1
|
Pujana-Vaquerizo M, Bozal-Basterra L, Carracedo A. Metabolic adaptations in prostate cancer. Br J Cancer 2024; 131:1250-1262. [PMID: 38969865 DOI: 10.1038/s41416-024-02762-z] [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: 03/13/2024] [Revised: 06/07/2024] [Accepted: 06/11/2024] [Indexed: 07/07/2024] Open
Abstract
Prostate cancer is one of the most commonly diagnosed cancers in men and is a major cause of cancer-related deaths worldwide. Among the molecular processes that contribute to this disease, the weight of metabolism has been placed under the limelight in recent years. Tumours exhibit metabolic adaptations to comply with their biosynthetic needs. However, metabolites also play an important role in supporting cell survival in challenging environments or remodelling the tumour microenvironment, thus being recognized as a hallmark in cancer. Prostate cancer is uniquely driven by androgen receptor signalling, and this knowledge has also influenced the paths of cancer metabolism research. This review provides a comprehensive perspective on the metabolic adaptations that support prostate cancer progression beyond androgen signalling, with a particular focus on tumour cell intrinsic and extrinsic pathways.
Collapse
Affiliation(s)
- Mikel Pujana-Vaquerizo
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Spain
- Centro de Investigación Biomédica En Red de Cáncer (CIBERONC), 28029, Madrid, Spain
| | - Laura Bozal-Basterra
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Spain.
| | - Arkaitz Carracedo
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Spain.
- Centro de Investigación Biomédica En Red de Cáncer (CIBERONC), 28029, Madrid, Spain.
- Traslational Prostate Cancer Research Lab, CIC bioGUNE-Basurto, Biobizkaia Health Research Institute, Baracaldo, Spain.
- Ikerbasque, Basque Foundation for Science, Bilbao, Spain.
- Biochemistry and Molecular Biology Department, University of the Basque Country (UPV/EHU), Leioa, Spain.
| |
Collapse
|
2
|
Zhakula-Kostadinova N, Taylor AM. Patterns of Aneuploidy and Signaling Consequences in Cancer. Cancer Res 2024; 84:2575-2587. [PMID: 38924459 PMCID: PMC11325152 DOI: 10.1158/0008-5472.can-24-0169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 03/29/2024] [Accepted: 06/20/2024] [Indexed: 06/28/2024]
Abstract
Aneuploidy, or a change in the number of whole chromosomes or chromosome arms, is a near-universal feature of cancer. Chromosomes affected by aneuploidy are not random, with observed cancer-specific and tissue-specific patterns. Recent advances in genome engineering methods have allowed the creation of models with targeted aneuploidy events. These models can be used to uncover the downstream effects of individual aneuploidies on cancer phenotypes including proliferation, apoptosis, metabolism, and immune signaling. Here, we review the current state of research into the patterns of aneuploidy in cancer and their impact on signaling pathways and biological processes.
Collapse
Affiliation(s)
- Nadja Zhakula-Kostadinova
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, New York
- Department of Genetics and Development, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York
| | - Alison M Taylor
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, New York
- Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York
| |
Collapse
|
3
|
Shahrouzi P, Forouz F, Mathelier A, Kristensen VN, Duijf PHG. Copy number alterations: a catastrophic orchestration of the breast cancer genome. Trends Mol Med 2024; 30:750-764. [PMID: 38772764 DOI: 10.1016/j.molmed.2024.04.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 04/12/2024] [Accepted: 04/26/2024] [Indexed: 05/23/2024]
Abstract
Breast cancer (BCa) is a prevalent malignancy that predominantly affects women around the world. Somatic copy number alterations (CNAs) are tumor-specific amplifications or deletions of DNA segments that often drive BCa development and therapy resistance. Hence, the complex patterns of CNAs complement BCa classification systems. In addition, understanding the precise contributions of CNAs is essential for tailoring personalized treatment approaches. This review highlights how tumor evolution drives the acquisition of CNAs, which in turn shape the genomic landscapes of BCas. It also discusses advanced methodologies for identifying recurrent CNAs, studying CNAs in BCa and their clinical impact.
Collapse
Affiliation(s)
- Parastoo Shahrouzi
- Department of Medical Genetics, Institute of Basic Medical Science, Faculty of Medicine, University of Oslo and Oslo University Hospital, Oslo, Norway.
| | - Farzaneh Forouz
- School of Pharmacy, University of Queensland, Woolloongabba, Brisbane, Australia
| | - Anthony Mathelier
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, 0318 Oslo, Norway; Center for Bioinformatics, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway; Department of Medical Genetics, Institute of Clinical Medicine, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Vessela N Kristensen
- Department of Medical Genetics, Institute of Clinical Medicine, University of Oslo and Oslo University Hospital, Oslo, Norway; Division of Medicine, Department of Clinical Molecular Biology and Laboratory Science (EpiGen), Akershus University Hospital, Lørenskog, Norway; Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Pascal H G Duijf
- Department of Medical Genetics, Institute of Clinical Medicine, University of Oslo and Oslo University Hospital, Oslo, Norway; Centre for Cancer Biology, UniSA Clinical and Health Sciences, University of South Australia and SA Pathology, Adelaide, Australia.
| |
Collapse
|
4
|
Reis-Cunha JL, Pimenta-Carvalho SA, Almeida LV, Coqueiro-Dos-Santos A, Marques CA, Black JA, Damasceno J, McCulloch R, Bartholomeu DC, Jeffares DC. Ancestral aneuploidy and stable chromosomal duplication resulting in differential genome structure and gene expression control in trypanosomatid parasites. Genome Res 2024; 34:441-453. [PMID: 38604731 PMCID: PMC11067883 DOI: 10.1101/gr.278550.123] [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: 09/22/2023] [Accepted: 03/14/2024] [Indexed: 04/13/2024]
Abstract
Aneuploidy is widely observed in both unicellular and multicellular eukaryotes, usually associated with adaptation to stress conditions. Chromosomal duplication stability is a tradeoff between the fitness cost of having unbalanced gene copies and the potential fitness gained from increased dosage of specific advantageous genes. Trypanosomatids, a family of protozoans that include species that cause neglected tropical diseases, are a relevant group to study aneuploidies. Their life cycle has several stressors that could select for different patterns of chromosomal duplications and/or losses, and their nearly universal use of polycistronic transcription increases their reliance on gene expansion/contraction, as well as post-transcriptional control as mechanisms for gene expression regulation. By evaluating the data from 866 isolates covering seven trypanosomatid genera, we have revealed that aneuploidy tolerance is an ancestral characteristic of trypanosomatids but has a reduced occurrence in a specific monophyletic clade that has undergone large genomic reorganization and chromosomal fusions. We have also identified an ancient chromosomal duplication that was maintained across these parasite's speciation, named collectively as the trypanosomatid ancestral supernumerary chromosome (TASC). TASC has most genes in the same coding strand, is expressed as a disomic chromosome (even having four copies), and has increased potential for functional variation, but it purges highly deleterious mutations more efficiently than other chromosomes. The evidence of stringent control over gene expression in this chromosome suggests that these parasites have adapted to mitigate the fitness cost associated with this ancient chromosomal duplication.
Collapse
Affiliation(s)
- João L Reis-Cunha
- York Biomedical Research Institute, Department of Biology, University of York, York YO10 5DD, United Kingdom;
| | - Samuel A Pimenta-Carvalho
- Instituto de Ciências Biológicas, Departamento de Parasitologia, Universidade Federal de Minas Gerais, Belo Horizonte, 31270-901, Brazil
| | - Laila V Almeida
- Instituto de Ciências Biológicas, Departamento de Parasitologia, Universidade Federal de Minas Gerais, Belo Horizonte, 31270-901, Brazil
| | - Anderson Coqueiro-Dos-Santos
- Instituto de Ciências Biológicas, Departamento de Parasitologia, Universidade Federal de Minas Gerais, Belo Horizonte, 31270-901, Brazil
| | - Catarina A Marques
- The Wellcome Centre for Integrative Parasitology, School of Infection and Immunity, University of Glasgow, Glasgow G12 8TA, United Kingdom
| | - Jennifer A Black
- The Wellcome Centre for Integrative Parasitology, School of Infection and Immunity, University of Glasgow, Glasgow G12 8TA, United Kingdom
- Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, 14049-900, Brazil
| | - Jeziel Damasceno
- The Wellcome Centre for Integrative Parasitology, School of Infection and Immunity, University of Glasgow, Glasgow G12 8TA, United Kingdom
| | - Richard McCulloch
- The Wellcome Centre for Integrative Parasitology, School of Infection and Immunity, University of Glasgow, Glasgow G12 8TA, United Kingdom
| | - Daniella C Bartholomeu
- Instituto de Ciências Biológicas, Departamento de Parasitologia, Universidade Federal de Minas Gerais, Belo Horizonte, 31270-901, Brazil
| | - Daniel C Jeffares
- York Biomedical Research Institute, Department of Biology, University of York, York YO10 5DD, United Kingdom
| |
Collapse
|
5
|
Bhatia S, Khanna KK, Duijf PHG. Targeting chromosomal instability and aneuploidy in cancer. Trends Pharmacol Sci 2024; 45:210-224. [PMID: 38355324 DOI: 10.1016/j.tips.2024.01.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 01/18/2024] [Accepted: 01/19/2024] [Indexed: 02/16/2024]
Abstract
Cancer development and therapy resistance are driven by chromosomal instability (CIN), which causes chromosome gains and losses (i.e., aneuploidy) and structural chromosomal alterations. Technical limitations and knowledge gaps have delayed therapeutic targeting of CIN and aneuploidy in cancers. However, our toolbox for creating and studying aneuploidy in cell models has greatly expanded recently. Moreover, accumulating evidence suggests that seven conventional antimitotic chemotherapeutic drugs achieve clinical response by inducing CIN instead of mitotic arrest, although additional anticancer activities may also contribute in vivo. In this review, we discuss these recent developments. We also highlight new discoveries, which together show that 25 chromosome arm aneuploidies (CAAs) may be targetable by 36 drugs across 14 types of cancer. Collectively, these advances offer many new opportunities to improve cancer treatment.
Collapse
Affiliation(s)
- Sugandha Bhatia
- Queensland University of Technology (QUT), School of Biomedical Sciences, Centre for Genomics and Personalised Health and Centre for Biomedical Technologies at the Translational Research Institute, Woolloongabba, QLD 4102, Australia.
| | - Kum Kum Khanna
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, QLD 4006, Australia; Mater Research Institute, The University of Queensland, Translational Research Institute, Woolloongabba, QLD 4102, Australia
| | - Pascal H G Duijf
- Queensland University of Technology (QUT), School of Biomedical Sciences, Centre for Genomics and Personalised Health and Centre for Biomedical Technologies at the Translational Research Institute, Woolloongabba, QLD 4102, Australia; Centre for Cancer Biology, Clinical and Health Sciences, University of South Australia and SA Pathology, Adelaide, SA 5001, Australia; Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway; Department of Medical Genetics, Oslo University Hospital, Oslo, Norway.
| |
Collapse
|
6
|
Mansur MB, deSouza NM, Natrajan R, Abegglen LM, Schiffman JD, Greaves M. Evolutionary determinants of curability in cancer. Nat Ecol Evol 2023; 7:1761-1770. [PMID: 37620552 DOI: 10.1038/s41559-023-02159-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 07/05/2023] [Indexed: 08/26/2023]
Abstract
The emergence of drug-resistant cells, most of which have a mutated TP53 gene, prevents curative treatment in most advanced and common metastatic cancers of adults. Yet, a few, rarer malignancies, all of which are TP53 wild type, have high cure rates. In this Perspective, we discuss how common features of curable cancers offer insights into the evolutionary and developmental determinants of drug resistance. Acquired loss of TP53 protein function is the most common genetic change in cancer. This probably reflects positive selection in the context of strong ecosystem pressures including microenvironmental hypoxia. Loss of TP53's functions results in multiple fitness benefits and enhanced evolvability of cancer cells. TP53-null cells survive apoptosis, and tolerate potent oncogenic signalling, DNA damage and genetic instability. In addition, critically, they provide an expanded pool of self-renewing, or stem, cells, the primary units of evolutionary selection in cancer, making subsequent adaptation to therapeutic challenge by drug resistance highly probable. The exceptional malignancies that are curable, including the common genetic subtype of childhood acute lymphoblastic leukaemia and testicular seminoma, differ from the common adult cancers in originating prenatally from embryonic or fetal cells that are developmentally primed for TP53-dependent apoptosis. Plus, they have other genetic and phenotypic features that enable dissemination without exposure to selective pressures for TP53 loss, retaining their intrinsic drug hypersensitivity.
Collapse
Affiliation(s)
| | - Nandita M deSouza
- Division of Radiotherapy and Imaging, The Institute of Cancer Research, London, UK
- Department of Imaging, The Royal Marsden National Health Service (NHS) Foundation Trust, London, UK
| | - Rachael Natrajan
- The Breast Cancer Now Toby Robins Research Centre, Division of Breast Cancer, The Institute of Cancer Research, London, UK
| | - Lisa M Abegglen
- Department of Pediatrics and Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Joshua D Schiffman
- Department of Pediatrics and Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
- Peel Therapeutics, Inc., Salt Lake City, UT, USA
| | - Mel Greaves
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK.
| |
Collapse
|
7
|
Mansur MB, Greaves M. Convergent TP53 loss and evolvability in cancer. BMC Ecol Evol 2023; 23:54. [PMID: 37743495 PMCID: PMC10518978 DOI: 10.1186/s12862-023-02146-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 08/10/2023] [Indexed: 09/26/2023] Open
Abstract
Cancer cell populations evolve by a stepwise process involving natural selection of the fittest variants within a tissue ecosystem context and as modified by therapy. Genomic scrutiny of patient samples reveals an extraordinary diversity of mutational profiles both between patients with similar cancers and within the cancer cell population of individual patients. Does this signify highly divergent evolutionary trajectories or are there repetitive and predictable patterns?Major evolutionary innovations or adaptations in different species are frequently repeated, or convergent, reflecting both common selective pressures and constraints on optimal solutions. We argue this is true of evolving cancer cells, especially with respect to the TP53 gene. Functional loss variants in TP53 are the most common genetic change in cancer. We discuss the likely microenvironmental selective pressures involved and the profound impact this has on cell fitness, evolvability and probability of subsequent drug resistance.
Collapse
Affiliation(s)
- Marcela Braga Mansur
- Centre for Evolution and Cancer, The Institute of Cancer Research, ICR, London, UK
| | - Mel Greaves
- Centre for Evolution and Cancer, The Institute of Cancer Research, ICR, London, UK.
| |
Collapse
|
8
|
Yang X, Zhang Q, Li S, Devarajan R, Luo B, Tan Z, Wang Z, Giannareas N, Wenta T, Ma W, Li Y, Yang Y, Manninen A, Wu S, Wei GH. GATA2 co-opts TGFβ1/SMAD4 oncogenic signaling and inherited variants at 6q22 to modulate prostate cancer progression. J Exp Clin Cancer Res 2023; 42:198. [PMID: 37550764 PMCID: PMC10408074 DOI: 10.1186/s13046-023-02745-7] [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: 01/21/2023] [Accepted: 06/30/2023] [Indexed: 08/09/2023] Open
Abstract
BACKGROUND Aberrant somatic genomic alteration including copy number amplification is a hallmark of cancer genomes. We previously profiled genomic landscapes of prostate cancer (PCa), yet the underlying causal genes with prognostic potential has not been defined. It remains unclear how a somatic genomic event cooperates with inherited germline variants contribute to cancer predisposition and progression. METHODS We applied integrated genomic and clinical data, experimental models and bioinformatic analysis to identify GATA2 as a highly prevalent metastasis-associated genomic amplification in PCa. Biological roles of GATA2 in PCa metastasis was determined in vitro and in vivo. Global chromatin co-occupancy and co-regulation of GATA2 and SMAD4 was investigated by coimmunoprecipitation, ChIP-seq and RNA-seq assays. Tumor cellular assays, qRT-PCR, western blot, ChIP, luciferase assays and CRISPR-Cas9 editing methods were performed to mechanistically understand the cooperation of GATA2 with SMAD4 in promoting TGFβ1 and AR signaling and mediating inherited PCa risk and progression. RESULTS In this study, by integrated genomics and experimental analysis, we identified GATA2 as a prevalent metastasis-associated genomic amplification to transcriptionally augment its own expression in PCa. Functional experiments demonstrated that GATA2 physically interacted and cooperated with SMAD4 for genome-wide chromatin co-occupancy and co-regulation of PCa genes and metastasis pathways like TGFβ signaling. Mechanistically, GATA2 was cooperative with SMAD4 to enhance TGFβ and AR signaling pathways, and activated the expression of TGFβ1 via directly binding to a distal enhancer of TGFβ1. Strinkingly, GATA2 and SMAD4 globally mediated inherited PCa risk and formed a transcriptional complex with HOXB13 at the PCa risk-associated rs339331/6q22 enhancer, leading to increased expression of the PCa susceptibility gene RFX6. CONCLUSIONS Our study prioritizes causal genomic amplification genes with prognostic values in PCa and reveals the pivotal roles of GATA2 in transcriptionally activating the expression of its own and TGFβ1, thereby co-opting to TGFβ1/SMAD4 signaling and RFX6 at 6q22 to modulate PCa predisposition and progression.
Collapse
Affiliation(s)
- Xiayun Yang
- Disease Networks Research Unit, Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland
- Institute of Urology, The Third Affiliated Hospital of Shenzhen University (Luohu Hospital Group), Shenzhen, China
| | - Qin Zhang
- Disease Networks Research Unit, Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Shuxuan Li
- Fudan University Shanghai Cancer Center & MOE Key Laboratory of Metabolism and Molecular Medicine and Department of Biochemistry and Molecular Biology of School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai, China
| | - Raman Devarajan
- Disease Networks Research Unit, Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Binjie Luo
- Disease Networks Research Unit, Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Zenglai Tan
- Disease Networks Research Unit, Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Zixian Wang
- Fudan University Shanghai Cancer Center & MOE Key Laboratory of Metabolism and Molecular Medicine and Department of Biochemistry and Molecular Biology of School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai, China
| | - Nikolaos Giannareas
- Disease Networks Research Unit, Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Tomasz Wenta
- Disease Networks Research Unit, Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Wenlong Ma
- Institute of Urology, The Third Affiliated Hospital of Shenzhen University (Luohu Hospital Group), Shenzhen, China
| | - Yuqing Li
- Institute of Urology, The Third Affiliated Hospital of Shenzhen University (Luohu Hospital Group), Shenzhen, China
| | - Yuehong Yang
- Disease Networks Research Unit, Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Aki Manninen
- Disease Networks Research Unit, Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland.
| | - Song Wu
- Institute of Urology, The Third Affiliated Hospital of Shenzhen University (Luohu Hospital Group), Shenzhen, China.
- Institute of Urology, South China Hospital of Shenzhen University, Shenzhen, China.
| | - Gong-Hong Wei
- Disease Networks Research Unit, Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland.
- Fudan University Shanghai Cancer Center & MOE Key Laboratory of Metabolism and Molecular Medicine and Department of Biochemistry and Molecular Biology of School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai, China.
| |
Collapse
|
9
|
Pompei S, Cosentino Lagomarsino M. A fitness trade-off explains the early fate of yeast aneuploids with chromosome gains. Proc Natl Acad Sci U S A 2023; 120:e2211687120. [PMID: 37018197 PMCID: PMC10104565 DOI: 10.1073/pnas.2211687120] [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: 07/07/2022] [Accepted: 02/19/2023] [Indexed: 04/06/2023] Open
Abstract
The early development of aneuploidy from an accidental chromosome missegregation shows contrasting effects. On the one hand, it is associated with significant cellular stress and decreased fitness. On the other hand, it often carries a beneficial effect and provides a quick (but typically transient) solution to external stress. These apparently controversial trends emerge in several experimental contexts, particularly in the presence of duplicated chromosomes. However, we lack a mathematical evolutionary modeling framework that comprehensively captures these trends from the mutational dynamics and the trade-offs involved in the early stages of aneuploidy. Here, focusing on chromosome gains, we address this point by introducing a fitness model where a fitness cost of chromosome duplications is contrasted by a fitness advantage from the dosage of specific genes. The model successfully captures the experimentally measured probability of emergence of extra chromosomes in a laboratory evolution setup. Additionally, using phenotypic data collected in rich media, we explored the fitness landscape, finding evidence supporting the existence of a per-gene cost of extra chromosomes. Finally, we show that the substitution dynamics of our model, evaluated in the empirical fitness landscape, explains the relative abundance of duplicated chromosomes observed in yeast population genomics data. These findings lay a firm framework for the understanding of the establishment of newly duplicated chromosomes, providing testable quantitative predictions for future observations.
Collapse
Affiliation(s)
- Simone Pompei
- IFOM ETS (Ente del Terzo Settore) - The AIRC (Associazione Italiana per la Ricerca sul Cancro) Institute of Molecular Oncology, Milano20139, Italy
| | - Marco Cosentino Lagomarsino
- IFOM ETS (Ente del Terzo Settore) - The AIRC (Associazione Italiana per la Ricerca sul Cancro) Institute of Molecular Oncology, Milano20139, Italy
- Dipartimento di Fisica, Università degli Studi di Milano, Milano20133, Italy
- Istituto Nazionale di Fisica Nucleare (INFN) sezione di Milano, Milano20133, Italy
| |
Collapse
|
10
|
Chacon-Barahona JA, MacKeigan JP, Lanning NJ. Unique Metabolic Contexts Sensitize Cancer Cells and Discriminate between Glycolytic Tumor Types. Cancers (Basel) 2023; 15:cancers15041158. [PMID: 36831501 PMCID: PMC9953999 DOI: 10.3390/cancers15041158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 02/06/2023] [Accepted: 02/08/2023] [Indexed: 02/15/2023] Open
Abstract
Cancer cells utilize variable metabolic programs in order to maintain homeostasis in response to environmental challenges. To interrogate cancer cell reliance on glycolytic programs under different nutrient availabilities, we analyzed a gene panel containing all glycolytic genes as well as pathways associated with glycolysis. Using this gene panel, we analyzed the impact of an siRNA library on cellular viability in cells containing only glucose or only pyruvate as the major bioenergetic nutrient source. From these panels, we aimed to identify genes that elicited conserved and glycolysis-dependent changes in cellular bioenergetics across glycolysis-promoting and OXPHOS-promoting conditions. To further characterize gene sets within this panel and identify similarities and differences amongst glycolytic tumor RNA-seq profiles across a pan-cancer cohort, we then used unsupervised statistical classification of RNA-seq profiles for glycolytic cancers and non-glycolytic cancer types. Here, Kidney renal clear cell carcinoma (KIRC); Head and Neck squamous cell carcinoma (HNSC); and Lung squamous cell carcinoma (LUSC) defined the glycolytic cancer group, while Prostate adenocarcinoma (PRAD), Thyroid carcinoma (THCA), and Thymoma (THYM) defined the non-glycolytic cancer group. These groups were defined based on glycolysis scoring from previous studies, where KIRC, HNSC, and LUSC had the highest glycolysis scores, meanwhile, PRAD, THCA, and THYM had the lowest. Collectively, these results aimed to identify multi-omic profiles across cancer types with demonstrated variably glycolytic rates. Our analyses provide further support for strategies aiming to classify tumors by metabolic phenotypes in order to therapeutically target tumor-specific vulnerabilities.
Collapse
Affiliation(s)
| | - Jeffrey P. MacKeigan
- Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA
- Department of Cell Biology, Van Andel Research Institute, Grand Rapids, MI 49503, USA
- Correspondence: (J.P.M.); (N.J.L.)
| | - Nathan J. Lanning
- Department of Biological Sciences, California State University, Los Angeles, CA 90032, USA
- Correspondence: (J.P.M.); (N.J.L.)
| |
Collapse
|
11
|
van den Bosch T, Derks S, Miedema DM. Chromosomal Instability, Selection and Competition: Factors That Shape the Level of Karyotype Intra-Tumor Heterogeneity. Cancers (Basel) 2022; 14:4986. [PMID: 36291770 PMCID: PMC9600040 DOI: 10.3390/cancers14204986] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 10/07/2022] [Accepted: 10/09/2022] [Indexed: 12/03/2022] Open
Abstract
Intra-tumor heterogeneity (ITH) is a pan-cancer predictor of survival, with high ITH being correlated to a dismal prognosis. The level of ITH is, hence, a clinically relevant characteristic of a malignancy. ITH of karyotypes is driven by chromosomal instability (CIN). However, not all new karyotypes generated by CIN are viable or competitive, which limits the amount of ITH. Here, we review the cellular processes and ecological properties that determine karyotype ITH. We propose a framework to understand karyotype ITH, in which cells with new karyotypes emerge through CIN, are selected by cell intrinsic and cell extrinsic selective pressures, and propagate through a cancer in competition with other malignant cells. We further discuss how CIN modulates the cell phenotype and immune microenvironment, and the implications this has for the subsequent selection of karyotypes. Together, we aim to provide a comprehensive overview of the biological processes that shape the level of karyotype heterogeneity.
Collapse
Affiliation(s)
- Tom van den Bosch
- Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Cancer Center Amsterdam and Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam University Medical Centers—Location AMC, 1105 AZ Amsterdam, The Netherlands
- Oncode Institute, 1105 AZ Amsterdam, The Netherlands
| | - Sarah Derks
- Oncode Institute, 1105 AZ Amsterdam, The Netherlands
- Department of Medical Oncology, Amsterdam University Medical Centers—Location VUmc, 1081 HV Amsterdam, The Netherlands
| | - Daniël M. Miedema
- Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Cancer Center Amsterdam and Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam University Medical Centers—Location AMC, 1105 AZ Amsterdam, The Netherlands
- Oncode Institute, 1105 AZ Amsterdam, The Netherlands
| |
Collapse
|
12
|
Markowska M, Cąkała T, Miasojedow B, Aybey B, Juraeva D, Mazur J, Ross E, Staub E, Szczurek E. CONET: copy number event tree model of evolutionary tumor history for single-cell data. Genome Biol 2022; 23:128. [PMID: 35681161 PMCID: PMC9185904 DOI: 10.1186/s13059-022-02693-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 05/23/2022] [Indexed: 11/10/2022] Open
Abstract
Copy number alterations constitute important phenomena in tumor evolution. Whole genome single-cell sequencing gives insight into copy number profiles of individual cells, but is highly noisy. Here, we propose CONET, a probabilistic model for joint inference of the evolutionary tree on copy number events and copy number calling. CONET employs an efficient, regularized MCMC procedure to search the space of possible model structures and parameters. We introduce a range of model priors and penalties for efficient regularization. CONET reveals copy number evolution in two breast cancer samples, and outperforms other methods in tree reconstruction, breakpoint identification and copy number calling.
Collapse
Affiliation(s)
- Magda Markowska
- University of Warsaw, Faculty of Mathematics, Informatics and Mechanics, Banacha 2, Warsaw, Poland
- Medical University of Warsaw, Postgraduate School of Molecular Medicine, Ks. Trojdena 2a Street, Warsaw, Poland
| | - Tomasz Cąkała
- University of Warsaw, Faculty of Mathematics, Informatics and Mechanics, Banacha 2, Warsaw, Poland
| | - BłaŻej Miasojedow
- University of Warsaw, Faculty of Mathematics, Informatics and Mechanics, Banacha 2, Warsaw, Poland
| | - Bogac Aybey
- Merck Healthcare KGaA, Translational Medicine, Oncology Bioinformatics, Frankfurter Str. 250, Darmstadt, 64293 Germany
| | - Dilafruz Juraeva
- Merck Healthcare KGaA, Translational Medicine, Oncology Bioinformatics, Frankfurter Str. 250, Darmstadt, 64293 Germany
| | - Johanna Mazur
- Merck Healthcare KGaA, Translational Medicine, Oncology Bioinformatics, Frankfurter Str. 250, Darmstadt, 64293 Germany
| | - Edith Ross
- Merck Healthcare KGaA, Translational Medicine, Oncology Bioinformatics, Frankfurter Str. 250, Darmstadt, 64293 Germany
| | - Eike Staub
- Merck Healthcare KGaA, Translational Medicine, Oncology Bioinformatics, Frankfurter Str. 250, Darmstadt, 64293 Germany
| | - Ewa Szczurek
- University of Warsaw, Faculty of Mathematics, Informatics and Mechanics, Banacha 2, Warsaw, Poland
| |
Collapse
|
13
|
Moiso E, Provero P. Cancer Metabolic Subtypes and Their Association with Molecular and Clinical Features. Cancers (Basel) 2022; 14:cancers14092145. [PMID: 35565274 PMCID: PMC9104370 DOI: 10.3390/cancers14092145] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 04/19/2022] [Accepted: 04/21/2022] [Indexed: 01/27/2023] Open
Abstract
Simple Summary The metabolic alterations characteristic of cancer cells play a significant role in tumors’ natural history and response to therapy. Recent technological advances have allowed the production of unprecedented amounts of data on many types of cancers. We exploited the most comprehensive collection of such data, The Cancer Genome Atlas (TCGA), to systematically investigate the associations between metabolic alterations and other tumor features. We used sets of genes known to be associated with specific metabolic pathways to classify patients into “metabolic subtypes”. Then, we systematically looked for associations between the metabolic subtypes and other tumor features, including histological classification, patient survival, and genome alterations. Our results, while correlative in nature, can provide a guide to the formulation of specific mechanistic hypotheses to be tested experimentally so as to improve our understanding of the biology of cancer and our ability to tailor therapeutic interventions to the specific features of each patient. Abstract The alterations of metabolic pathways in cancer have been investigated for many years, beginning long before the discovery of the role of oncogenes and tumor suppressors, and the last few years have witnessed renewed interest in this topic. Large-scale molecular and clinical data on tens of thousands of samples allow us to tackle the problem from a general point of view. Here, we show that transcriptomic profiles of tumors can be exploited to define metabolic cancer subtypes, which can be systematically investigated for associations with other molecular and clinical data. We find thousands of significant associations between metabolic subtypes and molecular features such as somatic mutations, structural variants, epigenetic modifications, protein abundance and activation, and with clinical/phenotypic data, including survival probability, tumor grade, and histological types, which we make available to the community in a dedicated web resource. Our work provides a methodological framework and a rich database of statistical associations, which will contribute to the understanding of the role of metabolic alterations in cancer and to the development of precision therapeutic strategies.
Collapse
Affiliation(s)
- Enrico Moiso
- Department of Molecular Biotechnology and Health Sciences, University of Turin, 10126 Turin, Italy
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Correspondence: (E.M.); (P.P.)
| | - Paolo Provero
- Department of Neurosciences “Rita Levi Montalcini”, University of Turin, 10126 Turin, Italy
- Center for Omics Sciences, San Raffaele Scientific Institute IRCSS, 20132 Milan, Italy
- Correspondence: (E.M.); (P.P.)
| |
Collapse
|
14
|
Schiavoni F, Zuazua-Villar P, Roumeliotis TI, Benstead-Hume G, Pardo M, Pearl FMG, Choudhary JS, Downs JA. Aneuploidy tolerance caused by BRG1 loss allows chromosome gains and recovery of fitness. Nat Commun 2022; 13:1731. [PMID: 35365638 PMCID: PMC8975814 DOI: 10.1038/s41467-022-29420-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 03/16/2022] [Indexed: 11/17/2022] Open
Abstract
Aneuploidy results in decreased cellular fitness in many species and model systems. However, aneuploidy is commonly found in cancer cells and often correlates with aggressive growth, suggesting that the impact of aneuploidy on cellular fitness is context dependent. The BRG1 (SMARCA4) subunit of the SWI/SNF chromatin remodelling complex is frequently lost in cancer. Here, we use a chromosomally stable cell line to test the effect of BRG1 loss on the evolution of aneuploidy. BRG1 deletion leads to an initial loss of fitness in this cell line that improves over time. Notably, we find increased tolerance to aneuploidy immediately upon loss of BRG1, and the fitness recovery over time correlates with chromosome gain. These data show that BRG1 loss creates an environment where karyotype changes can be explored without a fitness penalty. At least in some genetic backgrounds, therefore, BRG1 loss can affect the progression of tumourigenesis through tolerance of aneuploidy.
Collapse
Affiliation(s)
- Federica Schiavoni
- Epigenetics and Genome Stability Team, The Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB, UK
| | - Pedro Zuazua-Villar
- Epigenetics and Genome Stability Team, The Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB, UK
| | - Theodoros I Roumeliotis
- Functional Proteomics Team, The Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB, UK
| | - Graeme Benstead-Hume
- Functional Proteomics Team, The Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB, UK
- Bioinformatics Group, School of Life Sciences, University of Sussex, Falmer, Brighton, BN1 9QJ, UK
| | - Mercedes Pardo
- Functional Proteomics Team, The Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB, UK
| | - Frances M G Pearl
- Bioinformatics Group, School of Life Sciences, University of Sussex, Falmer, Brighton, BN1 9QJ, UK
| | - Jyoti S Choudhary
- Functional Proteomics Team, The Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB, UK
| | - Jessica A Downs
- Epigenetics and Genome Stability Team, The Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB, UK.
| |
Collapse
|
15
|
Mashat RM, Zielinska HA, Holly JMP, Perks CM. A Role for ER-Beta in the Effects of Low-Density Lipoprotein Cholesterol and 27-Hydroxycholesterol on Breast Cancer Progression: Involvement of the IGF Signalling Pathway? Cells 2021; 11:94. [PMID: 35011656 PMCID: PMC8749996 DOI: 10.3390/cells11010094] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 12/13/2021] [Accepted: 12/16/2021] [Indexed: 02/07/2023] Open
Abstract
Cholesterol-in particular, high levels of low-density lipoprotein (LDL) and its metabolite, 27-hydroxycholesterol (27-OHC)-is correlated with increases in the risks of breast cancer and obesity. Although the high expression of LDL/27-OHC has been reported in breast cancer, its effects and mechanism of action remain to be fully elucidated. In this study, we found that the effects of LDL on cell proliferation were mediated by the activation of the cytochrome P450 enzyme, sterol 27 hydroxylase, and cholesterol 27-hydroxylase (CYP27A1) in both ER-α-positive and ER-α-negative breast cancer cells. We found that treatment with 27-OHC only increased cell growth in oestrogen receptor-α (ER-α)-positive breast cancer cells in an ER-α-dependent manner, but, interestingly, the effects of 27-OHC on cell migration and invasion were independent of ER-α. Using ER-α-negative MDA-MB-231 cells, we found that 27-OHC similarly promoted cell invasion and migration, and this was mediated by oestrogen receptor β (ER-β). These results suggest that 27-OHC promotes breast cancer cell proliferation in ER-α-positive breast cancer cells via ER-α, but migration and invasion are mediated via ER-β in ER-α positive and negative cell lines. The addition of LDL/27OHC increased the production of IGF-I and the abundance of IGF-IR in TNBC. We further found that modulating ER-β using an agonist or antagonist increased or decreased, respectively, levels of the IGF-I and EGF receptors in TNBC. The inhibition of the insulin-like growth factor receptor blocked the effects of cholesterol on cell growth and the migration of TNBC. Using TCGA and METABRIC microarray expression data from invasive breast cancer carcinomas, we also observed that higher levels of ER-beta were associated with higher levels of IGF-IR. Thus, this study shows novel evidence that ER-β is central to the effects of LDL/27OHC on invasion, migration, and the IGF and EGF axes. Our data suggest that targeting ER-β in TNBC could be an alternative approach for downregulating IGF/EGF signalling and controlling the impact of LDL in breast cancer patients.
Collapse
Affiliation(s)
| | | | | | - Claire M. Perks
- IGFs & Metabolic Endocrinology Group, Translational Health Sciences, Bristol Medical School, Learning & Research Building, Southmead Hospital, Bristol BS10 5NB, UK; (R.M.M.); (H.A.Z.); (J.M.P.H.)
| |
Collapse
|
16
|
Šimčíková D, Gardáš D, Hložková K, Hruda M, Žáček P, Rob L, Heneberg P. Loss of hexokinase 1 sensitizes ovarian cancer to high-dose metformin. Cancer Metab 2021; 9:41. [PMID: 34895333 PMCID: PMC8666047 DOI: 10.1186/s40170-021-00277-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 11/16/2021] [Indexed: 02/06/2023] Open
Abstract
Background Hexokinases (HKs) are well-studied enzymes catalyzing the first step of glycolysis. However, non-canonical regulatory roles of HKs are still incompletely understood. Here, we hypothesized that HKs comprise one of the missing links between high-dose metformin and the inhibition of the respiratory chain in cancer. Methods We tested the isoenzyme-specific regulatory roles of HKs in ovarian cancer cells by examining the effects of the deletions of HK1 and HK2 in TOV-112D ovarian adenocarcinoma cells. We reverted these effects by re-introducing wild-type HK1 and HK2, and we compared the HK1 revertant with the knock-in of catalytically dead HK1 p.D656A. We subjected these cells to a battery of metabolic and proliferation assays and targeted GC×GC-MS metabolomics. Results We found that the HK1 depletion (but not the HK2 depletion) sensitized ovarian cancer cells to high-dose metformin during glucose starvation. We confirmed that this newly uncovered role of HK1 is glycolysis-independent by the introduction of the catalytically dead HK1. The expression of catalytically dead HK1 stimulated similar changes in levels of TCA intermediates, aspartate and cysteine, and in glutamate as were induced by the HK2 deletion. In contrast, HK1 deletion increased the levels of branched amino acids; this effect was completely eliminated by the expression of catalytically dead HK1. Furthermore, HK1 revertants but not HK2 revertants caused a strong increase of NADPH/NADP ratios independently on the presence of glucose or metformin. The HK1 deletion (but not HK2 deletion) suppressed the growth of xenotransplanted ovarian cancer cells and nearly abolished the tumor growth when the mice were fed the glucose-free diet. Conclusions We provided the evidence that HK1 is involved in the so far unknown glycolysis-independent HK1–metformin axis and influences metabolism even in glucose-free conditions. Supplementary Information The online version contains supplementary material available at 10.1186/s40170-021-00277-2.
Collapse
Affiliation(s)
- Daniela Šimčíková
- Third Faculty of Medicine, Charles University, Ruská 87, CZ-100 00, Prague, Czech Republic
| | - Dominik Gardáš
- Third Faculty of Medicine, Charles University, Ruská 87, CZ-100 00, Prague, Czech Republic
| | - Kateřina Hložková
- CLIP - Childhood Leukaemia Investigation Prague, Prague, Czech Republic.,Department of Pediatric Hematology and Oncology, Second Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Martin Hruda
- Third Faculty of Medicine, Charles University, Ruská 87, CZ-100 00, Prague, Czech Republic.,University Hospital Kralovské Vinohrady, Prague, Czech Republic
| | - Petr Žáček
- Faculty of Science, BIOCEV, Charles University, Vestec, Czech Republic
| | - Lukáš Rob
- Third Faculty of Medicine, Charles University, Ruská 87, CZ-100 00, Prague, Czech Republic.,University Hospital Kralovské Vinohrady, Prague, Czech Republic
| | - Petr Heneberg
- Third Faculty of Medicine, Charles University, Ruská 87, CZ-100 00, Prague, Czech Republic.
| |
Collapse
|
17
|
Andor N, Altrock PM, Jain N, Gomes AP. Tipping cancer cells over the edge: the context-dependent cost of high ploidy. Cancer Res 2021; 82:741-748. [PMID: 34785577 DOI: 10.1158/0008-5472.can-21-2794] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 09/27/2021] [Accepted: 11/10/2021] [Indexed: 11/16/2022]
Abstract
Tetraploidy is an aneuploidy-permissive condition that can fuel tumorgenesis. The tip-over hypothesis of cytotoxic therapy-sensitivity proposes that therapy is effective if it pushes a cell's aneuploidy above a viable tipping point. But elevated aneuploidy alone may not account for this tipping point. Tissue micro-environments (TMEs) that lack sufficient resources to support tetraploid cells can explain the fitness cost of aneuploidy. Raw materials needed to generate deoxynucleotides, the building blocks of DNA, are candidate rate-limiting factors for the evolution of high-ploidy cancer cells. Understanding the resource cost of high ploidy is key to uncover its therapeutic vulnerabilities across tissue sites with versatile energy supplies.
Collapse
Affiliation(s)
- Noemi Andor
- Integrated Mathematical Oncology, Moffitt Cancer Center
| | - Philipp M Altrock
- Department of Evolutionary Theory, Max Planck Institute for Evolutionary Biology
| | | | - Ana P Gomes
- Molecular Oncology, H. Lee Moffitt Cancer Center & Research Institute
| |
Collapse
|
18
|
Critical evaluation of CNA estimators for DNA data using matching confidence masks and WGS technology. Biomed Signal Process Control 2021. [DOI: 10.1016/j.bspc.2021.103004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
|
19
|
Joly JH, Lowry WE, Graham NA. Differential Gene Set Enrichment Analysis: a statistical approach to quantify the relative enrichment of two gene sets. Bioinformatics 2021; 36:5247-5254. [PMID: 32692836 DOI: 10.1093/bioinformatics/btaa658] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Revised: 06/24/2020] [Accepted: 07/15/2020] [Indexed: 01/30/2023] Open
Abstract
MOTIVATION Gene Set Enrichment Analysis (GSEA) is an algorithm widely used to identify statistically enriched gene sets in transcriptomic data. However, GSEA cannot examine the enrichment of two gene sets or pathways relative to one another. Here we present Differential Gene Set Enrichment Analysis (DGSEA), an adaptation of GSEA that quantifies the relative enrichment of two gene sets. RESULTS After validating the method using synthetic data, we demonstrate that DGSEA accurately captures the hypoxia-induced coordinated upregulation of glycolysis and downregulation of oxidative phosphorylation. We also show that DGSEA is more predictive than GSEA of the metabolic state of cancer cell lines, including lactate secretion and intracellular concentrations of lactate and AMP. Finally, we demonstrate the application of DGSEA to generate hypotheses about differential metabolic pathway activity in cellular senescence. Together, these data demonstrate that DGSEA is a novel tool to examine the relative enrichment of gene sets in transcriptomic data. AVAILABILITY AND IMPLEMENTATION DGSEA software and tutorials are available at https://jamesjoly.github.io/DGSEA/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- James H Joly
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, CA 90089, USA
| | - William E Lowry
- Department of Molecular, Cell, and Developmental Biology, Los Angeles, Los Angeles, CA 90095, USA.,Broad Center for Regenerative Medicine, Los Angeles, Los Angeles, CA 90095, USA.,Division of Dermatology, David Geffen School of Medicine, Los Angeles, Los Angeles, CA 90095, USA.,Molecular Biology Institute, Los Angeles, Los Angeles, CA 90095, USA.,Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Nicholas A Graham
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, CA 90089, USA.,Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90089, USA
| |
Collapse
|
20
|
Hirsch D, Hardt J, Sauer C, Heselmeyer-Hadded K, Witt SH, Kienle P, Ried T, Gaiser T. Molecular characterization of ulcerative colitis-associated colorectal carcinomas. Mod Pathol 2021; 34:1153-1166. [PMID: 33318582 PMCID: PMC8154647 DOI: 10.1038/s41379-020-00722-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Revised: 10/14/2020] [Accepted: 10/28/2020] [Indexed: 12/15/2022]
Abstract
Patients with ulcerative colitis (UC) are at increased risk for developing colorectal cancer (CRC). In contrast to sporadic colorectal tumorigenesis, TP53 mutations occur early in the progression from inflamed colonic epithelium to dysplasia to CRC, and are sometimes readily detectable in inflamed, (yet) non-dysplastic mucosa. Here, we analyzed formalin-fixed paraffin-embedded tissue samples from 19 patients with long-standing UC (median 18 years, range 3 to 34) who had developed CRC as a consequence of chronic inflammation of the large bowel. We performed microsatellite instability testing, copy number analysis by array-based comparative genomic hybridization, mutation analysis by targeted next generation sequencing (48-gene panel) and TP53 immunostaining. The results were compared to The Cancer Genome Atlas (TCGA) data on sporadic CRC. All UC-CRC lesions in our cohort were microsatellite stable. Overall, genomic imbalances of UC-CRCs showed patterns of chromosomal aneuploidies characteristic for sporadic CRC with the exception of gains of chromosome arm 5p (12 of 23 UC-CRC, 52%), which are rare in sporadic CRCs from TCGA (21 of 144, 15%; FDR adjusted P = 0.006). UC-CRCs showed a predilection for TP53 alterations, which was the most frequently mutated gene in our cohort (20 of 23, 87%). Interestingly, spatially separated tumor lesions from individual patients tended to harbor distinct TP53 mutations. Similar to CRCs arising in a background of Crohn's colitis, the genetic landscape of UC-CRCs was characterized by TP53 mutations and chromosomal aneuploidies including gains of chromosome arm 5p. Both alterations harbor the potential for early detection in precursor lesions, thus complementing morphologic diagnosis.
Collapse
Affiliation(s)
- Daniela Hirsch
- Institute of Pathology, University Medical Center Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany.
- Cancer Genomics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
| | - Julia Hardt
- Department of Surgery, University Medical Center Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Christian Sauer
- Institute of Pathology, University Medical Center Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Kerstin Heselmeyer-Hadded
- Cancer Genomics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Stephanie H Witt
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Peter Kienle
- General and Visceral Surgery, Theresienkrankenhaus and St. Hedwig-Klinik GmbH, Mannheim, Germany
| | - Thomas Ried
- Cancer Genomics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Timo Gaiser
- Institute of Pathology, University Medical Center Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| |
Collapse
|
21
|
Patkar S, Heselmeyer-Haddad K, Auslander N, Hirsch D, Camps J, Bronder D, Brown M, Chen WD, Lokanga R, Wangsa D, Wangsa D, Hu Y, Lischka A, Braun R, Emons G, Ghadimi BM, Gaedcke J, Grade M, Montagna C, Lazebnik Y, Difilippantonio MJ, Habermann JK, Auer G, Ruppin E, Ried T. Hard wiring of normal tissue-specific chromosome-wide gene expression levels is an additional factor driving cancer type-specific aneuploidies. Genome Med 2021; 13:93. [PMID: 34034815 PMCID: PMC8147418 DOI: 10.1186/s13073-021-00905-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 05/06/2021] [Indexed: 12/12/2022] Open
Abstract
Background Many carcinomas have recurrent chromosomal aneuploidies specific to the tissue of tumor origin. The reason for this specificity is not completely understood. Methods In this study, we looked at the frequency of chromosomal arm gains and losses in different cancer types from the The Cancer Genome Atlas (TCGA) and compared them to the mean gene expression of each chromosome arm in corresponding normal tissues of origin from the Genotype-Tissue Expression (GTEx) database, in addition to the distribution of tissue-specific oncogenes and tumor suppressors on different chromosome arms. Results This analysis revealed a complex picture of factors driving tumor karyotype evolution in which some recurrent chromosomal copy number reflect the chromosome arm-wide gene expression levels of the their normal tissue of tumor origin. Conclusions We conclude that the cancer type-specific distribution of chromosomal arm gains and losses is potentially “hardwiring” gene expression levels characteristic of the normal tissue of tumor origin, in addition to broadly modulating the expression of tissue-specific tumor driver genes. Supplementary Information The online version contains supplementary material available at 10.1186/s13073-021-00905-y.
Collapse
Affiliation(s)
- Sushant Patkar
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA.,Department of Computer Science, University of Maryland, College Park, USA
| | - Kerstin Heselmeyer-Haddad
- Section of Cancer Genomics, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Noam Auslander
- Department of Computer Science, University of Maryland, College Park, USA.,National Center for Biotechnology Information, NIH, Bethesda, MD, 20892, USA
| | - Daniela Hirsch
- Section of Cancer Genomics, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Jordi Camps
- Gastrointestinal and Pancreatic Oncology Team, Institut D'Investigacions Biomèdiques August Pi i Sunyer, (IDIBAPS), Hospital Clínic of Barcelona, CIBEREHD, 08036, Barcelona, Spain
| | - Daniel Bronder
- Section of Cancer Genomics, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Markus Brown
- Section of Cancer Genomics, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Wei-Dong Chen
- Section of Cancer Genomics, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Rachel Lokanga
- Section of Cancer Genomics, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Darawalee Wangsa
- Section of Cancer Genomics, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Danny Wangsa
- Section of Cancer Genomics, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Yue Hu
- Section of Cancer Genomics, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Annette Lischka
- Section of Cancer Genomics, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA.,Section for Translational Surgical Oncology and Biobanking, Department of Surgery, University Medical Center Schleswig Holstein, Campus Lübeck, Lübeck, Germany
| | - Rüdiger Braun
- Section of Cancer Genomics, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA.,Section for Translational Surgical Oncology and Biobanking, Department of Surgery, University Medical Center Schleswig Holstein, Campus Lübeck, Lübeck, Germany
| | - Georg Emons
- Section of Cancer Genomics, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA.,Department of General, Visceral and Pediatric Surgery, University Medical Center, Göttingen, Germany
| | - B Michael Ghadimi
- Department of General, Visceral and Pediatric Surgery, University Medical Center, Göttingen, Germany
| | - Jochen Gaedcke
- Department of General, Visceral and Pediatric Surgery, University Medical Center, Göttingen, Germany
| | - Marian Grade
- Department of General, Visceral and Pediatric Surgery, University Medical Center, Göttingen, Germany
| | - Cristina Montagna
- Department of Genetics and Pathology, Albert Einstein College of Medicine, Bronx, NY, USA
| | | | - Michael J Difilippantonio
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Jens K Habermann
- Section for Translational Surgical Oncology and Biobanking, Department of Surgery, University Medical Center Schleswig Holstein, Campus Lübeck, Lübeck, Germany
| | - Gert Auer
- Department of Oncology and Pathology, CancerCenter Karolinska, Karolinska Institute and University Hospital, Stockholm, Sweden
| | - Eytan Ruppin
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Thomas Ried
- Section of Cancer Genomics, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA.
| |
Collapse
|
22
|
Joly JH, Chew BTL, Graham NA. The landscape of metabolic pathway dependencies in cancer cell lines. PLoS Comput Biol 2021; 17:e1008942. [PMID: 33872312 PMCID: PMC8084347 DOI: 10.1371/journal.pcbi.1008942] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 04/29/2021] [Accepted: 04/06/2021] [Indexed: 01/22/2023] Open
Abstract
The metabolic reprogramming of cancer cells creates metabolic vulnerabilities that can be therapeutically targeted. However, our understanding of metabolic dependencies and the pathway crosstalk that creates these vulnerabilities in cancer cells remains incomplete. Here, by integrating gene expression data with genetic loss-of-function and pharmacological screening data from hundreds of cancer cell lines, we identified metabolic vulnerabilities at the level of pathways rather than individual genes. This approach revealed that metabolic pathway dependencies are highly context-specific such that cancer cells are vulnerable to inhibition of one metabolic pathway only when activity of another metabolic pathway is altered. Notably, we also found that the no single metabolic pathway was universally essential, suggesting that cancer cells are not invariably dependent on any metabolic pathway. In addition, we confirmed that cell culture medium is a major confounding factor for the analysis of metabolic pathway vulnerabilities. Nevertheless, we found robust associations between metabolic pathway activity and sensitivity to clinically approved drugs that were independent of cell culture medium. Lastly, we used parallel integration of pharmacological and genetic dependency data to confidently identify metabolic pathway vulnerabilities. Taken together, this study serves as a comprehensive characterization of the landscape of metabolic pathway vulnerabilities in cancer cell lines.
Collapse
Affiliation(s)
- James H Joly
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California, United States of America
| | - Brandon T L Chew
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California, United States of America
| | - Nicholas A Graham
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California, United States of America.,Norris Comprehensive Cancer Center, University of Southern California, University of Southern California, Los Angeles, California, United States of America.,Leonard Davis School of Gerontology, University of Southern California, Los Angeles, California, United States of America
| |
Collapse
|
23
|
Storchova Z. Consequences of mitotic failure - The penalties and the rewards. Semin Cell Dev Biol 2021; 117:149-158. [PMID: 33820699 DOI: 10.1016/j.semcdb.2021.03.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 03/12/2021] [Accepted: 03/13/2021] [Indexed: 12/14/2022]
Abstract
Eukaryotic cells are usually diploid, meaning they contain two copies of each chromosome. However, aberrant chromosome numbers due to both, chromosome gains and losses, are often observed in nature. They can occur as a planned developmental step, but are more often an uninvited result of mitotic failure. Recent discoveries have improved our understanding of the cellular effects of aneuploidy - uneven chromosome numbers, and polyploidy - multiplication of entire sets of chromosomes - in eukaryotic cells. The results show that mitotic errors lead to rapid and extensive modifications of many cellular processes and affect proliferation, proteome balance, genome stability and more. The findings picture the cellular response to aneuploidy and polyploidy as a complex, tissue and context dependent network of events. Here I review the latest discoveries, with an emphasis on pathological aspects of aneuploidy and polyploidy in human cells.
Collapse
Affiliation(s)
- Zuzana Storchova
- Department of Molecular Genetics, TU Kaiserslautern, Paul Ehrlich Str. 24, 67663 Kaiserslautern, Germany.
| |
Collapse
|
24
|
Narkar A, Johnson BA, Bharne P, Zhu J, Padmanaban V, Biswas D, Fraser A, Iglesias PA, Ewald AJ, Li R. On the role of p53 in the cellular response to aneuploidy. Cell Rep 2021; 34:108892. [PMID: 33761356 PMCID: PMC8051136 DOI: 10.1016/j.celrep.2021.108892] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 11/09/2020] [Accepted: 03/02/2021] [Indexed: 01/01/2023] Open
Abstract
Most solid tumors are aneuploid, and p53 has been implicated as the guardian of the euploid genome. Previous experiments using human cell lines showed that aneuploidy induction leads to p53 accumulation and p21-mediated G1 cell cycle arrest. We find that adherent 2-dimensional (2D) cultures of human immortalized or cancer cell lines activate p53 upon aneuploidy induction, whereas suspension cultures of a human lymphoid cell line undergo a p53-independent cell cycle arrest. Surprisingly, 3D human and mouse organotypic cultures from neural, intestinal, or mammary epithelial tissues do not activate p53 or arrest in G1 following aneuploidy induction. p53-deficient colon organoids have increased aneuploidy and frequent lagging chromosomes and multipolar spindles during mitosis. These data suggest that p53 may not act as a universal surveillance factor restricting the proliferation of aneuploid cells but instead helps directly or indirectly ensure faithful chromosome transmission likely by preventing polyploidization and influencing spindle mechanics.
Collapse
Affiliation(s)
- Akshay Narkar
- Center for Cell Dynamics and Department of Cell Biology, Johns Hopkins University, School of Medicine, Baltimore, MD 21205, USA; McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Blake A Johnson
- Center for Cell Dynamics and Department of Cell Biology, Johns Hopkins University, School of Medicine, Baltimore, MD 21205, USA; Medical Scientist Training Program, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Pandurang Bharne
- Center for Cell Dynamics and Department of Cell Biology, Johns Hopkins University, School of Medicine, Baltimore, MD 21205, USA
| | - Jin Zhu
- Center for Cell Dynamics and Department of Cell Biology, Johns Hopkins University, School of Medicine, Baltimore, MD 21205, USA
| | - Veena Padmanaban
- Center for Cell Dynamics and Department of Cell Biology, Johns Hopkins University, School of Medicine, Baltimore, MD 21205, USA
| | - Debojyoti Biswas
- Electrical and Computer Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Andrew Fraser
- Center for Cell Dynamics and Department of Cell Biology, Johns Hopkins University, School of Medicine, Baltimore, MD 21205, USA
| | - Pablo A Iglesias
- Center for Cell Dynamics and Department of Cell Biology, Johns Hopkins University, School of Medicine, Baltimore, MD 21205, USA; Electrical and Computer Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD 21218, USA; Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Andrew J Ewald
- Center for Cell Dynamics and Department of Cell Biology, Johns Hopkins University, School of Medicine, Baltimore, MD 21205, USA
| | - Rong Li
- Center for Cell Dynamics and Department of Cell Biology, Johns Hopkins University, School of Medicine, Baltimore, MD 21205, USA; Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD 21205, USA; Mechanobiology Institute and Department of Biological Sciences, National University of Singapore, Singapore 117411, Singapore.
| |
Collapse
|
25
|
Gong Y, Ji P, Yang YS, Xie S, Yu TJ, Xiao Y, Jin ML, Ma D, Guo LW, Pei YC, Chai WJ, Li DQ, Bai F, Bertucci F, Hu X, Jiang YZ, Shao ZM. Metabolic-Pathway-Based Subtyping of Triple-Negative Breast Cancer Reveals Potential Therapeutic Targets. Cell Metab 2021; 33:51-64.e9. [PMID: 33181091 DOI: 10.1016/j.cmet.2020.10.012] [Citation(s) in RCA: 232] [Impact Index Per Article: 77.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Revised: 08/16/2020] [Accepted: 10/13/2020] [Indexed: 02/06/2023]
Abstract
Triple-negative breast cancer (TNBC) remains an unmet medical challenge. We investigated metabolic dysregulation in TNBCs by using our multi-omics database (n = 465, the largest to date). TNBC samples were classified into three heterogeneous metabolic-pathway-based subtypes (MPSs) with distinct metabolic features: MPS1, the lipogenic subtype with upregulated lipid metabolism; MPS2, the glycolytic subtype with upregulated carbohydrate and nucleotide metabolism; and MPS3, the mixed subtype with partial pathway dysregulation. These subtypes were validated by metabolomic profiling of 72 samples. These three subtypes had distinct prognoses, molecular subtype distributions, and genomic alterations. Moreover, MPS1 TNBCs were more sensitive to metabolic inhibitors targeting fatty acid synthesis, whereas MPS2 TNBCs showed higher sensitivity to inhibitors targeting glycolysis. Importantly, inhibition of lactate dehydrogenase could enhance tumor response to anti-PD-1 immunotherapy in MPS2 TNBCs. Collectively, our analysis demonstrated the metabolic heterogeneity of TNBCs and enabled the development of personalized therapies targeting unique tumor metabolic profiles.
Collapse
Affiliation(s)
- Yue Gong
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, P.R. China
| | - Peng Ji
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, P.R. China
| | - Yun-Song Yang
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, P.R. China
| | - Shao Xie
- Institute of Pediatrics, Children's Hospital, Fudan University, Shanghai 201102, P.R. China
| | - Tian-Jian Yu
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, P.R. China
| | - Yi Xiao
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, P.R. China
| | - Ming-Liang Jin
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, P.R. China
| | - Ding Ma
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, P.R. China
| | - Lin-Wei Guo
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, P.R. China
| | - Yu-Chen Pei
- Precision Cancer Medicine Center, Fudan University Shanghai Cancer Center, Shanghai 200032, P.R. China
| | - Wen-Jun Chai
- Laboratory Animal Center, Fudan University Shanghai Cancer Center, Shanghai 200032, P.R. China
| | - Da-Qiang Li
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, P.R. China; Precision Cancer Medicine Center, Fudan University Shanghai Cancer Center, Shanghai 200032, P.R. China
| | - Fan Bai
- Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, P.R. China
| | - François Bertucci
- Predictive Oncology Laboratory and Department of Medical Oncology, CRCM, Institut Paoli-Calmettes, INSERM, CNRS, Aix-Marseille Université, Marseille, France
| | - Xin Hu
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, P.R. China; Precision Cancer Medicine Center, Fudan University Shanghai Cancer Center, Shanghai 200032, P.R. China.
| | - Yi-Zhou Jiang
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, P.R. China; Precision Cancer Medicine Center, Fudan University Shanghai Cancer Center, Shanghai 200032, P.R. China.
| | - Zhi-Ming Shao
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, P.R. China; Precision Cancer Medicine Center, Fudan University Shanghai Cancer Center, Shanghai 200032, P.R. China.
| |
Collapse
|
26
|
Zhu LL, Wu Z, Li RK, Xing X, Jiang YS, Li J, Wang YH, Hu LP, Wang X, Qin WT, Sun YW, Zhang ZG, Yang Q, Jiang SH. Deciphering the genomic and lncRNA landscapes of aerobic glycolysis identifies potential therapeutic targets in pancreatic cancer. Int J Biol Sci 2021; 17:107-118. [PMID: 33390837 PMCID: PMC7757027 DOI: 10.7150/ijbs.49243] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Accepted: 10/29/2020] [Indexed: 12/17/2022] Open
Abstract
Aerobic glycolysis, also known as the Warburg effect, is emerged as a hallmark of most cancer cells. Increased aerobic glycolysis is closely associated with tumor aggressiveness and predicts a poor prognosis. Pancreatic ductal adenocarcinoma (PDAC) is characterized by prominent genomic aberrations and increased glycolytic phenotype. However, the detailed molecular events implicated in aerobic glycolysis of PDAC are not well understood. In this study, we performed a comprehensive molecular characterization using multidimensional ''omic'' data from The Cancer Genome Atlas (TCGA). Detailed analysis of 89 informative PDAC tumors identified substantial copy number variations (MYC, GATA6, FGFR1, IDO1, and SMAD4) and mutations (KRAS, SMAD4, and RNF43) related to aerobic glycolysis. Moreover, integrated analysis of transcriptional profiles revealed many differentially expressed long non-coding RNAs involved in PDAC aerobic glycolysis. Loss-of-function studies showed that LINC01559 and UNC5B-AS1 knockdown significantly inhibited the glycolytic capacity of PDAC cells as revealed by reduced glucose uptake, lactate production, and extracellular acidification rate. Moreover, genetic silencing of LINC01559 and UNC5B-AS1 suppressed tumor growth and resulted in alterations in several signaling pathways, such as TNF signaling pathway, IL-17 signaling pathway, and transcriptional misregulation in cancer. Notably, high expression of LINC01559 and UNC5B-AS1 predicted poor patient prognosis and correlated with the maximum standard uptakevalue (SUVmax) in PDAC patients who received preoperative 18F-FDG PET/CT. Taken together, our results decipher the glycolysis-associated copy number variations, mutations, and lncRNA landscapes in PDAC. These findings improve our knowledge of the molecular mechanism of PDAC aerobic glycolysis and may have practical implications for precision cancer therapy.
Collapse
Affiliation(s)
- Li-Li Zhu
- State Key Laboratory of Oncogenes and Related Genes, Ren Ji Hospital, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, P.R. China.,State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, P.R. China
| | - Zheng Wu
- Department of Radiation Oncology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, PR China
| | - Rong-Kun Li
- Institute of Oncology, Affiliated Hospital of Jiangsu University, Zhenjiang 212001, P.R. China
| | - Xin Xing
- The Fengxian Hospital, Southern Medical University, Shanghai 201499, PR China
| | - Yong-Sheng Jiang
- Department of Biliary-Pancreatic Surgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200217, P.R. China
| | - Jun Li
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, P.R. China
| | - Ya-Hui Wang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, P.R. China
| | - Li-Peng Hu
- State Key Laboratory of Oncogenes and Related Genes, Ren Ji Hospital, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, P.R. China.,State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, P.R. China
| | - Xu Wang
- Institute of Oncology, Affiliated Hospital of Jiangsu University, Zhenjiang 212001, P.R. China
| | - Wei-Ting Qin
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, P.R. China
| | - Yong-Wei Sun
- Department of Biliary-Pancreatic Surgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200217, P.R. China
| | - Zhi-Gang Zhang
- State Key Laboratory of Oncogenes and Related Genes, Ren Ji Hospital, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, P.R. China.,State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, P.R. China
| | - Qin Yang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, P.R. China
| | - Shu-Heng Jiang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, P.R. China
| |
Collapse
|
27
|
Glycolytic phenotypes in an evaluation of ovarian carcinoma based on carcinogenesis and BRCA mutation. Eur J Radiol 2020; 133:109391. [PMID: 33171356 DOI: 10.1016/j.ejrad.2020.109391] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 10/15/2020] [Accepted: 10/29/2020] [Indexed: 11/23/2022]
Abstract
BACKGROUNDS Recently, a dualistic carcinogenesis model of ovarian cancer has emerged. We aimed to investigate differences in the glycolytic phenotypes of type I and type II ovarian carcinoma on the basis of FDG uptake and in the pathological features according to tumour grade and histology. MATERIALS AND METHODS In total, 386 epithelial ovarian carcinoma patients underwent debulking surgery, and the histopathological results of the patients were retrospectively reviewed from 2003 to 2017. Among these patients, 170 patients had histopathological data that were available due to primary cytoreductive surgery and could be analysed regarding FDG avidity in type I and type II ovarian cancer. The FDG uptake of the tumour (SUVmax), metabolic tumor volume (MTV) and total lesion glycolysis (TLG) were analysed according to the tumour grade, histology and type of ovarian carcinogenesis (type I and II) and prognosis. RESULTS Among the 386 patients, there was a significant difference in SUVmax among ovarian cancer subtypes. There was a significant increase in SUVmax as the tumour grade increased (8.08 ± 0.63, 10.5 ± 0.40, and 12.7 ± 0.38 for grades I, II and III, respectively, Kruskal-Wallis test, p < 0.0001). Among the 90 type I and 80 type II ovarian carcinoma patients, there was a significant difference in SUVmax (type I and II, 9.47 ± 0.54 and 12.97 ± 0.70, respectively, Mann-Whitney test, p = 0.0003). However, no significant change in SUVmax was observed between BRCA-positive and BRCA-negative patients (N = 80, 13.8 ± 5.78 and 12.4 ± 6.30, Student's t-test, p = 0.3075). Among clinicopathologic and metabolic parameters, type of ovarian cancer, MTV and CA125 were significant factors in the prediction of recurrence. CONCLUSIONS The glycolytic phenotype was related to tumour grade and histological subtype, with significant differences between type I and II ovarian cancer. SUVmax of the ovarian cancer would be considered in the differentiation of type I and II ovarian cancer.
Collapse
|
28
|
Thermodynamic energetics underlying genomic instability and whole-genome doubling in cancer. Proc Natl Acad Sci U S A 2020; 117:18880-18890. [PMID: 32694208 DOI: 10.1073/pnas.1920870117] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Genomic instability contributes to tumorigenesis through the amplification and deletion of cancer driver genes. DNA copy number (CN) profiling of ensembles of tumors allows a thermodynamic analysis of the profile for each tumor. The free energy of the distribution of CNs is found to be a monotonically increasing function of the average chromosomal ploidy. The dependence is universal across several cancer types. Surprisal analysis distinguishes two main known subgroups: tumors with cells that have or have not undergone whole-genome duplication (WGD). The analysis uncovers that CN states having a narrower distribution are energetically more favorable toward the WGD transition. Surprisal analysis also determines the deviations from a fully stable-state distribution. These deviations reflect constraints imposed by tumor fitness selection pressures. The results point to CN changes that are more common in high-ploidy tumors and thus support altered selection pressures upon WGD.
Collapse
|
29
|
Overall tumor genomic instability: an important predictor of recurrence-free survival in patients with localized clear cell renal cell carcinoma. Cancer Biol Ther 2020; 21:424-431. [PMID: 32116106 DOI: 10.1080/15384047.2020.1721251] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Measurement of a tumor's overall genomic instability has gathered recent interest over the identification of specific genomic imbalances, as it may provide a more robust measure of tumor aggressiveness. Here we demonstrate the association of tumor genomic instability in the prediction of disease recurrence in patients with clinically localized clear cell renal cell carcinoma (ccRCC). Genomic copy number analysis was performed using SNP-based microarrays on tumors from 103 ccRCC patients. The number of copy number alterations (CNAs) for each tumor was calculated, and a genomic imbalance threshold (GIT) associated with high stage and high-grade disease was determined. Cox proportional hazards regression analyzes were performed to assess the effect of GIT on recurrence-free survival adjusting for known confounders. In the cohort, copy number losses in chromosome arms 3p, 14q, 6q, 9p, and 1p and gains of 5q and 7p/q were common. CNA burden significantly increased with increasing stage (p < .001) and grade (p < .001). The median CNA burden associated with patients presenting with advanced stage (IV) and high-grade (III/IV) tumors was ≥9, defining the GIT. On regression analysis, GIT was a superior predictor of recurrence (Hazard Ratio 4.44 [CI 1.36-14.48], p = .01) independent of stage, with similar results adjusting for grade. These findings were confirmed using an alternative measure of genomic instability, weighted Genomic Integrity Index. Our data support a key role for genomic instability in ccRCC progression. More importantly, we have identified a GIT (≥ 9 CNAs) that is a superior and independent predictor of disease recurrence in high-risk ccRCC patients.
Collapse
|
30
|
Pinoli P, Stamoulakatou E, Nguyen AP, Rodríguez Martínez M, Ceri S. Pan-cancer analysis of somatic mutations and epigenetic alterations in insulated neighbourhood boundaries. PLoS One 2020; 15:e0227180. [PMID: 31945090 PMCID: PMC6964824 DOI: 10.1371/journal.pone.0227180] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 12/14/2019] [Indexed: 01/05/2023] Open
Abstract
Recent evidence shows that the disruption of constitutive insulated neighbourhoods might lead to oncogene dysregulation. We present here a systematic pan-cancer characterisation of the associations between constitutive boundaries and genome alterations in cancer. Specifically, we investigate the enrichment of somatic mutation, abnormal methylation, and copy number alteration events in the proximity of CTCF bindings overlapping with topological boundaries (junctions) in 26 cancer types. Focusing on CTCF motifs that are both in-boundary (overlapping with junctions) and active (overlapping with peaks of CTCF expression), we find a significant enrichment of somatic mutations in several cancer types. Furthermore, mutated junctions are significantly conserved across cancer types, and we also observe a positive selection of transversions rather than transitions in many cancer types. We also analyzed the mutational signature found on the different classes of CTCF motifs, finding some signatures (such as SBS26) to have a higher weight within in-boundary than off-bounday motifs. Regarding methylation, we find a significant number of over-methylated active in-boundary CTCF motifs in several cancer types; similarly to somatic-mutated junctions, they also have a significant conservation across cancer types. Finally, in several cancer types we observe that copy number alterations tend to overlap with active junctions more often than in matched normal samples. While several articles have recently reported a mutational enrichment at CTCF binding sites for specific cancer types, our analysis is pan-cancer and investigates abnormal methylation and copy number alterations in addition to somatic mutations. Our method is fully replicable and suggests several follow-up tumour-specific analyses.
Collapse
|
31
|
Cuevas D, Velasco A, Vaquero M, Santacana M, Gatius S, Eritja N, Estaran E, Matias‐Guiu X. Intratumour heterogeneity in endometrial serous carcinoma assessed by targeted sequencing and multiplex ligation‐dependent probe amplification: a descriptive study. Histopathology 2020; 76:447-460. [DOI: 10.1111/his.14001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 09/20/2019] [Indexed: 01/05/2023]
Affiliation(s)
- Dolors Cuevas
- Hospital Universitari Arnau de Vilanova Universitat de Lleida IRBLleida Ciberonc Lleida Spain
| | - Ana Velasco
- Hospital Universitari Arnau de Vilanova Universitat de Lleida IRBLleida Ciberonc Lleida Spain
| | - Marta Vaquero
- Hospital Universitari Arnau de Vilanova Universitat de Lleida IRBLleida Ciberonc Lleida Spain
| | - Maria Santacana
- Hospital Universitari Arnau de Vilanova Universitat de Lleida IRBLleida Ciberonc Lleida Spain
| | - Sònia Gatius
- Hospital Universitari Arnau de Vilanova Universitat de Lleida IRBLleida Ciberonc Lleida Spain
| | - Núria Eritja
- Hospital Universitari Arnau de Vilanova Universitat de Lleida IRBLleida Ciberonc Lleida Spain
| | - Elena Estaran
- Hospital Universitari Arnau de Vilanova Universitat de Lleida IRBLleida Ciberonc Lleida Spain
| | - Xavier Matias‐Guiu
- Hospital Universitari Arnau de Vilanova Universitat de Lleida IRBLleida Ciberonc Lleida Spain
- Hospital Universitari de Bellvitge Idibell Barcelona Spain
| |
Collapse
|
32
|
Seth Nanda C, Venkateswaran SV, Patani N, Yuneva M. Defining a metabolic landscape of tumours: genome meets metabolism. Br J Cancer 2020; 122:136-149. [PMID: 31819196 PMCID: PMC7051970 DOI: 10.1038/s41416-019-0663-7] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 11/06/2019] [Accepted: 11/08/2019] [Indexed: 12/13/2022] Open
Abstract
Cancer is a complex disease of multiple alterations occuring at the epigenomic, genomic, transcriptomic, proteomic and/or metabolic levels. The contribution of genetic mutations in cancer initiation, progression and evolution is well understood. However, although metabolic changes in cancer have long been acknowledged and considered a plausible therapeutic target, the crosstalk between genetic and metabolic alterations throughout cancer types is not clearly defined. In this review, we summarise the present understanding of the interactions between genetic drivers of cellular transformation and cancer-associated metabolic changes, and how these interactions contribute to metabolic heterogeneity of tumours. We discuss the essential question of whether changes in metabolism are a cause or a consequence in the formation of cancer. We highlight two modes of how metabolism contributes to tumour formation. One is when metabolic reprogramming occurs downstream of oncogenic mutations in signalling pathways and supports tumorigenesis. The other is where metabolic reprogramming initiates transformation being either downstream of mutations in oncometabolite genes or induced by chronic wounding, inflammation, oxygen stress or metabolic diseases. Finally, we focus on the factors that can contribute to metabolic heterogeneity in tumours, including genetic heterogeneity, immunomodulatory factors and tissue architecture. We believe that an in-depth understanding of cancer metabolic reprogramming, and the role of metabolic dysregulation in tumour initiation and progression, can help identify cellular vulnerabilities that can be exploited for therapeutic use.
Collapse
Affiliation(s)
| | | | - Neill Patani
- The Francis Crick Institute, 1 Midland Road, London, UK
| | - Mariia Yuneva
- The Francis Crick Institute, 1 Midland Road, London, UK.
| |
Collapse
|
33
|
Palaskas NJ, Garcia JD, Shirazi R, Shin DS, Puig-Saus C, Braas D, Ribas A, Graeber TG. Global alteration of T-lymphocyte metabolism by PD-L1 checkpoint involves a block of de novo nucleoside phosphate synthesis. Cell Discov 2019; 5:62. [PMID: 31798961 PMCID: PMC6877514 DOI: 10.1038/s41421-019-0130-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 09/18/2019] [Indexed: 12/29/2022] Open
Abstract
Metabolic obstacles of the tumor microenvironment remain a challenge to T-cell-mediated cancer immunotherapies. To better understand the interplay of immune checkpoint signaling and immune metabolism, this study developed and used an optimized metabolite extraction protocol for non-adherent primary human T-cells, to broadly profile in vitro metabolic changes effected by PD-1 signaling by mass spectrometry-based metabolomics and isotopomer analysis. Inhibitory signaling reduced aerobic glycolysis and glutaminolysis. A general scarcity across the panel of metabolites measured supported widespread metabolic regulation by PD-1. Glucose carbon fate analysis supported tricarboxylic acid cycle reliance on pyruvate carboxylation, catabolic-state fluxes into acetyl-CoA and succinyl-CoA, and a block in de novo nucleoside phosphate synthesis that was accompanied by reduced mTORC1 signaling. Nonetheless, exogenous administration of nucleosides was not sufficient to ameliorate proliferation of T-cells in the context of multiple metabolic insufficiencies due to PD-L1 treatment. Carbon fate analysis did not support the use of primarily glucose-derived carbons to fuel fatty acid beta oxidation, in contrast to reports on T-memory cells. These findings add to our understanding of metabolic dysregulation by PD-1 signaling and inform the effort to rationally develop metabolic interventions coupled with immune-checkpoint blockade for increased treatment efficacy.
Collapse
Affiliation(s)
- Nicolaos Jay Palaskas
- 1Division of Hematology and Oncology, Department of Medicine, University of California Los Angeles, Los Angeles, CA 90095 USA.,2Department of Molecular, Cellular, and Integrative Physiology, University of California Los Angeles, Los Angeles, CA 90095 USA
| | - Jacob David Garcia
- 3Department of Molecular, Cellular, and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095 USA
| | - Roksana Shirazi
- 4Department of Microbiology, Immunology, and Molecular Genetics, University of California Los Angeles, Los Angeles, CA 90095 USA
| | - Daniel Sanghoon Shin
- 1Division of Hematology and Oncology, Department of Medicine, University of California Los Angeles, Los Angeles, CA 90095 USA.,2Department of Molecular, Cellular, and Integrative Physiology, University of California Los Angeles, Los Angeles, CA 90095 USA
| | - Cristina Puig-Saus
- 1Division of Hematology and Oncology, Department of Medicine, University of California Los Angeles, Los Angeles, CA 90095 USA
| | - Daniel Braas
- 2Department of Molecular, Cellular, and Integrative Physiology, University of California Los Angeles, Los Angeles, CA 90095 USA.,5Crump Institute for Molecular Imaging, University of California Los Angeles, Los Angeles, CA 90095 USA.,6Metabolomics Center, University of California Los Angeles, Los Angeles, CA 90095 USA
| | - Antoni Ribas
- 1Division of Hematology and Oncology, Department of Medicine, University of California Los Angeles, Los Angeles, CA 90095 USA.,2Department of Molecular, Cellular, and Integrative Physiology, University of California Los Angeles, Los Angeles, CA 90095 USA.,7Department of Molecular and Medical Pharmacology, University of California Los Angeles, Los Angeles, CA 90095 USA.,8Jonsson Comprehensive Cancer Center, University of California Los Angeles, Los Angeles, CA 90095 USA.,9Division of Surgical Oncology, Department of Surgery, University of California Los Angeles, Los Angeles, CA 90095 USA
| | - Thomas Glen Graeber
- 2Department of Molecular, Cellular, and Integrative Physiology, University of California Los Angeles, Los Angeles, CA 90095 USA.,5Crump Institute for Molecular Imaging, University of California Los Angeles, Los Angeles, CA 90095 USA.,6Metabolomics Center, University of California Los Angeles, Los Angeles, CA 90095 USA.,7Department of Molecular and Medical Pharmacology, University of California Los Angeles, Los Angeles, CA 90095 USA.,8Jonsson Comprehensive Cancer Center, University of California Los Angeles, Los Angeles, CA 90095 USA
| |
Collapse
|
34
|
Ben-David U, Amon A. Context is everything: aneuploidy in cancer. Nat Rev Genet 2019; 21:44-62. [DOI: 10.1038/s41576-019-0171-x] [Citation(s) in RCA: 234] [Impact Index Per Article: 46.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/14/2019] [Indexed: 02/07/2023]
|
35
|
Yao DW, Balanis NG, Eskin E, Graeber TG. A linear mixed model approach to gene expression-tumor aneuploidy association studies. Sci Rep 2019; 9:11944. [PMID: 31420589 PMCID: PMC6697733 DOI: 10.1038/s41598-019-48302-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 08/02/2019] [Indexed: 11/09/2022] Open
Abstract
Aneuploidy, defined as abnormal chromosome number or somatic DNA copy number, is a characteristic of many aggressive tumors and is thought to drive tumorigenesis. Gene expression-aneuploidy association studies have previously been conducted to explore cellular mechanisms associated with aneuploidy. However, in an observational setting, gene expression is influenced by many factors that can act as confounders between gene expression and aneuploidy, leading to spurious correlations between the two variables. These factors include known confounders such as sample purity or batch effect, as well as gene co-regulation which induces correlations between the expression of causal genes and non-causal genes. We use a linear mixed-effects model (LMM) to account for confounding effects of tumor purity and gene co-regulation on gene expression-aneuploidy associations. When applied to patient tumor data across diverse tumor types, we observe that the LMM both accounts for the impact of purity on aneuploidy measurements and identifies a new association between histone gene expression and aneuploidy.
Collapse
Affiliation(s)
- Douglas W Yao
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA, USA.
| | - Nikolas G Balanis
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA.,Crump Institute for Molecular Imaging, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Eleazar Eskin
- Department of Computer Science, University of California, Los Angeles, CA, USA.,Department of Human Genetics, University of California, Los Angeles, CA, USA
| | - Thomas G Graeber
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA. .,Crump Institute for Molecular Imaging, David Geffen School of Medicine, University of California, Los Angeles, CA, USA. .,Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California, Los Angeles, CA, USA. .,California NanoSystems Institute, David Geffen School of Medicine, University of California, Los Angeles, CA, USA.
| |
Collapse
|
36
|
Ried T, Meijer GA, Harrison DJ, Grech G, Franch-Expósito S, Briffa R, Carvalho B, Camps J. The landscape of genomic copy number alterations in colorectal cancer and their consequences on gene expression levels and disease outcome. Mol Aspects Med 2019; 69:48-61. [PMID: 31365882 DOI: 10.1016/j.mam.2019.07.007] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 07/23/2019] [Accepted: 07/26/2019] [Indexed: 12/18/2022]
Abstract
Aneuploidy, the unbalanced state of the chromosome content, represents a hallmark of most solid tumors, including colorectal cancer. Such aneuploidies result in tumor specific genomic imbalances, which emerge in premalignant precursor lesions. Moreover, increasing levels of chromosomal instability have been observed in adenocarcinomas and are maintained in distant metastases. A number of studies have systematically integrated copy number alterations with gene expression changes in primary carcinomas, cell lines, and experimental models of aneuploidy. In fact, chromosomal aneuploidies target a number of genes conferring a selective advantage for the metabolism of the cancer cell. Copy number alterations not only have a positive correlation with expression changes of the majority of genes on the altered genomic segment, but also have effects on the transcriptional levels of genes genome-wide. Finally, copy number alterations have been associated with disease outcome; nevertheless, the translational applicability in clinical practice requires further studies. Here, we (i) review the spectrum of genetic alterations that lead to colorectal cancer, (ii) describe the most frequent copy number alterations at different stages of colorectal carcinogenesis, (iii) exemplify their positive correlation with gene expression levels, and (iv) discuss copy number alterations that are potentially involved in disease outcome of individual patients.
Collapse
Affiliation(s)
- Thomas Ried
- Genetics Branch, Center for Cancer Research, National Cancer Institute/National Institutes of Health, Bethesda, MD, USA.
| | - Gerrit A Meijer
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - David J Harrison
- School of Medicine, University of St Andrews, St Andrews, Scotland, UK
| | - Godfrey Grech
- Laboratory of Molecular Pathology, Department of Pathology, Faculty of Medicine and Surgery, University of Malta, Msida, Malta
| | - Sebastià Franch-Expósito
- Gastrointestinal and Pancreatic Oncology Group, Institut D'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), CIBEREHD, Barcelona, Spain
| | - Romina Briffa
- School of Medicine, University of St Andrews, St Andrews, Scotland, UK; Laboratory of Molecular Pathology, Department of Pathology, Faculty of Medicine and Surgery, University of Malta, Msida, Malta
| | - Beatriz Carvalho
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Jordi Camps
- Gastrointestinal and Pancreatic Oncology Group, Institut D'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), CIBEREHD, Barcelona, Spain; Unitat de Biologia Cel·lular i Genètica Mèdica, Departament de Biologia Cel·lular, Fisiologia i Immunologia, Facultat de Medicina, Universitat Autònoma de Barcelona, Bellaterra, Spain.
| |
Collapse
|
37
|
Balanis NG, Sheu KM, Esedebe FN, Patel SJ, Smith BA, Park JW, Alhani S, Gomperts BN, Huang J, Witte ON, Graeber TG. Pan-cancer Convergence to a Small-Cell Neuroendocrine Phenotype that Shares Susceptibilities with Hematological Malignancies. Cancer Cell 2019; 36:17-34.e7. [PMID: 31287989 PMCID: PMC6703903 DOI: 10.1016/j.ccell.2019.06.005] [Citation(s) in RCA: 105] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 03/04/2019] [Accepted: 06/06/2019] [Indexed: 01/01/2023]
Abstract
Small-cell neuroendocrine cancers (SCNCs) are an aggressive cancer subtype. Transdifferentiation toward an SCN phenotype has been reported as a resistance route in response to targeted therapies. Here, we identified a convergence to an SCN state that is widespread across epithelial cancers and is associated with poor prognosis. More broadly, non-SCN metastases have higher expression of SCN-associated transcription factors than non-SCN primary tumors. Drug sensitivity and gene dependency screens demonstrate that these convergent SCNCs have shared vulnerabilities. These common vulnerabilities are found across unannotated SCN-like epithelial cases, small-round-blue cell tumors, and unexpectedly in hematological malignancies. The SCN convergent phenotype and common sensitivity profiles with hematological cancers can guide treatment options beyond tissue-specific targeted therapies.
Collapse
Affiliation(s)
- Nikolas G Balanis
- Department of Molecular and Medical Pharmacology, UCLA, Los Angeles, CA 90095, USA
| | - Katherine M Sheu
- Department of Molecular and Medical Pharmacology, UCLA, Los Angeles, CA 90095, USA
| | - Favour N Esedebe
- Department of Molecular and Medical Pharmacology, UCLA, Los Angeles, CA 90095, USA
| | - Saahil J Patel
- Department of Molecular and Medical Pharmacology, UCLA, Los Angeles, CA 90095, USA
| | - Bryan A Smith
- Department of Microbiology, Immunology, and Molecular Genetics, UCLA, Los Angeles, CA 90095, USA
| | - Jung Wook Park
- Department of Microbiology, Immunology, and Molecular Genetics, UCLA, Los Angeles, CA 90095, USA
| | - Salwan Alhani
- Department of Molecular and Medical Pharmacology, UCLA, Los Angeles, CA 90095, USA
| | - Brigitte N Gomperts
- Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, CA 90095, USA; UCLA Children's Discovery and Innovation Institute, Mattel Children's Hospital UCLA, Department of Pediatrics, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA; Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, UCLA, Los Angeles, CA 90095, USA
| | - Jiaoti Huang
- Department of Pathology, Duke University School of Medicine, Durham, NC 27708, USA
| | - Owen N Witte
- Department of Microbiology, Immunology, and Molecular Genetics, UCLA, Los Angeles, CA 90095, USA; Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, CA 90095, USA; Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, UCLA, Los Angeles, CA 90095, USA.
| | - Thomas G Graeber
- Department of Molecular and Medical Pharmacology, UCLA, Los Angeles, CA 90095, USA; Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, CA 90095, USA; Crump Institute for Molecular Imaging, UCLA, Los Angeles, CA 90095, USA; California NanoSystems Institute, UCLA, Los Angeles, CA 90095, USA; Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, UCLA, Los Angeles, CA 90095, USA.
| |
Collapse
|
38
|
Delfarah A, Parrish S, Junge JA, Yang J, Seo F, Li S, Mac J, Wang P, Fraser SE, Graham NA. Inhibition of nucleotide synthesis promotes replicative senescence of human mammary epithelial cells. J Biol Chem 2019; 294:10564-10578. [PMID: 31138644 DOI: 10.1074/jbc.ra118.005806] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 05/18/2019] [Indexed: 12/15/2022] Open
Abstract
Cellular senescence is a mechanism by which cells permanently withdraw from the cell cycle in response to stresses including telomere shortening, DNA damage, or oncogenic signaling. Senescent cells contribute to both age-related degeneration and hyperplastic pathologies, including cancer. In culture, normal human epithelial cells enter senescence after a limited number of cell divisions, known as replicative senescence. Here, to investigate how metabolic pathways regulate replicative senescence, we used LC-MS-based metabolomics to analyze senescent primary human mammary epithelial cells (HMECs). We did not observe significant changes in glucose uptake or lactate secretion in senescent HMECs. However, analysis of intracellular metabolite pool sizes indicated that senescent cells exhibit depletion of metabolites from nucleotide synthesis pathways. Furthermore, stable isotope tracing with 13C-labeled glucose or glutamine revealed a dramatic blockage of flux of these two metabolites into nucleotide synthesis pathways in senescent HMECs. To test whether cellular immortalization would reverse these observations, we expressed telomerase in HMECs. In addition to preventing senescence, telomerase expression maintained metabolic flux from glucose into nucleotide synthesis pathways. Finally, we investigated whether inhibition of nucleotide synthesis in proliferating HMECs is sufficient to induce senescence. In proliferating HMECs, both pharmacological and genetic inhibition of ribonucleotide reductase regulatory subunit M2 (RRM2), a rate-limiting enzyme in dNTP synthesis, induced premature senescence with concomitantly decreased metabolic flux from glucose into nucleotide synthesis. Taken together, our results suggest that nucleotide synthesis inhibition plays a causative role in the establishment of replicative senescence in HMECs.
Collapse
Affiliation(s)
- Alireza Delfarah
- From the Mork Family Department of Chemical Engineering and Materials Science
| | - Sydney Parrish
- From the Mork Family Department of Chemical Engineering and Materials Science
| | - Jason A Junge
- the Translational Imaging Center, Molecular and Computational Biology, and
| | - Jesse Yang
- From the Mork Family Department of Chemical Engineering and Materials Science
| | - Frances Seo
- From the Mork Family Department of Chemical Engineering and Materials Science
| | - Si Li
- From the Mork Family Department of Chemical Engineering and Materials Science
| | - John Mac
- From the Mork Family Department of Chemical Engineering and Materials Science
| | - Pin Wang
- From the Mork Family Department of Chemical Engineering and Materials Science
| | - Scott E Fraser
- the Translational Imaging Center, Molecular and Computational Biology, and
| | - Nicholas A Graham
- From the Mork Family Department of Chemical Engineering and Materials Science, .,the Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California 90089
| |
Collapse
|
39
|
Follia L, Ferrero G, Mandili G, Beccuti M, Giordano D, Spadi R, Satolli MA, Evangelista A, Katayama H, Hong W, Momin AA, Capello M, Hanash SM, Novelli F, Cordero F. Integrative Analysis of Novel Metabolic Subtypes in Pancreatic Cancer Fosters New Prognostic Biomarkers. Front Oncol 2019; 9:115. [PMID: 30873387 PMCID: PMC6400843 DOI: 10.3389/fonc.2019.00115] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 02/07/2019] [Indexed: 12/25/2022] Open
Abstract
Background: Most of the patients with Pancreatic Ductal Adenocarcinoma (PDA) are not eligible for a curative surgical resection. For this reason there is an urgent need for personalized therapies. PDA is the result of complex interactions between tumor molecular profile and metabolites produced by its microenvironment. Despite recent studies identified PDA molecular subtypes, its metabolic classification is still lacking. Methods: We applied an integrative analysis on transcriptomic and genomic data of glycolytic genes in PDA. Data were collected from public datasets and molecular glycolytic subtypes were defined using hierarchical clustering. The grade of purity of the cancer samples was assessed estimating the different amount of stromal and immunological infiltrate among the identified PDA subtypes. Analyses of metabolomic data from a subset of PDA cell lines allowed us to identify the different metabolites produced by the metabolic subtypes. Sera of a cohort of 31 PDA patients were analyzed using Q-TOF mass spectrometer to measure the amount of metabolic circulating proteins present before and after chemotherapy. Results: Our integrative analysis of glycolytic genes identified two glycolytic and two non-glycolytic metabolic PDA subtypes. Glycolytic patients develop disease earlier, have poor prognosis, low immune-infiltrated tumors, and are characterized by a gain in chr12p13 genomic region. This gain results in the over-expression of GAPDH, TPI1, and FOXM1. PDA cell lines with the gain of chr12p13 are characterized by an higher lipid uptake and sensitivity to drug targeting the fatty acid metabolism. Our sera proteomic analysis confirms that TPI1 serum levels increase in poor prognosis gemcitabine-treated patients. Conclusions: We identify four metabolic PDA subtypes with different prognosis outcomes which may have pivotal role in setting personalized treatments. Moreover, our data suggest TPI1 as putative prognostic PDA biomarker.
Collapse
Affiliation(s)
- Laura Follia
- Center for Experimental Research and Medical Studies, Azienda Universitaria Ospedaliera Città della Salute e della Scienza di Torino, Turin, Italy
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, Italy
- Department of Computer Sciences, University of Turin, Turin, Italy
| | - Giulio Ferrero
- Department of Computer Sciences, University of Turin, Turin, Italy
| | - Giorgia Mandili
- Center for Experimental Research and Medical Studies, Azienda Universitaria Ospedaliera Città della Salute e della Scienza di Torino, Turin, Italy
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, Italy
| | - Marco Beccuti
- Department of Computer Sciences, University of Turin, Turin, Italy
| | - Daniele Giordano
- Center for Experimental Research and Medical Studies, Azienda Universitaria Ospedaliera Città della Salute e della Scienza di Torino, Turin, Italy
| | - Rosella Spadi
- Centro Oncologico Ematologico Subalpino, Azienda Universitaria Ospedaliera Città della Salute e della Scienza di Torino, Turin, Italy
| | - Maria Antonietta Satolli
- Centro Oncologico Ematologico Subalpino, Azienda Universitaria Ospedaliera Città della Salute e della Scienza di Torino, Turin, Italy
| | - Andrea Evangelista
- Servizio di Epidemiologia dei Tumori, Azienda Universitaria Ospedaliera Città della Salute e della Scienza di Torino, Turin, Italy
| | - Hiroyuki Katayama
- Department of Clinical Cancer Prevention Research, MD Anderson Cancer Center, Houston, TX, United States
| | - Wang Hong
- Department of Clinical Cancer Prevention Research, MD Anderson Cancer Center, Houston, TX, United States
| | - Amin A. Momin
- Department of Clinical Cancer Prevention Research, MD Anderson Cancer Center, Houston, TX, United States
| | - Michela Capello
- Department of Clinical Cancer Prevention Research, MD Anderson Cancer Center, Houston, TX, United States
| | - Samir M. Hanash
- Department of Clinical Cancer Prevention Research, MD Anderson Cancer Center, Houston, TX, United States
| | - Francesco Novelli
- Center for Experimental Research and Medical Studies, Azienda Universitaria Ospedaliera Città della Salute e della Scienza di Torino, Turin, Italy
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, Italy
- Molecular Biotechnology Center, University of Turin, Turin, Italy
| | | |
Collapse
|
40
|
Hydroxysteroid 11-Beta Dehydrogenase 1 Overexpression with Copy-Number Gain and Missense Mutations in Primary Gastrointestinal Stromal Tumors. J Clin Med 2018; 7:jcm7110408. [PMID: 30388854 PMCID: PMC6262574 DOI: 10.3390/jcm7110408] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 10/25/2018] [Accepted: 10/29/2018] [Indexed: 12/11/2022] Open
Abstract
The lipid-metabolizing enzymes remain underexplored in gastrointestinal stromal tumors (GISTs). Through transcriptomic reappraisal, hydroxysteroid 11-beta dehydrogenase-1 (HSD11B1) was identified as a top-upregulated, progression-associated gene. To validate the clinical relevance of HSD11B1, the informative results of Sanger sequencing (n = 58), mRNA quantification by branched-chain DNA in situ hybridization assay (n = 70), copy number assay by fluorescent in situ hybridization (n = 350), and immunohistochemistry (n = 350) were correlated with clincopathological variables, KIT/PDGFRA/BRAF genotypes, and disease-free survival (DFS). HSD11B1 was stably silenced to explore its oncogenic function. HSD11B1 mRNA varied between high-risk and non-high-risk groups (p = 0.009) and positively correlated with HSD11B1 immunoexpression (r = 0.783, p < 0.001). HSD11B1 copy-number gain (CNG), including polysomy (5.4%) and amplification (12%), associated with HSD11B1 overexpression (p < 0.001). Predominantly involving the homodimer interface-affecting exon 6 or exon 7, missense HSD11B1 mutations (17.2%) were related to high risk (p = 0.044), age ≥70 years (p = 0.007), and shorter DFS among relapsed cases (p = 0.033). CNG was related to unfavorable KIT/PDGFRA/BRAF genotypes (p = 0.015), while HSD11B1 overexpression was preferential in non-gastric cases (p < 0.001). Both abnormalities strongly associated with risk levels (both p < 0.001) and shorter univariate DFS (both p < 0.0001), and HSD11B1 CNG remained prognostically independent (p < 0.001) with a 3-fold increased hazard ratio. In vitro, HSD11B1 knockdown significantly inhibited proliferation and caused G2/M arrest. In conclusion, HSD11B1 overexpression may occur owing to CNG, confer a pro-proliferative function, and predict a worse prognosis in GISTs.
Collapse
|
41
|
Simões-Sousa S, Littler S, Thompson SL, Minshall P, Whalley H, Bakker B, Belkot K, Moralli D, Bronder D, Tighe A, Spierings DCJ, Bah N, Graham J, Nelson L, Green CM, Foijer F, Townsend PA, Taylor SS. The p38α Stress Kinase Suppresses Aneuploidy Tolerance by Inhibiting Hif-1α. Cell Rep 2018; 25:749-760.e6. [PMID: 30332653 PMCID: PMC6205844 DOI: 10.1016/j.celrep.2018.09.060] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 06/25/2018] [Accepted: 09/18/2018] [Indexed: 12/20/2022] Open
Abstract
Deviating from the normal karyotype dramatically changes gene dosage, in turn decreasing the robustness of biological networks. Consequently, aneuploidy is poorly tolerated by normal somatic cells and acts as a barrier to transformation. Paradoxically, however, karyotype heterogeneity drives tumor evolution and the emergence of therapeutic drug resistance. To better understand how cancer cells tolerate aneuploidy, we focused on the p38 stress response kinase. We show here that p38-deficient cells upregulate glycolysis and avoid post-mitotic apoptosis, leading to the emergence of aneuploid subclones. We also show that p38 deficiency upregulates the hypoxia-inducible transcription factor Hif-1α and that inhibiting Hif-1α restores apoptosis in p38-deficent cells. Because hypoxia and aneuploidy are both barriers to tumor progression, the ability of Hif-1α to promote cell survival following chromosome missegregation raises the possibility that aneuploidy tolerance coevolves with adaptation to hypoxia.
Collapse
Affiliation(s)
- Susana Simões-Sousa
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Cancer Research Centre, Wilmslow Road, Manchester M20 4QL, UK
| | - Samantha Littler
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Cancer Research Centre, Wilmslow Road, Manchester M20 4QL, UK
| | - Sarah L Thompson
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Cancer Research Centre, Wilmslow Road, Manchester M20 4QL, UK
| | - Paul Minshall
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Cancer Research Centre, Wilmslow Road, Manchester M20 4QL, UK
| | - Helen Whalley
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Cancer Research Centre, Wilmslow Road, Manchester M20 4QL, UK
| | - Bjorn Bakker
- European Research Institute for the Biology of Ageing (ERIBA), University of Groningen, University Medical Center Groningen, 9713 AV Groningen, the Netherlands
| | - Klaudyna Belkot
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Cancer Research Centre, Wilmslow Road, Manchester M20 4QL, UK
| | - Daniela Moralli
- Wellcome Centre Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Daniel Bronder
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Cancer Research Centre, Wilmslow Road, Manchester M20 4QL, UK
| | - Anthony Tighe
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Cancer Research Centre, Wilmslow Road, Manchester M20 4QL, UK
| | - Diana C J Spierings
- European Research Institute for the Biology of Ageing (ERIBA), University of Groningen, University Medical Center Groningen, 9713 AV Groningen, the Netherlands
| | - Nourdine Bah
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Cancer Research Centre, Wilmslow Road, Manchester M20 4QL, UK
| | - Joshua Graham
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Cancer Research Centre, Wilmslow Road, Manchester M20 4QL, UK
| | - Louisa Nelson
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Cancer Research Centre, Wilmslow Road, Manchester M20 4QL, UK
| | - Catherine M Green
- Wellcome Centre Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Floris Foijer
- European Research Institute for the Biology of Ageing (ERIBA), University of Groningen, University Medical Center Groningen, 9713 AV Groningen, the Netherlands
| | - Paul A Townsend
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Cancer Research Centre, Wilmslow Road, Manchester M20 4QL, UK
| | - Stephen S Taylor
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Cancer Research Centre, Wilmslow Road, Manchester M20 4QL, UK.
| |
Collapse
|
42
|
Smith BA, Balanis NG, Nanjundiah A, Sheu KM, Tsai BL, Zhang Q, Park JW, Thompson M, Huang J, Witte ON, Graeber TG. A Human Adult Stem Cell Signature Marks Aggressive Variants across Epithelial Cancers. Cell Rep 2018; 24:3353-3366.e5. [PMID: 30232014 PMCID: PMC6382070 DOI: 10.1016/j.celrep.2018.08.062] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 07/12/2018] [Accepted: 08/21/2018] [Indexed: 12/23/2022] Open
Abstract
Cancer progression to an aggressive phenotype often co-opts aspects of stem cell biology. Here, we developed gene signatures for normal human stem cell populations to understand the relationship between epithelial cancers and stem cell transcriptional programs. Using a pan-cancer approach, we reveal that aggressive epithelial cancers are enriched for a transcriptional signature shared by epithelial adult stem cells. The adult stem cell signature selected for epithelial cancers with worse overall survival and alterations of oncogenic drivers. Lethal small cell neuroendocrine lung, prostate, and bladder cancers transcriptionally converged onto the adult stem cell signature and not other stem cell signatures tested. We found that DNA methyltransferase expression correlated with adult stem cell signature status and was enriched in small cell neuroendocrine cancers. DNA methylation analysis uncovered a shared epigenomic profile between small cell neuroendocrine cancers. These pan-cancer findings establish a molecular link between human adult stem cells and aggressive epithelial cancers.
Collapse
Affiliation(s)
- Bryan A Smith
- Department of Microbiology, Immunology, and Molecular Genetics, UCLA, Los Angeles, CA 90095, USA
| | - Nikolas G Balanis
- Department of Molecular and Medical Pharmacology, UCLA, Los Angeles, CA 90095, USA
| | - Avinash Nanjundiah
- Department of Molecular and Medical Pharmacology, UCLA, Los Angeles, CA 90095, USA
| | - Katherine M Sheu
- Department of Molecular and Medical Pharmacology, UCLA, Los Angeles, CA 90095, USA
| | - Brandon L Tsai
- Department of Microbiology, Immunology, and Molecular Genetics, UCLA, Los Angeles, CA 90095, USA
| | - Qingfu Zhang
- Department of Pathology, Duke University School of Medicine, Durham, NC 27710, USA; Department of Pathology, The First Affiliated Hospital of China Medical University, 110001 Shenyang, China
| | - Jung Wook Park
- Department of Microbiology, Immunology, and Molecular Genetics, UCLA, Los Angeles, CA 90095, USA
| | - Michael Thompson
- Department of Molecular and Medical Pharmacology, UCLA, Los Angeles, CA 90095, USA
| | - Jiaoti Huang
- Department of Pathology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Owen N Witte
- Department of Microbiology, Immunology, and Molecular Genetics, UCLA, Los Angeles, CA 90095, USA; Department of Molecular and Medical Pharmacology, UCLA, Los Angeles, CA 90095, USA; Molecular Biology Institute, UCLA, Los Angeles, CA 90095, USA; Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, UCLA, Los Angeles, CA 90095, USA; Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, CA 90095, USA
| | - Thomas G Graeber
- Department of Molecular and Medical Pharmacology, UCLA, Los Angeles, CA 90095, USA; Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, UCLA, Los Angeles, CA 90095, USA; Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, CA 90095, USA; Crump Institute for Molecular Imaging, UCLA, Los Angeles, CA 90095, USA.
| |
Collapse
|
43
|
Bakhoum SF, Cantley LC. The Multifaceted Role of Chromosomal Instability in Cancer and Its Microenvironment. Cell 2018; 174:1347-1360. [PMID: 30193109 PMCID: PMC6136429 DOI: 10.1016/j.cell.2018.08.027] [Citation(s) in RCA: 394] [Impact Index Per Article: 65.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 08/03/2018] [Accepted: 08/13/2018] [Indexed: 02/07/2023]
Abstract
Chromosomal instability (CIN) is a hallmark of human cancer, and it is associated with poor prognosis, metastasis, and therapeutic resistance. CIN results from errors in chromosome segregation during mitosis, leading to structural and numerical chromosomal abnormalities. In addition to generating genomic heterogeneity that acts as a substrate for natural selection, CIN promotes inflammatory signaling by introducing double-stranded DNA into the cytosol, engaging the cGAS-STING anti-viral pathway. These multipronged effects distinguish CIN as a central driver of tumor evolution and as a genomic source for the crosstalk between the tumor and its microenvironment, in the course of immune editing and evasion.
Collapse
Affiliation(s)
- Samuel F Bakhoum
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
| | - Lewis C Cantley
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA
| |
Collapse
|
44
|
Tran HV, Kiemer AK, Helms V. Copy Number Alterations in Tumor Genomes Deleting Antineoplastic Drug Targets Partially Compensated by Complementary Amplifications. Cancer Genomics Proteomics 2018; 15:365-378. [PMID: 30194077 PMCID: PMC6199575 DOI: 10.21873/cgp.20095] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 07/14/2018] [Accepted: 07/17/2018] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND/AIM Genomic DNA copy number alterations (CNAs) are frequent in tumors and have been catalogued by The Cancer Genome Atlas project. Emergence of chemoresistance frequently renders drug therapies ineffective. MATERIALS AND METHODS We analyzed how CNAs recurrently found in the genomes of TCGA patients of thirty-one tumor types affect protein targets of antineoplastic (AN) agents. RESULTS CNA deletions more frequently affected the targets of AN agents than CNA amplifications. Interestingly, in seven tumors we observed signs of compensatory CNAs. For example, in glioblastoma multiforme, two target genes (FLT1, FLT3) of the experimental drug sorafenib were recurrently deleted, whereas another target (KDR) of sorafenib was recurrently amplified. In renal clear cell carcinoma, the target FLT1 of pazopanib, sunitinib, sorafenib, and axitinib was recurrently deleted, whereas FLT4 bound by the same drugs, was recurrently amplified. CONCLUSION Deletions of AN target proteins can be compensated by amplification of alternative targets.
Collapse
Affiliation(s)
- Ha Vu Tran
- Saarland University, Center for Bioinformatics, Saarbruecken, Germany
- Department of Computer Science, Faculty of Information Technology, Vietnam National University of Agriculture, Hanoi, Vietnam
| | - Alexandra K Kiemer
- Saarland University, Department of Pharmacy, Pharmaceutical Biology, Saarbruecken, Germany
| | - Volkhard Helms
- Saarland University, Center for Bioinformatics, Saarbruecken, Germany
| |
Collapse
|
45
|
Mishra S, Van Rechem C, Pal S, Clarke TL, Chakraborty D, Mahan SD, Black JC, Murphy SE, Lawrence MS, Daniels DL, Whetstine JR. Cross-talk between Lysine-Modifying Enzymes Controls Site-Specific DNA Amplifications. Cell 2018; 174:803-817.e16. [PMID: 30057114 PMCID: PMC6212369 DOI: 10.1016/j.cell.2018.06.018] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 04/02/2018] [Accepted: 06/08/2018] [Indexed: 12/28/2022]
Abstract
Acquired chromosomal DNA amplifications are features of many tumors. Although overexpression and stabilization of the histone H3 lysine 9/36 (H3K9/36) tri-demethylase KDM4A generates transient site-specific copy number gains (TSSGs), additional mechanisms directly controlling site-specific DNA copy gains are not well defined. In this study, we uncover a collection of H3K4-modifying chromatin regulators that function with H3K9 and H3K36 regulators to orchestrate TSSGs. Specifically, the H3K4 tri-demethylase KDM5A and specific COMPASS/KMT2 H3K4 methyltransferases modulate different TSSG loci through H3K4 methylation states and KDM4A recruitment. Furthermore, a distinct chromatin modifier network, MLL1-KDM4B-KDM5B, controls copy number regulation at a specific genomic locus in a KDM4A-independent manner. These pathways comprise an epigenetic addressing system for defining site-specific DNA rereplication and amplifications.
Collapse
Affiliation(s)
- Sweta Mishra
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, 13(th) Street, Charlestown, MA 02129, USA
| | - Capucine Van Rechem
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, 13(th) Street, Charlestown, MA 02129, USA
| | - Sangita Pal
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, 13(th) Street, Charlestown, MA 02129, USA
| | - Thomas L Clarke
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, 13(th) Street, Charlestown, MA 02129, USA
| | - Damayanti Chakraborty
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, 13(th) Street, Charlestown, MA 02129, USA
| | - Sarah D Mahan
- Promega Corporation, 2800 Woods Hollow Road, Madison, WI 53711, USA
| | - Joshua C Black
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, 13(th) Street, Charlestown, MA 02129, USA
| | - Sedona E Murphy
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, 13(th) Street, Charlestown, MA 02129, USA
| | - Michael S Lawrence
- Massachusetts General Hospital Cancer Center and Department of Pathology, Harvard Medical School, 13th Street, Charlestown, MA 02129, USA; Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA
| | | | - Johnathan R Whetstine
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, 13(th) Street, Charlestown, MA 02129, USA.
| |
Collapse
|
46
|
Tanner LB, Goglia AG, Wei MH, Sehgal T, Parsons LR, Park JO, White E, Toettcher JE, Rabinowitz JD. Four Key Steps Control Glycolytic Flux in Mammalian Cells. Cell Syst 2018; 7:49-62.e8. [PMID: 29960885 PMCID: PMC6062487 DOI: 10.1016/j.cels.2018.06.003] [Citation(s) in RCA: 220] [Impact Index Per Article: 36.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2017] [Revised: 03/29/2018] [Accepted: 06/04/2018] [Indexed: 12/18/2022]
Abstract
Altered glycolysis is a hallmark of diseases including diabetes and cancer. Despite intensive study of the contributions of individual glycolytic enzymes, systems-level analyses of flux control through glycolysis remain limited. Here, we overexpress in two mammalian cell lines the individual enzymes catalyzing each of the 12 steps linking extracellular glucose to excreted lactate, and find substantial flux control at four steps: glucose import, hexokinase, phosphofructokinase, and lactate export (and not at any steps of lower glycolysis). The four flux-controlling steps are specifically upregulated by the Ras oncogene: optogenetic Ras activation rapidly induces the transcription of isozymes catalyzing these four steps and enhances glycolysis. At least one isozyme catalyzing each of these four steps is consistently elevated in human tumors. Thus, in the studied contexts, flux control in glycolysis is concentrated in four key enzymatic steps. Upregulation of these steps in tumors likely underlies the Warburg effect.
Collapse
Affiliation(s)
- Lukas Bahati Tanner
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Alexander G Goglia
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Monica H Wei
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Talen Sehgal
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Lance R Parsons
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Junyoung O Park
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
| | - Eileen White
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08903, USA; Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, NJ 08854, USA
| | - Jared E Toettcher
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Joshua D Rabinowitz
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; Department of Chemistry, Princeton University, Princeton, NJ 08544, USA.
| |
Collapse
|
47
|
Balanis NG, Graeber TG. Making Mistakes Empowers Cancer Cells. Trends Cancer 2018; 4:461-463. [PMID: 29937042 DOI: 10.1016/j.trecan.2018.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 05/03/2018] [Indexed: 11/30/2022]
Abstract
Lethal cancers have genomes that can reflect a jigsaw puzzle put together in a hurricane. The missing, misjoined, and extra pieces contribute to the driving forces behind the cancer phenotypes. But is this the only reason genomic instability is so prevalent in aggressive cancers? New findings support that the hurricane winds themselves, not just their aftermath, contribute to the cancer phenotype of metastasis.
Collapse
Affiliation(s)
- Nikolas G Balanis
- Department of Molecular and Medical Pharmacology, University of California Los Angeles, Los Angeles, CA, USA
| | - Thomas G Graeber
- Department of Molecular and Medical Pharmacology, University of California Los Angeles, Los Angeles, CA, USA.
| |
Collapse
|
48
|
Ooft ML, van Ipenburg J, van de Loo RJM, de Jong R, Moelans CB, de Bree R, de Herdt MJ, Koljenović S, Baatenburg de Jong R, Hardillo J, Willems SM. Differences in cancer gene copy number alterations between Epstein-Barr virus-positive and Epstein-Barr virus-negative nasopharyngeal carcinoma. Head Neck 2018; 40:1986-1998. [PMID: 29927011 DOI: 10.1002/hed.25195] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2017] [Revised: 01/21/2018] [Accepted: 03/02/2018] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Nasopharyngeal carcinoma (NPC) treatment is mainly based on clinical staging. We hypothesize that better understanding of the molecular heterogeneity of NPC can aid in better treatment decisions. Therefore, the purpose of this study was to present our exploration of cancer gene copy-number alterations (CNAs) of Epstein-Barr virus (EBV)-positive and EBV-negative NPC. METHODS Multiplex ligation-dependent probe amplification was applied to detect CNAs of 36 cancer genes (n = 103). Correlation between CNAs, clinicopathological features, and survival were examined. RESULTS The CNAs occurred significantly more in EBV-negative NPC, with PIK3CA and MCCC1 (P < .001) gain/amplification occurring more frequently. Gain/amplification of cyclin-L1 (CCNL1) and PTK2 (P < .001) predict worse disease-free survival (DFS) in EBV-positive NPC. CONCLUSION The EBV-positive and EBV-negative NPC show some similarities in cancer gene CNAs suggesting a common pathogenic route but also important differences possibly indicating divergence in oncogenesis. Copy number gain/amplification of CCNL1 and PTK2 are possibly good predictors of survival in EBV-positive NPC.
Collapse
Affiliation(s)
- Marc Lucas Ooft
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Jolique van Ipenburg
- Department of Pathology, Erasmus University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Rob J M van de Loo
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Rick de Jong
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Cathy B Moelans
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Remco de Bree
- Department of Head and Neck Surgical Oncology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Martine J de Herdt
- Department of Otorhinolaryngology - Head and Neck Surgery, Erasmus Medical Center, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Senada Koljenović
- Department of Pathology, Erasmus University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - R Baatenburg de Jong
- Department of Otorhinolaryngology - Head and Neck Surgery, Erasmus Medical Center Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - J Hardillo
- Department of Otorhinolaryngology - Head and Neck Surgery, Erasmus Medical Center Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Stefan Martin Willems
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| |
Collapse
|
49
|
Zhu J, Tsai HJ, Gordon MR, Li R. Cellular Stress Associated with Aneuploidy. Dev Cell 2018; 44:420-431. [PMID: 29486194 DOI: 10.1016/j.devcel.2018.02.002] [Citation(s) in RCA: 123] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 01/29/2018] [Accepted: 01/31/2018] [Indexed: 01/10/2023]
Abstract
Aneuploidy, chromosome stoichiometry that deviates from exact multiples of the haploid compliment of an organism, exists in eukaryotic microbes, several normal human tissues, and the majority of solid tumors. Here, we review the current understanding about the cellular stress states that may result from aneuploidy. The topics of aneuploidy-induced proteotoxic, metabolic, replication, and mitotic stress are assessed in the context of the gene dosage imbalance observed in aneuploid cells. We also highlight emerging findings related to the downstream effects of aneuploidy-induced cellular stress on the immune surveillance against aneuploid cells.
Collapse
Affiliation(s)
- Jin Zhu
- Department of Cell Biology, Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Hung-Ji Tsai
- Department of Cell Biology, Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Molly R Gordon
- Department of Cell Biology, Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Rong Li
- Department of Cell Biology, Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD 21218, USA.
| |
Collapse
|
50
|
Bi J, Wu S, Zhang W, Mischel PS. Targeting cancer's metabolic co-dependencies: A landscape shaped by genotype and tissue context. Biochim Biophys Acta Rev Cancer 2018; 1870:76-87. [PMID: 29775654 DOI: 10.1016/j.bbcan.2018.05.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 05/13/2018] [Indexed: 12/25/2022]
Abstract
Tumors cells reprogram their metabolism to fuel rapid growth. The ability to trace nutrient fluxes in the context of specific alterations has provided new mechanistic insight into the process of oncogenic transformation. A broad array of complementary genetic, epigenetic, transcriptional and translational mechanisms has been identified, revealing a metabolic landscape of cancer. However, cancer metabolism is not a static or uniform process, including within a single tumor. Tumor cells adapt to changing environmental conditions, profoundly shaping the enzymatic dependencies of individual cells. The underlying molecular mechanisms of adaptation, and the specific interactions between tumor genotype, oncogenic signaling, and tissue/biochemical context, remain incompletely understood. In this review, we examine dynamic aspects of how metabolic dependencies develop in cancer, shaped both by genotype and biochemical environment, and review how these interlaced processes generate targetable metabolic vulnerabilities. This article is part of a Special Issue entitled: Cancer Metabolism edited by Dr. Chi Van Dang.
Collapse
Affiliation(s)
- Junfeng Bi
- Ludwig Institute for Cancer Research, University of California, San Diego, La Jolla, CA 92093, USA
| | - Sihan Wu
- Ludwig Institute for Cancer Research, University of California, San Diego, La Jolla, CA 92093, USA
| | - Wenjing Zhang
- Ludwig Institute for Cancer Research, University of California, San Diego, La Jolla, CA 92093, USA
| | - Paul S Mischel
- Ludwig Institute for Cancer Research, University of California, San Diego, La Jolla, CA 92093, USA; Department of Pathology, UCSD School of Medicine, La Jolla, CA 92093, USA; Moores Cancer Center, UCSD School of Medicine, La Jolla, CA 92093, USA.
| |
Collapse
|