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M. Swamynathan M, Mathew G, Aziz A, Gordon C, Hillowe A, Wang H, Jhaveri A, Kendall J, Cox H, Giarrizzo M, Azabdaftari G, Rizzo RC, Diermeier SD, Ojima I, Bialkowska AB, Kaczocha M, Trotman LC. FABP5 Inhibition against PTEN-Mutant Therapy Resistant Prostate Cancer. Cancers (Basel) 2023; 16:60. [PMID: 38201488 PMCID: PMC10871093 DOI: 10.3390/cancers16010060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 11/20/2023] [Accepted: 12/13/2023] [Indexed: 01/12/2024] Open
Abstract
Resistance to standard of care taxane and androgen deprivation therapy (ADT) causes the vast majority of prostate cancer (PC) deaths worldwide. We have developed RapidCaP, an autochthonous genetically engineered mouse model of PC. It is driven by the loss of PTEN and p53, the most common driver events in PC patients with life-threatening diseases. As in human ADT, surgical castration of RapidCaP animals invariably results in disease relapse and death from the metastatic disease burden. Fatty Acid Binding Proteins (FABPs) are a large family of signaling lipid carriers. They have been suggested as drivers of multiple cancer types. Here we combine analysis of primary cancer cells from RapidCaP (RCaP cells) with large-scale patient datasets to show that among the 10 FABP paralogs, FABP5 is the PC-relevant target. Next, we show that RCaP cells are uniquely insensitive to both ADT and taxane treatment compared to a panel of human PC cell lines. Yet, they share an exquisite sensitivity to the small-molecule FABP5 inhibitor SBFI-103. We show that SBFI-103 is well tolerated and can strongly eliminate RCaP tumor cells in vivo. This provides a pre-clinical platform to fight incurable PC and suggests an important role for FABP5 in PTEN-deficient PC.
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Affiliation(s)
- Manojit M. Swamynathan
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA (A.J.)
- Department of Molecular and Cell Biology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Grinu Mathew
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA (A.J.)
- The Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Andrei Aziz
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA (A.J.)
| | - Chris Gordon
- Department of Anesthesiology, Stony Brook University, Stony Brook, NY 11794, USA; (C.G.); (A.H.)
| | - Andrew Hillowe
- Department of Anesthesiology, Stony Brook University, Stony Brook, NY 11794, USA; (C.G.); (A.H.)
| | - Hehe Wang
- Department of Chemistry, Stony Brook University, Stony Brook, NY 11794, USA (I.O.)
| | - Aashna Jhaveri
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA (A.J.)
| | - Jude Kendall
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA (A.J.)
| | - Hilary Cox
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA (A.J.)
| | - Michael Giarrizzo
- Department of Medicine, Stony Brook University, Stony Brook, NY 11794, USA; (M.G.); (A.B.B.)
| | - Gissou Azabdaftari
- Department of Anatomic Pathology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Robert C. Rizzo
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794, USA
- Institute of Chemical Biology and Drug Discovery, Stony Brook University, Stony Brook, NY 11794, USA
| | - Sarah D. Diermeier
- Department of Biochemistry, University of Otago, Dunedin 9016, New Zealand;
| | - Iwao Ojima
- Department of Chemistry, Stony Brook University, Stony Brook, NY 11794, USA (I.O.)
- Institute of Chemical Biology and Drug Discovery, Stony Brook University, Stony Brook, NY 11794, USA
| | - Agnieszka B. Bialkowska
- Department of Medicine, Stony Brook University, Stony Brook, NY 11794, USA; (M.G.); (A.B.B.)
- Institute of Chemical Biology and Drug Discovery, Stony Brook University, Stony Brook, NY 11794, USA
| | - Martin Kaczocha
- Department of Anesthesiology, Stony Brook University, Stony Brook, NY 11794, USA; (C.G.); (A.H.)
- Institute of Chemical Biology and Drug Discovery, Stony Brook University, Stony Brook, NY 11794, USA
| | - Lloyd C. Trotman
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA (A.J.)
- Department of Molecular and Cell Biology, Stony Brook University, Stony Brook, NY 11794, USA
- Institute of Chemical Biology and Drug Discovery, Stony Brook University, Stony Brook, NY 11794, USA
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2
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Ramírez-Mena A, Andrés-León E, Alvarez-Cubero MJ, Anguita-Ruiz A, Martinez-Gonzalez LJ, Alcala-Fdez J. Explainable artificial intelligence to predict and identify prostate cancer tissue by gene expression. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2023; 240:107719. [PMID: 37453366 DOI: 10.1016/j.cmpb.2023.107719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 06/16/2023] [Accepted: 07/08/2023] [Indexed: 07/18/2023]
Abstract
BACKGROUND AND OBJECTIVE Prostate cancer is one of the most prevalent forms of cancer in men worldwide. Traditional screening strategies such as serum PSA levels, which are not necessarily cancer-specific, or digital rectal exams, which are often inconclusive, are still the screening methods used for the disease. Some studies have focused on identifying biomarkers of the disease but none have been reported for diagnosis in routine clinical practice and few studies have provided tools to assist the pathologist in the decision-making process when analyzing prostate tissue. Therefore, a classifier is proposed to predict the occurrence of PCa that provides physicians with accurate predictions and understandable explanations. METHODS A selection of 47 genes was made based on differential expression between PCa and normal tissue, GO gene ontology as well as the literature to be used as input predictors for different machine learning methods based on eXplainable Artificial Intelligence. These methods were trained using different class-balancing strategies to build accurate classifiers using gene expression data from 550 samples from 'The Cancer Genome Atlas'. Our model was validated in four external cohorts with different ancestries, totaling 463 samples. In addition, a set of SHapley Additive exPlanations was provided to help clinicians understand the underlying reasons for each decision. RESULTS An in-depth analysis showed that the Random Forest algorithm combined with majority class downsampling was the best performing approach with robust statistical significance. Our method achieved an average sensitivity and specificity of 0.90 and 0.8 with an AUC of 0.84 across all databases. The relevance of DLX1, MYL9 and FGFR genes for PCa screening was demonstrated in addition to the important role of novel genes such as CAV2 and MYLK. CONCLUSIONS This model has shown good performance in 4 independent external cohorts of different ancestries and the explanations provided are consistent with each other and with the literature, opening a horizon for its application in clinical practice. In the near future, these genes, in combination with our model, could be applied to liquid biopsy to improve PCa screening.
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Affiliation(s)
- Alberto Ramírez-Mena
- GENYO, Centre for Genomics and Oncological Research: Pfizer -University of Granada - Andalusian Regional Government, Granada, 18016, Spain.
| | - Eduardo Andrés-León
- Institute of Parasitology and Biomedicine "López-Neyra" (IPBLN), Spanish National Research Council (CSIC), Granada, 18016, Spain.
| | - Maria Jesus Alvarez-Cubero
- GENYO, Centre for Genomics and Oncological Research: Pfizer -University of Granada - Andalusian Regional Government, Granada, 18016, Spain; Department of Biochemistry and Molecular Biology III and Immunology, University of Granada, Granada, 18071, Spain.
| | | | - Luis Javier Martinez-Gonzalez
- GENYO, Centre for Genomics and Oncological Research: Pfizer -University of Granada - Andalusian Regional Government, Granada, 18016, Spain.
| | - Jesus Alcala-Fdez
- Department of Computer Science and Artificial Intelligence, Andalusian Research Institute in Data Science and Computational Intelligence (DaSCI), University of Granada, Granada, 18071, Spain.
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3
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Baslan T, Morris JP, Zhao Z, Reyes J, Ho YJ, Tsanov KM, Bermeo J, Tian S, Zhang S, Askan G, Yavas A, Lecomte N, Erakky A, Varghese AM, Zhang A, Kendall J, Ghiban E, Chorbadjiev L, Wu J, Dimitrova N, Chadalavada K, Nanjangud GJ, Bandlamudi C, Gong Y, Donoghue MTA, Socci ND, Krasnitz A, Notta F, Leach SD, Iacobuzio-Donahue CA, Lowe SW. Ordered and deterministic cancer genome evolution after p53 loss. Nature 2022; 608:795-802. [PMID: 35978189 PMCID: PMC9402436 DOI: 10.1038/s41586-022-05082-5] [Citation(s) in RCA: 98] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Accepted: 07/06/2022] [Indexed: 11/08/2022]
Abstract
Although p53 inactivation promotes genomic instability1 and presents a route to malignancy for more than half of all human cancers2,3, the patterns through which heterogenous TP53 (encoding human p53) mutant genomes emerge and influence tumorigenesis remain poorly understood. Here, in a mouse model of pancreatic ductal adenocarcinoma that reports sporadic p53 loss of heterozygosity before cancer onset, we find that malignant properties enabled by p53 inactivation are acquired through a predictable pattern of genome evolution. Single-cell sequencing and in situ genotyping of cells from the point of p53 inactivation through progression to frank cancer reveal that this deterministic behaviour involves four sequential phases-Trp53 (encoding mouse p53) loss of heterozygosity, accumulation of deletions, genome doubling, and the emergence of gains and amplifications-each associated with specific histological stages across the premalignant and malignant spectrum. Despite rampant heterogeneity, the deletion events that follow p53 inactivation target functionally relevant pathways that can shape genomic evolution and remain fixed as homogenous events in diverse malignant populations. Thus, loss of p53-the 'guardian of the genome'-is not merely a gateway to genetic chaos but, rather, can enable deterministic patterns of genome evolution that may point to new strategies for the treatment of TP53-mutant tumours.
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Affiliation(s)
- Timour Baslan
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - John P Morris
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Zhen Zhao
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Pathology, Molecular and Cell-based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jose Reyes
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Yu-Jui Ho
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kaloyan M Tsanov
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jonathan Bermeo
- Rubinstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sha Tian
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sean Zhang
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Gokce Askan
- Rubinstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Aslihan Yavas
- Rubinstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nicolas Lecomte
- Rubinstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Amanda Erakky
- Rubinstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Anna M Varghese
- Rubinstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Amy Zhang
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Jude Kendall
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Elena Ghiban
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Lubomir Chorbadjiev
- Technical School of Electronic Systems, Technical University of Sofia, Sofia, Bulgaria
| | - Jie Wu
- Phillips Research North America, Oncology Informatics and Genomics, Cambridge, MA, USA
| | - Nevenka Dimitrova
- Phillips Research North America, Oncology Informatics and Genomics, Cambridge, MA, USA
| | - Kalyani Chadalavada
- Molecular Cytogenetics Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Gouri J Nanjangud
- Molecular Cytogenetics Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Chaitanya Bandlamudi
- Marie-Josee and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yixiao Gong
- Marie-Josee and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mark T A Donoghue
- Marie-Josee and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nicholas D Socci
- Marie-Josee and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alex Krasnitz
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Faiyaz Notta
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Steve D Leach
- Rubinstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Dartmouth Cancer Center, Hanover, NH, USA
| | | | - Scott W Lowe
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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4
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Ali A, Du Feu A, Oliveira P, Choudhury A, Bristow RG, Baena E. Prostate zones and cancer: lost in transition? Nat Rev Urol 2022; 19:101-115. [PMID: 34667303 DOI: 10.1038/s41585-021-00524-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/17/2021] [Indexed: 12/16/2022]
Abstract
Localized prostate cancer shows great clinical, genetic and environmental heterogeneity; however, prostate cancer treatment is currently guided solely by clinical staging, serum PSA levels and histology. Increasingly, the roles of differential genomics, multifocality and spatial distribution in tumorigenesis are being considered to further personalize treatment. The human prostate is divided into three zones based on its histological features: the peripheral zone (PZ), the transition zone (TZ) and the central zone (CZ). Each zone has variable prostate cancer incidence, prognosis and outcomes, with TZ prostate tumours having better clinical outcomes than PZ and CZ tumours. Molecular and cell biological studies can improve understanding of the unique molecular, genomic and zonal cell type features that underlie the differences in tumour progression and aggression between the zones. The unique biology of each zonal tumour type could help to guide individualized treatment and patient risk stratification.
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Affiliation(s)
- Amin Ali
- Prostate Oncobiology Group, Cancer Research UK Manchester Institute, The University of Manchester, Manchester, UK.,The Christie NHS Foundation Trust, Manchester Academic Health Sciences Centre, Manchester, UK
| | - Alexander Du Feu
- Prostate Oncobiology Group, Cancer Research UK Manchester Institute, The University of Manchester, Manchester, UK
| | - Pedro Oliveira
- The Christie NHS Foundation Trust, Manchester Academic Health Sciences Centre, Manchester, UK
| | - Ananya Choudhury
- The Christie NHS Foundation Trust, Manchester Academic Health Sciences Centre, Manchester, UK.,The University of Manchester, Manchester Cancer Research Centre, Manchester, UK.,Belfast-Manchester Movember Centre of Excellence, Cancer Research UK Manchester Institute, The University of Manchester, Manchester, UK
| | - Robert G Bristow
- The Christie NHS Foundation Trust, Manchester Academic Health Sciences Centre, Manchester, UK.,The University of Manchester, Manchester Cancer Research Centre, Manchester, UK.,Belfast-Manchester Movember Centre of Excellence, Cancer Research UK Manchester Institute, The University of Manchester, Manchester, UK
| | - Esther Baena
- Prostate Oncobiology Group, Cancer Research UK Manchester Institute, The University of Manchester, Manchester, UK. .,Belfast-Manchester Movember Centre of Excellence, Cancer Research UK Manchester Institute, The University of Manchester, Manchester, UK.
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5
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Abstract
Bladder cancer is the most common malignant tumour of the urinary system that is characterised by significant intra-tumoural heterogeneity. While large-scale sequencing projects have provided a preliminary understanding of tumour heterogeneity, these findings are based on the average signals obtained from the pooled populations of diverse cells. Recent advances in single-cell sequencing (SCS) technologies have been critical in this regard, opening up new ways of understanding the nuanced tumour biology by identifying distinct cellular subpopulations, dissecting the tumour microenvironment, and characterizing cellular genomic mutations. By integrating these novel insights, SCS technologies are expected to make powerful and meaningful changes to the current diagnosis and treatment of bladder cancer through the identification and usage of novel biomarkers as well as targeted therapeutics. SCS can discriminate complex heterogeneity in a large population of tumour cells and determine the key molecular properties that influence clinical outcomes. Here, we review the advances in single-cell technologies and discuss their applications in cancer research and clinical practice, with a specific focus on bladder cancer.
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6
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Tu J, Zhou Y, Tao Y, Lu N, Yang Y, Lu Z. Sensitivity to copy number variation analysis in single cell genomics. Gene 2022; 808:145995. [PMID: 34627941 DOI: 10.1016/j.gene.2021.145995] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 09/13/2021] [Accepted: 10/04/2021] [Indexed: 11/24/2022]
Abstract
While previous studies have given some guidance, the sensitivity of copy number calling in single-cell genomics is still not comprehensive. We studied the impact of sequencing depth and other factors on single-cell copy number analysis. Sequencing Data from 26 datasets were retrieved, and 2946 single cells passed the filter. Thirty-eight single cells were independently downscaled to evaluate copy number variation (CNV) detection sensitivity at different bin sizes. The sensitivity of whole genome amplification (WGA) approaches and cell types to CNV calling were evaluated using downsampling of 101 and 70 cells. Cluster analysis based on t-SNE was executed to evaluate CNV calling performance. Our results suggest 0.75× sequencing depth with moderate resolution (250 kb bin size) may be a practical guideline considering both sequencing cost and performance of copy number calling, which can be appropriately optimized based on amplification approach, cell type, and sample complexity.
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Affiliation(s)
- Jing Tu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China.
| | - Yue Zhou
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Yuhan Tao
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Na Lu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Yixuan Yang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Zuhong Lu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China.
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7
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Accurate genomic variant detection in single cells with primary template-directed amplification. Proc Natl Acad Sci U S A 2021; 118:2024176118. [PMID: 34099548 PMCID: PMC8214697 DOI: 10.1073/pnas.2024176118] [Citation(s) in RCA: 75] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Improvements in whole genome amplification (WGA) would enable new types of basic and applied biomedical research, including studies of intratissue genetic diversity that require more accurate single-cell genotyping. Here, we present primary template-directed amplification (PTA), an isothermal WGA method that reproducibly captures >95% of the genomes of single cells in a more uniform and accurate manner than existing approaches, resulting in significantly improved variant calling sensitivity and precision. To illustrate the types of studies that are enabled by PTA, we developed direct measurement of environmental mutagenicity (DMEM), a tool for mapping genome-wide interactions of mutagens with single living human cells at base-pair resolution. In addition, we utilized PTA for genome-wide off-target indel and structural variant detection in cells that had undergone CRISPR-mediated genome editing, establishing the feasibility for performing single-cell evaluations of biopsies from edited tissues. The improved precision and accuracy of variant detection with PTA overcomes the current limitations of accurate WGA, which is the major obstacle to studying genetic diversity and evolution at cellular resolution.
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8
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Erickson A, Hayes A, Rajakumar T, Verrill C, Bryant RJ, Hamdy FC, Wedge DC, Woodcock DJ, Mills IG, Lamb AD. A Systematic Review of Prostate Cancer Heterogeneity: Understanding the Clonal Ancestry of Multifocal Disease. Eur Urol Oncol 2021; 4:358-369. [PMID: 33888445 DOI: 10.1016/j.euo.2021.02.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 01/31/2021] [Accepted: 02/26/2021] [Indexed: 11/24/2022]
Abstract
CONTEXT Studies characterising genomic changes in prostate cancer (PCa) during natural progression have greatly increased our understanding of the disease. A better understanding of the evolutionary history of PCa would allow advances in diagnostics, prognostication, and novel therapies that together will improve patient outcomes. OBJECTIVE To review the molecular heterogeneity of PCa and assess recent efforts to profile intratumoural heterogeneity and clonal evolution. EVIDENCE ACQUISITION We screened a total of 1313 abstracts from PubMed published between 2009 and 2020, of which we reviewed 84 full-text articles. We excluded 49, resulting in 35 studies for qualitative analysis. EVIDENCE SYNTHESIS In studies of primary disease (16 studies, 4793 specimens), there is a lack of consensus regarding the monoclonal or polyclonal origin of primary PCa. There is no consistent mutation giving rise to primary PCa. Detailed clonal analysis of primary PCa has been limited by current techniques. By contrast, clonal relationships between PCa metastases and a potentiating clone have been consistently identified (19 studies, 732 specimens). Metastatic specimens demonstrate consistent truncal genomic aberrations that suggest monoclonal metastatic progenitors. CONCLUSIONS The relationship between the clonal dynamics of PCa and clinical outcomes needs further investigation. It is likely that this will provide a biological rationale for whether radical treatment of the primary tumour benefits patients with oligometastatic PCa. Future studies on the mutational burden in primary disease at single-cell resolution should permit the identification of clonal patterns underpinning the origin of lethal PCa. PATIENT SUMMARY Prostate cancers arise in different parts of the prostate because of DNA mutations that occur by chance at different times. These cancer cells and their origin can be tracked by DNA mapping. In this review we summarise the state of the art and outline what further science is needed to provide the missing answers.
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Affiliation(s)
- Andrew Erickson
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | - Alicia Hayes
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK; Oxford NIHR Biomedical Research Centre, University of Oxford, UK
| | - Timothy Rajakumar
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | - Clare Verrill
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK; Department of Cellular Pathology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Oxford National Institute for Health Research Biomedical Research Centre, Oxford, UK; Oxford NIHR Biomedical Research Centre, University of Oxford, UK
| | - Richard J Bryant
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK; Department of Urology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Oxford NIHR Biomedical Research Centre, University of Oxford, UK
| | - Freddie C Hamdy
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK; Department of Urology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Oxford NIHR Biomedical Research Centre, University of Oxford, UK
| | - David C Wedge
- Manchester Cancer Research Centre, University of Manchester, Manchester, UK
| | - Dan J Woodcock
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK; Oxford Big Data Institute, University of Oxford, Oxford, UK
| | - Ian G Mills
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK; Oxford NIHR Biomedical Research Centre, University of Oxford, UK
| | - Alastair D Lamb
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK; Department of Urology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Oxford NIHR Biomedical Research Centre, University of Oxford, UK.
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9
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Haffner MC, Zwart W, Roudier MP, True LD, Nelson WG, Epstein JI, De Marzo AM, Nelson PS, Yegnasubramanian S. Genomic and phenotypic heterogeneity in prostate cancer. Nat Rev Urol 2021; 18:79-92. [PMID: 33328650 PMCID: PMC7969494 DOI: 10.1038/s41585-020-00400-w] [Citation(s) in RCA: 232] [Impact Index Per Article: 77.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/05/2020] [Indexed: 02/07/2023]
Abstract
From a clinical, morphological and molecular perspective, prostate cancer is a heterogeneous disease. Primary prostate cancers are often multifocal, having topographically and morphologically distinct tumour foci. Sequencing studies have revealed that individual tumour foci can arise as clonally distinct lesions with no shared driver gene alterations. This finding demonstrates that multiple genomically and phenotypically distinct primary prostate cancers can be present in an individual patient. Lethal metastatic prostate cancer seems to arise from a single clone in the primary tumour but can exhibit subclonal heterogeneity at the genomic, epigenetic and phenotypic levels. Collectively, this complex heterogeneous constellation of molecular alterations poses obstacles for the diagnosis and treatment of prostate cancer. However, advances in our understanding of intra-tumoural heterogeneity and the development of novel technologies will allow us to navigate these challenges, refine approaches for translational research and ultimately improve patient care.
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Affiliation(s)
- Michael C. Haffner
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA, USA,Department of Pathology, University of Washington, Seattle, WA, USA,Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA,
| | - Wilbert Zwart
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | | | - Lawrence D. True
- Department of Pathology, University of Washington, Seattle, WA, USA
| | - William G. Nelson
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA,Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA,Department of Urology, James Buchanan Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jonathan I. Epstein
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA,Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA,Department of Urology, James Buchanan Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Angelo M. De Marzo
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA,Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA,Department of Urology, James Buchanan Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Peter S. Nelson
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
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10
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Zhang W, Li Y, Zou X. SCCLRR: A Robust Computational Method for Accurate Clustering Single Cell RNA-Seq Data. IEEE J Biomed Health Inform 2021; 25:247-256. [PMID: 32356764 DOI: 10.1109/jbhi.2020.2991172] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Single-cell RNA transcriptome data present a tremendous opportunity for studying the cellular heterogeneity. Identifying subpopulations based on scRNA-seq data is a hot topic in recent years, although many researchers have been focused on designing elegant computational methods for identifying new cell types; however, the performance of these methods is still unsatisfactory due to the high dimensionality, sparsity and noise of scRNA-seq data. In this study, we propose a new cell type detection method by learning a robust and accurate similarity matrix, named SCCLRR. The method simultaneously captures both global and local intrinsic properties of data based on a low rank representation (LRR) framework mathematical model. The integrated normalized Euclidean distance and cosine similarity are used to balance the intrinsic linear and nonlinear manifold of data in the local regularization term. To solve the non-convex optimization model, we present an iterative optimization procedure using the alternating direction method of multipliers (ADMM) algorithm. We evaluate the performance of the SCCLRR method on nine real scRNA-seq datasets and compare it with seven state-of-the-art methods. The simulation results show that the SCCLRR outperforms other methods and is robust and effective for clustering scRNA-seq data. (The code of SCCLRR is free available for academic https://github.com/wzhangwhu/SCCLRR).
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11
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Lin XD, Lin N, Lin TT, Wu YP, Huang P, Ke ZB, Lin YZ, Chen SH, Zheng QS, Wei Y, Xue XY, Lin RJ, Xu N. Identification of marker genes and cell subtypes in castration-resistant prostate cancer cells. J Cancer 2021; 12:1249-1257. [PMID: 33442423 PMCID: PMC7797644 DOI: 10.7150/jca.49409] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 12/01/2020] [Indexed: 12/15/2022] Open
Abstract
The diverse tumor cell populations may be the critical roles in relapse and resistance to treatment in prostate cancer patients. This study aimed to identify new marker genes and cell subtypes among castration-resistant prostate cancer (CRPC) cells. We downloaded single-cell RNA seq profiles (GSE67980) from the Gene Expression Omnibus (GEO) database. Principal component (PC) analysis and t-Distributed Stochastic Neighbor Embedding (TSNE) analysis were performed to identify marker genes. CRPC cells were clustered and annotated. GO and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses among marker genes were performed. A total of 1500 genes with larger standardized variance were obtained. The top 20 genes were demonstrated in each identified 20 PCs. PC with P-value < 0.05 was selected, including PC1, PC7, PC8, and PC14. The TSNE analysis classified cells as two clusters. The top 6 genes in cluster 0 included HBB, CCL5, SLITRK4, GZMB, BBIP1, and PF4V1. Plus, the top 6 genes in cluster 1 included MLEC, CCT8, CCT3, EPCAM, TMPRSS2, EIF4G2. The GO analysis revealed that these marker genes were mainly enriched in RNA catabolic process, translational initiation, mitochondrial inner membrane, cytosolic part, ribosome, cell adhesion molecule binding, cadherin binding, and structural constituent of ribosome. The KEGG analysis showed that these marker genes mainly enriched in metabolism associated pathways, including carbon metabolism, cysteine and methionine metabolism, propanoate metabolism, pyruvate metabolism, and citrate cycle pathways. To conclude, our results provide essential insights into the spectrum of cellular heterogeneity within human CRPC cells. These marker genes, GO terms and pathways may be critical in the development and progression of human CRPC.
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Affiliation(s)
- Xiao-Dan Lin
- Department of Urology, the First Affiliated Hospital of Fujian Medical University, Fuzhou 350005, China
| | - Ning Lin
- Department of Urology, the First Affiliated Hospital of Fujian Medical University, Fuzhou 350005, China
| | - Ting-Ting Lin
- Department of Urology, the First Affiliated Hospital of Fujian Medical University, Fuzhou 350005, China
| | - Yu-Peng Wu
- Department of Urology, the First Affiliated Hospital of Fujian Medical University, Fuzhou 350005, China
| | - Peng Huang
- Department of Urology, the First Affiliated Hospital of Fujian Medical University, Fuzhou 350005, China
| | - Zhi-Bin Ke
- Department of Urology, the First Affiliated Hospital of Fujian Medical University, Fuzhou 350005, China
| | - Yun-Zhi Lin
- Department of Urology, the First Affiliated Hospital of Fujian Medical University, Fuzhou 350005, China
| | - Shao-Hao Chen
- Department of Urology, the First Affiliated Hospital of Fujian Medical University, Fuzhou 350005, China
| | - Qing-Shui Zheng
- Department of Urology, the First Affiliated Hospital of Fujian Medical University, Fuzhou 350005, China
| | - Yong Wei
- Department of Urology, the First Affiliated Hospital of Fujian Medical University, Fuzhou 350005, China
| | - Xue-Yi Xue
- Department of Urology, the First Affiliated Hospital of Fujian Medical University, Fuzhou 350005, China
| | - Rong-Jin Lin
- Department of Nursing, the First Affiliated Hospital of Fujian Medical University, Fuzhou 350005, China
| | - Ning Xu
- Department of Urology, the First Affiliated Hospital of Fujian Medical University, Fuzhou 350005, China
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12
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Carretta C, Mallia S, Genovese E, Parenti S, Rontauroli S, Bianchi E, Fantini S, Sartini S, Tavernari L, Tagliafico E, Manfredini R. Genomic Analysis of Hematopoietic Stem Cell at the Single-Cell Level: Optimization of Cell Fixation and Whole Genome Amplification (WGA) Protocol. Int J Mol Sci 2020; 21:E7366. [PMID: 33036143 PMCID: PMC7582552 DOI: 10.3390/ijms21197366] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 09/30/2020] [Accepted: 10/03/2020] [Indexed: 12/15/2022] Open
Abstract
Single-cell genomics has become the method of choice for the study of heterogeneous cell populations and represents an elective application in defining the architecture and clonal evolution in hematological neoplasms. Reconstructing the clonal evolution of a neoplastic population therefore represents the main way to understand more deeply the pathogenesis of the neoplasm, but it is also a potential tool to understand the evolution of the tumor population with respect to its response to therapy. Pre-analytical phase for single-cell genomics analysis is crucial to obtain a cell population suitable for single-cell sorting, and whole genome amplification is required to obtain the necessary amount of DNA from a single cell in order to proceed with sequencing. Here, we evaluated the impact of different methods of cellular immunostaining, fixation and whole genome amplification on the efficiency and yield of single-cell sequencing.
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Affiliation(s)
- Chiara Carretta
- Centre for Regenerative Medicine “S. Ferrari”, University of Modena and Reggio Emilia, 41125 Modena, Italy; (C.C.); (S.M.); (E.G.); (S.P.); (S.R.); (E.B.); (S.F.); (S.S.); (L.T.)
| | - Selene Mallia
- Centre for Regenerative Medicine “S. Ferrari”, University of Modena and Reggio Emilia, 41125 Modena, Italy; (C.C.); (S.M.); (E.G.); (S.P.); (S.R.); (E.B.); (S.F.); (S.S.); (L.T.)
| | - Elena Genovese
- Centre for Regenerative Medicine “S. Ferrari”, University of Modena and Reggio Emilia, 41125 Modena, Italy; (C.C.); (S.M.); (E.G.); (S.P.); (S.R.); (E.B.); (S.F.); (S.S.); (L.T.)
| | - Sandra Parenti
- Centre for Regenerative Medicine “S. Ferrari”, University of Modena and Reggio Emilia, 41125 Modena, Italy; (C.C.); (S.M.); (E.G.); (S.P.); (S.R.); (E.B.); (S.F.); (S.S.); (L.T.)
| | - Sebastiano Rontauroli
- Centre for Regenerative Medicine “S. Ferrari”, University of Modena and Reggio Emilia, 41125 Modena, Italy; (C.C.); (S.M.); (E.G.); (S.P.); (S.R.); (E.B.); (S.F.); (S.S.); (L.T.)
| | - Elisa Bianchi
- Centre for Regenerative Medicine “S. Ferrari”, University of Modena and Reggio Emilia, 41125 Modena, Italy; (C.C.); (S.M.); (E.G.); (S.P.); (S.R.); (E.B.); (S.F.); (S.S.); (L.T.)
| | - Sebastian Fantini
- Centre for Regenerative Medicine “S. Ferrari”, University of Modena and Reggio Emilia, 41125 Modena, Italy; (C.C.); (S.M.); (E.G.); (S.P.); (S.R.); (E.B.); (S.F.); (S.S.); (L.T.)
| | - Stefano Sartini
- Centre for Regenerative Medicine “S. Ferrari”, University of Modena and Reggio Emilia, 41125 Modena, Italy; (C.C.); (S.M.); (E.G.); (S.P.); (S.R.); (E.B.); (S.F.); (S.S.); (L.T.)
| | - Lara Tavernari
- Centre for Regenerative Medicine “S. Ferrari”, University of Modena and Reggio Emilia, 41125 Modena, Italy; (C.C.); (S.M.); (E.G.); (S.P.); (S.R.); (E.B.); (S.F.); (S.S.); (L.T.)
| | - Enrico Tagliafico
- Center for Genome Research, University of Modena and Reggio Emilia, 41125 Modena, Italy;
- Department of Medical and Surgical Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Rossella Manfredini
- Centre for Regenerative Medicine “S. Ferrari”, University of Modena and Reggio Emilia, 41125 Modena, Italy; (C.C.); (S.M.); (E.G.); (S.P.); (S.R.); (E.B.); (S.F.); (S.S.); (L.T.)
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13
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Chorbadjiev L, Kendall J, Alexander J, Zhygulin V, Song J, Wigler M, Krasnitz A. Integrated Computational Pipeline for Single-Cell Genomic Profiling. JCO Clin Cancer Inform 2020; 4:464-471. [PMID: 32432904 PMCID: PMC7265781 DOI: 10.1200/cci.19.00171] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
PURPOSE Copy-number profiling of multiple individual cells from sparse sequencing may be used to reveal a detailed picture of genomic heterogeneity and clonal organization in a tissue biopsy specimen. We sought to provide a comprehensive computational pipeline for single-cell genomics, to facilitate adoption of this molecular technology for basic and translational research. MATERIALS AND METHODS The pipeline comprises software tools programmed in Python and in R and depends on Bowtie, HISAT2, Matplotlib, and Qt. It is installed and used with Anaconda. RESULTS Here we describe a complete pipeline for sparse single-cell genomic data, encompassing all steps of single-nucleus DNA copy-number profiling, from raw sequence processing to clonal structure analysis and visualization. For the latter, a specialized graphical user interface termed the single-cell genome viewer (SCGV) is provided. With applications to cancer diagnostics in mind, the SCGV allows for zooming and linkage to the University of California at Santa Cruz Genome Browser from each of the multiple integrated views of single-cell copy-number profiles. The latter can be organized by clonal substructure or by any of the associated metadata such as anatomic location and histologic characterization. CONCLUSION The pipeline is available as open-source software for Linux and OS X. Its modular structure, extensive documentation, and ease of deployment using Anaconda facilitate its adoption by researchers and practitioners of single-cell genomics. With open-source availability and Massachusetts Institute of Technology licensing, it provides a basis for additional development by the cancer bioinformatics community.
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Affiliation(s)
- Lubomir Chorbadjiev
- Technological School of Electronic Systems, Technical University of Sofia, Sofia, Bulgaria
| | - Jude Kendall
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
| | | | - Viacheslav Zhygulin
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY.,Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY
| | - Junyan Song
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY.,Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY
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14
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Baslan T, Kendall J, Volyanskyy K, McNamara K, Cox H, D'Italia S, Ambrosio F, Riggs M, Rodgers L, Leotta A, Song J, Mao Y, Wu J, Shah R, Gularte-Mérida R, Chadalavada K, Nanjangud G, Varadan V, Gordon A, Curtis C, Krasnitz A, Dimitrova N, Harris L, Wigler M, Hicks J. Novel insights into breast cancer copy number genetic heterogeneity revealed by single-cell genome sequencing. eLife 2020; 9:e51480. [PMID: 32401198 PMCID: PMC7220379 DOI: 10.7554/elife.51480] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 04/03/2020] [Indexed: 11/13/2022] Open
Abstract
Copy number alterations (CNAs) play an important role in molding the genomes of breast cancers and have been shown to be clinically useful for prognostic and therapeutic purposes. However, our knowledge of intra-tumoral genetic heterogeneity of this important class of somatic alterations is limited. Here, using single-cell sequencing, we comprehensively map out the facets of copy number alteration heterogeneity in a cohort of breast cancer tumors. Ou/var/www/html/elife/12-05-2020/backup/r analyses reveal: genetic heterogeneity of non-tumor cells (i.e. stroma) within the tumor mass; the extent to which copy number heterogeneity impacts breast cancer genomes and the importance of both the genomic location and dosage of sub-clonal events; the pervasive nature of genetic heterogeneity of chromosomal amplifications; and the association of copy number heterogeneity with clinical and biological parameters such as polyploidy and estrogen receptor negative status. Our data highlight the power of single-cell genomics in dissecting, in its many forms, intra-tumoral genetic heterogeneity of CNAs, the magnitude with which CNA heterogeneity affects the genomes of breast cancers, and the potential importance of CNA heterogeneity in phenomena such as therapeutic resistance and disease relapse.
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Affiliation(s)
- Timour Baslan
- Cold Spring Harbor LaboratoryCold Spring HarborUnited States
- Department of Molecular and Cellular Biology, Stony Brook UniversityStony BrookUnited States
| | - Jude Kendall
- Cold Spring Harbor LaboratoryCold Spring HarborUnited States
| | | | - Katherine McNamara
- Department of Genetics, Stanford University School of MedicineStanfordUnited States
| | - Hilary Cox
- Cold Spring Harbor LaboratoryCold Spring HarborUnited States
| | - Sean D'Italia
- Cold Spring Harbor LaboratoryCold Spring HarborUnited States
| | - Frank Ambrosio
- Cold Spring Harbor LaboratoryCold Spring HarborUnited States
| | - Michael Riggs
- Cold Spring Harbor LaboratoryCold Spring HarborUnited States
| | - Linda Rodgers
- Cold Spring Harbor LaboratoryCold Spring HarborUnited States
| | - Anthony Leotta
- Cold Spring Harbor LaboratoryCold Spring HarborUnited States
| | - Junyan Song
- Cold Spring Harbor LaboratoryCold Spring HarborUnited States
- Department of Applied Mathematics and Statistics, Stony Brook UniversityStony BrookUnited States
| | - Yong Mao
- Philips Research North America, Biomedical InformaticsCambridgeUnited States
| | - Jie Wu
- Philips Research North America, Biomedical InformaticsCambridgeUnited States
| | - Ronak Shah
- Center for Molecular Oncology, Memorial Sloan Kettering Cancer CenterNew YorkUnited States
| | | | - Kalyani Chadalavada
- Molecular Cytogenetics Core Facility, Memorial Sloan Kettering Cancer CenterNew YorkUnited States
| | - Gouri Nanjangud
- Molecular Cytogenetics Core Facility, Memorial Sloan Kettering Cancer CenterNew YorkUnited States
| | - Vinay Varadan
- Case Comprehensive Cancer Center, Case Western Reserve UniversityClevelandUnited States
| | | | - Christina Curtis
- Department of Genetics, Stanford University School of MedicineStanfordUnited States
| | - Alex Krasnitz
- Cold Spring Harbor LaboratoryCold Spring HarborUnited States
| | - Nevenka Dimitrova
- Philips Research North America, Biomedical InformaticsCambridgeUnited States
| | - Lyndsay Harris
- Case Comprehensive Cancer Center, Case Western Reserve UniversityClevelandUnited States
- Division of Hematology/Oncology, Department of Medicine, Case Western Reserve University School of MedicineClevelandUnited States
- Seidman Cancer Center, University Hospitals of Case WesternClevelandUnited States
| | - Michael Wigler
- Cold Spring Harbor LaboratoryCold Spring HarborUnited States
| | - James Hicks
- Cold Spring Harbor LaboratoryCold Spring HarborUnited States
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15
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Lim B, Lin Y, Navin N. Advancing Cancer Research and Medicine with Single-Cell Genomics. Cancer Cell 2020; 37:456-470. [PMID: 32289270 PMCID: PMC7899145 DOI: 10.1016/j.ccell.2020.03.008] [Citation(s) in RCA: 165] [Impact Index Per Article: 41.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 03/01/2020] [Accepted: 03/09/2020] [Indexed: 01/21/2023]
Abstract
Single-cell sequencing (SCS) has impacted many areas of cancer research and improved our understanding of intratumor heterogeneity, the tumor microenvironment, metastasis, and therapeutic resistance. The development and refinement of SCS technologies has led to massive reductions in costs, increased cell throughput, and improved reproducibility, paving the way for clinical applications. However, before translational applications can be realized, there are a number of logistical and technical challenges that must be overcome. This review discusses past cancer research studies, emerging technologies, and future clinical applications that are bound to transform cancer medicine.
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Affiliation(s)
- Bora Lim
- Department of Breast Medical Oncology, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yiyun Lin
- Department of Genetics, UT MD Anderson Cancer Center, Houston, TX 77030, USA; Graduate School of Biomedical Sciences, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Nicholas Navin
- Department of Genetics, UT MD Anderson Cancer Center, Houston, TX 77030, USA; Graduate School of Biomedical Sciences, UT MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Bioinformatics and Computational Biology, UT MD Anderson Cancer Center, Houston, TX 77030, USA.
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16
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Li S, Kendall J, Park S, Wang Z, Alexander J, Moffitt A, Ranade N, Danyko C, Gegenhuber B, Fischer S, Robinson BD, Lepor H, Tollkuhn J, Gillis J, Brouzes E, Krasnitz A, Levy D, Wigler M. Copolymerization of single-cell nucleic acids into balls of acrylamide gel. Genome Res 2019; 30:49-61. [PMID: 31727682 PMCID: PMC6961581 DOI: 10.1101/gr.253047.119] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 11/13/2019] [Indexed: 01/06/2023]
Abstract
We show the use of 5′-Acrydite oligonucleotides to copolymerize single-cell DNA or RNA into balls of acrylamide gel (BAGs). Combining this step with split-and-pool techniques for creating barcodes yields a method with advantages in cost and scalability, depth of coverage, ease of operation, minimal cross-contamination, and efficient use of samples. We perform DNA copy number profiling on mixtures of cell lines, nuclei from frozen prostate tumors, and biopsy washes. As applied to RNA, the method has high capture efficiency of transcripts and sufficient consistency to clearly distinguish the expression patterns of cell lines and individual nuclei from neurons dissected from the mouse brain. By using varietal tags (UMIs) to achieve sequence error correction, we show extremely low levels of cross-contamination by tracking source-specific SNVs. The method is readily modifiable, and we will discuss its adaptability and diverse applications.
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Affiliation(s)
- Siran Li
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Jude Kendall
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Sarah Park
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Zihua Wang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Joan Alexander
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Andrea Moffitt
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Nissim Ranade
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Cassidy Danyko
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Bruno Gegenhuber
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Stephan Fischer
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Brian D Robinson
- Department of Pathology and Laboratory Medicine, Weill Medical College of Cornell University, New York, New York 10021, USA
| | - Herbert Lepor
- Department of Urology, New York University Langone Medical Center, New York, New York 10017, USA
| | - Jessica Tollkuhn
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Jesse Gillis
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Eric Brouzes
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, New York 11794, USA
| | - Alex Krasnitz
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Dan Levy
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Michael Wigler
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
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17
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Anaparthy N, Ho YJ, Martelotto L, Hammell M, Hicks J. Single-Cell Applications of Next-Generation Sequencing. Cold Spring Harb Perspect Med 2019; 9:a026898. [PMID: 30617056 PMCID: PMC6771363 DOI: 10.1101/cshperspect.a026898] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The single cell is considered the basic unit of biology, and the pursuit of understanding how heterogeneous populations of cells can functionally coexist in tissues, organisms, microbial ecosystems, and even cancer, makes them the subject of intense study. Next-generation sequencing (NGS) of RNA and DNA has opened a new frontier of (single)-cell biology. Hundreds to millions of cells now can be assayed in parallel, providing the molecular profile of each cell in its milieu inexpensively and in a manner that can be analyzed mathematically. The goal of this article is to provide a high-level overview of single-cell sequencing for the nonexpert and show how its applications are influencing both basic and applied clinical studies in embryology, developmental genetics, and cancer.
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Affiliation(s)
- Naishitha Anaparthy
- Department of Molecular and Cellular Biology, Stony Brook University, Stony Brook, New York 11794
| | - Yu-Jui Ho
- Watson School of Biological Science, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724
| | - Luciano Martelotto
- University of Melbourne, Centre for Cancer Research, Victoria Comprehensive Cancer Centre, 3000 Victoria, Australia
| | - Molly Hammell
- Watson School of Biological Science, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724
| | - James Hicks
- Michelson Center for Convergent Biosciences, Dornsife College, University of Southern California, Los Angeles, California 90089
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18
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Prabakar RK, Xu L, Hicks J, Smith AD. SMURF-seq: efficient copy number profiling on long-read sequencers. Genome Biol 2019; 20:134. [PMID: 31287019 PMCID: PMC6615205 DOI: 10.1186/s13059-019-1732-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Accepted: 06/06/2019] [Indexed: 12/21/2022] Open
Abstract
We present SMURF-seq, a protocol to efficiently sequence short DNA molecules on a long-read sequencer by randomly ligating them to form long molecules. Applying SMURF-seq using the Oxford Nanopore MinION yields up to 30 fragments per read, providing an average of 6.2 and up to 7.5 million mappable fragments per run, increasing information throughput for read-counting applications. We apply SMURF-seq on the MinION to generate copy number profiles. A comparison with profiles from Illumina sequencing reveals that SMURF-seq attains similar accuracy. More broadly, SMURF-seq expands the utility of long-read sequencers for read-counting applications.
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Affiliation(s)
- Rishvanth K. Prabakar
- Quantitative and Computational Biology Section, Department of Biological Sciences, University of Southern California, 1050 Childs Way, Los Angeles, 90089 USA
| | - Liya Xu
- Michelson Center for Convergent Bioscience, University of Southern California, 1002 Childs Way, Los Angeles, 90089 USA
| | - James Hicks
- Michelson Center for Convergent Bioscience, University of Southern California, 1002 Childs Way, Los Angeles, 90089 USA
| | - Andrew D. Smith
- Quantitative and Computational Biology Section, Department of Biological Sciences, University of Southern California, 1050 Childs Way, Los Angeles, 90089 USA
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19
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Sun S, Chen Y, Liu Y, Shang X. A fast and efficient count-based matrix factorization method for detecting cell types from single-cell RNAseq data. BMC SYSTEMS BIOLOGY 2019; 13:28. [PMID: 30953530 PMCID: PMC6449882 DOI: 10.1186/s12918-019-0699-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Background Single-cell RNA sequencing (scRNAseq) data always involves various unwanted variables, which would be able to mask the true signal to identify cell-types. More efficient way of dealing with this issue is to extract low dimension information from high dimensional gene expression data to represent cell-type structure. In the past two years, several powerful matrix factorization tools were developed for scRNAseq data, such as NMF, ZIFA, pCMF and ZINB-WaVE. But the existing approaches either are unable to directly model the raw count of scRNAseq data or are really time-consuming when handling a large number of cells (e.g. n>500). Results In this paper, we developed a fast and efficient count-based matrix factorization method (single-cell negative binomial matrix factorization, scNBMF) based on the TensorFlow framework to infer the low dimensional structure of cell types. To make our method scalable, we conducted a series of experiments on three public scRNAseq data sets, brain, embryonic stem, and pancreatic islet. The experimental results show that scNBMF is more powerful to detect cell types and 10 - 100 folds faster than the scRNAseq bespoke tools. Conclusions In this paper, we proposed a fast and efficient count-based matrix factorization method, scNBMF, which is more powerful for detecting cell type purposes. A series of experiments were performed on three public scRNAseq data sets. The results show that scNBMF is a more powerful tool in large-scale scRNAseq data analysis. scNBMF was implemented in R and Python, and the source code are freely available at https://github.com/sqsun.
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Affiliation(s)
- Shiquan Sun
- School of Computer Science, Northwestern Polytechnical University, Xi'an, Shaanxi, 710129, People's Republic of China.,Key Laboratory of Big Data Storage and Management, Northwestern Polytechnical University, Ministry of Industry and Information Technology, Xi'an, Shaanxi, 710129, People's Republic of China.,Centre for Multidisciplinary Convergence Computing (CMCC), School of Computer Science, Northwestern Polytechnical University, Xi'an, Shaanxi, 710129, People's Republic of China.,Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yabo Chen
- School of Computer Science, Northwestern Polytechnical University, Xi'an, Shaanxi, 710129, People's Republic of China
| | - Yang Liu
- School of Computer Science, Northwestern Polytechnical University, Xi'an, Shaanxi, 710129, People's Republic of China
| | - Xuequn Shang
- School of Computer Science, Northwestern Polytechnical University, Xi'an, Shaanxi, 710129, People's Republic of China. .,Key Laboratory of Big Data Storage and Management, Northwestern Polytechnical University, Ministry of Industry and Information Technology, Xi'an, Shaanxi, 710129, People's Republic of China.
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20
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Boutros PC. The Promise and Perils of Sequencing Individual Prostate Cancer Nuclei. Eur Urol 2018; 74:560-561. [PMID: 30075977 DOI: 10.1016/j.eururo.2018.07.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2018] [Accepted: 07/19/2018] [Indexed: 11/26/2022]
Affiliation(s)
- Paul C Boutros
- Ontario Institute for Cancer Research, Toronto, Canada; Department of Pharmacology & Toxicology, University of Toronto, Toronto, Canada; Department of Medical Biophysics, University of Toronto, Toronto, Canada.
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Prostate cancer: Singled out: single-cell genomics for diagnosis. Nat Rev Urol 2017; 15:69. [PMID: 29256491 DOI: 10.1038/nrurol.2017.217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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