1
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Mulet-Lazaro R, Delwel R. Oncogenic Enhancers in Leukemia. Blood Cancer Discov 2024; 5:303-317. [PMID: 39093124 PMCID: PMC11369600 DOI: 10.1158/2643-3230.bcd-23-0211] [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: 03/01/2024] [Revised: 06/06/2024] [Accepted: 07/17/2024] [Indexed: 08/04/2024] Open
Abstract
Although the study of leukemogenesis has traditionally focused on protein-coding genes, the role of enhancer dysregulation is becoming increasingly recognized. The advent of high-throughput sequencing, together with a better understanding of enhancer biology, has revealed how various genetic and epigenetic lesions produce oncogenic enhancers that drive transformation. These aberrations include translocations that lead to enhancer hijacking, point mutations that modulate enhancer activity, and copy number alterations that modify enhancer dosage. In this review, we describe these mechanisms in the context of leukemia and discuss potential therapeutic avenues to target these regulatory elements. Significance: Large-scale sequencing projects have uncovered recurrent gene mutations in leukemia, but the picture remains incomplete: some patients harbor no such aberrations, whereas others carry only a few that are insufficient to bring about transformation on their own. One of the missing pieces is enhancer dysfunction, which only recently has emerged as a critical driver of leukemogenesis. Knowledge of the various mechanisms of enhancer dysregulation is thus key for a complete understanding of leukemia and its causes, as well as the development of targeted therapies in the era of precision medicine.
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Affiliation(s)
- Roger Mulet-Lazaro
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands.
- Oncode Institute, Utrecht, the Netherlands.
| | - Ruud Delwel
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands.
- Oncode Institute, Utrecht, the Netherlands.
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2
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Jayne ND, Liang Z, Lim DH, Chen PB, Diaz C, Arimoto KI, Xia L, Liu M, Ren B, Fu XD, Zhang DE. RUNX1 C-terminal mutations impair blood cell differentiation by perturbing specific enhancer-promoter networks. Blood Adv 2024; 8:2410-2423. [PMID: 38513139 PMCID: PMC11112616 DOI: 10.1182/bloodadvances.2023011484] [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: 08/19/2023] [Revised: 01/02/2024] [Accepted: 02/15/2024] [Indexed: 03/23/2024] Open
Abstract
ABSTRACT The transcription factor RUNX1 is a master regulator of hematopoiesis and is frequently mutated in myeloid malignancies. Mutations in its runt homology domain (RHD) frequently disrupt DNA binding and result in loss of RUNX1 function. However, it is not clearly understood how other RUNX1 mutations contribute to disease development. Here, we characterized RUNX1 mutations outside of the RHD. Our analysis of the patient data sets revealed that mutations within the C-terminus frequently occur in hematopoietic disorders. Remarkably, most of these mutations were nonsense or frameshift mutations and were predicted to be exempt from nonsense-mediated messenger RNA decay. Therefore, this class of mutation is projected to produce DNA-binding proteins that contribute to the pathogenesis in a distinct manner. To model this, we introduced the RUNX1R320∗ mutation into the endogenous gene locus and demonstrated the production of RUNX1R320∗ protein. Expression of RUNX1R320∗ resulted in the disruption of RUNX1 regulated processes such as megakaryocytic differentiation, through a transcriptional signature different from RUNX1 depletion. To understand the underlying mechanisms, we used Global RNA Interactions with DNA by deep sequencing (GRID-seq) to examine enhancer-promoter connections. We identified widespread alterations in the enhancer-promoter networks within RUNX1 mutant cells. Additionally, we uncovered enrichment of RUNX1R320∗ and FOXK2 binding at the MYC super enhancer locus, significantly upregulating MYC transcription and signaling pathways. Together, our study demonstrated that most RUNX1 mutations outside the DNA-binding domain are not subject to nonsense-mediated decay, producing protein products that act in concert with additional cofactors to dysregulate hematopoiesis through mechanisms distinct from those induced by RUNX1 depletion.
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Affiliation(s)
- Nathan D. Jayne
- Moores UCSD Cancer Center, University of California San Diego, La Jolla, CA
- School of Biological Sciences, University of California San Diego, La Jolla, CA
| | - Zhengyu Liang
- School of Medicine, University of California San Diego, La Jolla, CA
| | - Do-Hwan Lim
- School of Medicine, University of California San Diego, La Jolla, CA
| | - Poshen B. Chen
- School of Medicine, University of California San Diego, La Jolla, CA
| | - Cristina Diaz
- Moores UCSD Cancer Center, University of California San Diego, La Jolla, CA
- School of Biological Sciences, University of California San Diego, La Jolla, CA
| | - Kei-Ichiro Arimoto
- Moores UCSD Cancer Center, University of California San Diego, La Jolla, CA
| | - Lingbo Xia
- Moores UCSD Cancer Center, University of California San Diego, La Jolla, CA
- School of Biological Sciences, University of California San Diego, La Jolla, CA
| | - Mengdan Liu
- Moores UCSD Cancer Center, University of California San Diego, La Jolla, CA
- School of Biological Sciences, University of California San Diego, La Jolla, CA
| | - Bing Ren
- School of Medicine, University of California San Diego, La Jolla, CA
| | - Xiang-Dong Fu
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
| | - Dong-Er Zhang
- Moores UCSD Cancer Center, University of California San Diego, La Jolla, CA
- School of Biological Sciences, University of California San Diego, La Jolla, CA
- School of Medicine, University of California San Diego, La Jolla, CA
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3
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Rosean S, Sosa EA, O'Shea D, Raj SM, Seoighe C, Greally JM. Regulatory landscape enrichment analysis (RLEA): a computational toolkit for non-coding variant enrichment and cell type prioritization. BMC Bioinformatics 2024; 25:179. [PMID: 38714913 PMCID: PMC11075237 DOI: 10.1186/s12859-024-05794-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 04/22/2024] [Indexed: 05/12/2024] Open
Abstract
BACKGROUND As genomic studies continue to implicate non-coding sequences in disease, testing the roles of these variants requires insights into the cell type(s) in which they are likely to be mediating their effects. Prior methods for associating non-coding variants with cell types have involved approaches using linkage disequilibrium or ontological associations, incurring significant processing requirements. GaiaAssociation is a freely available, open-source software that enables thousands of genomic loci implicated in a phenotype to be tested for enrichment at regulatory loci of multiple cell types in minutes, permitting insights into the cell type(s) mediating the studied phenotype. RESULTS In this work, we present Regulatory Landscape Enrichment Analysis (RLEA) by GaiaAssociation and demonstrate its capability to test the enrichment of 12,133 variants across the cis-regulatory regions of 44 cell types. This analysis was completed in 134.0 ± 2.3 s, highlighting the efficient processing provided by GaiaAssociation. The intuitive interface requires only four inputs, offers a collection of customizable functions, and visualizes variant enrichment in cell-type regulatory regions through a heatmap matrix. GaiaAssociation is available on PyPi for download as a command line tool or Python package and the source code can also be installed from GitHub at https://github.com/GreallyLab/gaiaAssociation . CONCLUSIONS GaiaAssociation is a novel package that provides an intuitive and efficient resource to understand the enrichment of non-coding variants across the cis-regulatory regions of different cells, empowering studies seeking to identify disease-mediating cell types.
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Affiliation(s)
- Samuel Rosean
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Eric A Sosa
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Dónal O'Shea
- School of Mathematics, Statistics & Applied Mathematics, National University of Ireland Galway, Galway, H91 TK33, Ireland
| | - Srilakshmi M Raj
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Cathal Seoighe
- School of Mathematics, Statistics & Applied Mathematics, National University of Ireland Galway, Galway, H91 TK33, Ireland
| | - John M Greally
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA.
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4
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Nuno K, Azizi A, Koehnke T, Lareau C, Ediriwickrema A, Corces MR, Satpathy AT, Majeti R. Convergent epigenetic evolution drives relapse in acute myeloid leukemia. eLife 2024; 13:e93019. [PMID: 38647535 PMCID: PMC11034943 DOI: 10.7554/elife.93019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 03/26/2024] [Indexed: 04/25/2024] Open
Abstract
Relapse of acute myeloid leukemia (AML) is highly aggressive and often treatment refractory. We analyzed previously published AML relapse cohorts and found that 40% of relapses occur without changes in driver mutations, suggesting that non-genetic mechanisms drive relapse in a large proportion of cases. We therefore characterized epigenetic patterns of AML relapse using 26 matched diagnosis-relapse samples with ATAC-seq. This analysis identified a relapse-specific chromatin accessibility signature for mutationally stable AML, suggesting that AML undergoes epigenetic evolution at relapse independent of mutational changes. Analysis of leukemia stem cell (LSC) chromatin changes at relapse indicated that this leukemic compartment underwent significantly less epigenetic evolution than non-LSCs, while epigenetic changes in non-LSCs reflected overall evolution of the bulk leukemia. Finally, we used single-cell ATAC-seq paired with mitochondrial sequencing (mtscATAC) to map clones from diagnosis into relapse along with their epigenetic features. We found that distinct mitochondrially-defined clones exhibit more similar chromatin accessibility at relapse relative to diagnosis, demonstrating convergent epigenetic evolution in relapsed AML. These results demonstrate that epigenetic evolution is a feature of relapsed AML and that convergent epigenetic evolution can occur following treatment with induction chemotherapy.
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Affiliation(s)
- Kevin Nuno
- Cancer Biology Graduate Program, Stanford University School of MedicineStanfordUnited States
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of MedicineStanfordUnited States
- Cancer Institute, Stanford University School of MedicineStanfordUnited States
- Department of Medicine, Division of Hematology, Stanford University School of MedicineStanfordUnited States
| | - Armon Azizi
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of MedicineStanfordUnited States
- Cancer Institute, Stanford University School of MedicineStanfordUnited States
- Department of Medicine, Division of Hematology, Stanford University School of MedicineStanfordUnited States
- University of California Irvine School of MedicineIrvineUnited States
| | - Thomas Koehnke
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of MedicineStanfordUnited States
- Cancer Institute, Stanford University School of MedicineStanfordUnited States
- Department of Medicine, Division of Hematology, Stanford University School of MedicineStanfordUnited States
| | - Caleb Lareau
- Department of Pathology, Stanford UniversityStanfordUnited States
- Program in Immunology, Stanford UniversityStanfordUnited States
| | - Asiri Ediriwickrema
- Cancer Biology Graduate Program, Stanford University School of MedicineStanfordUnited States
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of MedicineStanfordUnited States
- Cancer Institute, Stanford University School of MedicineStanfordUnited States
- Department of Medicine, Division of Hematology, Stanford University School of MedicineStanfordUnited States
| | - M Ryan Corces
- Cancer Biology Graduate Program, Stanford University School of MedicineStanfordUnited States
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of MedicineStanfordUnited States
- Cancer Institute, Stanford University School of MedicineStanfordUnited States
- Department of Medicine, Division of Hematology, Stanford University School of MedicineStanfordUnited States
- Gladstone Institute of Neurological DiseaseSan FranciscoUnited States
- Gladstone Institute of Data Science and BiotechnologySan FranciscoUnited States
- Department of Neurology, University of California, San FranciscoSan FranciscoUnited States
| | - Ansuman T Satpathy
- Department of Pathology, Stanford UniversityStanfordUnited States
- Program in Immunology, Stanford UniversityStanfordUnited States
- Parker Institute for Cancer Immunotherapy, Stanford UniversityStanfordUnited States
- Gladstone-UCSF Institute of Genomic ImmunologySan FranciscoUnited States
| | - Ravindra Majeti
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of MedicineStanfordUnited States
- Cancer Institute, Stanford University School of MedicineStanfordUnited States
- Department of Medicine, Division of Hematology, Stanford University School of MedicineStanfordUnited States
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5
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Wright S, Zhao X, Rosikiewicz W, Mryncza S, Hyle J, Qi W, Liu Z, Yi S, Cheng Y, Xu B, Li C. Systematic characterization of the HOXA9 downstream targets in MLL-r leukemia by noncoding CRISPR screens. Nat Commun 2023; 14:7464. [PMID: 38016946 PMCID: PMC10684515 DOI: 10.1038/s41467-023-43264-5] [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: 10/20/2022] [Accepted: 11/02/2023] [Indexed: 11/30/2023] Open
Abstract
Accumulating evidence indicates that HOXA9 dysregulation is necessary and sufficient for leukemic transformation and maintenance. However, it remains largely unknown how HOXA9, as a homeobox transcriptional factor, binds to noncoding regulatory sequences and controls the downstream genes. Here, we conduct dropout CRISPR screens against 229 HOXA9-bound peaks identified by ChIP-seq. Integrative data analysis identifies reproducible noncoding hits, including those located in the distal enhancer of FLT3 and intron of CDK6. The Cas9-editing and dCas9-KRAB silencing of the HOXA9-bound sites significantly reduce corresponding gene transcription and impair cell proliferation in vitro, and in vivo by transplantation into NSG female mice. In addition, RNA-seq, Q-PCR analysis, chromatin accessibility change, and chromatin conformation evaluation uncover the noncoding regulation mechanism of HOXA9 and its functional downstream genes. In summary, our work improves our understanding of how HOXA9-associated transcription programs reconstruct the regulatory network specifying MLL-r dependency.
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Affiliation(s)
- Shaela Wright
- Department of Tumor Cell Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Xujie Zhao
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
- Zhongda Hospital, School of Life Sciences and Technology, Advanced Institute for Life and Health, Southeast University, Nanjing, 210096, China
| | - Wojciech Rosikiewicz
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Shelby Mryncza
- Department of Biology, Rhodes College, 2000 North Pkwy, Memphis, TN, 38112, USA
| | - Judith Hyle
- Department of Tumor Cell Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Wenjie Qi
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Zhenling Liu
- Department of Tumor Cell Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Siqi Yi
- Department of Hematology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Yong Cheng
- Department of Hematology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Beisi Xu
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Chunliang Li
- Department of Tumor Cell Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA.
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6
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Wang Z, Luo M, Liang Q, Zhao K, Hu Y, Wang W, Feng X, Hu B, Teng J, You T, Li R, Bao Z, Pan W, Yang T, Zhang C, Li T, Dong X, Yi X, Liu B, Zhao L, Li M, Chen K, Song W, Yang J, Li MJ. Landscape of enhancer disruption and functional screen in melanoma cells. Genome Biol 2023; 24:248. [PMID: 37904237 PMCID: PMC10614365 DOI: 10.1186/s13059-023-03087-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 10/12/2023] [Indexed: 11/01/2023] Open
Abstract
BACKGROUND The high mutation rate throughout the entire melanoma genome presents a major challenge in stratifying true driver events from the background mutations. Numerous recurrent non-coding alterations, such as those in enhancers, can shape tumor evolution, thereby emphasizing the importance in systematically deciphering enhancer disruptions in melanoma. RESULTS Here, we leveraged 297 melanoma whole-genome sequencing samples to prioritize highly recurrent regions. By performing a genome-scale CRISPR interference (CRISPRi) screen on highly recurrent region-associated enhancers in melanoma cells, we identified 66 significant hits which could have tumor-suppressive roles. These functional enhancers show unique mutational patterns independent of classical significantly mutated genes in melanoma. Target gene analysis for the essential enhancers reveal many known and hidden mechanisms underlying melanoma growth. Utilizing extensive functional validation experiments, we demonstrate that a super enhancer element could modulate melanoma cell proliferation by targeting MEF2A, and another distal enhancer is able to sustain PTEN tumor-suppressive potential via long-range interactions. CONCLUSIONS Our study establishes a catalogue of crucial enhancers and their target genes in melanoma growth and progression, and illuminates the identification of novel mechanisms of dysregulation for melanoma driver genes and new therapeutic targeting strategies.
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Affiliation(s)
- Zhao Wang
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Institute of Aging, Key Laboratory of Alzheimer's Disease of Zhejiang Province, The Second Affiliated Hospital, Wenzhou Medical University, Wenzhou, China.
- Department of Epidemiology and Biostatistics, Tianjin Key Laboratory of Molecular Cancer Epidemiology, The Province and Ministry Co-Sponsored Collaborative Innovation Center for Medical Epigenetics, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China.
| | - Menghan Luo
- Department of Epidemiology and Biostatistics, Tianjin Key Laboratory of Molecular Cancer Epidemiology, The Province and Ministry Co-Sponsored Collaborative Innovation Center for Medical Epigenetics, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
- Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Qian Liang
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Institute of Aging, Key Laboratory of Alzheimer's Disease of Zhejiang Province, The Second Affiliated Hospital, Wenzhou Medical University, Wenzhou, China
- Department of Epidemiology and Biostatistics, Tianjin Key Laboratory of Molecular Cancer Epidemiology, The Province and Ministry Co-Sponsored Collaborative Innovation Center for Medical Epigenetics, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
- Scientific Research Center, Wenzhou Medical University, Wenzhou, China
| | - Ke Zhao
- Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Yuelin Hu
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Institute of Aging, Key Laboratory of Alzheimer's Disease of Zhejiang Province, The Second Affiliated Hospital, Wenzhou Medical University, Wenzhou, China
| | - Wei Wang
- Department of Epidemiology and Biostatistics, Tianjin Key Laboratory of Molecular Cancer Epidemiology, The Province and Ministry Co-Sponsored Collaborative Innovation Center for Medical Epigenetics, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Xiangling Feng
- Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Bolang Hu
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Institute of Aging, Key Laboratory of Alzheimer's Disease of Zhejiang Province, The Second Affiliated Hospital, Wenzhou Medical University, Wenzhou, China
| | - Jianjin Teng
- Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Tianyi You
- Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Ran Li
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Institute of Aging, Key Laboratory of Alzheimer's Disease of Zhejiang Province, The Second Affiliated Hospital, Wenzhou Medical University, Wenzhou, China
| | - Zhengkai Bao
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Institute of Aging, Key Laboratory of Alzheimer's Disease of Zhejiang Province, The Second Affiliated Hospital, Wenzhou Medical University, Wenzhou, China
| | - Wenhao Pan
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Institute of Aging, Key Laboratory of Alzheimer's Disease of Zhejiang Province, The Second Affiliated Hospital, Wenzhou Medical University, Wenzhou, China
| | - Tielong Yang
- Department of Bone and Soft Tissue Tumor, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Chao Zhang
- Department of Bone and Soft Tissue Tumor, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Ting Li
- Department of Bone and Soft Tissue Tumor, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Xiaobao Dong
- Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Xianfu Yi
- Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Ben Liu
- Department of Epidemiology and Biostatistics, Tianjin Key Laboratory of Molecular Cancer Epidemiology, The Province and Ministry Co-Sponsored Collaborative Innovation Center for Medical Epigenetics, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Li Zhao
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Miaoxin Li
- Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
| | - Kexin Chen
- Department of Epidemiology and Biostatistics, Tianjin Key Laboratory of Molecular Cancer Epidemiology, The Province and Ministry Co-Sponsored Collaborative Innovation Center for Medical Epigenetics, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Weihong Song
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Institute of Aging, Key Laboratory of Alzheimer's Disease of Zhejiang Province, The Second Affiliated Hospital, Wenzhou Medical University, Wenzhou, China.
| | - Jilong Yang
- Department of Bone and Soft Tissue Tumor, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China.
| | - Mulin Jun Li
- Department of Epidemiology and Biostatistics, Tianjin Key Laboratory of Molecular Cancer Epidemiology, The Province and Ministry Co-Sponsored Collaborative Innovation Center for Medical Epigenetics, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China.
- Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China.
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7
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Nuno KA, Azizi A, Köhnke T, Lareau CA, Ediwirickrema A, Ryan Corces M, Satpathy AT, Majeti R. Convergent Epigenetic Evolution Drives Relapse in Acute Myeloid Leukemia. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.10.561642. [PMID: 37873452 PMCID: PMC10592718 DOI: 10.1101/2023.10.10.561642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Relapse of acute myeloid leukemia (AML) is highly aggressive and often treatment refractory. We analyzed previously published AML relapse cohorts and found that 40% of relapses occur without changes in driver mutations, suggesting that non-genetic mechanisms drive relapse in a large proportion of cases. We therefore characterized epigenetic patterns of AML relapse using 26 matched diagnosis-relapse samples with ATAC-seq. This analysis identified a relapse-specific chromatin accessibility signature for mutationally stable AML, suggesting that AML undergoes epigenetic evolution at relapse independent of mutational changes. Analysis of leukemia stem cell (LSC) chromatin changes at relapse indicated that this leukemic compartment underwent significantly less epigenetic evolution than non-LSCs, while epigenetic changes in non-LSCs reflected overall evolution of the bulk leukemia. Finally, we used single-cell ATAC-seq paired with mitochondrial sequencing (mtscATAC) to map clones from diagnosis into relapse along with their epigenetic features. We found that distinct mitochondrially-defined clones exhibit more similar chromatin accessibility at relapse relative to diagnosis, demonstrating convergent epigenetic evolution in relapsed AML. These results demonstrate that epigenetic evolution is a feature of relapsed AML and that convergent epigenetic evolution can occur following treatment with induction chemotherapy.
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Affiliation(s)
- Kevin A Nuno
- Cancer Biology Graduate Program, Stanford University School of Medicine, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medicine, Division of Hematology, Stanford University School of Medicine, Stanford, CA, USA
- These authors contributed to this work equally
| | - Armon Azizi
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medicine, Division of Hematology, Stanford University School of Medicine, Stanford, CA, USA
- University of California Irvine School of Medicine, Irvine, California
- These authors contributed to this work equally
| | - Thomas Köhnke
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medicine, Division of Hematology, Stanford University School of Medicine, Stanford, CA, USA
| | - Caleb A Lareau
- Department of Pathology, Stanford University, Stanford, CA, USA
- Program in Immunology, Stanford University, Stanford, CA, USA
| | - Asiri Ediwirickrema
- Cancer Biology Graduate Program, Stanford University School of Medicine, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medicine, Division of Hematology, Stanford University School of Medicine, Stanford, CA, USA
| | - M Ryan Corces
- Cancer Biology Graduate Program, Stanford University School of Medicine, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medicine, Division of Hematology, Stanford University School of Medicine, Stanford, CA, USA
- Gladstone Institute of Neurological Disease, San Francisco, California
- Gladstone Institute of Data Science and Biotechnology, San Francisco, California
- Department of Neurology, University of California San Francisco, San Francisco, California
| | - Ansuman T Satpathy
- Department of Pathology, Stanford University, Stanford, CA, USA
- Program in Immunology, Stanford University, Stanford, CA, USA
- Parker Institute for Cancer Immunotherapy, Stanford University, Stanford, CA, USA
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
| | - Ravindra Majeti
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medicine, Division of Hematology, Stanford University School of Medicine, Stanford, CA, USA
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8
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Tanaka M, Nakamura T. Targeting epigenetic aberrations of sarcoma in CRISPR era. Genes Chromosomes Cancer 2023; 62:510-525. [PMID: 36967299 DOI: 10.1002/gcc.23142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 03/21/2023] [Accepted: 03/22/2023] [Indexed: 03/29/2023] Open
Abstract
Sarcomas are rare malignancies that exhibit diverse biological, genetic, morphological, and clinical characteristics. Genetic alterations, such as gene fusions, mutations in transcriptional machinery components, histones, and DNA methylation regulatory molecules, play an essential role in sarcomagenesis. These mutations induce and/or cooperate with specific epigenetic aberrations required for the growth and maintenance of sarcomas. Appropriate mouse models have been developed to clarify the significance of genetic and epigenetic interactions in sarcomas. Studies using the mouse models for human sarcomas have demonstrated major advances in our understanding the developmental processes as well as tumor microenvironment of sarcomas. Recent technological progresses in epigenome editing will not only improve the studies using animal models but also provide a direct clue for epigenetic therapies. In this manuscript, we review important epigenetic aberrations in sarcomas and their representative mouse models, current methods of epigenetic editing using CRISPR/dCas9 systems, and potential applications in sarcoma studies and therapeutics.
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Affiliation(s)
- Miwa Tanaka
- Project for Cancer Epigenomics, The Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
- Department of Experimental Pathology, Institute of Medical Science, Tokyo Medical University, Tokyo, Japan
| | - Takuro Nakamura
- Department of Experimental Pathology, Institute of Medical Science, Tokyo Medical University, Tokyo, Japan
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9
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Esposito R, Lanzós A, Uroda T, Ramnarayanan S, Büchi I, Polidori T, Guillen-Ramirez H, Mihaljevic A, Merlin BM, Mela L, Zoni E, Hovhannisyan L, McCluggage F, Medo M, Basile G, Meise DF, Zwyssig S, Wenger C, Schwarz K, Vancura A, Bosch-Guiteras N, Andrades Á, Tham AM, Roemmele M, Medina PP, Ochsenbein AF, Riether C, Kruithof-de Julio M, Zimmer Y, Medová M, Stroka D, Fox A, Johnson R. Tumour mutations in long noncoding RNAs enhance cell fitness. Nat Commun 2023; 14:3342. [PMID: 37291246 PMCID: PMC10250536 DOI: 10.1038/s41467-023-39160-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 06/01/2023] [Indexed: 06/10/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) are linked to cancer via pathogenic changes in their expression levels. Yet, it remains unclear whether lncRNAs can also impact tumour cell fitness via function-altering somatic "driver" mutations. To search for such driver-lncRNAs, we here perform a genome-wide analysis of fitness-altering single nucleotide variants (SNVs) across a cohort of 2583 primary and 3527 metastatic tumours. The resulting 54 mutated and positively-selected lncRNAs are significantly enriched for previously-reported cancer genes and a range of clinical and genomic features. A number of these lncRNAs promote tumour cell proliferation when overexpressed in in vitro models. Our results also highlight a dense SNV hotspot in the widely-studied NEAT1 oncogene. To directly evaluate the functional significance of NEAT1 SNVs, we use in cellulo mutagenesis to introduce tumour-like mutations in the gene and observe a significant and reproducible increase in cell fitness, both in vitro and in a mouse model. Mechanistic studies reveal that SNVs remodel the NEAT1 ribonucleoprotein and boost subnuclear paraspeckles. In summary, this work demonstrates the utility of driver analysis for mapping cancer-promoting lncRNAs, and provides experimental evidence that somatic mutations can act through lncRNAs to enhance pathological cancer cell fitness.
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Affiliation(s)
- Roberta Esposito
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, 3010, Bern, Switzerland.
- Department for BioMedical Research, University of Bern, 3008, Bern, Switzerland.
- Institute of Genetics and Biophysics "Adriano Buzzati-Traverso", CNR, 80131, Naples, Italy.
| | - Andrés Lanzós
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, 3010, Bern, Switzerland
- Department for BioMedical Research, University of Bern, 3008, Bern, Switzerland
- Graduate School of Cellular and Biomedical Sciences, University of Bern, 3012, Bern, Switzerland
| | - Tina Uroda
- School of Biology and Environmental Science, University College Dublin, Dublin, D04 V1W8, Ireland
- Conway Institute for Biomolecular and Biomedical Research, University College Dublin, Dublin, D04 V1W8, Ireland
| | - Sunandini Ramnarayanan
- School of Biology and Environmental Science, University College Dublin, Dublin, D04 V1W8, Ireland
- Conway Institute for Biomolecular and Biomedical Research, University College Dublin, Dublin, D04 V1W8, Ireland
- The SFI Centre for Research Training in Genomics Data Science, Dublin, Ireland
| | - Isabel Büchi
- Department for BioMedical Research, University of Bern, 3008, Bern, Switzerland
- Department of Visceral Surgery and Medicine, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Taisia Polidori
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, 3010, Bern, Switzerland
- Department for BioMedical Research, University of Bern, 3008, Bern, Switzerland
| | - Hugo Guillen-Ramirez
- School of Biology and Environmental Science, University College Dublin, Dublin, D04 V1W8, Ireland
- Conway Institute for Biomolecular and Biomedical Research, University College Dublin, Dublin, D04 V1W8, Ireland
| | - Ante Mihaljevic
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, 3010, Bern, Switzerland
- Department for BioMedical Research, University of Bern, 3008, Bern, Switzerland
| | - Bernard Mefi Merlin
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, 3010, Bern, Switzerland
- Department for BioMedical Research, University of Bern, 3008, Bern, Switzerland
| | - Lia Mela
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, 3010, Bern, Switzerland
- Department for BioMedical Research, University of Bern, 3008, Bern, Switzerland
| | - Eugenio Zoni
- Department for BioMedical Research, University of Bern, 3008, Bern, Switzerland
- Department of Urology, Inselspital, Bern University Hospital, Bern, Switzerland
| | - Lusine Hovhannisyan
- Department for BioMedical Research, University of Bern, 3008, Bern, Switzerland
- Department of Radiation Oncology, Inselspital, Bern University Hospital and University of Bern, Bern, Switzerland
| | - Finn McCluggage
- School of Molecular Sciences, University of Western Australia, Crawley, WA, Australia
- School of Human Sciences, University of Western Australia, Crawley, WA, Australia
| | - Matúš Medo
- Department for BioMedical Research, University of Bern, 3008, Bern, Switzerland
- Department of Radiation Oncology, Inselspital, Bern University Hospital and University of Bern, Bern, Switzerland
| | - Giulia Basile
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, 3010, Bern, Switzerland
- Department for BioMedical Research, University of Bern, 3008, Bern, Switzerland
| | - Dominik F Meise
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, 3010, Bern, Switzerland
- Department for BioMedical Research, University of Bern, 3008, Bern, Switzerland
| | - Sandra Zwyssig
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, 3010, Bern, Switzerland
- Department for BioMedical Research, University of Bern, 3008, Bern, Switzerland
| | - Corina Wenger
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, 3010, Bern, Switzerland
- Department for BioMedical Research, University of Bern, 3008, Bern, Switzerland
| | - Kyriakos Schwarz
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, 3010, Bern, Switzerland
- Department for BioMedical Research, University of Bern, 3008, Bern, Switzerland
| | - Adrienne Vancura
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, 3010, Bern, Switzerland
- Department for BioMedical Research, University of Bern, 3008, Bern, Switzerland
| | - Núria Bosch-Guiteras
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, 3010, Bern, Switzerland
- Department for BioMedical Research, University of Bern, 3008, Bern, Switzerland
- Graduate School of Cellular and Biomedical Sciences, University of Bern, 3012, Bern, Switzerland
| | - Álvaro Andrades
- GENYO, Centre for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Government, Granada, 18016, Spain
- Instituto de Investigación Biosanitaria, Granada, 18014, Spain
- Department of Biochemistry and Molecular Biology I, University of Granada, Granada, 18071, Spain
| | - Ai Ming Tham
- School of Biology and Environmental Science, University College Dublin, Dublin, D04 V1W8, Ireland
- Conway Institute for Biomolecular and Biomedical Research, University College Dublin, Dublin, D04 V1W8, Ireland
| | - Michaela Roemmele
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, 3010, Bern, Switzerland
- Department for BioMedical Research, University of Bern, 3008, Bern, Switzerland
| | - Pedro P Medina
- GENYO, Centre for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Government, Granada, 18016, Spain
- Instituto de Investigación Biosanitaria, Granada, 18014, Spain
- Department of Biochemistry and Molecular Biology I, University of Granada, Granada, 18071, Spain
| | - Adrian F Ochsenbein
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, 3010, Bern, Switzerland
- Department for BioMedical Research, University of Bern, 3008, Bern, Switzerland
| | - Carsten Riether
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, 3010, Bern, Switzerland
- Department for BioMedical Research, University of Bern, 3008, Bern, Switzerland
| | - Marianna Kruithof-de Julio
- Department for BioMedical Research, University of Bern, 3008, Bern, Switzerland
- Department of Urology, Inselspital, Bern University Hospital, Bern, Switzerland
| | - Yitzhak Zimmer
- Department for BioMedical Research, University of Bern, 3008, Bern, Switzerland
- Department of Radiation Oncology, Inselspital, Bern University Hospital and University of Bern, Bern, Switzerland
| | - Michaela Medová
- Department for BioMedical Research, University of Bern, 3008, Bern, Switzerland
- Department of Radiation Oncology, Inselspital, Bern University Hospital and University of Bern, Bern, Switzerland
| | - Deborah Stroka
- Department for BioMedical Research, University of Bern, 3008, Bern, Switzerland
- Department of Visceral Surgery and Medicine, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Archa Fox
- School of Molecular Sciences, University of Western Australia, Crawley, WA, Australia
- School of Human Sciences, University of Western Australia, Crawley, WA, Australia
| | - Rory Johnson
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, 3010, Bern, Switzerland.
- Department for BioMedical Research, University of Bern, 3008, Bern, Switzerland.
- School of Biology and Environmental Science, University College Dublin, Dublin, D04 V1W8, Ireland.
- Conway Institute for Biomolecular and Biomedical Research, University College Dublin, Dublin, D04 V1W8, Ireland.
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10
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Lyu J, Liu Y, Gong L, Chen M, Madanat YF, Zhang Y, Cai F, Gu Z, Cao H, Kaphle P, Kim YJ, Kalkan FN, Stephens H, Dickerson KE, Ni M, Chen W, Patel P, Mims AS, Borate U, Burd A, Cai SF, Yin CC, You MJ, Chung SS, Collins RH, DeBerardinis RJ, Liu X, Xu J. Disabling Uncompetitive Inhibition of Oncogenic IDH Mutations Drives Acquired Resistance. Cancer Discov 2023; 13:170-193. [PMID: 36222845 PMCID: PMC9827114 DOI: 10.1158/2159-8290.cd-21-1661] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 08/31/2022] [Accepted: 10/04/2022] [Indexed: 01/16/2023]
Abstract
Mutations in IDH genes occur frequently in acute myeloid leukemia (AML) and other human cancers to generate the oncometabolite R-2HG. Allosteric inhibition of mutant IDH suppresses R-2HG production in a subset of patients with AML; however, acquired resistance emerges as a new challenge, and the underlying mechanisms remain incompletely understood. Here we establish isogenic leukemia cells containing common IDH oncogenic mutations by CRISPR base editing. By mutational scanning of IDH single amino acid variants in base-edited cells, we describe a repertoire of IDH second-site mutations responsible for therapy resistance through disabling uncompetitive enzyme inhibition. Recurrent mutations at NADPH binding sites within IDH heterodimers act in cis or trans to prevent the formation of stable enzyme-inhibitor complexes, restore R-2HG production in the presence of inhibitors, and drive therapy resistance in IDH-mutant AML cells and patients. We therefore uncover a new class of pathogenic mutations and mechanisms for acquired resistance to targeted cancer therapies. SIGNIFICANCE Comprehensive scanning of IDH single amino acid variants in base-edited leukemia cells uncovers recurrent mutations conferring resistance to IDH inhibition through disabling NADPH-dependent uncompetitive inhibition. Together with targeted sequencing, structural, and functional studies, we identify a new class of pathogenic mutations and mechanisms for acquired resistance to IDH-targeting cancer therapies. This article is highlighted in the In This Issue feature, p. 1.
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Affiliation(s)
- Junhua Lyu
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, Texas
- Department of Pediatrics, Harold C. Simmons Comprehensive Cancer Center, and Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Yuxuan Liu
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, Texas
- Department of Pediatrics, Harold C. Simmons Comprehensive Cancer Center, and Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Lihu Gong
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, Department of Obstetrics and Gynecology, and Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Mingyi Chen
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Yazan F. Madanat
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Yuannyu Zhang
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, Texas
- Department of Pediatrics, Harold C. Simmons Comprehensive Cancer Center, and Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Feng Cai
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Zhimin Gu
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, Texas
- Department of Pediatrics, Harold C. Simmons Comprehensive Cancer Center, and Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Hui Cao
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, Texas
- Department of Pediatrics, Harold C. Simmons Comprehensive Cancer Center, and Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Pranita Kaphle
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, Texas
- Department of Pediatrics, Harold C. Simmons Comprehensive Cancer Center, and Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Yoon Jung Kim
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, Texas
- Department of Pediatrics, Harold C. Simmons Comprehensive Cancer Center, and Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Fatma N. Kalkan
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Helen Stephens
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Kathryn E. Dickerson
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, Texas
- Department of Pediatrics, Harold C. Simmons Comprehensive Cancer Center, and Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Min Ni
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Weina Chen
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Prapti Patel
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Alice S. Mims
- Division of Hematology, Department of Internal Medicine, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio
| | - Uma Borate
- Division of Hematology and Medical Oncology, Department of Medicine, Oregon Health and Science University, Portland, Oregon
| | - Amy Burd
- The Leukemia & Lymphoma Society, Rye Brook, New York
| | - Sheng F. Cai
- Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - C. Cameron Yin
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - M. James You
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Stephen S. Chung
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Robert H. Collins
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Ralph J. DeBerardinis
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, Texas
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Xin Liu
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, Department of Obstetrics and Gynecology, and Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Jian Xu
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, Texas
- Department of Pediatrics, Harold C. Simmons Comprehensive Cancer Center, and Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas
- Corresponding Author: Jian Xu, Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, 6000 Harry Hines Boulevard, Dallas, TX 75235. Phone: 214-648-6125; E-mail:
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11
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Botten GA, Lee M, Xu J. Dissecting Locus-Specific Chromatin Interactions by CRISPR CAPTURE. Methods Mol Biol 2023; 2599:69-97. [PMID: 36427144 PMCID: PMC10395504 DOI: 10.1007/978-1-0716-2847-8_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] [Indexed: 06/16/2023]
Abstract
The spatiotemporal control of tissue-specific gene expression is coordinated by cis-regulatory elements (CREs) and associated trans-acting factors. Despite major advances in genome-wide annotation of candidate CREs, the in situ regulatory composition of the vast majority of CREs remain unknown. To address this challenge, we developed the CRISPR affinity purification in situ of regulatory elements (CAPTURE) toolbox that employs an in vivo biotinylated nuclease-deficient Cas9 (dCas9) protein and programmable single-guide RNAs (sgRNAs) to identify CRE-associated macromolecular complexes and chromatin looping. In this chapter, we provide a detailed protocol for implementing the latest iteration of the CRISPR-based CAPTURE methods to interrogate the molecular composition of locus-specific chromatin complexes and configuration in a mammalian genome.
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Affiliation(s)
- Giovanni A Botten
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Pediatrics, Harold C. Simmons Comprehensive Cancer Center, and Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Michael Lee
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Pediatrics, Harold C. Simmons Comprehensive Cancer Center, and Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jian Xu
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA.
- Department of Pediatrics, Harold C. Simmons Comprehensive Cancer Center, and Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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12
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Cappelletti L, Petrini A, Gliozzo J, Casiraghi E, Schubach M, Kircher M, Valentini G. Boosting tissue-specific prediction of active cis-regulatory regions through deep learning and Bayesian optimization techniques. BMC Bioinformatics 2022; 23:154. [PMID: 36510125 PMCID: PMC9743524 DOI: 10.1186/s12859-022-04582-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 01/20/2022] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Cis-regulatory regions (CRRs) are non-coding regions of the DNA that fine control the spatio-temporal pattern of transcription; they are involved in a wide range of pivotal processes such as the development of specific cell-lines/tissues and the dynamic cell response to physiological stimuli. Recent studies showed that genetic variants occurring in CRRs are strongly correlated with pathogenicity or deleteriousness. Considering the central role of CRRs in the regulation of physiological and pathological conditions, the correct identification of CRRs and of their tissue-specific activity status through Machine Learning methods plays a major role in dissecting the impact of genetic variants on human diseases. Unfortunately, the problem is still open, though some promising results have been already reported by (deep) machine-learning based methods that predict active promoters and enhancers in specific tissues or cell lines by encoding epigenetic or spectral features directly extracted from DNA sequences. RESULTS We present the experiments we performed to compare two Deep Neural Networks, a Feed-Forward Neural Network model working on epigenomic features, and a Convolutional Neural Network model working only on genomic sequence, targeted to the identification of enhancer- and promoter-activity in specific cell lines. While performing experiments to understand how the experimental setup influences the prediction performance of the methods, we particularly focused on (1) automatic model selection performed by Bayesian optimization and (2) exploring different data rebalancing setups for reducing negative unbalancing effects. CONCLUSIONS Results show that (1) automatic model selection by Bayesian optimization improves the quality of the learner; (2) data rebalancing considerably impacts the prediction performance of the models; test set rebalancing may provide over-optimistic results, and should therefore be cautiously applied; (3) despite working on sequence data, convolutional models obtain performance close to those of feed forward models working on epigenomic information, which suggests that also sequence data carries informative content for CRR-activity prediction. We therefore suggest combining both models/data types in future works.
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Affiliation(s)
- Luca Cappelletti
- grid.4708.b0000 0004 1757 2822AnacletoLab, Dipartimento di Informatica, Università degli Studi di Milano, Milan, Italy
| | - Alessandro Petrini
- grid.4708.b0000 0004 1757 2822AnacletoLab, Dipartimento di Informatica, Università degli Studi di Milano, Milan, Italy
| | - Jessica Gliozzo
- grid.4708.b0000 0004 1757 2822AnacletoLab, Dipartimento di Informatica, Università degli Studi di Milano, Milan, Italy
| | - Elena Casiraghi
- grid.4708.b0000 0004 1757 2822AnacletoLab, Dipartimento di Informatica, Università degli Studi di Milano, Milan, Italy
| | - Max Schubach
- grid.6363.00000 0001 2218 4662Berlin Institute of Health at Charité, Universitätsmedizin Berlin, Berlin, Germany
| | - Martin Kircher
- grid.6363.00000 0001 2218 4662Berlin Institute of Health at Charité, Universitätsmedizin Berlin, Berlin, Germany
| | - Giorgio Valentini
- grid.4708.b0000 0004 1757 2822AnacletoLab, Dipartimento di Informatica, Università degli Studi di Milano, Milan, Italy ,European Laboratory for Learning and Intelligent Systems (ELLIS), Berlin, Germany ,CINI National Laboratory of Artificial Intelligence and Intelligent Systems (AIIS), Rome, Italy ,grid.4708.b0000 0004 1757 2822Data Science Research Center, Università degli Studi di Milano, Milan, Italy
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13
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Jayaprakash S, Hegde M, Girisa S, Alqahtani MS, Abbas M, Lee EHC, Yap KCH, Sethi G, Kumar AP, Kunnumakkara AB. Demystifying the Functional Role of Nuclear Receptors in Esophageal Cancer. Int J Mol Sci 2022; 23:ijms231810952. [PMID: 36142861 PMCID: PMC9501100 DOI: 10.3390/ijms231810952] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Revised: 09/14/2022] [Accepted: 09/14/2022] [Indexed: 11/16/2022] Open
Abstract
Esophageal cancer (EC), an aggressive and poorly understood disease, is one of the top causes of cancer-related fatalities. GLOBOCAN 2020 reports that there are 544,076 deaths and 604,100 new cases expected worldwide. Even though there are various advancements in treatment procedures, this cancer has been reported as one of the most difficult cancers to cure, and to increase patient survival; treatment targets still need to be established. Nuclear receptors (NRs) are a type of transcription factor, which has a key role in several biological processes such as reproduction, development, cellular differentiation, stress response, immunity, metabolism, lipids, and drugs, and are essential regulators of several diseases, including cancer. Numerous studies have demonstrated the importance of NRs in tumor immunology and proved the well-known roles of multiple NRs in modulating proliferation, differentiation, and apoptosis. There are surplus of studies conducted on NRs and their implications in EC, but only a few studies have demonstrated the diagnostic and prognostic potential of NRs. Therefore, there is still a paucity of the role of NRs and different ways to target them in EC cells to stop them from spreading malignancy. This review emphasizes the significance of NRs in EC by discussing their diverse agonists as well as antagonists and their response to tumor progression. Additionally, we emphasize NRs’ potential to serve as a novel therapeutic target and their capacity to treat and prevent EC.
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Affiliation(s)
- Sujitha Jayaprakash
- Cancer Biology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology (IIT) Guwahati, Guwahati 781039, Assam, India
| | - Mangala Hegde
- Cancer Biology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology (IIT) Guwahati, Guwahati 781039, Assam, India
| | - Sosmitha Girisa
- Cancer Biology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology (IIT) Guwahati, Guwahati 781039, Assam, India
| | - Mohammed S. Alqahtani
- Radiological Sciences Department, College of Applied Medical Sciences, King Khalid University, Abha 61421, Saudi Arabia
- BioImaging Unit, Space Research Centre, Michael Atiyah Building, University of Leicester, Leicester LE1 7RH, UK
| | - Mohamed Abbas
- Electrical Engineering Department, College of Engineering, King Khalid University, Abha 61421, Saudi Arabia
- Electronics and Communications Department, College of Engineering, Delta University for Science and Technology, Gamasa 35712, Egypt
| | - E. Hui Clarissa Lee
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117600, Singapore
- NUS Center for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore
| | - Kenneth Chun-Hong Yap
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117600, Singapore
- NUS Center for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore
| | - Gautam Sethi
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117600, Singapore
- NUS Center for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore
| | - Alan Prem Kumar
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117600, Singapore
- NUS Center for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore
- Correspondence: (A.P.K.); (A.B.K.)
| | - Ajaikumar B. Kunnumakkara
- Cancer Biology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology (IIT) Guwahati, Guwahati 781039, Assam, India
- Correspondence: (A.P.K.); (A.B.K.)
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14
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Song H, Liu Y, Tan Y, Zhang Y, Jin W, Chen L, Wu S, Yan J, Li J, Chen Z, Chen S, Wang K. Recurrent noncoding somatic and germline WT1 variants converge to disrupt MYB binding in acute promyelocytic leukemia. Blood 2022; 140:1132-1144. [PMID: 35653587 PMCID: PMC9461475 DOI: 10.1182/blood.2021014945] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Accepted: 05/24/2022] [Indexed: 11/22/2022] Open
Abstract
Genetic alternations can occur at noncoding regions, but how they contribute to cancer pathogenesis is poorly understood. Here, we established a mutational landscape of cis-regulatory regions (CREs) in acute promyelocytic leukemia (APL) based on whole-genome sequencing analysis of paired tumor and germline samples from 24 patients and epigenetic profiling of 16 patients. Mutations occurring in CREs occur preferentially in active enhancers bound by the complex of master transcription factors in APL. Among significantly enriched mutated CREs, we found a recurrently mutated region located within the third intron of WT1, an essential regulator of normal and malignant hematopoiesis. Focusing on noncoding mutations within this WT1 intron, an analysis on 169 APL patients revealed that somatic mutations were clustered into a focal hotspot region, including one site identified as a germline polymorphism contributing to APL risk. Significantly decreased WT1 expression was observed in APL patients bearing somatic and/or germline noncoding WT1 variants. Furthermore, biallelic WT1 inactivation was recurrently found in APL patients with noncoding WT1 variants, which resulted in the complete loss of WT1. The high incidence of biallelic inactivation suggested the tumor suppressor activity of WT1 in APL. Mechanistically, noncoding WT1 variants disrupted MYB binding on chromatin and suppressed the enhancer activity and WT1 expression through destroying the chromatin looping formation. Our study highlights the important role of noncoding variants in the leukemogenesis of APL.
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Affiliation(s)
- Huan Song
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yabin Liu
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yun Tan
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yi Zhang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wen Jin
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Sino-French Research Center for Life Sciences and Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; and
| | - Li Chen
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shishuang Wu
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jinsong Yan
- Department of Hematology, the Second Hospital of Dalian Medical University, Dalian, China
| | - Junmin Li
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhu Chen
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Saijuan Chen
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Kankan Wang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Sino-French Research Center for Life Sciences and Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; and
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15
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Zou H, Pan T, Gao Y, Chen R, Li S, Guo J, Tian Z, Xu G, Xu J, Ma Y, Li Y. Pan-cancer assessment of mutational landscape in intrinsically disordered hotspots reveals potential driver genes. Nucleic Acids Res 2022; 50:e49. [PMID: 35061901 PMCID: PMC9122534 DOI: 10.1093/nar/gkac028] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 12/22/2021] [Accepted: 01/10/2022] [Indexed: 11/13/2022] Open
Abstract
Large-scale cancer genome sequencing has enabled the catalogs of somatic mutations; however, the mutational impact on intrinsically disordered protein regions (IDRs) has not been systematically investigated to date. Here, we comprehensively characterized the mutational landscapes of IDRs and found that IDRs have higher mutation frequencies across diverse cancers. We thus developed a computational method, ROI-Driver, to identify putative driver genes enriching IDR and domain hotspots in cancer. Numerous well-known cancer-related oncogenes or tumor suppressors that play important roles in cancer signaling regulation, development and immune response were identified at a higher resolution. In particular, the incorporation of IDR structures helps in the identification of novel potential driver genes that play central roles in human protein-protein interaction networks. Interestingly, we found that the putative driver genes with IDR hotspots were significantly enriched with predicted phase separation propensities, suggesting that IDR mutations disrupt phase separation in key cellular pathways. We also identified an appreciable number of clinically relevant genes enriching IDR mutational hotspots that exhibited differential expression patterns and are associated with cancer patient survival. In summary, combinations of mutational effects on IDRs significantly increase the sensitivity of driver detection and are likely to open new therapeutic avenues for various cancers.
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Affiliation(s)
- Haozhe Zou
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Provincial Key Laboratory for Human Reproductive Medicine and Genetic Research, International Technology Cooperation Base ‘China–Myanmar Joint Research Center for Prevention and Treatment of Regional Major Disease’ by the Ministry of Science and Technology of China, Hainan Provincial Clinical Research Center for Thalassemia, The First Affiliated Hospital of Hainan Medical University, College of Biomedical Information and Engineering, Hainan Medical University, Haikou 571199, China
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Tao Pan
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Provincial Key Laboratory for Human Reproductive Medicine and Genetic Research, International Technology Cooperation Base ‘China–Myanmar Joint Research Center for Prevention and Treatment of Regional Major Disease’ by the Ministry of Science and Technology of China, Hainan Provincial Clinical Research Center for Thalassemia, The First Affiliated Hospital of Hainan Medical University, College of Biomedical Information and Engineering, Hainan Medical University, Haikou 571199, China
| | - Yueying Gao
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Provincial Key Laboratory for Human Reproductive Medicine and Genetic Research, International Technology Cooperation Base ‘China–Myanmar Joint Research Center for Prevention and Treatment of Regional Major Disease’ by the Ministry of Science and Technology of China, Hainan Provincial Clinical Research Center for Thalassemia, The First Affiliated Hospital of Hainan Medical University, College of Biomedical Information and Engineering, Hainan Medical University, Haikou 571199, China
| | - Renwei Chen
- Hainan Women and Children’s Medical Center, Hainan Medical University, Haikou 571199, China
| | - Si Li
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Provincial Key Laboratory for Human Reproductive Medicine and Genetic Research, International Technology Cooperation Base ‘China–Myanmar Joint Research Center for Prevention and Treatment of Regional Major Disease’ by the Ministry of Science and Technology of China, Hainan Provincial Clinical Research Center for Thalassemia, The First Affiliated Hospital of Hainan Medical University, College of Biomedical Information and Engineering, Hainan Medical University, Haikou 571199, China
| | - Jing Guo
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Provincial Key Laboratory for Human Reproductive Medicine and Genetic Research, International Technology Cooperation Base ‘China–Myanmar Joint Research Center for Prevention and Treatment of Regional Major Disease’ by the Ministry of Science and Technology of China, Hainan Provincial Clinical Research Center for Thalassemia, The First Affiliated Hospital of Hainan Medical University, College of Biomedical Information and Engineering, Hainan Medical University, Haikou 571199, China
| | - Zhanyu Tian
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Provincial Key Laboratory for Human Reproductive Medicine and Genetic Research, International Technology Cooperation Base ‘China–Myanmar Joint Research Center for Prevention and Treatment of Regional Major Disease’ by the Ministry of Science and Technology of China, Hainan Provincial Clinical Research Center for Thalassemia, The First Affiliated Hospital of Hainan Medical University, College of Biomedical Information and Engineering, Hainan Medical University, Haikou 571199, China
| | - Gang Xu
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Provincial Key Laboratory for Human Reproductive Medicine and Genetic Research, International Technology Cooperation Base ‘China–Myanmar Joint Research Center for Prevention and Treatment of Regional Major Disease’ by the Ministry of Science and Technology of China, Hainan Provincial Clinical Research Center for Thalassemia, The First Affiliated Hospital of Hainan Medical University, College of Biomedical Information and Engineering, Hainan Medical University, Haikou 571199, China
| | - Juan Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Yanlin Ma
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Provincial Key Laboratory for Human Reproductive Medicine and Genetic Research, International Technology Cooperation Base ‘China–Myanmar Joint Research Center for Prevention and Treatment of Regional Major Disease’ by the Ministry of Science and Technology of China, Hainan Provincial Clinical Research Center for Thalassemia, The First Affiliated Hospital of Hainan Medical University, College of Biomedical Information and Engineering, Hainan Medical University, Haikou 571199, China
| | - Yongsheng Li
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Provincial Key Laboratory for Human Reproductive Medicine and Genetic Research, International Technology Cooperation Base ‘China–Myanmar Joint Research Center for Prevention and Treatment of Regional Major Disease’ by the Ministry of Science and Technology of China, Hainan Provincial Clinical Research Center for Thalassemia, The First Affiliated Hospital of Hainan Medical University, College of Biomedical Information and Engineering, Hainan Medical University, Haikou 571199, China
- Hainan Women and Children’s Medical Center, Hainan Medical University, Haikou 571199, China
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16
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Yoshino S, Suzuki HI. The molecular understanding of super-enhancer dysregulation in cancer. NAGOYA JOURNAL OF MEDICAL SCIENCE 2022; 84:216-229. [PMID: 35967935 PMCID: PMC9350580 DOI: 10.18999/nagjms.84.2.216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 01/20/2022] [Indexed: 11/30/2022]
Abstract
Abnormalities in the regulation of gene expression are associated with various pathological conditions. Among the distal regulatory elements in the genome, the activation of target genes by enhancers plays a central role in the formation of cell type-specific gene expression patterns. Super-enhancers are a subclass of enhancers that frequently contain multiple enhancer-like elements and are characterized by dense binding of master transcription factors and Mediator complexes and high signals of active histone marks. Super-enhancers have been studied in detail as important regulatory regions that control cell identity and contribute to the pathogenesis of diverse diseases. In cancer, super-enhancers have multifaceted roles by activating various oncogenes and other cancer-related genes and shaping characteristic gene expression patterns in cancer cells. Alterations in super-enhancer activities in cancer involve multiple mechanisms, including the dysregulation of transcription factors and the super-enhancer-associated genomic abnormalities. The study of super-enhancers could contribute to the identification of effective biomarkers and the development of cancer therapeutics targeting transcriptional addiction. In this review, we summarize the roles of super-enhancers in cancer biology, with a particular focus on hematopoietic malignancies, in which multiple super-enhancer alteration mechanisms have been reported.
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Affiliation(s)
- Seiko Yoshino
- Division of Molecular Oncology, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Japan.
| | - Hiroshi I. Suzuki
- Division of Molecular Oncology, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Japan.
,Institute for Glyco-core Research (iGCORE), Nagoya University, Nagoya, Japan
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17
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A primary hierarchically organized patient-derived model enables in depth interrogation of stemness driven by the coding and non-coding genome. Leukemia 2022; 36:2690-2704. [PMID: 36131042 PMCID: PMC9613464 DOI: 10.1038/s41375-022-01697-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 08/23/2022] [Accepted: 09/01/2022] [Indexed: 11/30/2022]
Abstract
Many cancers are organized as cellular hierarchies sustained by cancer stem cells (CSC), whose eradication is crucial for achieving long-term remission. Difficulties to isolate and undertake in vitro and in vivo experimental studies of rare CSC under conditions that preserve their original properties currently constitute a bottleneck for identifying molecular mechanisms involving coding and non-coding genomic regions that govern stemness. We focussed on acute myeloid leukemia (AML) as a paradigm of the CSC model and developed a patient-derived system termed OCI-AML22 that recapitulates the cellular hierarchy driven by leukemia stem cells (LSC). Through classical flow sorting and functional analyses, we established that a single phenotypic population is highly enriched for LSC. The LSC fraction can be easily isolated and serially expanded in culture or in xenografts while faithfully recapitulating functional, transcriptional and epigenetic features of primary LSCs. A novel non-coding regulatory element was identified with a new computational approach using functionally validated primary AML LSC fractions and its role in LSC stemness validated through efficient CRISPR editing using methods optimized for OCI-AML22 LSC. Collectively, OCI-AML22 constitutes a valuable resource to uncover mechanisms governing CSC driven malignancies.
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18
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Liu Y, Gu Z, Cao H, Kaphle P, Lyu J, Zhang Y, Hu W, Chung SS, Dickerson KE, Xu J. Convergence of oncogenic cooperation at single-cell and single-gene levels drives leukemic transformation. Nat Commun 2021; 12:6323. [PMID: 34732703 PMCID: PMC8566485 DOI: 10.1038/s41467-021-26582-4] [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: 08/18/2020] [Accepted: 10/13/2021] [Indexed: 12/17/2022] Open
Abstract
Cancers develop from the accumulation of somatic mutations, yet it remains unclear how oncogenic lesions cooperate to drive cancer progression. Using a mouse model harboring NRasG12D and EZH2 mutations that recapitulates leukemic progression, we employ single-cell transcriptomic profiling to map cellular composition and gene expression alterations in healthy or diseased bone marrows during leukemogenesis. At cellular level, NRasG12D induces myeloid lineage-biased differentiation and EZH2-deficiency impairs myeloid cell maturation, whereas they cooperate to promote myeloid neoplasms with dysregulated transcriptional programs. At gene level, NRasG12D and EZH2-deficiency independently and synergistically deregulate gene expression. We integrate results from histopathology, leukemia repopulation, and leukemia-initiating cell assays to validate transcriptome-based cellular profiles. We use this resource to relate developmental hierarchies to leukemia phenotypes, evaluate oncogenic cooperation at single-cell and single-gene levels, and identify GEM as a regulator of leukemia-initiating cells. Our studies establish an integrative approach to deconvolute cancer evolution at single-cell resolution in vivo.
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Affiliation(s)
- Yuxuan Liu
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
- Department of Pediatrics, Harold C. Simmons Comprehensive Cancer Center, and Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Zhimin Gu
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
- Department of Pediatrics, Harold C. Simmons Comprehensive Cancer Center, and Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Hui Cao
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
- Department of Pediatrics, Harold C. Simmons Comprehensive Cancer Center, and Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Pranita Kaphle
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
- Department of Pediatrics, Harold C. Simmons Comprehensive Cancer Center, and Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Junhua Lyu
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
- Department of Pediatrics, Harold C. Simmons Comprehensive Cancer Center, and Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Yuannyu Zhang
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
- Department of Pediatrics, Harold C. Simmons Comprehensive Cancer Center, and Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Wenhuo Hu
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Stephen S Chung
- Division of Hematology Oncology, Department of Internal Medicine, and Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Kathryn E Dickerson
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
- Department of Pediatrics, Harold C. Simmons Comprehensive Cancer Center, and Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Jian Xu
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
- Department of Pediatrics, Harold C. Simmons Comprehensive Cancer Center, and Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
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19
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Zhao Z, Xu Q, Wei R, Huang L, Wang W, Wei G, Ni T. Comprehensive characterization of somatic variants associated with intronic polyadenylation in human cancers. Nucleic Acids Res 2021; 49:10369-10381. [PMID: 34508351 PMCID: PMC8501991 DOI: 10.1093/nar/gkab772] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 08/16/2021] [Accepted: 08/26/2021] [Indexed: 11/29/2022] Open
Abstract
Somatic single nucleotide variants (SNVs) in cancer genome affect gene expression through various mechanisms depending on their genomic location. While somatic SNVs near canonical splice sites have been reported to cause abnormal splicing of cancer-related genes, whether these SNVs can affect gene expression through other mechanisms remains an open question. Here, we analyzed RNA sequencing and exome data from 4,998 cancer patients covering ten cancer types and identified 152 somatic SNVs near splice sites that were associated with abnormal intronic polyadenylation (IPA). IPA-associated somatic variants favored the localization near the donor splice sites compared to the acceptor splice sites. A proportion of SNV-associated IPA events overlapped with premature cleavage and polyadenylation events triggered by U1 small nuclear ribonucleoproteins (snRNP) inhibition. GC content, intron length and polyadenylation signal were three genomic features that differentiated between SNV-associated IPA and intron retention. Notably, IPA-associated SNVs were enriched in tumor suppressor genes (TSGs), including the well-known TSGs such as PTEN and CDH1 with recurrent SNV-associated IPA events. Minigene assay confirmed that SNVs from PTEN, CDH1, VEGFA, GRHL2, CUL3 and WWC2 could lead to IPA. This work reveals that IPA acts as a novel mechanism explaining the functional consequence of somatic SNVs in human cancer.
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Affiliation(s)
- Zhaozhao Zhao
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Human Phenome Institute, School of Life Sciences and Huashan Hospital, Fudan University, Shanghai 200438, P.R. China
| | - Qiushi Xu
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Human Phenome Institute, School of Life Sciences and Huashan Hospital, Fudan University, Shanghai 200438, P.R. China
| | - Ran Wei
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Human Phenome Institute, School of Life Sciences and Huashan Hospital, Fudan University, Shanghai 200438, P.R. China.,Department of Pathology, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, P.R. China
| | - Leihuan Huang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Human Phenome Institute, School of Life Sciences and Huashan Hospital, Fudan University, Shanghai 200438, P.R. China
| | - Weixu Wang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Human Phenome Institute, School of Life Sciences and Huashan Hospital, Fudan University, Shanghai 200438, P.R. China
| | - Gang Wei
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Human Phenome Institute, School of Life Sciences and Huashan Hospital, Fudan University, Shanghai 200438, P.R. China.,MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai 200438, P.R. China
| | - Ting Ni
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Human Phenome Institute, School of Life Sciences and Huashan Hospital, Fudan University, Shanghai 200438, P.R. China.,Shanghai Engineering Research Center of Industrial Microorganisms, School of Life Sciences, Fudan University, Shanghai 200438, P.R. China
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20
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Abstract
Tumour formation involves random mutagenic events and positive evolutionary selection acting on a subset of such events, referred to as driver mutations. A decade of careful surveying of tumour DNA using exome-based analyses has revealed a multitude of protein-coding somatic driver mutations, some of which are clinically actionable. Today, a transition towards whole-genome analysis is well under way, technically enabling the discovery of potential driver mutations occurring outside protein-coding sequences. Mutations are abundant in this vast non-coding space, which is more than 50 times larger than the coding exome, but reliable identification of selection signals in non-coding DNA remains a challenge. In this Review, we discuss recent findings in the field, where the emerging landscape is one in which non-coding driver mutations appear to be relatively infrequent. Nevertheless, we highlight several notable discoveries. We consider possible reasons for the relative absence of non-coding driver events, as well as the difficulties associated with detecting signals of positive selection in non-coding DNA.
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Affiliation(s)
- Kerryn Elliott
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Erik Larsson
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden.
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21
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Yang Z, Gimple RC, Zhou N, Zhao L, Gustafsson JÅ, Zhou S. Targeting Nuclear Receptors for Cancer Therapy: Premises, Promises, and Challenges. Trends Cancer 2021; 7:541-556. [PMID: 33341430 DOI: 10.1016/j.trecan.2020.11.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 11/17/2020] [Accepted: 11/18/2020] [Indexed: 12/12/2022]
Abstract
Nuclear receptors are a family of transcription factors localized in cell nuclei, sensing specific ligands and fine-tuning a variety of cell physiological events. They have been intensively investigated in cancer biology. With their excellent properties of druggability and actionability, nuclear receptors have demonstrated much promise as novel therapeutic targets for different cancer types. Accumulating evidence has highlighted the essential roles of certain nuclear receptors in tumor immunology, suggesting the possibility for them to serve as cancer immunotherapeutic targets. Here, we summarize the roles of nuclear receptors in cancer biology and tumor immunology, and underscore the current advances of clinical trials for nuclear receptor-based cancer therapeutics.
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Affiliation(s)
- Zhengnan Yang
- Department of Obstetrics and Gynecology, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE and State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Ryan C Gimple
- Division of Regenerative Medicine, Department of Medicine, University of California, San Diego, CA, USA; Department of Pathology, Case Western Reserve University, Cleveland, OH, USA
| | - Nianxin Zhou
- Department of Obstetrics and Gynecology, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE and State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Linjie Zhao
- Division of Regenerative Medicine, Department of Medicine, University of California, San Diego, CA, USA.
| | - Jan-Åke Gustafsson
- Department of Biology and Biochemistry, Center for Nuclear Receptors and Cell Signaling, University of Houston, Houston, TX, USA; Center for Medical Innovation, Department of Biosciences and Nutrition at Novum, Karolinska Institute, Stockholm, Sweden.
| | - Shengtao Zhou
- Department of Obstetrics and Gynecology, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE and State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China.
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22
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van Galen P. Decoding the Noncoding Cancer Genome. Cancer Discov 2021; 10:646-647. [PMID: 32357969 DOI: 10.1158/2159-8290.cd-20-0285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
In this issue of Cancer Discovery, Li and colleagues provide a blueprint for the identification and functional validation of cancer-associated mutations in noncoding regions of the genome. Integration of whole-genome sequencing and high-throughput epigenome editing screens is starting to reveal the extent to which noncoding genetic lesions contribute to cancer.See related article by Li et al., p. 724.
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Affiliation(s)
- Peter van Galen
- Division of Hematology, Brigham and Women's Hospital, Boston, Massachusetts. Department of Medicine, Harvard Medical School, Boston, Massachusetts. Broad Institute of MIT and Harvard, Cambridge, Massachusetts.
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23
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Belver L, Albero R, Ferrando AA. Deregulation of enhancer structure, function, and dynamics in acute lymphoblastic leukemia. Trends Immunol 2021; 42:418-431. [PMID: 33858773 PMCID: PMC8091164 DOI: 10.1016/j.it.2021.03.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 03/09/2021] [Accepted: 03/10/2021] [Indexed: 12/25/2022]
Abstract
Enhancers control dynamic changes in gene expression and orchestrate the tightly controlled transcriptional circuitries that direct and coordinate cell growth, proliferation, survival, lineage commitment, and differentiation during lymphoid development. Enhancer hijacking and neoenhancer formation at oncogene loci, as well as aberrant activation of oncogene-associated enhancers, can induce constitutive activation of self-perpetuating oncogenic transcriptional circuitries, and contribute to the malignant transformation of immature lymphoid progenitors in acute lymphoblastic leukemia (ALL). In this review, we present recent discoveries of the role of enhancer dynamics in mouse and human lymphoid development, and discuss how genetic and epigenetic alterations of enhancer function can promote leukemogenesis, and potential strategies for targeting the enhancer machinery in the treatment of ALL.
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Affiliation(s)
- Laura Belver
- Institute for Cancer Genetics, Columbia University, New York, NY, 10032, USA; Josep Carreras Leukaemia Research Institute, Badalona, Barcelona, 08916, Spain
| | - Robert Albero
- Institute for Cancer Genetics, Columbia University, New York, NY, 10032, USA
| | - Adolfo A Ferrando
- Institute for Cancer Genetics, Columbia University, New York, NY, 10032, USA; Department of Systems Biology, Columbia University, New York, NY, 10032, USA; Department of Pediatrics, Columbia University Medical Center, New York, NY, 10032, USA; Department of Pathology, Columbia University Medical Center, New York, NY, 10032, USA.
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24
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Gu Z, Liu Y, Zhang Y, Cao H, Lyu J, Wang X, Wylie A, Newkirk SJ, Jones AE, Lee M, Botten GA, Deng M, Dickerson KE, Zhang CC, An W, Abrams JM, Xu J. Silencing of LINE-1 retrotransposons is a selective dependency of myeloid leukemia. Nat Genet 2021; 53:672-682. [PMID: 33833453 PMCID: PMC8270111 DOI: 10.1038/s41588-021-00829-8] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 02/26/2021] [Indexed: 02/07/2023]
Abstract
Transposable elements or transposons are major players in genetic variability and genome evolution. Aberrant activation of long interspersed element-1 (LINE-1 or L1) retrotransposons is common in human cancers, yet their tumor-type-specific functions are poorly characterized. We identified MPHOSPH8/MPP8, a component of the human silencing hub (HUSH) complex, as an acute myeloid leukemia (AML)-selective dependency by epigenetic regulator-focused CRISPR screening. Although MPP8 is dispensable for steady-state hematopoiesis, MPP8 loss inhibits AML development by reactivating L1s to induce the DNA damage response and cell cycle exit. Activation of endogenous or ectopic L1s mimics the phenotype of MPP8 loss, whereas blocking retrotransposition abrogates MPP8-deficiency-induced phenotypes. Expression of AML oncogenic mutations promotes L1 suppression, and enhanced L1 silencing is associated with poor prognosis in human AML. Hence, while retrotransposons are commonly recognized for their cancer-promoting functions, we describe a tumor-suppressive role for L1 retrotransposons in myeloid leukemia.
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Affiliation(s)
- Zhimin Gu
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Pediatrics, Harold C. Simmons Comprehensive Cancer Center and Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Yuxuan Liu
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Pediatrics, Harold C. Simmons Comprehensive Cancer Center and Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Yuannyu Zhang
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Pediatrics, Harold C. Simmons Comprehensive Cancer Center and Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Hui Cao
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Pediatrics, Harold C. Simmons Comprehensive Cancer Center and Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Junhua Lyu
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Pediatrics, Harold C. Simmons Comprehensive Cancer Center and Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Xun Wang
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Annika Wylie
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Simon J Newkirk
- Department of Pharmaceutical Sciences, South Dakota State University, Brookings, SD, USA
| | - Amanda E Jones
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Michael Lee
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Pediatrics, Harold C. Simmons Comprehensive Cancer Center and Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Giovanni A Botten
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Pediatrics, Harold C. Simmons Comprehensive Cancer Center and Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Mi Deng
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Kathryn E Dickerson
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Pediatrics, Harold C. Simmons Comprehensive Cancer Center and Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Cheng Cheng Zhang
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Wenfeng An
- Department of Pharmaceutical Sciences, South Dakota State University, Brookings, SD, USA
| | - John M Abrams
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jian Xu
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA.
- Department of Pediatrics, Harold C. Simmons Comprehensive Cancer Center and Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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25
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Tottone L, Lancho O, Loh JW, Singh A, Kimura S, Roels J, Kuchmiy A, Strubbe S, Lawlor MA, da Silva-Diz V, Luo S, Gachet S, García-Prieto CA, Hagelaar R, Esteller M, Meijerink JPP, Soulier J, Taghon T, Van Vlierberghe P, Mullighan CG, Khiabanian H, Rocha PP, Herranz D. A Tumor Suppressor Enhancer of PTEN in T-cell development and leukemia. Blood Cancer Discov 2020; 2:92-109. [PMID: 33458694 DOI: 10.1158/2643-3230.bcd-20-0201] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Long-range oncogenic enhancers play an important role in cancer. Yet, whether similar regulation of tumor suppressor genes is relevant remains unclear. Loss of expression of PTEN is associated with the pathogenesis of various cancers, including T-cell leukemia (T-ALL). Here, we identify a highly conserved distal enhancer (PE) that interacts with the PTEN promoter in multiple hematopoietic populations, including T-cells, and acts as a hub of relevant transcription factors in T-ALL. Consistently, loss of PE leads to reduced PTEN levels in T-ALL cells. Moreover, PE-null mice show reduced Pten levels in thymocytes and accelerated development of NOTCH1-induced T-ALL. Furthermore, secondary loss of PE in established leukemias leads to accelerated progression and a gene expression signature driven by Pten loss. Finally, we uncovered recurrent deletions encompassing PE in T-ALL, which are associated with decreased PTEN levels. Altogether, our results identify PE as the first long-range tumor suppressor enhancer directly implicated in cancer.
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Affiliation(s)
- Luca Tottone
- Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, New Jersey
| | - Olga Lancho
- Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, New Jersey
| | - Jui-Wan Loh
- Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, New Jersey
- Center for Systems and Computational Biology, Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, New Jersey
| | - Amartya Singh
- Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, New Jersey
- Center for Systems and Computational Biology, Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, New Jersey
| | - Shunsuke Kimura
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Juliette Roels
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Anna Kuchmiy
- Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Steven Strubbe
- Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Matthew A Lawlor
- Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, New Jersey
| | - Victoria da Silva-Diz
- Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, New Jersey
| | - Shirley Luo
- Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, New Jersey
| | - Stéphanie Gachet
- INSERM U944 and University de Paris, Hopital Saint-Louis, Paris, France
| | - Carlos A García-Prieto
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Catalonia, Spain
- Barcelona Supercomputing Center (BSC), Barcelona, Catalonia, Spain
| | - Rico Hagelaar
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Manel Esteller
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Catalonia, Spain
- Centro de Investigación Biomédica en Red de Cancer (CIBERONC), Madrid, Spain
- Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona (UB), Barcelona, Catalonia, Spain
- Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain
| | | | - Jean Soulier
- INSERM U944 and University de Paris, Hopital Saint-Louis, Paris, France
| | - Tom Taghon
- Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Pieter Van Vlierberghe
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium
| | - Charles G Mullighan
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Hossein Khiabanian
- Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, New Jersey
- Center for Systems and Computational Biology, Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, New Jersey
- Department of Pathology and Laboratory Medicine, Rutgers Robert Wood Johnson Medical School, Rutgers University, New Brunswick, New Jersey
| | - Pedro P Rocha
- Unit on Genome Structure and Regulation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland
- National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Daniel Herranz
- Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, New Jersey.
- Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, New Jersey
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26
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Rovirosa L, Ramos-Morales A, Javierre BM. The Genome in a Three-Dimensional Context: Deciphering the Contribution of Noncoding Mutations at Enhancers to Blood Cancer. Front Immunol 2020; 11:592087. [PMID: 33117405 PMCID: PMC7575776 DOI: 10.3389/fimmu.2020.592087] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 09/21/2020] [Indexed: 11/13/2022] Open
Abstract
Associations between blood cancer and genetic predisposition, including both inherited variants and acquired mutations and epimutations, have been well characterized. However, the majority of these variants affect noncoding regions, making their mechanisms difficult to hypothesize and hindering the translation of these insights into patient benefits. Fueled by unprecedented progress in next-generation sequencing and computational integrative analysis, studies have started applying combinations of epigenetic, genome architecture, and functional assays to bridge the gap between noncoding variants and blood cancer. These complementary tools have not only allowed us to understand the potential malignant role of these variants but also to differentiate key variants, cell-types, and conditions from misleading ones. Here, we briefly review recent studies that have provided fundamental insights into our understanding of how noncoding mutations at enhancers predispose and promote blood malignancies in the context of spatial genome architecture.
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Affiliation(s)
- Llorenç Rovirosa
- 3D Chromatin Organization Group, Josep Carreras Leukaemia Research Institute (IJC), Germans Trias i Pujol, Badalona, Spain
| | - Alberto Ramos-Morales
- 3D Chromatin Organization Group, Josep Carreras Leukaemia Research Institute (IJC), Germans Trias i Pujol, Badalona, Spain
| | - Biola M Javierre
- 3D Chromatin Organization Group, Josep Carreras Leukaemia Research Institute (IJC), Germans Trias i Pujol, Badalona, Spain.,Institute for Health Science Research Germans Trias i Pujol (IGTP), Badalona, Spain
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27
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Noorani I, Bradley A, de la Rosa J. CRISPR and transposon in vivo screens for cancer drivers and therapeutic targets. Genome Biol 2020; 21:204. [PMID: 32811551 PMCID: PMC7437018 DOI: 10.1186/s13059-020-02118-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 07/23/2020] [Indexed: 02/07/2023] Open
Abstract
Human cancers harbor substantial genetic, epigenetic, and transcriptional changes, only some of which drive oncogenesis at certain times during cancer evolution. Identifying the cancer-driver alterations amongst the vast swathes of "passenger" changes still remains a major challenge. Transposon and CRISPR screens in vivo provide complementary methods for achieving this, and each platform has its own advantages. Here, we review recent major technological breakthroughs made with these two approaches and highlight future directions. We discuss how each genetic screening platform can provide unique insight into cancer evolution, including intra-tumoral heterogeneity, metastasis, and immune evasion, presenting transformative opportunities for targeted therapeutic intervention.
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Affiliation(s)
- Imran Noorani
- Department of Medicine, University of Cambridge School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK.
- Department of Neurosurgery, University of Cambridge, Cambridge, CB2 0QQ, UK.
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK.
| | - Allan Bradley
- Department of Medicine, University of Cambridge School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK
| | - Jorge de la Rosa
- Department of Medicine, University of Cambridge School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK.
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