passage MM cultures, mouse xenografts and human tumour explants. We demonstrate that BAP1 deubiquitinase activity and its association with ASXL1 to form the Polycomb repressive deubiquitinase complex (PR-DUB) impacts TRAIL sensitivity implicating transcriptional modulation as an underlying mechanism. Death receptor agonists are well-tolerated anti-cancer agents demonstrating limited therapeutic benefit in trials without a targeting biomarker. We identify BAP1 loss-of-function mutations, which are frequent in MM, as a potential genomic stratification tool for TRAIL sensitivity with immediate and actionable therapeutic implications.
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Affiliation(s)
- Krishna Kalyan Kolluri
- Lungs for Living Research Centre, UCL RespiratoryUniversity College LondonLondonUnited Kingdom
| | | | - Neelam Kumar
- Lungs for Living Research Centre, UCL RespiratoryUniversity College LondonLondonUnited Kingdom
| | - Yuki Ishii
- Lungs for Living Research Centre, UCL RespiratoryUniversity College LondonLondonUnited Kingdom
| | - Stacey Price
- Wellcome Trust Sanger InstituteCambridgeUnited Kingdom
| | | | | | - Syd Barthorpe
- Wellcome Trust Sanger InstituteCambridgeUnited Kingdom
| | | | - Sara Busacca
- CRUK Leicester Centre, Department of Cancer studiesUniversity of LeicesterLeicesterUnited Kingdom
| | - Annabel Sharkey
- CRUK Leicester Centre, Department of Cancer studiesUniversity of LeicesterLeicesterUnited Kingdom
| | - Zhenqiang Yuan
- Lungs for Living Research Centre, UCL RespiratoryUniversity College LondonLondonUnited Kingdom
| | - Elizabeth K Sage
- Lungs for Living Research Centre, UCL RespiratoryUniversity College LondonLondonUnited Kingdom
| | - Sabarinath Vallath
- Lungs for Living Research Centre, UCL RespiratoryUniversity College LondonLondonUnited Kingdom
| | - John Le Quesne
- CRUK Leicester Centre, Department of Cancer studiesUniversity of LeicesterLeicesterUnited Kingdom
| | - David A Tice
- Oncology Research, MedImmune, Inc.GaithersburgUnited States
| | - Doraid Alrifai
- Lungs for Living Research Centre, UCL RespiratoryUniversity College LondonLondonUnited Kingdom
| | - Sylvia von Karstedt
- Centre for Cell Death, Cancer and InflammationUCL Cancer Institute, University College LondonLondonUnited Kingdom
| | - Antonella Montinaro
- Centre for Cell Death, Cancer and InflammationUCL Cancer Institute, University College LondonLondonUnited Kingdom
| | - Naomi Guppy
- UCL Advanced DiagnosticsUniversity College LondonLondonUnited Kingdom
| | - David A Waller
- Department of Thoracic SurgeryGlenfield Hospital, University Hospitals of LeicesterLeicesterUnited Kingdom
| | - Apostolos Nakas
- Department of Thoracic SurgeryGlenfield Hospital, University Hospitals of LeicesterLeicesterUnited Kingdom
| | - Robert Good
- UCL School of PharmacyUniversity College LondonLondonUnited Kingdom
| | - Alan Holmes
- UCL School of PharmacyUniversity College LondonLondonUnited Kingdom
| | - Henning Walczak
- Centre for Cell Death, Cancer and InflammationUCL Cancer Institute, University College LondonLondonUnited Kingdom
| | - Dean A Fennell
- CRUK Leicester Centre, Department of Cancer studiesUniversity of LeicesterLeicesterUnited Kingdom
| | | | - Francesco Iorio
- European Molecular Biology LaboratoryEuropean Bioinformatics InstituteCambridgeUnited Kingdom
| | | | | | - Samuel M Janes
- Lungs for Living Research Centre, UCL RespiratoryUniversity College LondonLondonUnited Kingdom
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40
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Abstract
Differences between genomes can be due to single nucleotide variants (SNPs), translocations, inversions and copy number variants (CNVs, gain or loss of DNA). The latter can range from sub-microscopic events to complete chromosomal aneuploidies. Small CNVs are often benign but those larger than 250 kb are strongly associated with morbid consequences such as developmental disorders and cancer. Detecting CNVs within and between populations is essential to better understand the plasticity of our genome and to elucidate its possible contribution to disease or phenotypic traits.While the link between SNPs and disease susceptibility has been well studied, to date there are still very few published CNV genome-wide association studies; probably owing to the fact that CNV analysis remains a slightly more complex task than SNP analysis (both in term of bioinformatics workflow and uncertainty in the CNV calling leading to high false positive rates and unknown false negative rates). This chapter aims at explaining computational methods for the analysis of CNVs, ranging from study design, data processing and quality control, up to genome-wide association study with clinical traits.
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Affiliation(s)
- Aurélien Macé
- Institute of Social and Preventive Medicine, University Hospital of Lausanne, Lausanne, Switzerland.,Department of Computational Biology, University of Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Zoltán Kutalik
- Institute of Social and Preventive Medicine, University Hospital of Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
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41
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Renault V, Tost J, Pichon F, Wang-Renault SF, Letouzé E, Imbeaud S, Zucman-Rossi J, Deleuze JF, How-Kit A. aCNViewer: Comprehensive genome-wide visualization of absolute copy number and copy neutral variations. PLoS One 2017; 12:e0189334. [PMID: 29261730 PMCID: PMC5736239 DOI: 10.1371/journal.pone.0189334] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 11/23/2017] [Indexed: 11/26/2022] Open
Abstract
Motivation Copy number variations (CNV) include net gains or losses of part or whole chromosomal regions. They differ from copy neutral loss of heterozygosity (cn-LOH) events which do not induce any net change in the copy number and are often associated with uniparental disomy. These phenomena have long been reported to be associated with diseases and particularly in cancer. Losses/gains of genomic regions are often correlated with lower/higher gene expression. On the other hand, loss of heterozygosity (LOH) and cn-LOH are common events in cancer and may be associated with the loss of a functional tumor suppressor gene. Therefore, identifying recurrent CNV and cn-LOH events can be important as they may highlight common biological components and give insights into the development or mechanisms of a disease. However, no currently available tools allow a comprehensive whole-genome visualization of recurrent CNVs and cn-LOH in groups of samples providing absolute quantification of the aberrations leading to the loss of potentially important information. Results To overcome these limitations, we developed aCNViewer (Absolute CNV Viewer), a visualization tool for absolute CNVs and cn-LOH across a group of samples. aCNViewer proposes three graphical representations: dendrograms, bi-dimensional heatmaps showing chromosomal regions sharing similar abnormality patterns, and quantitative stacked histograms facilitating the identification of recurrent absolute CNVs and cn-LOH. We illustrated aCNViewer using publically available hepatocellular carcinomas (HCCs) Affymetrix SNP Array data (Fig 1A). Regions 1q and 8q present a similar percentage of total gains but significantly different copy number gain categories (p-value of 0.0103 with a Fisher exact test), validated by another cohort of HCCs (p-value of 5.6e-7) (Fig 2B). Availability and implementation aCNViewer is implemented in python and R and is available with a GNU GPLv3 license on GitHub https://github.com/FJD-CEPH/aCNViewer and Docker https://hub.docker.com/r/fjdceph/acnviewer/. Contact aCNViewer@cephb.fr
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Affiliation(s)
- Victor Renault
- Laboratory for Bioinformatics, Fondation Jean Dausset–CEPH, Paris, France
- Laboratory of Excellence GenMed, Paris, France
- * E-mail: (VR); (AHK)
| | - Jörg Tost
- Laboratory for Epigenetics and Environment, Centre National de Recherche en Génomique Humaine, Institut de Biologie François Jacob, CEA, Evry, France
| | - Fabien Pichon
- Laboratory for Epigenetics and Environment, Centre National de Recherche en Génomique Humaine, Institut de Biologie François Jacob, CEA, Evry, France
| | - Shu-Fang Wang-Renault
- Laboratory for Epigenetics and Environment, Centre National de Recherche en Génomique Humaine, Institut de Biologie François Jacob, CEA, Evry, France
| | - Eric Letouzé
- Inserm, UMR-1162, Génomique fonctionnelle des tumeurs solides, Institut Universitaire d'Hématologie (IUH), Paris, France
| | - Sandrine Imbeaud
- Inserm, UMR-1162, Génomique fonctionnelle des tumeurs solides, Institut Universitaire d'Hématologie (IUH), Paris, France
| | - Jessica Zucman-Rossi
- Inserm, UMR-1162, Génomique fonctionnelle des tumeurs solides, Institut Universitaire d'Hématologie (IUH), Paris, France
| | - Jean-François Deleuze
- Laboratory for Bioinformatics, Fondation Jean Dausset–CEPH, Paris, France
- Laboratory of Excellence GenMed, Paris, France
- Laboratory for Epigenetics and Environment, Centre National de Recherche en Génomique Humaine, Institut de Biologie François Jacob, CEA, Evry, France
- Laboratory for Genomics, Fondation Jean Dausset–CEPH, Paris, France
| | - Alexandre How-Kit
- Laboratory of Excellence GenMed, Paris, France
- Laboratory for Genomics, Fondation Jean Dausset–CEPH, Paris, France
- * E-mail: (VR); (AHK)
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42
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Xu J, Peng X, Chen Y, Zhang Y, Ma Q, Liang L, Carter AC, Lu X, Wu CI. Free-living human cells reconfigure their chromosomes in the evolution back to uni-cellularity. eLife 2017; 6. [PMID: 29251591 PMCID: PMC5734875 DOI: 10.7554/elife.28070] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 10/28/2017] [Indexed: 01/06/2023] Open
Abstract
Cells of multi-cellular organisms evolve toward uni-cellularity in the form of cancer and, if humans intervene, continue to evolve in cell culture. During this process, gene dosage relationships may evolve in novel ways to cope with the new environment and may regress back to the ancestral uni-cellular state. In this context, the evolution of sex chromosomes vis-a-vis autosomes is of particular interest. Here, we report the chromosomal evolution in ~ 600 cancer cell lines. Many of them jettisoned either Y or the inactive X; thus, free-living male and female cells converge by becoming ‘de-sexualized’. Surprisingly, the active X often doubled, accompanied by the addition of one haploid complement of autosomes, leading to an X:A ratio of 2:3 from the extant ratio of 1:2. Theoretical modeling of the frequency distribution of X:A karyotypes suggests that the 2:3 ratio confers a higher fitness and may reflect aspects of sex chromosome evolution. Multicellular life relies on a group of cells working together for a common interest. To study these cells, researchers take them out of the organism and grow them in the laboratory. Instead of growing as part of organs and tissues, the cells normally have a free-living lifestyle. Because multicellular life evolved from single-celled organisms, laboratory-grown cells can be considered as life forms that are evolving backward from a multicellular to a single-celled existence. Normally, the cells that make up most of the tissues in the human body have 22 pairs of chromosomes known as autosomes and a pair of sex chromosomes. The cells of women have two X sex chromosomes, one of which is inactive, while those of men have one X and one Y chromosome. However, free-living single cells do not need to distinguish between male and female cells. Xu, Peng, Chen et al. have now studied the chromosomes of cancer cells taken from over 600 people and grown in the laboratory. As the cells evolved in response to their free-living lifestyle, they became ‘de-sexualized’; male cells lost their Y chromosome, while female cells abandoned their inactive X chromosome. The cells then evolved toward a new state in which they possessed two active X chromosomes and three sets of autosomes. This new configuration suggests that the current X chromosome to autosome ratio may not be optimal for fitness and hence sheds some light on how mammalian sex chromosomes evolved. It is currently thought that as cancerous tumors grow, their cells evolve to favor their own interests over the common interests of the rest of the organism. In this way, they develop characteristics more like those of single cells. Further research is therefore needed to investigate whether changes occur to the chromosomes of cancer cells growing within the body, and whether this gives them an advantage over normal cells.
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Affiliation(s)
- Jin Xu
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Xinxin Peng
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Yuxin Chen
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Yuezheng Zhang
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Qin Ma
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Liang Liang
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Ava C Carter
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, United States
| | - Xuemei Lu
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China.,CAS Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - Chung-I Wu
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China.,Department of Ecology and Evolution, University of Chicago, Chicago, United States
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43
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Gong X, Litchfield LM, Webster Y, Chio LC, Wong SS, Stewart TR, Dowless M, Dempsey J, Zeng Y, Torres R, Boehnke K, Mur C, Marugán C, Baquero C, Yu C, Bray SM, Wulur IH, Bi C, Chu S, Qian HR, Iversen PW, Merzoug FF, Ye XS, Reinhard C, De Dios A, Du J, Caldwell CW, Lallena MJ, Beckmann RP, Buchanan SG. Genomic Aberrations that Activate D-type Cyclins Are Associated with Enhanced Sensitivity to the CDK4 and CDK6 Inhibitor Abemaciclib. Cancer Cell 2017; 32:761-776.e6. [PMID: 29232554 DOI: 10.1016/j.ccell.2017.11.006] [Citation(s) in RCA: 171] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Revised: 08/10/2017] [Accepted: 11/08/2017] [Indexed: 12/11/2022]
Abstract
Most cancers preserve functional retinoblastoma (Rb) and may, therefore, respond to inhibition of D-cyclin-dependent Rb kinases, CDK4 and CDK6. To date, CDK4/6 inhibitors have shown promising clinical activity in breast cancer and lymphomas, but it is not clear which additional Rb-positive cancers might benefit from these agents. No systematic survey to compare relative sensitivities across tumor types and define molecular determinants of response has been described. We report a subset of cancers highly sensitive to CDK4/6 inhibition and characterized by various genomic aberrations known to elevate D-cyclin levels and describe a recurrent CCND1 3'UTR mutation associated with increased expression in endometrial cancer. The results suggest multiple additional classes of cancer that may benefit from CDK4/6-inhibiting drugs such as abemaciclib.
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Affiliation(s)
- Xueqian Gong
- Eli Lilly and Company, Indianapolis, IN 46285, USA
| | | | - Yue Webster
- Eli Lilly and Company, Indianapolis, IN 46285, USA
| | - Li-Chun Chio
- Eli Lilly and Company, Indianapolis, IN 46285, USA
| | | | | | | | - Jack Dempsey
- Eli Lilly and Company, Indianapolis, IN 46285, USA
| | - Yi Zeng
- Eli Lilly and Company, Indianapolis, IN 46285, USA
| | | | | | - Cecilia Mur
- Eli Lilly and Company, Alcobendas, Madrid, Spain
| | | | | | | | | | | | - Chen Bi
- Eli Lilly and Company, Indianapolis, IN 46285, USA
| | - Shaoyou Chu
- Eli Lilly and Company, Indianapolis, IN 46285, USA
| | | | | | | | | | | | | | - Jian Du
- Eli Lilly and Company, Indianapolis, IN 46285, USA
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44
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Hughesman CB, Lu XJD, Liu KYP, Zhu Y, Towle RM, Haynes C, Poh CF. Detection of clinically relevant copy number alterations in oral cancer progression using multiplexed droplet digital PCR. Sci Rep 2017; 7:11855. [PMID: 28928368 PMCID: PMC5605662 DOI: 10.1038/s41598-017-11201-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 08/21/2017] [Indexed: 02/06/2023] Open
Abstract
Copy number alterations (CNAs), a common genomic event during carcinogenesis, are known to affect a large fraction of the genome. Common recurrent gains or losses of specific chromosomal regions occur at frequencies that they may be considered distinctive features of tumoral cells. Here we introduce a novel multiplexed droplet digital PCR (ddPCR) assay capable of detecting recurrent CNAs that drive tumorigenesis of oral squamous cell carcinoma. Applied to DNA extracted from oral cell lines and clinical samples of various disease stages, we found good agreement between CNAs detected by our ddPCR assay with those previously reported using comparative genomic hybridization or single nucleotide polymorphism arrays. Furthermore, we demonstrate that the ability to target specific locations of the genome permits detection of clinically relevant oncogenic events such as small, submicroscopic homozygous deletions. Additional capabilities of the multiplexed ddPCR assay include the ability to infer ploidy level, quantify the change in copy number of target loci with high-level gains, and simultaneously assess the status and viral load for high-risk human papillomavirus types 16 and 18. This novel multiplexed ddPCR assay therefore may have clinical value in differentiating between benign oral lesions from those that are at risk of progressing to oral cancer.
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Affiliation(s)
- Curtis B Hughesman
- Department of Oral Medical and Biological Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, V5Z 1L3, Canada
| | - X J David Lu
- Department of Oral Medical and Biological Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, V5Z 1L3, Canada
| | - Kelly Y P Liu
- Department of Oral Medical and Biological Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, V5Z 1L3, Canada
| | - Yuqi Zhu
- Department of Oral Medical and Biological Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, V5Z 1L3, Canada
| | - Rebecca M Towle
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, V5Z 1L3, Canada
| | - Charles Haynes
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada.
| | - Catherine F Poh
- Department of Oral Medical and Biological Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada.
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, V5Z 1L3, Canada.
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, V6T 2B5, Canada.
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45
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Chen W, Robertson AJ, Ganesamoorthy D, Coin LJM. sCNAphase: using haplotype resolved read depth to genotype somatic copy number alterations from low cellularity aneuploid tumors. Nucleic Acids Res 2017; 45:e34. [PMID: 27903916 PMCID: PMC5389684 DOI: 10.1093/nar/gkw1086] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 10/26/2016] [Indexed: 02/03/2023] Open
Abstract
Accurate identification of copy number alterations is an essential step in understanding the events driving tumor progression. While a variety of algorithms have been developed to use high-throughput sequencing data to profile copy number changes, no tool is able to reliably characterize ploidy and genotype absolute copy number from tumor samples that contain less than 40% tumor cells. To increase our power to resolve the copy number profile from low-cellularity tumor samples, we developed a novel approach that pre-phases heterozygote germline single nucleotide polymorphisms (SNPs) in order to replace the commonly used ‘B-allele frequency’ with a more powerful ‘parental-haplotype frequency’. We apply our tool—sCNAphase—to characterize the copy number and loss-of-heterozygosity profiles of four publicly available breast cancer cell-lines. Comparisons to previous spectral karyotyping and microarray studies revealed that sCNAphase reliably identified overall ploidy as well as the individual copy number mutations from each cell-line. Analysis of artificial cell-line mixtures demonstrated the capacity of this method to determine the level of tumor cellularity, consistently identify sCNAs and characterize ploidy in samples with as little as 10% tumor cells. This novel methodology has the potential to bring sCNA profiling to low-cellularity tumors, a form of cancer unable to be accurately studied by current methods.
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Affiliation(s)
- Wenhan Chen
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland, 4072, Australia
| | - Alan J Robertson
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland, 4072, Australia
| | - Devika Ganesamoorthy
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland, 4072, Australia
| | - Lachlan J M Coin
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland, 4072, Australia
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46
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Analysis of renal cancer cell lines from two major resources enables genomics-guided cell line selection. Nat Commun 2017; 8:15165. [PMID: 28489074 PMCID: PMC5436135 DOI: 10.1038/ncomms15165] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 03/06/2017] [Indexed: 12/19/2022] Open
Abstract
The utility of cancer cell lines is affected by the similarity to endogenous tumour cells. Here we compare genomic data from 65 kidney-derived cell lines from the Cancer Cell Line Encyclopedia and the COSMIC Cell Lines Project to three renal cancer subtypes from The Cancer Genome Atlas: clear cell renal cell carcinoma (ccRCC, also known as kidney renal clear cell carcinoma), papillary (pRCC, also known as kidney papillary) and chromophobe (chRCC, also known as kidney chromophobe) renal cell carcinoma. Clustering copy number alterations shows that most cell lines resemble ccRCC, a few (including some often used as models of ccRCC) resemble pRCC, and none resemble chRCC. Human ccRCC tumours clustering with cell lines display clinical and genomic features of more aggressive disease, suggesting that cell lines best represent aggressive tumours. We stratify mutations and copy number alterations for important kidney cancer genes by the consistency between databases, and classify cell lines into established gene expression-based indolent and aggressive subtypes. Our results could aid investigators in analysing appropriate renal cancer cell lines.
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47
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Rosenbloom DIS, Camara PG, Chu T, Rabadan R. Evolutionary scalpels for dissecting tumor ecosystems. Biochim Biophys Acta Rev Cancer 2016; 1867:69-83. [PMID: 27923679 DOI: 10.1016/j.bbcan.2016.11.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 11/20/2016] [Indexed: 02/06/2023]
Abstract
Amidst the growing literature on cancer genomics and intratumor heterogeneity, essential principles in evolutionary biology recur time and time again. Here we use these principles to guide the reader through major advances in cancer research, highlighting issues of "hit hard, hit early" treatment strategies, drug resistance, and metastasis. We distinguish between two frameworks for understanding heterogeneous tumors, both of which can inform treatment strategies: (1) The tumor as diverse ecosystem, a Darwinian population of sometimes-competing, sometimes-cooperating cells; (2) The tumor as tightly integrated, self-regulating organ, which may hijack developmental signals to restore functional heterogeneity after treatment. While the first framework dominates literature on cancer evolution, the second framework enjoys support as well. Throughout this review, we illustrate how mathematical models inform understanding of tumor progression and treatment outcomes. Connecting models to genomic data faces computational and technical hurdles, but high-throughput single-cell technologies show promise to clear these hurdles. This article is part of a Special Issue entitled: Evolutionary principles - heterogeneity in cancer?, edited by Dr. Robert A. Gatenby.
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Affiliation(s)
- Daniel I S Rosenbloom
- Department of Systems Biology, Columbia University College of Physicians and Surgeons, 1130 St. Nicholas Avenue, New York, NY 10032, USA; Department of Biomedical Informatics, Columbia University College of Physicians and Surgeons, 1130 St. Nicholas Avenue, New York, NY 10032, USA.
| | - Pablo G Camara
- Department of Systems Biology, Columbia University College of Physicians and Surgeons, 1130 St. Nicholas Avenue, New York, NY 10032, USA; Department of Biomedical Informatics, Columbia University College of Physicians and Surgeons, 1130 St. Nicholas Avenue, New York, NY 10032, USA
| | - Tim Chu
- Department of Systems Biology, Columbia University College of Physicians and Surgeons, 1130 St. Nicholas Avenue, New York, NY 10032, USA; Department of Biomedical Informatics, Columbia University College of Physicians and Surgeons, 1130 St. Nicholas Avenue, New York, NY 10032, USA
| | - Raul Rabadan
- Department of Systems Biology, Columbia University College of Physicians and Surgeons, 1130 St. Nicholas Avenue, New York, NY 10032, USA; Department of Biomedical Informatics, Columbia University College of Physicians and Surgeons, 1130 St. Nicholas Avenue, New York, NY 10032, USA.
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48
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Garcia E, Hayden A, Birts C, Britton E, Cowie A, Pickard K, Mellone M, Choh C, Derouet M, Duriez P, Noble F, White MJ, Primrose JN, Strefford JC, Rose-Zerilli M, Thomas GJ, Ang Y, Sharrocks AD, Fitzgerald RC, Underwood TJ. Authentication and characterisation of a new oesophageal adenocarcinoma cell line: MFD-1. Sci Rep 2016; 6:32417. [PMID: 27600491 PMCID: PMC5013399 DOI: 10.1038/srep32417] [Citation(s) in RCA: 18] [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: 04/14/2016] [Accepted: 08/04/2016] [Indexed: 12/16/2022] Open
Abstract
New biological tools are required to understand the functional significance of genetic events revealed by whole genome sequencing (WGS) studies in oesophageal adenocarcinoma (OAC). The MFD-1 cell line was isolated from a 55-year-old male with OAC without recombinant-DNA transformation. Somatic genetic variations from MFD-1, tumour, normal oesophagus, and leucocytes were analysed with SNP6. WGS was performed in tumour and leucocytes. RNAseq was performed in MFD-1, and two classic OAC cell lines FLO1 and OE33. Transposase-accessible chromatin sequencing (ATAC-seq) was performed in MFD-1, OE33, and non-neoplastic HET1A cells. Functional studies were performed. MFD-1 had a high SNP genotype concordance with matched germline/tumour. Parental tumour and MFD-1 carried four somatically acquired mutations in three recurrent mutated genes in OAC: TP53, ABCB1 and SEMA5A, not present in FLO-1 or OE33. MFD-1 displayed high expression of epithelial and glandular markers and a unique fingerprint of open chromatin. MFD-1 was tumorigenic in SCID mouse and proliferative and invasive in 3D cultures. The clinical utility of whole genome sequencing projects will be delivered using accurate model systems to develop molecular-phenotype therapeutics. We have described the first such system to arise from the oesophageal International Cancer Genome Consortium project.
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Affiliation(s)
- Edwin Garcia
- Faculty of Medicine, University of Southampton, Southampton General Hospital, Mailpoint 801, South Academic Block, Tremona Road, Southampton, SO16 6YD, United Kingdom
| | - Annette Hayden
- Faculty of Medicine, University of Southampton, Southampton General Hospital, Mailpoint 801, South Academic Block, Tremona Road, Southampton, SO16 6YD, United Kingdom
| | - Charles Birts
- Faculty of Medicine, University of Southampton, Southampton General Hospital, Mailpoint 801, South Academic Block, Tremona Road, Southampton, SO16 6YD, United Kingdom
| | - Edward Britton
- Faculty of Biology, Medicine and Health, Oxford Road, University of Manchester, Manchester, M13 9PT, UK
| | - Andrew Cowie
- Faculty of Medicine, University of Southampton, Southampton General Hospital, Mailpoint 801, South Academic Block, Tremona Road, Southampton, SO16 6YD, United Kingdom
| | - Karen Pickard
- Faculty of Medicine, University of Southampton, Southampton General Hospital, Mailpoint 801, South Academic Block, Tremona Road, Southampton, SO16 6YD, United Kingdom
| | - Massimiliano Mellone
- Faculty of Medicine, University of Southampton, Southampton General Hospital, Mailpoint 801, South Academic Block, Tremona Road, Southampton, SO16 6YD, United Kingdom
| | - Clarisa Choh
- Faculty of Medicine, University of Southampton, Southampton General Hospital, Mailpoint 801, South Academic Block, Tremona Road, Southampton, SO16 6YD, United Kingdom
| | - Mathieu Derouet
- Faculty of Medicine, University of Southampton, Southampton General Hospital, Mailpoint 801, South Academic Block, Tremona Road, Southampton, SO16 6YD, United Kingdom
| | - Patrick Duriez
- Faculty of Medicine, University of Southampton, Southampton General Hospital, Mailpoint 801, South Academic Block, Tremona Road, Southampton, SO16 6YD, United Kingdom
| | - Fergus Noble
- Faculty of Medicine, University of Southampton, Southampton General Hospital, Mailpoint 801, South Academic Block, Tremona Road, Southampton, SO16 6YD, United Kingdom
| | - Michael J. White
- Faculty of Medicine, University of Southampton, Southampton General Hospital, Mailpoint 801, South Academic Block, Tremona Road, Southampton, SO16 6YD, United Kingdom
| | - John N. Primrose
- Faculty of Medicine, University of Southampton, Southampton General Hospital, Mailpoint 801, South Academic Block, Tremona Road, Southampton, SO16 6YD, United Kingdom
| | - Jonathan C. Strefford
- Faculty of Medicine, University of Southampton, Southampton General Hospital, Mailpoint 801, South Academic Block, Tremona Road, Southampton, SO16 6YD, United Kingdom
| | - Matthew Rose-Zerilli
- Faculty of Medicine, University of Southampton, Southampton General Hospital, Mailpoint 801, South Academic Block, Tremona Road, Southampton, SO16 6YD, United Kingdom
| | - Gareth J. Thomas
- Faculty of Medicine, University of Southampton, Southampton General Hospital, Mailpoint 801, South Academic Block, Tremona Road, Southampton, SO16 6YD, United Kingdom
| | - Yeng Ang
- Faculty of Biology, Medicine and Health, Oxford Road, University of Manchester, Manchester, M13 9PT, UK
| | - Andrew D. Sharrocks
- Faculty of Biology, Medicine and Health, Oxford Road, University of Manchester, Manchester, M13 9PT, UK
| | - Rebecca C. Fitzgerald
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Box 197, Cambridge Biomedical Campus, Cambridge, CB2 0XZ United Kingdom
| | - Timothy J. Underwood
- Faculty of Medicine, University of Southampton, Southampton General Hospital, Mailpoint 801, South Academic Block, Tremona Road, Southampton, SO16 6YD, United Kingdom
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49
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Reproducible pharmacogenomic profiling of cancer cell line panels. Nature 2016; 533:333-7. [PMID: 27193678 DOI: 10.1038/nature17987] [Citation(s) in RCA: 205] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Accepted: 04/07/2016] [Indexed: 12/21/2022]
Abstract
The use of large-scale genomic and drug response screening of cancer cell lines depends crucially on the reproducibility of results. Here we consider two previously published screens, plus a later critique of these studies. Using independent data, we show that consistency is achievable, and provide a systematic description of the best laboratory and analysis practices for future studies.
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50
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Bueno R, Stawiski EW, Goldstein LD, Durinck S, De Rienzo A, Modrusan Z, Gnad F, Nguyen TT, Jaiswal BS, Chirieac LR, Sciaranghella D, Dao N, Gustafson CE, Munir KJ, Hackney JA, Chaudhuri A, Gupta R, Guillory J, Toy K, Ha C, Chen YJ, Stinson J, Chaudhuri S, Zhang N, Wu TD, Sugarbaker DJ, de Sauvage FJ, Richards WG, Seshagiri S. Comprehensive genomic analysis of malignant pleural mesothelioma identifies recurrent mutations, gene fusions and splicing alterations. Nat Genet 2016; 48:407-16. [PMID: 26928227 DOI: 10.1038/ng.3520] [Citation(s) in RCA: 673] [Impact Index Per Article: 74.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2015] [Accepted: 02/04/2016] [Indexed: 02/06/2023]
Abstract
We analyzed transcriptomes (n = 211), whole exomes (n = 99) and targeted exomes (n = 103) from 216 malignant pleural mesothelioma (MPM) tumors. Using RNA-seq data, we identified four distinct molecular subtypes: sarcomatoid, epithelioid, biphasic-epithelioid (biphasic-E) and biphasic-sarcomatoid (biphasic-S). Through exome analysis, we found BAP1, NF2, TP53, SETD2, DDX3X, ULK2, RYR2, CFAP45, SETDB1 and DDX51 to be significantly mutated (q-score ≥ 0.8) in MPMs. We identified recurrent mutations in several genes, including SF3B1 (∼2%; 4/216) and TRAF7 (∼2%; 5/216). SF3B1-mutant samples showed a splicing profile distinct from that of wild-type tumors. TRAF7 alterations occurred primarily in the WD40 domain and were, except in one case, mutually exclusive with NF2 alterations. We found recurrent gene fusions and splice alterations to be frequent mechanisms for inactivation of NF2, BAP1 and SETD2. Through integrated analyses, we identified alterations in Hippo, mTOR, histone methylation, RNA helicase and p53 signaling pathways in MPMs.
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Affiliation(s)
- Raphael Bueno
- Division of Thoracic Surgery, The Lung Center and the International Mesothelioma Program, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Eric W Stawiski
- Bioinformatics and Computational Biology Department, Genentech, Inc., South San Francisco, California, USA.,Molecular Biology Department, Genentech, Inc., South San Francisco, California, USA
| | - Leonard D Goldstein
- Bioinformatics and Computational Biology Department, Genentech, Inc., South San Francisco, California, USA.,Molecular Biology Department, Genentech, Inc., South San Francisco, California, USA
| | - Steffen Durinck
- Bioinformatics and Computational Biology Department, Genentech, Inc., South San Francisco, California, USA.,Molecular Biology Department, Genentech, Inc., South San Francisco, California, USA
| | - Assunta De Rienzo
- Division of Thoracic Surgery, The Lung Center and the International Mesothelioma Program, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Zora Modrusan
- Molecular Biology Department, Genentech, Inc., South San Francisco, California, USA
| | - Florian Gnad
- Bioinformatics and Computational Biology Department, Genentech, Inc., South San Francisco, California, USA
| | - Thong T Nguyen
- Molecular Biology Department, Genentech, Inc., South San Francisco, California, USA
| | - Bijay S Jaiswal
- Molecular Biology Department, Genentech, Inc., South San Francisco, California, USA
| | - Lucian R Chirieac
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Daniele Sciaranghella
- Division of Thoracic Surgery, The Lung Center and the International Mesothelioma Program, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Nhien Dao
- Division of Thoracic Surgery, The Lung Center and the International Mesothelioma Program, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Corinne E Gustafson
- Division of Thoracic Surgery, The Lung Center and the International Mesothelioma Program, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Kiara J Munir
- Division of Thoracic Surgery, The Lung Center and the International Mesothelioma Program, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Jason A Hackney
- Bioinformatics and Computational Biology Department, Genentech, Inc., South San Francisco, California, USA
| | - Amitabha Chaudhuri
- Bioinformatics Department, MedGenome Labs, Pvt., Ltd., Narayana Health City, Bangalore, India
| | - Ravi Gupta
- Bioinformatics Department, MedGenome Labs, Pvt., Ltd., Narayana Health City, Bangalore, India
| | - Joseph Guillory
- Molecular Biology Department, Genentech, Inc., South San Francisco, California, USA
| | - Karen Toy
- Molecular Biology Department, Genentech, Inc., South San Francisco, California, USA
| | - Connie Ha
- Molecular Biology Department, Genentech, Inc., South San Francisco, California, USA
| | - Ying-Jiun Chen
- Molecular Biology Department, Genentech, Inc., South San Francisco, California, USA
| | - Jeremy Stinson
- Molecular Biology Department, Genentech, Inc., South San Francisco, California, USA
| | - Subhra Chaudhuri
- Molecular Biology Department, Genentech, Inc., South San Francisco, California, USA
| | - Na Zhang
- Molecular Biology Department, Genentech, Inc., South San Francisco, California, USA
| | - Thomas D Wu
- Bioinformatics and Computational Biology Department, Genentech, Inc., South San Francisco, California, USA
| | - David J Sugarbaker
- Division of Thoracic Surgery, Baylor College of Medicine, Houston, Texas, USA
| | - Frederic J de Sauvage
- Molecular Oncology Department, Genentech, Inc., South San Francisco, California, USA
| | - William G Richards
- Division of Thoracic Surgery, The Lung Center and the International Mesothelioma Program, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Somasekar Seshagiri
- Molecular Biology Department, Genentech, Inc., South San Francisco, California, USA
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