51
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Shi P, Nie Y, Yang J, Zhang W, Tang Z, Xu J. Fundamental and practical approaches for single-cell ATAC-seq analysis. ABIOTECH 2022; 3:212-223. [PMID: 36313930 PMCID: PMC9590475 DOI: 10.1007/s42994-022-00082-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 09/07/2022] [Indexed: 11/28/2022]
Abstract
Assays for transposase-accessible chromatin through high-throughput sequencing (ATAC-seq) are effective tools in the study of genome-wide chromatin accessibility landscapes. With the rapid development of single-cell technology, open chromatin regions that play essential roles in epigenetic regulation have been measured at the single-cell level using single-cell ATAC-seq approaches. The application of scATAC-seq has become as popular as that of scRNA-seq. However, owing to the nature of scATAC-seq data, which are sparse and noisy, processing the data requires different methodologies and empirical experience. This review presents a practical guide for processing scATAC-seq data, from quality evaluation to downstream analysis, for various applications. In addition to the epigenomic profiling from scATAC-seq, we also discuss recent studies in which the function of non-coding variants has been investigated based on cell type-specific cis-regulatory elements and how to use the by-product genetic information obtained from scATAC-seq to infer single-cell copy number variants and trace cell lineage. We anticipate that this review will assist researchers in designing and implementing scATAC-seq assays to facilitate research in diverse fields.
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Affiliation(s)
- Peiyu Shi
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275 China
| | - Yage Nie
- Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510275 China
| | - Jiawen Yang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275 China
| | - Weixing Zhang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275 China
| | - Zhongjie Tang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275 China
| | - Jin Xu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275 China
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52
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Szeitz B, Megyesfalvi Z, Woldmar N, Valkó Z, Schwendenwein A, Bárány N, Paku S, László V, Kiss H, Bugyik E, Lang C, Szász AM, Pizzatti L, Bogos K, Hoda MA, Hoetzenecker K, Marko-Varga G, Horvatovich P, Döme B, Schelch K, Rezeli M. In-depth proteomic analysis reveals unique subtype-specific signatures in human small-cell lung cancer. Clin Transl Med 2022; 12:e1060. [PMID: 36149789 PMCID: PMC9506422 DOI: 10.1002/ctm2.1060] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 08/31/2022] [Accepted: 09/06/2022] [Indexed: 11/12/2022] Open
Abstract
Background Small‐cell lung cancer (SCLC) molecular subtypes have been primarily characterized based on the expression pattern of the following key transcription regulators: ASCL1 (SCLC‐A), NEUROD1 (SCLC‐N), POU2F3 (SCLC‐P) and YAP1 (SCLC‐Y). Here, we investigated the proteomic landscape of these molecular subsets with the aim to identify novel subtype‐specific proteins of diagnostic and therapeutic relevance. Methods Pellets and cell media of 26 human SCLC cell lines were subjected to label‐free shotgun proteomics for large‐scale protein identification and quantitation, followed by in‐depth bioinformatic analyses. Proteomic data were correlated with the cell lines’ phenotypic characteristics and with public transcriptomic data of SCLC cell lines and tissues. Results Our quantitative proteomic data highlighted that four molecular subtypes are clearly distinguishable at the protein level. The cell lines exhibited diverse neuroendocrine and epithelial–mesenchymal characteristics that varied by subtype. A total of 367 proteins were identified in the cell pellet and 34 in the culture media that showed significant up‐ or downregulation in one subtype, including known druggable proteins and potential blood‐based markers. Pathway enrichment analysis and parallel investigation of transcriptomics from SCLC cell lines outlined unique signatures for each subtype, such as upregulated oxidative phosphorylation in SCLC‐A, DNA replication in SCLC‐N, neurotrophin signalling in SCLC‐P and epithelial–mesenchymal transition in SCLC‐Y. Importantly, we identified the YAP1‐driven subtype as the most distinct SCLC subgroup. Using sparse partial least squares discriminant analysis, we identified proteins that clearly distinguish four SCLC subtypes based on their expression pattern, including potential diagnostic markers for SCLC‐Y (e.g. GPX8, PKD2 and UFO). Conclusions We report for the first time, the protein expression differences among SCLC subtypes. By shedding light on potential subtype‐specific therapeutic vulnerabilities and diagnostic biomarkers, our results may contribute to a better understanding of SCLC biology and the development of novel therapies.
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Affiliation(s)
- Beáta Szeitz
- Division of Oncology, Department of Internal Medicine and Oncology, Semmelweis University, Budapest, Hungary
| | - Zsolt Megyesfalvi
- National Korányi Institute of Pulmonology, Budapest, Hungary.,Department of Thoracic Surgery, Medical University of Vienna, Vienna, Austria.,Department of Thoracic Surgery, National Institute of Oncology, Semmelweis University, Budapest, Hungary
| | - Nicole Woldmar
- Division of Clinical Protein Science, & Imaging, Department of Clinical Sciences (Lund) and Department of Biomedical Engineering, Lund University, Lund, Sweden.,Laboratory of Molecular Biology and Proteomics of Blood/LADETEC, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Zsuzsanna Valkó
- National Korányi Institute of Pulmonology, Budapest, Hungary.,Department of Thoracic Surgery, Medical University of Vienna, Vienna, Austria
| | - Anna Schwendenwein
- Department of Thoracic Surgery, Medical University of Vienna, Vienna, Austria
| | - Nándor Bárány
- National Korányi Institute of Pulmonology, Budapest, Hungary.,Department of Thoracic Surgery, Medical University of Vienna, Vienna, Austria.,First Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Sándor Paku
- First Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Viktória László
- National Korányi Institute of Pulmonology, Budapest, Hungary.,Department of Thoracic Surgery, Medical University of Vienna, Vienna, Austria
| | - Helga Kiss
- Department of Thoracic Surgery, National Institute of Oncology, Semmelweis University, Budapest, Hungary.,University of Pécs, Pécs, Hungary
| | - Edina Bugyik
- National Korányi Institute of Pulmonology, Budapest, Hungary.,First Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Christian Lang
- Department of Thoracic Surgery, Medical University of Vienna, Vienna, Austria
| | - Attila Marcell Szász
- National Korányi Institute of Pulmonology, Budapest, Hungary.,Department of Bioinformatics, Semmelweis University, Budapest, Hungary
| | - Luciana Pizzatti
- Laboratory of Molecular Biology and Proteomics of Blood/LADETEC, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Krisztina Bogos
- National Korányi Institute of Pulmonology, Budapest, Hungary
| | - Mir Alireza Hoda
- Department of Thoracic Surgery, Medical University of Vienna, Vienna, Austria
| | - Konrad Hoetzenecker
- Department of Thoracic Surgery, Medical University of Vienna, Vienna, Austria
| | - György Marko-Varga
- Division of Clinical Protein Science, & Imaging, Department of Clinical Sciences (Lund) and Department of Biomedical Engineering, Lund University, Lund, Sweden
| | - Peter Horvatovich
- Department of Analytical Biochemistry, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, The Netherlands
| | - Balázs Döme
- National Korányi Institute of Pulmonology, Budapest, Hungary.,Department of Thoracic Surgery, Medical University of Vienna, Vienna, Austria.,Department of Thoracic Surgery, National Institute of Oncology, Semmelweis University, Budapest, Hungary.,Department of Translational Medicine, Lund University, Lund, Sweden
| | - Karin Schelch
- Center for Cancer Research, Medical University of Vienna, Vienna, Austria
| | - Melinda Rezeli
- Division of Clinical Protein Science, & Imaging, Department of Clinical Sciences (Lund) and Department of Biomedical Engineering, Lund University, Lund, Sweden
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53
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Jingyao C, Xiangyu P, Feifei N, Xuelan C, Chong C. Epigenetic reprogramming in small cell lung cancer. Cancer Biol Med 2022; 19:j.issn.2095-3941.2022.0343. [PMID: 36069525 PMCID: PMC9425178 DOI: 10.20892/j.issn.2095-3941.2022.0343] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Affiliation(s)
- Chen Jingyao
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610044, China
| | - Pan Xiangyu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610044, China
| | - Na Feifei
- Department of Thoracic Oncology, West China Hospital, Sichuan University, Chengdu 610044, China
| | - Chen Xuelan
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610044, China
| | - Chen Chong
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610044, China
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54
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Keogh A, Finn S, Radonic T. Emerging Biomarkers and the Changing Landscape of Small Cell Lung Cancer. Cancers (Basel) 2022; 14:cancers14153772. [PMID: 35954436 PMCID: PMC9367597 DOI: 10.3390/cancers14153772] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 07/26/2022] [Accepted: 07/26/2022] [Indexed: 12/26/2022] Open
Abstract
Simple Summary Small cell lung cancer (SCLC) is an aggressive cancer representing 15% of all lung cancers. Unlike other types of lung cancer, treatments for SCLC have changed very little in the past 20 years and therefore, the survival rate remains low. This is due, in part, to the lack of understanding of the biological basis of this disease and the previous idea that all SCLCs are the same. Multiple recent studies have identified that SCLCs have varying biological activity and can be divided into four different groups. The advantage of this is that each of these four groups responds differently to new treatments, which hopefully will dramatically improve survival. Additionally, the aim of these new treatments is to specifically target these biological differences in SCLC so normal/non cancer cells are unaffected, leading to decreased side effects and a better quality of life. There is still a lot unknown about SCLC, but these new findings offer a glimmer of hope for patients in the future. Abstract Small cell lung cancer (SCLC) is a high-grade neuroendocrine malignancy with an aggressive behavior and dismal prognosis. 5-year overall survival remains a disappointing 7%. Genomically, SCLCs are homogeneous compared to non-small cell lung cancers and are characterized almost always by functional inactivation of RB1 and TP53 with no actionable mutations. Additionally, SCLCs histologically appear uniform. Thus, SCLCs are currently managed as a single disease with platinum-based chemotherapy remaining the cornerstone of treatment. Recent studies have identified expression of dominant transcriptional signatures which may permit classification of SCLCs into four biologically distinct subtypes, namely, SCLC-A, SCLC-N, SCLC-P, and SCLC-I. These groups are readily detectable by immunohistochemistry and also have potential predictive utility for emerging therapies, including PARPi, immune checkpoint inhibitors, and DLL3 targeted therapies. In contrast with their histology, studies have identified that SCLCs display both inter- and intra-tumoral heterogeneity. Identification of subpopulations of cells with high expression of PLCG2 has been linked with risk of metastasis. SCLCs also display subtype switching under therapy pressure which may contribute furthermore to metastatic ability and chemoresistance. In this review, we summarize the recent developments in the understanding of the biology of SCLCs, and discuss the potential diagnostic, prognostic, and treatment opportunities the four proposed subtypes may present for the future. We also discuss the emerging evidence of tumor heterogeneity and plasticity in SCLCs which have been implicated in metastasis and acquired therapeutic resistance seen in these aggressive tumors.
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Affiliation(s)
- Anna Keogh
- Department of Histopathology, St. James’s Hospital, D08 NHY1 Dublin, Ireland;
- Department of Histopathology and Morbid Anatomy, Trinity Translational Medicine Institute, Trinity College Dublin, D08 HD53 Dublin, Ireland
- Correspondence:
| | - Stephen Finn
- Department of Histopathology, St. James’s Hospital, D08 NHY1 Dublin, Ireland;
- Department of Histopathology and Morbid Anatomy, Trinity Translational Medicine Institute, Trinity College Dublin, D08 HD53 Dublin, Ireland
| | - Teodora Radonic
- Department of Pathology, Amsterdam University Medical Center, VUMC, University Amsterdam, 1081 HV Amsterdam, The Netherlands;
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55
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Harkins D, Harvey TJ, Atterton C, Miller I, Currey L, Oishi S, Kasherman M, Davila RA, Harris L, Green K, Piper H, Parton RG, Thor S, Cooper HM, Piper M. Hydrocephalus in Nfix−/− Mice Is Underpinned by Changes in Ependymal Cell Physiology. Cells 2022; 11:cells11152377. [PMID: 35954220 PMCID: PMC9368351 DOI: 10.3390/cells11152377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 07/27/2022] [Accepted: 07/29/2022] [Indexed: 02/04/2023] Open
Abstract
Nuclear factor one X (NFIX) is a transcription factor required for normal ependymal development. Constitutive loss of Nfix in mice (Nfix−/−) is associated with hydrocephalus and sloughing of the dorsal ependyma within the lateral ventricles. Previous studies have implicated NFIX in the transcriptional regulation of genes encoding for factors essential to ependymal development. However, the cellular and molecular mechanisms underpinning hydrocephalus in Nfix−/− mice are unknown. To investigate the role of NFIX in hydrocephalus, we examined ependymal cells in brains from postnatal Nfix−/− and control (Nfix+/+) mice using a combination of confocal and electron microscopy. This revealed that the ependymal cells in Nfix−/− mice exhibited abnormal cilia structure and disrupted localisation of adhesion proteins. Furthermore, we modelled ependymal cell adhesion using epithelial cell culture and revealed changes in extracellular matrix and adherens junction gene expression following knockdown of NFIX. Finally, the ablation of Nfix from ependymal cells in the adult brain using a conditional approach culminated in enlarged ventricles, sloughing of ependymal cells from the lateral ventricles and abnormal localisation of adhesion proteins, which are phenotypes observed during development. Collectively, these data demonstrate a pivotal role for NFIX in the regulation of cell adhesion within ependymal cells of the lateral ventricles.
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Affiliation(s)
- Danyon Harkins
- School of Biomedical Sciences, The University of Queensland, Brisbane 4072, Australia; (D.H.); (T.J.H.); (C.A.); (I.M.); (L.C.); (S.O.); (M.K.); (R.A.D.); (H.P.); (S.T.)
| | - Tracey J. Harvey
- School of Biomedical Sciences, The University of Queensland, Brisbane 4072, Australia; (D.H.); (T.J.H.); (C.A.); (I.M.); (L.C.); (S.O.); (M.K.); (R.A.D.); (H.P.); (S.T.)
| | - Cooper Atterton
- School of Biomedical Sciences, The University of Queensland, Brisbane 4072, Australia; (D.H.); (T.J.H.); (C.A.); (I.M.); (L.C.); (S.O.); (M.K.); (R.A.D.); (H.P.); (S.T.)
| | - Ingrid Miller
- School of Biomedical Sciences, The University of Queensland, Brisbane 4072, Australia; (D.H.); (T.J.H.); (C.A.); (I.M.); (L.C.); (S.O.); (M.K.); (R.A.D.); (H.P.); (S.T.)
| | - Laura Currey
- School of Biomedical Sciences, The University of Queensland, Brisbane 4072, Australia; (D.H.); (T.J.H.); (C.A.); (I.M.); (L.C.); (S.O.); (M.K.); (R.A.D.); (H.P.); (S.T.)
| | - Sabrina Oishi
- School of Biomedical Sciences, The University of Queensland, Brisbane 4072, Australia; (D.H.); (T.J.H.); (C.A.); (I.M.); (L.C.); (S.O.); (M.K.); (R.A.D.); (H.P.); (S.T.)
| | - Maria Kasherman
- School of Biomedical Sciences, The University of Queensland, Brisbane 4072, Australia; (D.H.); (T.J.H.); (C.A.); (I.M.); (L.C.); (S.O.); (M.K.); (R.A.D.); (H.P.); (S.T.)
| | - Raul Ayala Davila
- School of Biomedical Sciences, The University of Queensland, Brisbane 4072, Australia; (D.H.); (T.J.H.); (C.A.); (I.M.); (L.C.); (S.O.); (M.K.); (R.A.D.); (H.P.); (S.T.)
| | - Lucy Harris
- Centre for Microscopy and Microanalysis, The University of Queensland, Brisbane 4072, Australia; (L.H.); (K.G.); (R.G.P.)
| | - Kathryn Green
- Centre for Microscopy and Microanalysis, The University of Queensland, Brisbane 4072, Australia; (L.H.); (K.G.); (R.G.P.)
| | - Hannah Piper
- School of Biomedical Sciences, The University of Queensland, Brisbane 4072, Australia; (D.H.); (T.J.H.); (C.A.); (I.M.); (L.C.); (S.O.); (M.K.); (R.A.D.); (H.P.); (S.T.)
| | - Robert G. Parton
- Centre for Microscopy and Microanalysis, The University of Queensland, Brisbane 4072, Australia; (L.H.); (K.G.); (R.G.P.)
- Institute for Molecular Biosciences, The University of Queensland, Brisbane 4072, Australia
| | - Stefan Thor
- School of Biomedical Sciences, The University of Queensland, Brisbane 4072, Australia; (D.H.); (T.J.H.); (C.A.); (I.M.); (L.C.); (S.O.); (M.K.); (R.A.D.); (H.P.); (S.T.)
| | - Helen M. Cooper
- Queensland Brain Institute, The University of Queensland, Brisbane 4072, Australia;
| | - Michael Piper
- School of Biomedical Sciences, The University of Queensland, Brisbane 4072, Australia; (D.H.); (T.J.H.); (C.A.); (I.M.); (L.C.); (S.O.); (M.K.); (R.A.D.); (H.P.); (S.T.)
- Queensland Brain Institute, The University of Queensland, Brisbane 4072, Australia;
- Correspondence:
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56
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Wang C, Yang J. Mechanical forces: The missing link between idiopathic pulmonary fibrosis and lung cancer. Eur J Cell Biol 2022; 101:151234. [DOI: 10.1016/j.ejcb.2022.151234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 05/05/2022] [Accepted: 05/05/2022] [Indexed: 11/25/2022] Open
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57
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Sou IF, Hamer G, Tee WW, Vader G, McClurg UL. Cancer and meiotic gene expression: Two sides of the same coin? Curr Top Dev Biol 2022; 151:43-68. [PMID: 36681477 DOI: 10.1016/bs.ctdb.2022.06.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Meiosis increases genetic diversity in offspring by generating genetically unique haploid gametes with reshuffled chromosomes. This process requires a specialized set of meiotic proteins, which facilitate chromosome recombination and segregation. However, re-expression of meiotic proteins in mitosis can have catastrophic oncogenic consequences and aberrant expression of meiotic proteins is a common occurrence in human tumors. Mechanistically, re-activation of meiotic genes in cancer promotes oncogenesis likely because cancers-conversely to healthy mitosis-are fueled by genetic instability which promotes tumor evolution, and evasion of immune response and treatment pressure. In this review, we explore similarities between meiotic and cancer cells with a particular focus on the oncogenic activation of meiotic genes in cancer. We emphasize the role of histones and their modifications, DNA methylation, genome organization, R-loops and the availability of distal enhancers.
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Affiliation(s)
- Ieng Fong Sou
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom; Chromatin Dynamics and Disease Epigenetics Group, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Geert Hamer
- Center for Reproductive Medicine, Reproductive Biology Laboratory, Amsterdam Reproduction and Development Research Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Wee-Wei Tee
- Chromatin Dynamics and Disease Epigenetics Group, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore; Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Gerben Vader
- Center for Reproductive Medicine, Reproductive Biology Laboratory, Amsterdam Reproduction and Development Research Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands; Section of Oncogenetics, Department of Human Genetics, Amsterdam UMC, Vrije Universiteit, Amsterdam, The Netherlands; Cancer Center Amsterdam, Cancer Biology and Immunology, Amsterdam, The Netherlands
| | - Urszula Lucja McClurg
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom.
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58
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Hwang WL, Jagadeesh KA, Guo JA, Hoffman HI, Yadollahpour P, Reeves JW, Mohan R, Drokhlyansky E, Van Wittenberghe N, Ashenberg O, Farhi SL, Schapiro D, Divakar P, Miller E, Zollinger DR, Eng G, Schenkel JM, Su J, Shiau C, Yu P, Freed-Pastor WA, Abbondanza D, Mehta A, Gould J, Lambden C, Porter CBM, Tsankov A, Dionne D, Waldman J, Cuoco MS, Nguyen L, Delorey T, Phillips D, Barth JL, Kem M, Rodrigues C, Ciprani D, Roldan J, Zelga P, Jorgji V, Chen JH, Ely Z, Zhao D, Fuhrman K, Fropf R, Beechem JM, Loeffler JS, Ryan DP, Weekes CD, Ferrone CR, Qadan M, Aryee MJ, Jain RK, Neuberg DS, Wo JY, Hong TS, Xavier R, Aguirre AJ, Rozenblatt-Rosen O, Mino-Kenudson M, Castillo CFD, Liss AS, Ting DT, Jacks T, Regev A. Single-nucleus and spatial transcriptome profiling of pancreatic cancer identifies multicellular dynamics associated with neoadjuvant treatment. Nat Genet 2022; 54:1178-1191. [PMID: 35902743 DOI: 10.1038/s41588-022-01134-8] [Citation(s) in RCA: 116] [Impact Index Per Article: 58.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Accepted: 06/16/2022] [Indexed: 12/24/2022]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a highly lethal and treatment-refractory cancer. Molecular stratification in pancreatic cancer remains rudimentary and does not yet inform clinical management or therapeutic development. Here, we construct a high-resolution molecular landscape of the cellular subtypes and spatial communities that compose PDAC using single-nucleus RNA sequencing and whole-transcriptome digital spatial profiling (DSP) of 43 primary PDAC tumor specimens that either received neoadjuvant therapy or were treatment naive. We uncovered recurrent expression programs across malignant cells and fibroblasts, including a newly identified neural-like progenitor malignant cell program that was enriched after chemotherapy and radiotherapy and associated with poor prognosis in independent cohorts. Integrating spatial and cellular profiles revealed three multicellular communities with distinct contributions from malignant, fibroblast and immune subtypes: classical, squamoid-basaloid and treatment enriched. Our refined molecular and cellular taxonomy can provide a framework for stratification in clinical trials and serve as a roadmap for therapeutic targeting of specific cellular phenotypes and multicellular interactions.
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Affiliation(s)
- William L Hwang
- Center for Systems Biology and Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Koch Institute for Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Karthik A Jagadeesh
- Center for Systems Biology and Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jimmy A Guo
- Center for Systems Biology and Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA.,School of Medicine, University of California, San Francisco, San Francisco, CA, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Biological and Biomedical Sciences Program, Harvard Medical School, Boston, MA, USA
| | - Hannah I Hoffman
- Center for Systems Biology and Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Koch Institute for Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.,Harvard-MIT MD/PhD and Health Sciences and Technology Program, Harvard Medical School, Boston, MA, USA
| | - Payman Yadollahpour
- Center for Systems Biology and Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Rahul Mohan
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | | | - Orr Ashenberg
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Denis Schapiro
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA, USA.,Institute for Computational Biomedicine and Institute of Pathology, Faculty of Medicine, Heidelberg University and Heidelberg University Hospital, Heidelberg, Germany
| | | | | | | | - George Eng
- Koch Institute for Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.,Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Jason M Schenkel
- Koch Institute for Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.,Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Jennifer Su
- Center for Systems Biology and Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Koch Institute for Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Carina Shiau
- Center for Systems Biology and Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Patrick Yu
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - William A Freed-Pastor
- Koch Institute for Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | | | - Arnav Mehta
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Department of Medical Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Joshua Gould
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | | | | | | | - Julia Waldman
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Lan Nguyen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Toni Delorey
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Devan Phillips
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Genentech, South San Francisco, CA, USA
| | - Jaimie L Barth
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Marina Kem
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Clifton Rodrigues
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Debora Ciprani
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Jorge Roldan
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Piotr Zelga
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Vjola Jorgji
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Jonathan H Chen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Zackery Ely
- Koch Institute for Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | | | | | | | - Jay S Loeffler
- Center for Systems Biology and Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - David P Ryan
- Department of Medical Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Colin D Weekes
- Department of Medical Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Cristina R Ferrone
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Motaz Qadan
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Martin J Aryee
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Rakesh K Jain
- Center for Systems Biology and Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.,Edwin L. Steele Laboratory for Tumor Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Donna S Neuberg
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jennifer Y Wo
- Center for Systems Biology and Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Theodore S Hong
- Center for Systems Biology and Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Ramnik Xavier
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Andrew J Aguirre
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Orit Rozenblatt-Rosen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Genentech, South San Francisco, CA, USA
| | - Mari Mino-Kenudson
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Andrew S Liss
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - David T Ting
- Department of Medical Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Tyler Jacks
- Koch Institute for Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Aviv Regev
- Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Genentech, South San Francisco, CA, USA.
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59
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Miyakawa K, Miyashita N, Horie M, Terasaki Y, Tanaka H, Urushiyama H, Fukuda K, Okabe Y, Ishii T, Kuwahara N, Suzuki HI, Nagase T, Saito A. ASCL1 regulates super-enhancer-associated miRNAs to define molecular subtypes of small cell lung cancer. Cancer Sci 2022; 113:3932-3946. [PMID: 35789143 PMCID: PMC9633298 DOI: 10.1111/cas.15481] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 06/23/2022] [Accepted: 06/27/2022] [Indexed: 11/29/2022] Open
Abstract
Small cell lung cancer (SCLC) is a highly aggressive neuroendocrine tumor with dismal prognosis. Recently, molecular subtypes of SCLC have been defined by the expression status of ASCL1, NEUROD1, YAP1, and POU2F3 transcription regulators. ASCL1 is essential for neuroendocrine differentiation and is expressed in the majority of SCLC. Although previous studies investigated ASCL1 target genes in SCLC cells, ASCL1‐mediated regulation of miRNAs and its relationship to molecular subtypes remain poorly explored. Here, we performed genome‐wide profiling of chromatin modifications (H3K27me3, H3K4me3, and H3K27ac) by CUT&Tag assay and ASCL1 knockdown followed by RNA sequencing and miRNA array analyses in SCLC cells. ASCL1 could preferentially regulate genes associated with super‐enhancers (SEs) defined by enrichment of H3K27ac marking. Moreover, ASCL1 positively regulated several SE‐associated miRNAs, such as miR‐7, miR‐375, miR‐200b‐3p, and miR‐429, leading to repression of their targets, whereas ASCL1 suppressed miR‐455‐3p, an abundant miRNA in other molecular subtypes. We further elucidated unique patterns of SE‐associated miRNAs in different SCLC molecular subtypes, highlighting subtype‐specific miRNA networks with functional relevance. Notably, we found apparent de‐repression of common target genes of different miRNAs following ASCL1 knockdown, suggesting combinatorial action of multiple miRNAs underlying molecular heterogeneity of SCLC (e.g., co‐targeting of YAP1 by miR‐9 and miR‐375). Our comprehensive analyses provide novel insights into SCLC pathogenesis and a clue to understanding subtype‐dependent phenotypic differences.
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Affiliation(s)
- Kazuko Miyakawa
- Department of Respiratory Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Naoya Miyashita
- Department of Respiratory Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Masafumi Horie
- Department of Molecular and Cellular Pathology, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Yasuhiro Terasaki
- Department of Analytic Human Pathology, Nippon Medical School, Tokyo, Japan
| | - Hidenori Tanaka
- Department of Molecular and Cellular Pathology, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan.,Department of Otorhinolaryngology-Head and Neck Surgery, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Hirokazu Urushiyama
- Department of Respiratory Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Kensuke Fukuda
- Department of Respiratory Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yugo Okabe
- Department of Respiratory Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Takashi Ishii
- Department of Respiratory Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Division for Health Service Promotion, The University of Tokyo, Tokyo, Japan
| | - Naomi Kuwahara
- Department of Analytic Human Pathology, Nippon Medical School, Tokyo, 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, Japan
| | - Takahide Nagase
- Department of Respiratory Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Akira Saito
- Department of Respiratory Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
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60
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Jin Y, Zhao Q, Zhu W, Feng Y, Xiao T, Zhang P, Jiang L, Hou Y, Guo C, Huang H, Chen Y, Tong X, Cao J, Li F, Zhu X, Qin J, Gao D, Liu XY, Zhang H, Chen L, Thomas RK, Wong KK, Zhang L, Wang Y, Hu L, Ji H. Identification of TAZ as the essential molecular switch in orchestrating SCLC phenotypic transition and metastasis. Natl Sci Rev 2022; 9:nwab232. [PMID: 35967587 PMCID: PMC9365451 DOI: 10.1093/nsr/nwab232] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 11/30/2021] [Accepted: 12/01/2021] [Indexed: 11/13/2022] Open
Abstract
Small-cell lung cancer (SCLC) is a recalcitrant cancer characterized by high metastasis. However, the exact cell type contributing to metastasis remains elusive. Using a Rb1 L/L /Trp53 L/L mouse model, we identify the NCAMhiCD44lo/- subpopulation as the SCLC metastasizing cell (SMC), which is progressively transitioned from the non-metastasizing NCAMloCD44hi cell (non-SMC). Integrative chromatin accessibility and gene expression profiling studies reveal the important role of the SWI/SNF complex, and knockout of its central component, Brg1, significantly inhibits such phenotypic transition and metastasis. Mechanistically, TAZ is silenced by the SWI/SNF complex during SCLC malignant progression, and its knockdown promotes SMC transition and metastasis. Importantly, ectopic TAZ expression reversely drives SMC-to-non-SMC transition and alleviates metastasis. Single-cell RNA-sequencing analyses identify SMC as the dominant subpopulation in human SCLC metastasis, and immunostaining data show a positive correlation between TAZ and patient prognosis. These data uncover high SCLC plasticity and identify TAZ as the key molecular switch in orchestrating SCLC phenotypic transition and metastasis.
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Affiliation(s)
- Yujuan Jin
- State Key Laboratory of Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
- Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
- Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Qiqi Zhao
- State Key Laboratory of Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
- Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
- Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Weikang Zhu
- Center for Excellence in Mathematical Sciences, National Center for Mathematics and Interdisciplinary Sciences, Key Laboratory of Management, Decision and Information System, Hua Loo-Keng Center for Mathematical Sciences, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing 100190, China
| | - Yan Feng
- State Key Laboratory of Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
- Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
- Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Tian Xiao
- Shenzhen Key Laboratory of Translational Medicine of Tumor, Department of Cell Biology and Genetics, Shenzhen University Health Sciences Center, Shenzhen 518060, China
| | - Peng Zhang
- Shanghai Pulmonary Hospital, Tongji University, Shanghai 200092, China
| | - Liyan Jiang
- Shanghai Chest Hospital, Shanghai Jiaotong University, Shanghai 200030, China
| | - Yingyong Hou
- Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Chenchen Guo
- State Key Laboratory of Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
- Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
- Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Hsinyi Huang
- State Key Laboratory of Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
- Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
- Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yabin Chen
- State Key Laboratory of Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
- Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
- Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Xinyuan Tong
- State Key Laboratory of Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
- Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
- Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Jiayu Cao
- State Key Laboratory of Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
- Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
- Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Fei Li
- Department of Pathology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Xueliang Zhu
- State Key Laboratory of Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
- Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
- Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
- School of Life Science and Technology, Shanghai Tech University, Shanghai 200120, China
| | - Jun Qin
- CAS Key Laboratory of Tissue Microenvironment and Tumor, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Nutrition and Health Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Dong Gao
- State Key Laboratory of Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
- Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
- Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Xin-Yuan Liu
- State Key Laboratory of Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
- Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
- Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Hua Zhang
- Laura and Isaac Perlmutter Cancer Center, New York University Langone Medical Center, New York, NY 10016, USA
| | - Luonan Chen
- State Key Laboratory of Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
- Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
- Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
- School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
| | - Roman K Thomas
- Department of Translational Genomics, Center of Integrated Oncology Cologne-Bonn, Medical Faculty, University of Cologne, Cologne 50931, Germany
- Department of Pathology, University Hospital Cologne, Cologne 50937, Germany
| | - Kwok-Kin Wong
- Laura and Isaac Perlmutter Cancer Center, New York University Langone Medical Center, New York, NY 10016, USA
| | - Lei Zhang
- State Key Laboratory of Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
- Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
- Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
- School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
| | - Yong Wang
- Center for Excellence in Mathematical Sciences, National Center for Mathematics and Interdisciplinary Sciences, Key Laboratory of Management, Decision and Information System, Hua Loo-Keng Center for Mathematical Sciences, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing 100190, China
- School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
| | - Liang Hu
- State Key Laboratory of Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
- Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
- Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Hongbin Ji
- State Key Laboratory of Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
- Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
- Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
- School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
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61
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Rebbeck CA, Xian J, Bornelöv S, Geradts J, Hobeika A, Geiger H, Alvarez JF, Rozhkova E, Nicholls A, Robine N, Lyerly HK, Hannon GJ. Gene expression signatures of individual ductal carcinoma in situ lesions identify processes and biomarkers associated with progression towards invasive ductal carcinoma. Nat Commun 2022; 13:3399. [PMID: 35697697 PMCID: PMC9192778 DOI: 10.1038/s41467-022-30573-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 05/06/2022] [Indexed: 12/27/2022] Open
Abstract
Ductal carcinoma in situ (DCIS) is considered a non-invasive precursor to breast cancer, and although associated with an increased risk of developing invasive disease, many women with DCIS will never progress beyond their in situ diagnosis. The path from normal duct to invasive ductal carcinoma (IDC) is not well understood, and efforts to do so are hampered by the substantial heterogeneity that exists between patients, and even within patients. Here we show gene expression analysis from > 2,000 individually micro-dissected ductal lesions representing 145 patients. Combining all samples into one continuous trajectory we show there is a progressive loss in basal layer integrity heading towards IDC, coupled with two epithelial to mesenchymal transitions, one early and a second coinciding with the convergence of DCIS and IDC expression profiles. We identify early processes and potential biomarkers, including CAMK2N1, MNX1, ADCY5, HOXC11 and ANKRD22, whose reduced expression is associated with the progression of DCIS to invasive breast cancer.
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Affiliation(s)
- Clare A Rebbeck
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK.
| | - Jian Xian
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Susanne Bornelöv
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Joseph Geradts
- Department of Pathology & Laboratory Medicine, East Carolina University Brody School of Medicine, Greenville, NC, USA
| | - Amy Hobeika
- Department of Surgery, Duke University Medical Center, Durham, NC, USA
| | | | - Jose Franco Alvarez
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Elena Rozhkova
- Department of Dermatology, Boston University School of Medicine, Boston, MA, USA
| | - Ashley Nicholls
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | | | - Herbert K Lyerly
- Department of Surgery, Duke University Medical Center, Durham, NC, USA.
| | - Gregory J Hannon
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK.
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62
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Zhou L, Wang QL, Mao LH, Chen SY, Yang ZH, Liu X, Gao YH, Li XQ, Zhou ZH, He S. Hepatocyte-Specific Knock-Out of Nfib Aggravates Hepatocellular Tumorigenesis via Enhancing Urea Cycle. Front Mol Biosci 2022; 9:875324. [PMID: 35655758 PMCID: PMC9152321 DOI: 10.3389/fmolb.2022.875324] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 03/28/2022] [Indexed: 12/23/2022] Open
Abstract
Nuclear Factor I B (NFIB) has been reported to promote tumor growth, metastasis, and liver regeneration, but its mechanism in liver cancer is not fully elucidated. The present study aims to reveal the role of NFIB in hepatocellular carcinogenesis. In our study, we constructed hepatocyte-specific NFIB gene knockout mice with CRISPR/Cas9 technology (Nfib-/-; Alb-cre), and induced liver cancer mouse model by intraperitoneal injection of DEN/CCl4. First, we found that Nfib-/- mice developed more tumor nodules and had heavier livers than wild-type mice. H&E staining indicated that the liver histological severity of Nfib-/- group was more serious than that of WT group. Then we found that the differentially expressed genes in the tumor tissue between Nfib-/- mice and wild type mice were enriched in urea cycle. Furthermore, ASS1 and CPS1, the core enzymes of the urea cycle, were significantly upregulated in Nfib-/- tumors. Subsequently, we validated that the expression of ASS1 and CPS1 increased after knockdown of NFIB by lentivirus in normal hepatocytes and also promoted cell proliferation in vitro. In addition, ChIP assay confirmed that NFIB can bind with promoter region of both ASS1 and CPS1 gene. Our study reveals for the first time that hepatocyte-specific knock-out of Nfib aggravates hepatocellular tumor development by enhancing the urea cycle.
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Affiliation(s)
- Li Zhou
- Department of Gastroenterology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Qing-Liang Wang
- Department of Pathology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Lin-Hong Mao
- Department of Gastroenterology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China.,Department of Gastroenterology, Chengdu Second People's Hospital, Sichuan, China
| | - Si-Yuan Chen
- Department of Gastroenterology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Zi-Han Yang
- Department of Biomedical Science, City University of Hong Kong, Hong Kong, China
| | - Xue Liu
- Department of Pathology, College of Basic Medicine, Jining Medical University, Jining, China
| | - Yu-Hua Gao
- Key Laboratory of Precision Oncology in Universities of Shandong, Institute of Precision Medicine, Jining Medical University, Jining, China
| | - Xiao-Qin Li
- Department of Gastroenterology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Zhi-Hang Zhou
- Department of Gastroenterology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Song He
- Department of Gastroenterology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
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63
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Na F, Pan X, Chen J, Chen X, Wang M, Chi P, You L, Zhang L, Zhong A, Zhao L, Dai S, Zhang M, Wang Y, Wang B, Zheng J, Wang Y, Xu J, Wang J, Wu B, Chen M, Liu H, Xue J, Huang M, Gong Y, Zhu J, Zhou L, Zhang Y, Yu M, Tian P, Fan M, Lu Z, Xue Z, Zhao Y, Yang H, Zhao C, Wang Y, Han J, Yang S, Xie D, Chen L, Zhong Q, Zeng M, Lowe SW, Lu Y, Liu Y, Wei Y, Chen C. KMT2C deficiency promotes small cell lung cancer metastasis through DNMT3A-mediated epigenetic reprogramming. NATURE CANCER 2022; 3:753-767. [PMID: 35449309 PMCID: PMC9969417 DOI: 10.1038/s43018-022-00361-6] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 03/10/2022] [Indexed: 02/02/2023]
Abstract
Small cell lung cancer (SCLC) is notorious for its early and frequent metastases, which contribute to it as a recalcitrant malignancy. To understand the molecular mechanisms underlying SCLC metastasis, we generated SCLC mouse models with orthotopically transplanted genome-edited lung organoids and performed multiomics analyses. We found that a deficiency of KMT2C, a histone H3 lysine 4 methyltransferase frequently mutated in extensive-stage SCLC, promoted multiple-organ metastases in mice. Metastatic and KMT2C-deficient SCLC displayed both histone and DNA hypomethylation. Mechanistically, KMT2C directly regulated the expression of DNMT3A, a de novo DNA methyltransferase, through histone methylation. Forced DNMT3A expression restrained metastasis of KMT2C-deficient SCLC through repressing metastasis-promoting MEIS/HOX genes. Further, S-(5'-adenosyl)-L-methionine, the common cofactor of histone and DNA methyltransferases, inhibited SCLC metastasis. Thus, our study revealed a concerted epigenetic reprogramming of KMT2C- and DNMT3A-mediated histone and DNA hypomethylation underlying SCLC metastasis, which suggested a potential epigenetic therapeutic vulnerability.
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Affiliation(s)
- Feifei Na
- Department of Thoracic Oncology, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China,These authors contributed equally: Feifei Na, Xiangyu Pan, Jingyao Chen, Xuelan Chen
| | - Xiangyu Pan
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China,These authors contributed equally: Feifei Na, Xiangyu Pan, Jingyao Chen, Xuelan Chen
| | - Jingyao Chen
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China,These authors contributed equally: Feifei Na, Xiangyu Pan, Jingyao Chen, Xuelan Chen
| | - Xuelan Chen
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China,These authors contributed equally: Feifei Na, Xiangyu Pan, Jingyao Chen, Xuelan Chen
| | - Manli Wang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Pengliang Chi
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Liting You
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Lanxin Zhang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Ailing Zhong
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Lei Zhao
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Siqi Dai
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Mengsha Zhang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Yiyun Wang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Bo Wang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Jianan Zheng
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Yuying Wang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Jing Xu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Jian Wang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Baohong Wu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Mei Chen
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Hongyu Liu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Jianxin Xue
- Department of Thoracic Oncology, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Meijuan Huang
- Department of Thoracic Oncology, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Youling Gong
- Department of Thoracic Oncology, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Jiang Zhu
- Department of Thoracic Oncology, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Lin Zhou
- Department of Thoracic Oncology, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Yan Zhang
- Department of Thoracic Oncology, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Min Yu
- Department of Thoracic Oncology, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Panwen Tian
- Department of Respiratory and Critical Care Medicine, West China Hospital of Sichuan University, Chengdu, China
| | - Mingyu Fan
- Lung Cancer Treatment Center, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Zhenghao Lu
- Department of Thoracic Oncology, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China,Chengdu OrganoidMed Medical Laboratory, West China Health Valley, Chengdu, China
| | - Zhihong Xue
- Department of Thoracic Oncology, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Yinglan Zhao
- Department of Thoracic Oncology, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Hanshuo Yang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Chengjian Zhao
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Yuan Wang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Junhong Han
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Shengyong Yang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Dan Xie
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Lu Chen
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Qian Zhong
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Musheng Zeng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Scott W. Lowe
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA,Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - You Lu
- Department of Thoracic Oncology, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Yu Liu
- Department of Thoracic Oncology, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Yuquan Wei
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Chong Chen
- Department of Thoracic Oncology, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China. .,State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China.
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64
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Grandi FC, Modi H, Kampman L, Corces MR. Chromatin accessibility profiling by ATAC-seq. Nat Protoc 2022; 17:1518-1552. [PMID: 35478247 PMCID: PMC9189070 DOI: 10.1038/s41596-022-00692-9] [Citation(s) in RCA: 112] [Impact Index Per Article: 56.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 02/22/2022] [Indexed: 12/13/2022]
Abstract
The assay for transposase-accessible chromatin using sequencing (ATAC-seq) provides a simple and scalable way to detect the unique chromatin landscape associated with a cell type and how it may be altered by perturbation or disease. ATAC-seq requires a relatively small number of input cells and does not require a priori knowledge of the epigenetic marks or transcription factors governing the dynamics of the system. Here we describe an updated and optimized protocol for ATAC-seq, called Omni-ATAC, that is applicable across a broad range of cell and tissue types. The ATAC-seq workflow has five main steps: sample preparation, transposition, library preparation, sequencing and data analysis. This protocol details the steps to generate and sequence ATAC-seq libraries, with recommendations for sample preparation and downstream bioinformatic analysis. ATAC-seq libraries for roughly 12 samples can be generated in 10 h by someone familiar with basic molecular biology, and downstream sequencing analysis can be implemented using benchmarked pipelines by someone with basic bioinformatics skills and with access to a high-performance computing environment.
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Affiliation(s)
- Fiorella C Grandi
- Gladstone Institute of Neurological Disease, San Francisco, CA, USA
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Hailey Modi
- Gladstone Institute of Neurological Disease, San Francisco, CA, USA
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Lucas Kampman
- Gladstone Institute of Neurological Disease, San Francisco, CA, USA
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - M Ryan Corces
- Gladstone Institute of Neurological Disease, San Francisco, CA, USA.
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA.
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA.
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65
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Yang D, Jones MG, Naranjo S, Rideout WM, Min KHJ, Ho R, Wu W, Replogle JM, Page JL, Quinn JJ, Horns F, Qiu X, Chen MZ, Freed-Pastor WA, McGinnis CS, Patterson DM, Gartner ZJ, Chow ED, Bivona TG, Chan MM, Yosef N, Jacks T, Weissman JS. Lineage tracing reveals the phylodynamics, plasticity, and paths of tumor evolution. Cell 2022; 185:1905-1923.e25. [PMID: 35523183 DOI: 10.1016/j.cell.2022.04.015] [Citation(s) in RCA: 103] [Impact Index Per Article: 51.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 02/09/2022] [Accepted: 04/08/2022] [Indexed: 12/19/2022]
Abstract
Tumor evolution is driven by the progressive acquisition of genetic and epigenetic alterations that enable uncontrolled growth and expansion to neighboring and distal tissues. The study of phylogenetic relationships between cancer cells provides key insights into these processes. Here, we introduced an evolving lineage-tracing system with a single-cell RNA-seq readout into a mouse model of Kras;Trp53(KP)-driven lung adenocarcinoma and tracked tumor evolution from single-transformed cells to metastatic tumors at unprecedented resolution. We found that the loss of the initial, stable alveolar-type2-like state was accompanied by a transient increase in plasticity. This was followed by the adoption of distinct transcriptional programs that enable rapid expansion and, ultimately, clonal sweep of stable subclones capable of metastasizing. Finally, tumors develop through stereotypical evolutionary trajectories, and perturbing additional tumor suppressors accelerates progression by creating novel trajectories. Our study elucidates the hierarchical nature of tumor evolution and, more broadly, enables in-depth studies of tumor progression.
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Affiliation(s)
- Dian Yang
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Matthew G Jones
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Biological and Medical Informatics Graduate Program, University of California, San Francisco, San Francisco, CA 94158, USA; Integrative Program in Quantitative Biology, University of California, San Francisco, San Francisco, CA 94158, USA; Center for Computational Biology, University of California, Berkeley, Berkeley, CA 94720, USA; David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Santiago Naranjo
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - William M Rideout
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Kyung Hoi Joseph Min
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Raymond Ho
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Wei Wu
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94158, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Joseph M Replogle
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA 94158, USA; Tetrad Graduate Program, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Jennifer L Page
- Cell and Genome Engineering Core, University of California San Francisco, San Francisco, CA 94158, USA
| | - Jeffrey J Quinn
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Felix Horns
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Xiaojie Qiu
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Michael Z Chen
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Medical Scientist Training Program, Harvard Medical School, Boston, MA 02115, USA
| | - William A Freed-Pastor
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Christopher S McGinnis
- Tetrad Graduate Program, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - David M Patterson
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Zev J Gartner
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA; Chan Zuckerberg BioHub Investigator, University of California, San Francisco, San Francisco, CA 94158, USA; Center for Cellular Construction, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Eric D Chow
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA; Center for Advanced Technology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Trever G Bivona
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94158, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Michelle M Chan
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Nir Yosef
- Center for Computational Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Chan Zuckerberg BioHub Investigator, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Electrical Engineering and Computer Science, University of California Berkeley, Berkeley, CA 94720, USA; Ragon Institute of Massachusetts General Hospital, MIT and Harvard University, Cambridge, MA, USA.
| | - Tyler Jacks
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.
| | - Jonathan S Weissman
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.
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66
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Lee MK, Brown MS, Wilkins OM, Pattabiraman DR, Christensen BC. Distinct cytosine modification profiles define epithelial-to-mesenchymal cell-state transitions. Epigenomics 2022; 14:519-535. [PMID: 35382559 PMCID: PMC9118069 DOI: 10.2217/epi-2022-0023] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 03/28/2022] [Indexed: 12/02/2022] Open
Abstract
Background: Epithelial-to-mesenchymal transition (EMT) is an early step in the invasion-metastasis cascade, involving progression through intermediate cell states. Due to challenges with isolating intermediate cell states, genome-wide cytosine modifications that define transition are not completely understood. Methods: The authors measured multiple DNA cytosine modification marks and chromatin accessibility across clonal populations residing in specific EMT states. Results: Clones exhibiting more intermediate EMT phenotypes demonstrated increased 5-hydroxymethylcytosine and decreased 5-methylcytosine. Open chromatin regions containing increased 5-hydroxymethylcytosine CpG loci were enriched in EMT transcription factor motifs and were associated with Rho GTPases. Conclusion: The results indicate the importance of both distinct and shared epigenetic profiles associated with EMT processes that may be targeted to prevent EMT progression.
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Affiliation(s)
- Min Kyung Lee
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
| | - Meredith S Brown
- Department of Molecular & Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
| | - Owen M Wilkins
- Norris Cotton Cancer Center, Dartmouth-Hitchcock Medical Center, Lebanon, NH 03756, USA
| | - Diwakar R Pattabiraman
- Department of Molecular & Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
| | - Brock C Christensen
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
- Department of Molecular & Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
- Department of Community & Family Medicine, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
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67
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Gurova K. Can aggressive cancers be identified by the "aggressiveness" of their chromatin? Bioessays 2022; 44:e2100212. [PMID: 35452144 DOI: 10.1002/bies.202100212] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 04/08/2022] [Accepted: 04/12/2022] [Indexed: 12/15/2022]
Abstract
Phenotypic plasticity is a crucial feature of aggressive cancer, providing the means for cancer progression. Stochastic changes in tumor cell transcriptional programs increase the chances of survival under any condition. I hypothesize that unstable chromatin permits stochastic transitions between transcriptional programs in aggressive cancers and supports non-genetic heterogeneity of tumor cells as a basis for their adaptability. I present a mechanistic model for unstable chromatin which includes destabilized nucleosomes, mobile chromatin fibers and random enhancer-promoter contacts, resulting in stochastic transcription. I suggest potential markers for "unsettled" chromatin in tumors associated with poor prognosis. Although many of the characteristics of unstable chromatin have been described, they were mostly used to explain changes in the transcription of individual genes. I discuss approaches to evaluate the role of unstable chromatin in non-genetic tumor cell heterogeneity and suggest using the degree of chromatin instability and transcriptional noise in tumor cells to predict cancer aggressiveness.
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Affiliation(s)
- Katerina Gurova
- Department of Cell Stress Biology, Roswell Park Comprehensive Cancer Center, Buffalo, New York, USA
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68
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Gao Y, Huang Y. Circ_0007841 knockdown confers cisplatin sensitivity to ovarian cancer cells by down-regulation of NFIB expression in a miR-532-5p-dependent manner. J Chemother 2022; 35:117-130. [PMID: 35380509 DOI: 10.1080/1120009x.2022.2056995] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Cisplatin (DDP) is first-line management for ovarian cancer (OC). Previous data have suggested that circular RNA_0007841 (circ_0007841) regulates OC progression; however, there is no data on its role in the sensitivity of OC cells to DDP. RNA expression of circ_0007841, microRNA-532-5p (miR-532-5p) and nuclear factor I B (NFIB) was detected by quantitative real-time polymerase chain reaction in OC patient samples and OC cell lines. Protein expression was checked by Western blotting analysis. Cell viability, proliferation, cell apoptotic rate, migration and invasion were investigated by 3-(4,5)-dimethylthiahiazo (-z-y1)-3,5-diphenytetrazoliumromide, 5-Ethynyl-29-deoxyuridine, flow cytometry analysis, scratch test and transwell assays, respectively. The interactions among circ_0007841, miR-532-5p and NFIB were identified by a dual-luciferase reporter assay. Xenograft mouse model assay was performed to determine the effect of circ_0007841 on DDP sensitivity in vivo. Circ_0007841 and NFIB expression were upregulated, whereas miR-532-5p was downregulated in DDP-resistant OC tissues and cells compared with controls. Circ_0007841 silencing improved DDP sensitivity, inhibited cell proliferation, invasion and migration, but induced cell apoptosis in DDP-resistant OC cells. Circ_0007841 acted as a miR-532-5p sponge and regulated DDP resistance and OC cell malignancy through miR-532-5p in DDP-resistant OC cells. Besides, the overexpression of NFIB, a target of miR-532-5p, remitted miR-532-5p-mediated effects in DDP-resistant OC cells. Circ_0007841 depletion conferred DDP sensitivity to DDP-resistant OC cells in vivo. Further, circ_0007841 was secreted from DDP-resistant OC cells through being packaged into exosomes. Circ_0007841 conferred DDP resistance to DDP-resistant OC cells through the miR-532-5p/NFIB axis, suggesting the potential of circ_0007841 as a therapeutic target for OC.
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Affiliation(s)
- Yuan Gao
- Department of Pharmacy, Wuhan Sixth Hospital, Wuhan, China
| | - Yan Huang
- Department of Pharmacy, Wuhan Sixth Hospital, Wuhan, China
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69
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Abstract
Drug resistance and metastasis-the major complications in cancer-both entail adaptation of cancer cells to stress, whether a drug or a lethal new environment. Intriguingly, these adaptive processes share similar features that cannot be explained by a pure Darwinian scheme, including dormancy, increased heterogeneity, and stress-induced plasticity. Here, we propose that learning theory offers a framework to explain these features and may shed light on these two intricate processes. In this framework, learning is performed at the single-cell level, by stress-driven exploratory trial-and-error. Such a process is not contingent on pre-existing pathways but on a random search for a state that diminishes the stress. We review underlying mechanisms that may support this search, and show by using a learning model that such exploratory learning is feasible in a high-dimensional system as the cell. At the population level, we view the tissue as a network of exploring agents that communicate, restraining cancer formation in health. In this view, disease results from the breakdown of homeostasis between cellular exploratory drive and tissue homeostasis.
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Affiliation(s)
- Aseel Shomar
- Department of Chemical Engineering, Israel Institute of Technology, Haifa 32000, Israel
- Network Biology Research Laboratory, Israel Institute of Technology, Haifa 32000, Israel
| | - Omri Barak
- Network Biology Research Laboratory, Israel Institute of Technology, Haifa 32000, Israel
- Rappaport Faculty of Medicine Technion, Israel Institute of Technology, Haifa 32000, Israel
| | - Naama Brenner
- Department of Chemical Engineering, Israel Institute of Technology, Haifa 32000, Israel
- Network Biology Research Laboratory, Israel Institute of Technology, Haifa 32000, Israel
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70
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Abstract
Small cell lung cancer (SCLC) is a rapidly growing, highly metastatic, and relatively immune-cold lung cancer subtype. Historically viewed in the laboratory and clinic as a single disease, new discoveries suggest that SCLC comprises multiple molecular subsets. Expression of MYC family members and lineage-related transcription factors ASCL1, NEUROD1, and POU2F3 (and, in some studies, YAP1) define unique molecular states that have been associated with distinct responses to a variety of therapies. However, SCLC tumors exhibit a high degree of intratumoral heterogeneity, with recent studies suggesting the existence of tumor cell plasticity and phenotypic switching between subtype states. While SCLC plasticity is correlated with, and likely drives, therapeutic resistance, the mechanisms underlying this plasticity are still largely unknown. Subtype states are also associated with immune-related gene expression, which likely impacts response to immune checkpoint blockade and may reveal novel targets for alternative immunotherapeutic approaches. In this review, we synthesize recent discoveries on the mechanisms of SCLC plasticity and how these processes may impinge on antitumor immunity.
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Affiliation(s)
- Kate D Sutherland
- Australian Cancer Research Foundation (ACRF) Cancer Biology and Stem Cells Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria 3052, Australia
| | - Abbie S Ireland
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah 84112, USA
| | - Trudy G Oliver
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah 84112, USA
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71
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Zibetti C. Deciphering the Retinal Epigenome during Development, Disease and Reprogramming: Advancements, Challenges and Perspectives. Cells 2022; 11:cells11050806. [PMID: 35269428 PMCID: PMC8908986 DOI: 10.3390/cells11050806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 02/15/2022] [Accepted: 02/18/2022] [Indexed: 02/01/2023] Open
Abstract
Retinal neurogenesis is driven by concerted actions of transcription factors, some of which are expressed in a continuum and across several cell subtypes throughout development. While seemingly redundant, many factors diversify their regulatory outcome on gene expression, by coordinating variations in chromatin landscapes to drive divergent retinal specification programs. Recent studies have furthered the understanding of the epigenetic contribution to the progression of age-related macular degeneration, a leading cause of blindness in the elderly. The knowledge of the epigenomic mechanisms that control the acquisition and stabilization of retinal cell fates and are evoked upon damage, holds the potential for the treatment of retinal degeneration. Herein, this review presents the state-of-the-art approaches to investigate the retinal epigenome during development, disease, and reprogramming. A pipeline is then reviewed to functionally interrogate the epigenetic and transcriptional networks underlying cell fate specification, relying on a truly unbiased screening of open chromatin states. The related work proposes an inferential model to identify gene regulatory networks, features the first footprinting analysis and the first tentative, systematic query of candidate pioneer factors in the retina ever conducted in any model organism, leading to the identification of previously uncharacterized master regulators of retinal cell identity, such as the nuclear factor I, NFI. This pipeline is virtually applicable to the study of genetic programs and candidate pioneer factors in any developmental context. Finally, challenges and limitations intrinsic to the current next-generation sequencing techniques are discussed, as well as recent advances in super-resolution imaging, enabling spatio-temporal resolution of the genome.
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Affiliation(s)
- Cristina Zibetti
- Department of Ophthalmology, Institute of Clinical Medicine, University of Oslo, Kirkeveien 166, Building 36, 0455 Oslo, Norway
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72
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Mattos ACD, Florindo JB, Adam RL, Lorand-Metze I, Metze K. The Fractal Dimension Suggests Two Chromatin Configurations in Small Cell Neuroendocrine Lung Cancer and Is an Independent Unfavorable Prognostic Factor for Overall Survival. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2022; 28:1-5. [PMID: 35193724 DOI: 10.1017/s1431927622000113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Experimental studies have shown that in small cell neuroendocrine lung carcinomas (SCLC) global opening of the chromatin structure is associated with a higher transcription activity and increase of tumor aggressiveness and metastasis. The study of the fractal characteristics (FD) of nuclear chromatin has been widely used to describe the cell nuclear texture and its changes correspond to changes in nuclear metabolic and transcription activity. Hence, we investigated whether the nuclear fractal dimension could be a prognostic factor in SCLC. Hematoxylin-eosin stained brush cytology slides from 49 patients with SCLC were retrieved from our files. The chromatin (FD) was calculated in digitalized and interactively segmented nuclei using a differential box-counting method. The 3,575 nuclei studied showed a bimodal distribution (peaks at FD1 = 2.115 and FD2 = 2.180). The 75 percentile of the FD was an independent unfavorable prognostic factor for overall survival when tested together with ECOG (Eastern Cooperative Oncology Group) performance status, tumor extension, and therapy in a multivariate Cox regression. Our study corroborates the concept of two main chromatin configurations in small cell neuroendocrine carcinomas and that globally more open chromatin indicates a higher risk of metastasis and therefore a shorter survival of the patient.
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Affiliation(s)
- Amilcar Castro de Mattos
- Department of Pathology, Faculty of Medical Sciences, University of Campinas (UNICAMP), Campinas, SP, Brazil
- Laboratory of Pathology, Pontifical Catholic University of Campinas PUCC, Campinas, Brazil
| | - João Batista Florindo
- Institute of Mathematics, Statistics and Scientific Computing, University of Campinas (UNICAMP), Campinas, Brazil
| | - Randall L Adam
- Department of Pathology, Faculty of Medical Sciences, University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - Irene Lorand-Metze
- Department of Internal Medicine, Faculty of Medical Sciences, University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - Konradin Metze
- Department of Pathology, Faculty of Medical Sciences, University of Campinas (UNICAMP), Campinas, SP, Brazil
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Zhang B, Lin J, Zhang J, Wang X, Deng X. Integrated Chromatin Accessibility and Transcriptome Landscapes of 5-Fluorouracil-Resistant Colon Cancer Cells. Front Cell Dev Biol 2022; 10:838332. [PMID: 35252200 PMCID: PMC8891516 DOI: 10.3389/fcell.2022.838332] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 01/26/2022] [Indexed: 12/11/2022] Open
Abstract
Background: 5-Fluorouracil (5-FU) is one of the most effective and widely used chemotherapeutic drugs in the treatment of colon cancer, yet chemoresistance is a common feature of colon cancer treatment, resulting in poor prognosis and short survival. Dynamic reprogramming of chromatin accessibility is crucial for proper regulation of gene transcription associated with cancer drug resistance by providing the gene regulatory machinery with rapid access to the open genomic DNA. Methods: Here, we explored the global chromatin accessibility and transcription changes by the assay for transposase-accessible chromatin using sequencing (ATAC-seq) in combination with transcriptome sequencing of both parental and 5-FU-resistant HCT15 cells, followed by integrative analysis to better understand the regulatory network underlying 5-FU resistance in colon cancer cells. Results: A total of 3,175 differentially expressed mRNAs (DEGs), lncRNAs (DELs), and miRNAs (DEMs) related to 5-FU resistance were identified, including significantly upregulated IL33, H19, and miR-17-5p; the downregulated AKR1B10, LINC01012, and miR-125b-5p; and chromatin modifiers such as INO80C, HDAC6, and KDM5A. The construction of the ceRNA regulatory network revealed that H19, HOXA11-AS, and NEAT1 might function as ceRNAs associated with 5-FU resistance in HCT15 cells. Moreover, 9,868 differentially accessible regions (DARs) were obtained, which were positively (r = 0.58) correlated with their nearest DEGs and DELs. The upregulated genes related to 4,937 hyper-accessible regions were significantly enriched in signaling pathways of MAPK, FOX, and WNT, while the 4,931 hypo-accessible regions were considered to be involved in declined biosynthesis of amino acids and nucleotide sugars, signaling pathways of Notch, and HIF-1. Analyses of the DAR sequences revealed that besides the AP-1 family, the TF motifs of FOX and KLF family members were highly enriched in hyper- and hypo-accessible regions, respectively. Finally, we obtained several critical TFs and their potential targets associated with DARs and 5-FU resistance, including FOXA1 and KLF3. Conclusion: These data provided clear insights and valuable resources for an improved understanding of the non-genetic landscape of 5-FU-resistant colon cancer cells based on chromatin accessibility and transcript levels, which allowed for genome-wide detection of TF binding sites, potential cis-regulatory elements and therapeutic targets.
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Affiliation(s)
- Bishu Zhang
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Research Institute of Pancreatic Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- State Key Laboratory of Oncogenes and Related Genes, Shanghai, China
- Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jiewei Lin
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Research Institute of Pancreatic Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- State Key Laboratory of Oncogenes and Related Genes, Shanghai, China
- Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jiaqiang Zhang
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Research Institute of Pancreatic Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- State Key Laboratory of Oncogenes and Related Genes, Shanghai, China
- Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
- *Correspondence: Jiaqiang Zhang, ; Xuelong Wang, ; Xiaxing Deng,
| | - Xuelong Wang
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Research Institute of Pancreatic Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
- *Correspondence: Jiaqiang Zhang, ; Xuelong Wang, ; Xiaxing Deng,
| | - Xiaxing Deng
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Research Institute of Pancreatic Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- State Key Laboratory of Oncogenes and Related Genes, Shanghai, China
- Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
- *Correspondence: Jiaqiang Zhang, ; Xuelong Wang, ; Xiaxing Deng,
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Kadur Lakshminarasimha Murthy P, Xi R, Arguijo D, Everitt JI, Kocak DD, Kobayashi Y, Bozec A, Vicent S, Ding S, Crawford GE, Hsu D, Tata PR, Reddy T, Shen X. Epigenetic basis of oncogenic-Kras-mediated epithelial-cellular proliferation and plasticity. Dev Cell 2022; 57:310-328.e9. [PMID: 35134344 PMCID: PMC8938988 DOI: 10.1016/j.devcel.2022.01.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Revised: 09/15/2021] [Accepted: 01/06/2022] [Indexed: 12/13/2022]
Abstract
Oncogenic Kras induces a hyper-proliferative state that permits cells to progress to neoplasms in diverse epithelial tissues. Depending on the cell of origin, this also involves lineage transformation. Although a multitude of downstream factors have been implicated in these processes, the precise chronology of molecular events controlling them remains elusive. Using mouse models, primary human tissues, and cell lines, we show that, in Kras-mutant alveolar type II cells (AEC2), FOSL1-based AP-1 factor guides the mSWI/SNF complex to increase chromatin accessibility at genomic loci controlling the expression of genes necessary for neoplastic transformation. We identified two orthogonal processes in Kras-mutant distal airway club cells. The first promoted their transdifferentiation into an AEC2-like state through NKX2.1, and the second controlled oncogenic transformation through the AP-1 complex. Our results suggest that neoplasms retain an epigenetic memory of their cell of origin through cell-type-specific transcription factors. Our analysis showed that a cross-tissue-conserved AP-1-dependent chromatin remodeling program regulates carcinogenesis.
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Affiliation(s)
- Preetish Kadur Lakshminarasimha Murthy
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA; Sibley School of Mechanical and Aerospace Engineering, Cornell University, Ithaca, NY 14853, USA; Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA. :
| | - Rui Xi
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA; Center for Genomics and Computational Biology, Duke University, Durham, NC 27708, USA
| | - Diana Arguijo
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
| | - Jeffrey I Everitt
- Department of Pathology, Duke University Medical Center, Durham, NC 27710, USA
| | - Dewran D Kocak
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA; Center for Genomics and Computational Biology, Duke University, Durham, NC 27708, USA
| | - Yoshihiko Kobayashi
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - Aline Bozec
- Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Department of Internal Medicine 3 - Rheumatology and Immunology, Universitätsklinikum Erlangen, Erlangen, Germany
| | - Silvestre Vicent
- University of Navarra, Center for Applied Medical Research, Program in Solid Tumors, Pamplona, Spain; University of Navarra, Department of Pathology, Anatomy and Physiology, Pamplona, Spain; IdiSNA, Navarra Institute for Health Research, Pamplona, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Shengli Ding
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA; Center for Genomics and Computational Biology, Duke University, Durham, NC 27708, USA; Center for Advanced Genomic Technologies, Duke University, Durham, NC 27708, USA
| | - Gregory E Crawford
- Center for Genomics and Computational Biology, Duke University, Durham, NC 27708, USA; Center for Advanced Genomic Technologies, Duke University, Durham, NC 27708, USA; Department of Pediatrics, Division of Medical Genetics, Duke University, Durham, NC 27710, USA
| | - David Hsu
- Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA
| | - Purushothama Rao Tata
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA; Center for Advanced Genomic Technologies, Duke University, Durham, NC 27708, USA
| | - Timothy Reddy
- Center for Genomics and Computational Biology, Duke University, Durham, NC 27708, USA; Center for Advanced Genomic Technologies, Duke University, Durham, NC 27708, USA; Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, NC 27710, USA
| | - Xiling Shen
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA; Center for Genomics and Computational Biology, Duke University, Durham, NC 27708, USA; Center for Advanced Genomic Technologies, Duke University, Durham, NC 27708, USA; Terasaki Institute for Biomedical Innovation, Los Angeles, CA 90024, USA.
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75
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SETD2 loss perturbs the kidney cancer epigenetic landscape to promote metastasis and engenders actionable dependencies on histone chaperone complexes. NATURE CANCER 2022; 3:188-202. [PMID: 35115713 PMCID: PMC8885846 DOI: 10.1038/s43018-021-00316-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 11/24/2021] [Indexed: 12/13/2022]
Abstract
SETD2 is a H3K36 trimethyltransferase that is mutated with high prevalence (13%) in clear cell renal cell carcinoma (ccRCC). Genomic profiling of primary ccRCC tumors reveals a positive correlation between SETD2 mutations and metastasis. However, whether and how SETD2 loss promotes metastasis remains unclear. In this study, we used SETD2-mutant metastatic ccRCC patient-derived cell line and xenograft models and showed that H3K36me3 restoration greatly reduced distant metastases of ccRCC in mice in an MMP1-dependent manner. An integrated multi-omics analysis using ATAC-seq, ChIP-seq, and RNA-seq established a tumor suppressor model in which loss of SETD2-mediated H3K36me3 activates enhancers to drive oncogenic transcriptional output through regulation of chromatin accessibility. Furthermore, we uncovered mechanism-based therapeutic strategies for SETD2-deficient cancer through the targeting of specific histone chaperone complexes including ASF1A/B and SPT16. Overall, SETD2 loss creates a permissive epigenetic landscape for cooperating oncogenic drivers to amplify transcriptional output, providing unique therapeutic opportunities.
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76
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Uluca B, Lektemur Esen C, Saritas Erdogan S, Kumbasar A. NFI transcriptionally represses CDON and is required for SH-SY5Y cell survival. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2022; 1865:194798. [PMID: 35151899 DOI: 10.1016/j.bbagrm.2022.194798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 01/14/2022] [Accepted: 01/30/2022] [Indexed: 06/14/2023]
Abstract
Nuclear Factor One (NFI) family of transcription factors regulate proliferation and multiple aspects of differentiation, playing analogous roles in embryonic development and various types of cancer. While all NFI family members are expressed in the developing brain and are involved in progression of brain cancers, their role in neuroblastoma has not been studied. Here we show that NFIB is required for the survival and proliferation of SH-SY5Y neuroblastoma cells, assessed by viability and colony formation assays. Cdon, an Ig superfamily member, is a SHH dependence receptor that acts as a tumor suppressor in neuroblastoma. In the absence of NFI, Cdon is upregulated in the developing mouse brain, however the mechanisms by which its transcription is regulated remains unknown. We report CDON as a downstream target of NFIs in SH-SY5Y cells. There are three putative NFI binding sites within the one kb CDON promoter, two of which are occupied by NFIs in SH-SY5Y cells and human neural stem cells. In dual-luciferase assays, Nfib directly represses CDON proximal promoter activity. Moreover, silencing NFIB leads to upregulation of CDON in SH-SY5Y cells, however, decreased cell proliferation in NFIB silenced cells could not be rescued by concomitantly silencing CDON, suggesting other molecular players are involved. For instance, p21, an NFI target in glioblastoma and breast cancer cells, is also upregulated upon NFIB knock-down. We propose that NFIB is indispensable for SH-SY5Y cells which may involve regulation of apoptosis inducer proteins CDON and p21.
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Affiliation(s)
- Betül Uluca
- Department of Molecular Biology and Genetics, Istanbul Technical University, Maslak, Istanbul 34469, Turkey; Department of Molecular Biotechnology, Turkish-German University, Beykoz, Istanbul 34820, Turkey
| | - Cemre Lektemur Esen
- Department of Molecular Biology and Genetics, Istanbul Technical University, Maslak, Istanbul 34469, Turkey
| | - Sinem Saritas Erdogan
- Department of Molecular Biology and Genetics, Istanbul Technical University, Maslak, Istanbul 34469, Turkey
| | - Asli Kumbasar
- Department of Molecular Biology and Genetics, Istanbul Technical University, Maslak, Istanbul 34469, Turkey.
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77
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Du J, Lan T, Liao H, Feng X, Chen X, Liao W, Hou G, Xu L, Feng Q, Xie K, Liao M, Chen X, Huang J, Yuan K, Zeng Y. CircNFIB inhibits tumor growth and metastasis through suppressing MEK1/ERK signaling in intrahepatic cholangiocarcinoma. Mol Cancer 2022; 21:18. [PMID: 35039066 PMCID: PMC8762882 DOI: 10.1186/s12943-021-01482-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 12/09/2021] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Considerable evidence shows that circular RNAs (circRNAs) play an important role in tumor development. However, their function in intrahepatic cholangiocarcinoma (ICC) metastasis and the underlying mechanisms are incompletely understood. METHODS circNFIB (hsa_circ_0086376, termed as cNFIB hereafter) was identified in human ICC tissues through circRNAs sequencing. The biological role of cNFIB was determined in vitro and in vivo by gain or loss of functional experiments. Fluorescence in situ hybridization (FISH), RNA immunoprecipitation (RIP) and RNA pull-down assays were conducted to analyze the interaction of cNFIB with dual specificity mitogen-activated protein kinase kinase1 (MEK1). Duolink in situ proximity ligation assay (PLA) and coimmunoprecipitation (co-IP) assay were used to investigate the effects of cNFIB on the interaction between MEK1 and mitogen-activated protein kinase 2 (ERK2). Finally, a series of in vitro and in vivo experiments were performed to explore the influences of cNFIB on the anti-tumor activity of trametinib (a MEK inhibitor). RESULTS cNFIB was significantly down-regulated in human ICC tissues with postoperative metastases. The loss of cNFIB was highly associated with aggressive characteristics and predicted unfavorable prognosis in ICC patients. Functional studies revealed that cNFIB inhibited the proliferation and metastasis of ICC cells in vitro and in vivo. Mechanistically, cNFIB competitively interacted with MEK1, which induced the dissociation between MEK1 and ERK2, thereby resulting in the suppression of ERK signaling and tumor metastasis. Moreover, we found that ICC cells with high levels of cNFIB held the potential to delay the trametinib resistance. Consistently, in vivo and in vitro studies demonstrated that cotreatment with trametinib and lentivirus vector encoding cNFIB showed greater inhibitory effect than isolated trametinib treatment. CONCLUSIONS Our findings identified that cNFIB played a key role in ICC growth and metastasis by regulating MEK1/ERK signaling. Given the efficacy of cNFIB modulation on ICC suppression and trametinib sensitivity, cNFIB appears to be a potential therapeutic molecule for ICC treatment.
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Affiliation(s)
- Jinpeng Du
- Department of Liver Surgery & Liver Transplantation, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, 610041, China
| | - Tian Lan
- Department of Liver Surgery & Liver Transplantation, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, 610041, China
| | - Haotian Liao
- Department of Liver Surgery & Liver Transplantation, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, 610041, China
| | - Xuping Feng
- Department of Liver Surgery & Liver Transplantation, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, 610041, China
- Laboratory of Liver Surgery, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Xing Chen
- Department of Liver Surgery & Liver Transplantation, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, 610041, China
| | - Wenwei Liao
- Department of Liver Surgery & Liver Transplantation, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, 610041, China
| | - Guimin Hou
- Department of Liver Surgery & Liver Transplantation, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, 610041, China
| | - Lin Xu
- Department of Liver Surgery & Liver Transplantation, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, 610041, China
- Laboratory of Liver Surgery, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Qingbo Feng
- Department of Liver Surgery & Liver Transplantation, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, 610041, China
| | - Kunlin Xie
- Department of Liver Surgery & Liver Transplantation, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, 610041, China
| | - Mingheng Liao
- Department of Liver Surgery & Liver Transplantation, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, 610041, China
| | - Xiangzheng Chen
- Department of Liver Surgery & Liver Transplantation, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, 610041, China
- Laboratory of Liver Surgery, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Jiwei Huang
- Department of Liver Surgery & Liver Transplantation, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, 610041, China
| | - Kefei Yuan
- Department of Liver Surgery & Liver Transplantation, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, 610041, China.
- Laboratory of Liver Surgery, West China Hospital, Sichuan University, Chengdu, 610041, China.
| | - Yong Zeng
- Department of Liver Surgery & Liver Transplantation, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, 610041, China.
- Laboratory of Liver Surgery, West China Hospital, Sichuan University, Chengdu, 610041, China.
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78
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Huang H, Jin J, Wu L, Wu H, Pi H, Dong Y, Xiang R. A de novo Non-sense Nuclear Factor I B Mutation (p.Tyr290*) Is Responsible for Brain Malformation and Lung Lobulation Defects. Front Pediatr 2022; 10:865181. [PMID: 35433561 PMCID: PMC9005976 DOI: 10.3389/fped.2022.865181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 03/07/2022] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Nuclear factor I B (NFIB) plays an important role in regulating the transcription of multiple biological processes. Mutations in NFIB cause intellectual disability and macrocephaly. However, studies on abnormal brain and lung development caused by NFIB mutations are lacking. METHODS In the present study, we enrolled a fetus with brain malformation and lung lobulation defects from China. Whole-exome sequencing (WES) was performed to detect the candidate genes and Sanger sequencing was performed for mutational analysis. RESULTS After data filtering and bioinformatics prediction, a novel non-sense mutation of NFIB (NM_001190737:c.870C > A;p.Tyr290*) was identified in the fetus. This variant was predicted to produce a truncated NFIB protein because of a premature stop codon and was absent in 200 healthy controls. CONCLUSION To the best of our knowledge, this is the first case of brain malformation and lung lobulation defects caused by a NFIB variant in Asia. These findings contribute to genetic diagnosis and family counseling and expand our understanding of NFIB mutations as well as brain and lung maturation.
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Affiliation(s)
- Hao Huang
- Department of Nephrology, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China.,Department of Cell Biology, School of Life Sciences, Central South University, Changsha, China
| | - Jieyuan Jin
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China.,Department of Cell Biology, School of Life Sciences, Central South University, Changsha, China
| | - Liping Wu
- Department of Medical Genetics and Prenatal Diagnosis, Shenzhen Longgang District Maternity and Child Healthcare Hospital, Shenzhen, China
| | - Huifen Wu
- Obstetric Inpatient Department, Shenzhen Longgang District Maternity and Child Healthcare Hospital, Shenzhen, China
| | - Huichun Pi
- Department of Medical Genetics and Prenatal Diagnosis, Shenzhen Longgang District Maternity and Child Healthcare Hospital, Shenzhen, China
| | - Yi Dong
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China.,Department of Cell Biology, School of Life Sciences, Central South University, Changsha, China
| | - Rong Xiang
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China.,Department of Cell Biology, School of Life Sciences, Central South University, Changsha, China
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79
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Perumal N, Kanchan RK, Doss D, Bastola N, Atri P, Chirravuri-Venkata R, Thapa I, Vengoji R, Maurya SK, Klinkebiel D, Talmon GA, Nasser MW, Batra SK, Mahapatra S. MiR-212-3p functions as a tumor suppressor gene in group 3 medulloblastoma via targeting nuclear factor I/B (NFIB). Acta Neuropathol Commun 2021; 9:195. [PMID: 34922631 PMCID: PMC8684142 DOI: 10.1186/s40478-021-01299-z] [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: 10/04/2021] [Accepted: 12/01/2021] [Indexed: 12/30/2022] Open
Abstract
Haploinsufficiency of chromosome 17p and c-Myc amplification distinguish group 3 medulloblastomas which are associated with early metastasis, rapid recurrence, and swift mortality. Tumor suppressor genes on this locus have not been adequately characterized. We elucidated the role of miR-212-3p in the pathophysiology of group 3 tumors. First, we learned that miR-212-3p undergoes epigenetic silencing by histone modifications in group 3 tumors. Restoring its expression reduced cancer cell proliferation, migration, colony formation, and wound healing in vitro and attenuated tumor burden and improved survival in vivo. MiR-212-3p also triggered c-Myc destabilization and degradation, leading to elevated apoptosis. We then isolated an oncogenic target of miR-212-3p, i.e. NFIB, a nuclear transcription factor implicated in metastasis and recurrence in various cancers. Increased expression of NFIB was confirmed in group 3 tumors and associated with poor survival. NFIB silencing reduced cancer cell proliferation, migration, and invasion. Concurrently, reduced medullosphere formation and stem cell markers (Nanog, Oct4, Sox2, CD133) were noted. These results substantiate the tumor-suppressive role of miR-212-3p in group 3 MB and identify a novel oncogenic target implicated in metastasis and tumor recurrence.
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Affiliation(s)
- Naveenkumar Perumal
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Ranjana K Kanchan
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - David Doss
- Department of Biomedical Sciences, Creighton University School of Medicine, Omaha, NE, 68124, USA
| | - Noah Bastola
- Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Pranita Atri
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | | | - Ishwor Thapa
- School of Interdisciplinary Informatics, University of Nebraska at Omaha, Omaha, NE, 68182, USA
| | - Raghupathy Vengoji
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Shailendra K Maurya
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - David Klinkebiel
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Geoffrey A Talmon
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Mohd W Nasser
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Surinder K Batra
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Sidharth Mahapatra
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, 68198, USA.
- Department of Pediatrics, University of Nebraska Medical Center, Omaha, NE, 68198, USA.
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80
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Amin R, Shukla A, Zhu JJ, Kim S, Wang P, Tian SZ, Tran AD, Paul D, Cappell SD, Burkett S, Liu H, Lee MP, Kruhlak MJ, Dwyer JE, Simpson RM, Hager GL, Ruan Y, Hunter KW. Nuclear pore protein NUP210 depletion suppresses metastasis through heterochromatin-mediated disruption of tumor cell mechanical response. Nat Commun 2021; 12:7216. [PMID: 34903738 PMCID: PMC8669001 DOI: 10.1038/s41467-021-27451-w] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 11/16/2021] [Indexed: 12/26/2022] Open
Abstract
Mechanical signals from the extracellular microenvironment have been implicated in tumor and metastatic progression. Here, we identify nucleoporin NUP210 as a metastasis susceptibility gene for human estrogen receptor positive (ER+) breast cancer and a cellular mechanosensor. Nup210 depletion suppresses lung metastasis in mouse models of breast cancer. Mechanistically, NUP210 interacts with LINC complex protein SUN2 which connects the nucleus to the cytoskeleton. In addition, the NUP210/SUN2 complex interacts with chromatin via the short isoform of BRD4 and histone H3.1/H3.2 at the nuclear periphery. In Nup210 knockout cells, mechanosensitive genes accumulate H3K27me3 heterochromatin modification, mediated by the polycomb repressive complex 2 and differentially reposition within the nucleus. Transcriptional repression in Nup210 knockout cells results in defective mechanotransduction and focal adhesion necessary for their metastatic capacity. Our study provides an important role of nuclear pore protein in cellular mechanosensation and metastasis. The involvement of nuclear pore proteins in cellular mechanosensing and metastasis is unclear. Here the authors identify that nuclear pore protein NUP210 promotes metastasis through the interaction with mechanotransducer LINC complex protein and chromatin to regulate mechanosensitive genes.
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Affiliation(s)
- Ruhul Amin
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA.
| | - Anjali Shukla
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
| | | | - Sohyoung Kim
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Ping Wang
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | | | - Andy D Tran
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA.,Confocal Microscopy Core Facility, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Debasish Paul
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Steven D Cappell
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Sandra Burkett
- Molecular Cytogenetics Core Facility, National Cancer Institute, NIH, Frederick, MD, USA
| | - Huaitian Liu
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA.,High-Dimension Data Analysis Group, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Maxwell P Lee
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA.,High-Dimension Data Analysis Group, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Michael J Kruhlak
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA.,Confocal Microscopy Core Facility, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Jennifer E Dwyer
- Molecular Pathology Unit, Laboratory of Cancer Biology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
| | - R Mark Simpson
- Molecular Pathology Unit, Laboratory of Cancer Biology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Gordon L Hager
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Yijun Ruan
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Kent W Hunter
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA.
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81
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Gui P, Bivona TG. Evolution of metastasis: new tools and insights. Trends Cancer 2021; 8:98-109. [PMID: 34872888 DOI: 10.1016/j.trecan.2021.11.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 11/01/2021] [Accepted: 11/05/2021] [Indexed: 02/07/2023]
Abstract
Metastasis is an evolutionary process occurring across multiple organs and timescales. Due to its continuous and dynamic nature, this multifaceted process has been challenging to investigate and remains incompletely understood, in part due to the lack of tools capable of probing genomic evolution at high enough resolution. However, technological advances in genetic sequencing and editing have provided new and powerful methods to refine our understanding of the complex series of events that lead to metastatic dissemination. In this review, we summarize the latest genetic and lineage-tracing approaches developed to unravel the genetic evolution of metastasis. The findings that have emerged have enhanced our comprehension of the mechanistic trajectories and timescales of metastasis and could provide new strategies for therapy.
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Affiliation(s)
- Philippe Gui
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA.
| | - Trever G Bivona
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA.
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82
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Ciampricotti M, Karakousi T, Richards AL, Quintanal-Villalonga À, Karatza A, Caeser R, Costa EA, Allaj V, Manoj P, Spainhower KB, Kombak FE, Sanchez-Rivera FJ, Jaspers JE, Zavitsanou AM, Maddalo D, Ventura A, Rideout WM, Akama-Garren EH, Jacks T, Donoghue MTA, Sen T, Oliver TG, Poirier JT, Papagiannakopoulos T, Rudin CM. Rlf-Mycl Gene Fusion Drives Tumorigenesis and Metastasis in a Mouse Model of Small Cell Lung Cancer. Cancer Discov 2021; 11:3214-3229. [PMID: 34344693 PMCID: PMC8810895 DOI: 10.1158/2159-8290.cd-21-0441] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 06/28/2021] [Accepted: 07/29/2021] [Indexed: 11/16/2022]
Abstract
Small cell lung cancer (SCLC) has limited therapeutic options and an exceptionally poor prognosis. Understanding the oncogenic drivers of SCLC may help define novel therapeutic targets. Recurrent genomic rearrangements have been identified in SCLC, most notably an in-frame gene fusion between RLF and MYCL found in up to 7% of the predominant ASCL1-expressing subtype. To explore the role of this fusion in oncogenesis and tumor progression, we used CRISPR/Cas9 somatic editing to generate a Rlf-Mycl-driven mouse model of SCLC. RLF-MYCL fusion accelerated transformation and proliferation of murine SCLC and increased metastatic dissemination and the diversity of metastatic sites. Tumors from the RLF-MYCL genetically engineered mouse model displayed gene expression similarities with human RLF-MYCL SCLC. Together, our studies support RLF-MYCL as the first demonstrated fusion oncogenic driver in SCLC and provide a new preclinical mouse model for the study of this subtype of SCLC. SIGNIFICANCE The biological and therapeutic implications of gene fusions in SCLC, an aggressive metastatic lung cancer, are unknown. Our study investigates the functional significance of the in-frame RLF-MYCL gene fusion by developing a Rlf-Mycl-driven genetically engineered mouse model and defining the impact on tumor growth and metastasis. This article is highlighted in the In This Issue feature, p. 2945.
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Affiliation(s)
- Metamia Ciampricotti
- Department of Medicine, Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Triantafyllia Karakousi
- Department of Pathology, New York University School of Medicine, New York, NY, USA
- These authors contributed equally
| | - Allison L Richards
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- These authors contributed equally
| | - Àlvaro Quintanal-Villalonga
- Department of Medicine, Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Angeliki Karatza
- Perlmutter Cancer Center, New York University Langone Health, New York, NY, USA
| | - Rebecca Caeser
- Department of Medicine, Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Emily A Costa
- Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, New York, NY, USA
| | - Viola Allaj
- Department of Medicine, Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Parvathy Manoj
- Department of Medicine, Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kyle B Spainhower
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Faruk E Kombak
- Precision Pathology Biobanking Center, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Francisco J Sanchez-Rivera
- Department of Cancer Biology and Genetics, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Janneke E Jaspers
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Danilo Maddalo
- Department of Cancer Biology and Genetics, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Current address: Department of Translational Oncology, Genentech, South San Francisco, CA, USA
| | - Andrea Ventura
- Department of Cancer Biology and Genetics, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - William M Rideout
- David H. Koch Institute for Integrative Cancer Research, Department of Biology, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Elliot H Akama-Garren
- David H. Koch Institute for Integrative Cancer Research, Department of Biology, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Tyler Jacks
- David H. Koch Institute for Integrative Cancer Research, Department of Biology, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Mark T A Donoghue
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Triparna Sen
- Department of Medicine, Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Trudy G Oliver
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - John T Poirier
- Perlmutter Cancer Center, New York University Langone Health, New York, NY, USA
| | - Thales Papagiannakopoulos
- Department of Pathology, New York University School of Medicine, New York, NY, USA
- Perlmutter Cancer Center, New York University Langone Health, New York, NY, USA
| | - Charles M Rudin
- Department of Medicine, Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Lead contact
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83
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Arnal-Estapé A, Foggetti G, Starrett JH, Nguyen DX, Politi K. Preclinical Models for the Study of Lung Cancer Pathogenesis and Therapy Development. Cold Spring Harb Perspect Med 2021; 11:a037820. [PMID: 34518338 PMCID: PMC8634791 DOI: 10.1101/cshperspect.a037820] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Experimental preclinical models have been a cornerstone of lung cancer translational research. Work in these model systems has provided insights into the biology of lung cancer subtypes and their origins, contributed to our understanding of the mechanisms that underlie tumor progression, and revealed new therapeutic vulnerabilities. Initially patient-derived lung cancer cell lines were the main preclinical models available. The landscape is very different now with numerous preclinical models for research each with unique characteristics. These include genetically engineered mouse models (GEMMs), patient-derived xenografts (PDXs) and three-dimensional culture systems ("organoid" cultures). Here we review the development and applications of these models and describe their contributions to lung cancer research.
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Affiliation(s)
- Anna Arnal-Estapé
- Department of Pathology
- Yale Cancer Center, Yale University School of Medicine, New Haven, Connecticut 06510, USA
| | | | | | - Don X Nguyen
- Department of Pathology
- Department of Internal Medicine (Section of Medical Oncology)
- Yale Cancer Center, Yale University School of Medicine, New Haven, Connecticut 06510, USA
| | - Katerina Politi
- Department of Pathology
- Department of Internal Medicine (Section of Medical Oncology)
- Yale Cancer Center, Yale University School of Medicine, New Haven, Connecticut 06510, USA
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84
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Reddy J, Fonseca MAS, Corona RI, Nameki R, Segato Dezem F, Klein IA, Chang H, Chaves-Moreira D, Afeyan LK, Malta TM, Lin X, Abbasi F, Font-Tello A, Sabedot T, Cejas P, Rodríguez-Malavé N, Seo JH, Lin DC, Matulonis U, Karlan BY, Gayther SA, Pasaniuc B, Gusev A, Noushmehr H, Long H, Freedman ML, Drapkin R, Young RA, Abraham BJ, Lawrenson K. Predicting master transcription factors from pan-cancer expression data. SCIENCE ADVANCES 2021; 7:eabf6123. [PMID: 34818047 PMCID: PMC8612691 DOI: 10.1126/sciadv.abf6123] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Critical developmental “master transcription factors” (MTFs) can be subverted during tumorigenesis to control oncogenic transcriptional programs. Current approaches to identifying MTFs rely on ChIP-seq data, which is unavailable for many cancers. We developed the CaCTS (Cancer Core Transcription factor Specificity) algorithm to prioritize candidate MTFs using pan-cancer RNA sequencing data. CaCTS identified candidate MTFs across 34 tumor types and 140 subtypes including predictions for cancer types/subtypes for which MTFs are unknown, including e.g. PAX8, SOX17, and MECOM as candidates in ovarian cancer (OvCa). In OvCa cells, consistent with known MTF properties, these factors are required for viability, lie proximal to superenhancers, co-occupy regulatory elements globally, co-bind loci encoding OvCa biomarkers, and are sensitive to pharmacologic inhibition of transcription. Our predictions of MTFs, especially for tumor types with limited understanding of transcriptional drivers, pave the way to therapeutic targeting of MTFs in a broad spectrum of cancers.
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Affiliation(s)
- Jessica Reddy
- Women’s Cancer Research Program at the Samuel
Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles,
CA, USA
- Division of Gynecologic Oncology, Department of
Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA,
USA
| | - Marcos A. S. Fonseca
- Women’s Cancer Research Program at the Samuel
Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles,
CA, USA
- Division of Gynecologic Oncology, Department of
Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA,
USA
| | - Rosario I. Corona
- Women’s Cancer Research Program at the Samuel
Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles,
CA, USA
- Division of Gynecologic Oncology, Department of
Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA,
USA
- Center for Bioinformatics and Functional Genomics,
Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Robbin Nameki
- Women’s Cancer Research Program at the Samuel
Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles,
CA, USA
- Division of Gynecologic Oncology, Department of
Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA,
USA
| | - Felipe Segato Dezem
- Women’s Cancer Research Program at the Samuel
Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles,
CA, USA
- Division of Gynecologic Oncology, Department of
Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA,
USA
- Center for Bioinformatics and Functional Genomics,
Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Isaac A. Klein
- Whitehead Institute for Biomedical Research,
Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer
Institute, Boston, MA, USA
| | - Heidi Chang
- Women’s Cancer Research Program at the Samuel
Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles,
CA, USA
- Division of Gynecologic Oncology, Department of
Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA,
USA
| | | | - Lena K. Afeyan
- Whitehead Institute for Biomedical Research,
Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of
Technology, Cambridge, MA, USA
| | | | - Xianzhi Lin
- Women’s Cancer Research Program at the Samuel
Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles,
CA, USA
- Division of Gynecologic Oncology, Department of
Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA,
USA
| | - Forough Abbasi
- Women’s Cancer Research Program at the Samuel
Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles,
CA, USA
- Division of Gynecologic Oncology, Department of
Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA,
USA
- Center for Bioinformatics and Functional Genomics,
Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Alba Font-Tello
- Center for Functional Cancer Epigenetics, Dana-Farber
Cancer Institute, Boston, MA, USA
| | | | - Paloma Cejas
- Center for Functional Cancer Epigenetics, Dana-Farber
Cancer Institute, Boston, MA, USA
| | - Norma Rodríguez-Malavé
- Center for Bioinformatics and Functional Genomics,
Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Ji-Heui Seo
- Department of Medical Oncology, Dana-Farber Cancer
Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber
Cancer Institute, Boston, MA, USA
| | - De-Chen Lin
- Department of Medicine, Cedars-Sinai Medical
Center, Los Angeles, CA, USA
| | - Ursula Matulonis
- Division of Gynecologic Oncology, Dana Farber
Cancer Institute, Boston, MA, USA
| | - Beth Y. Karlan
- Women’s Cancer Research Program at the Samuel
Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles,
CA, USA
- Division of Gynecologic Oncology, Department of
Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA,
USA
- Cancer Population Genetics, Jonsson Comprehensive
Cancer Center, David Geffen School of Medicine, University of California, Los
Angeles, Los Angeles, CA, USA
| | - Simon A. Gayther
- Center for Bioinformatics and Functional Genomics,
Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Bogdan Pasaniuc
- Bioinformatics Interdepartmental Program,
University of California, Los Angeles, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School
of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Pathology and Laboratory Medicine,
David Geffen School of Medicine, University of California, Los Angeles, Los
Angeles, CA, USA
- Department of Computational Medicine, David Geffen
School of Medicine, University of California, Los Angeles, Los Angeles, CA,
USA
| | - Alexander Gusev
- Center for Functional Cancer Epigenetics, Dana-Farber
Cancer Institute, Boston, MA, USA
- McGraw/Patterson Center for Population Sciences,
Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - Henry Long
- Center for Functional Cancer Epigenetics, Dana-Farber
Cancer Institute, Boston, MA, USA
| | - Matthew L. Freedman
- Department of Medical Oncology, Dana-Farber Cancer
Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber
Cancer Institute, Boston, MA, USA
- The Eli and Edythe L. Broad Institute, Cambridge,
MA, USA
| | - Ronny Drapkin
- Penn Ovarian Cancer Research Center, University of
Pennsylvania, Philadelphia, PA, USA
| | - Richard A. Young
- Whitehead Institute for Biomedical Research,
Cambridge, MA, USA
- Department of Biology, M.I.T., Cambridge, MA,
USA
| | - Brian J. Abraham
- Department of Computational Biology, St. Jude
Children’s Research Hospital, Memphis, TN, USA
- Corresponding author.
(B.J.A.);
(K.L.)
| | - Kate Lawrenson
- Women’s Cancer Research Program at the Samuel
Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles,
CA, USA
- Division of Gynecologic Oncology, Department of
Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA,
USA
- Center for Bioinformatics and Functional Genomics,
Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Corresponding author.
(B.J.A.);
(K.L.)
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85
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Lyu P, Hoang T, Santiago CP, Thomas ED, Timms AE, Appel H, Gimmen M, Le N, Jiang L, Kim DW, Chen S, Espinoza DF, Telger AE, Weir K, Clark BS, Cherry TJ, Qian J, Blackshaw S. Gene regulatory networks controlling temporal patterning, neurogenesis, and cell-fate specification in mammalian retina. Cell Rep 2021; 37:109994. [PMID: 34788628 PMCID: PMC8642835 DOI: 10.1016/j.celrep.2021.109994] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 09/30/2021] [Accepted: 10/21/2021] [Indexed: 12/30/2022] Open
Abstract
Gene regulatory networks (GRNs), consisting of transcription factors and their target sites, control neurogenesis and cell-fate specification in the developing central nervous system. In this study, we use integrated single-cell RNA and single-cell ATAC sequencing (scATAC-seq) analysis in developing mouse and human retina to identify multiple interconnected, evolutionarily conserved GRNs composed of cell-type-specific transcription factors that both activate genes within their own network and inhibit genes in other networks. These GRNs control temporal patterning in primary progenitors, regulate transition from primary to neurogenic progenitors, and drive specification of each major retinal cell type. We confirm that NFI transcription factors selectively activate expression of genes promoting late-stage temporal identity in primary retinal progenitors and identify other transcription factors that regulate rod photoreceptor specification in postnatal retina. This study inventories cis- and trans-acting factors that control retinal development and can guide cell-based therapies aimed at replacing retinal neurons lost to disease.
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Affiliation(s)
- Pin Lyu
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Thanh Hoang
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Clayton P Santiago
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Eric D Thomas
- Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Andrew E Timms
- Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Haley Appel
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Megan Gimmen
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Nguyet Le
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Lizhi Jiang
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Dong Won Kim
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Siqi Chen
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - David F Espinoza
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Ariel E Telger
- Department of Ophthalmology and Visual Sciences, Brotman Baty Institute, Seattle, WA 98195, USA
| | - Kurt Weir
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Brian S Clark
- Department of Ophthalmology and Visual Sciences, Brotman Baty Institute, Seattle, WA 98195, USA; Brotman Baty Institute, Seattle, WA 98195, USA; Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Timothy J Cherry
- Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA 98101, USA; Brotman Baty Institute, Seattle, WA 98195, USA; Department of Pediatrics, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Jiang Qian
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
| | - Seth Blackshaw
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Kavli Neuroscience Discovery Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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86
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Chen J, Guanizo A, Luong Q, Jayasekara WSN, Jayasinghe D, Inampudi C, Szczepny A, Garama DJ, Russell PA, Ganju V, Cain JE, Watkins DN, Gough DJ. Lineage-restricted neoplasia driven by Myc defaults to small cell lung cancer when combined with loss of p53 and Rb in the airway epithelium. Oncogene 2021; 41:138-145. [PMID: 34675406 DOI: 10.1038/s41388-021-02070-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 10/06/2021] [Accepted: 10/08/2021] [Indexed: 11/09/2022]
Abstract
Small cell lung cancer (SCLC) is an aggressive neuroendocrine cancer characterized by loss of function TP53 and RB1 mutations in addition to mutations in other oncogenes including MYC. Overexpression of MYC together with Trp53 and Rb1 loss in pulmonary neuroendocrine cells of the mouse lung drives an aggressive neuroendocrine low variant subtype of SCLC. However, the transforming potential of MYC amplification alone on airway epithelium is unclear. Therefore, we selectively and conditionally overexpressed MYC stochastically throughout the airway or specifically in neuroendocrine, club, or alveolar type II cells in the adult mouse lung. We observed that MYC overexpression induced carcinoma in situ which did not progress to invasive disease. The formation of adenoma or SCLC carcinoma in situ was dependent on the cell of origin. In contrast, MYC overexpression combined with conditional deletion of both Trp53 and Rb1 exclusively gave rise to SCLC, irrespective of the cell lineage of origin. However, cell of origin influenced disease latency, metastatic potential, and the transcriptional profile of the SCLC phenotype. Together this reveals that MYC overexpression alone provides a proliferative advantage but when combined with deletion of Trp53 and Rb1 it facilitates the formation of aggressive SCLC from multiple cell lineages.
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Affiliation(s)
- Jasmine Chen
- Centre for Cancer Research, Hudson Institute of Medical Research, 27-31 Wright Street, Clayton, VIC, 3168, Australia.,Department of Molecular and Translational Science, Monash University, 27-31 Wright Street, Clayton, VIC, 3168, Australia
| | - Aleks Guanizo
- Centre for Cancer Research, Hudson Institute of Medical Research, 27-31 Wright Street, Clayton, VIC, 3168, Australia.,Department of Molecular and Translational Science, Monash University, 27-31 Wright Street, Clayton, VIC, 3168, Australia
| | - Quinton Luong
- Centre for Cancer Research, Hudson Institute of Medical Research, 27-31 Wright Street, Clayton, VIC, 3168, Australia.,Department of Molecular and Translational Science, Monash University, 27-31 Wright Street, Clayton, VIC, 3168, Australia
| | - W Samantha N Jayasekara
- Centre for Cancer Research, Hudson Institute of Medical Research, 27-31 Wright Street, Clayton, VIC, 3168, Australia.,Department of Molecular and Translational Science, Monash University, 27-31 Wright Street, Clayton, VIC, 3168, Australia
| | - Dhilshan Jayasinghe
- Centre for Cancer Research, Hudson Institute of Medical Research, 27-31 Wright Street, Clayton, VIC, 3168, Australia.,Department of Molecular and Translational Science, Monash University, 27-31 Wright Street, Clayton, VIC, 3168, Australia
| | - Chaitanya Inampudi
- Centre for Cancer Research, Hudson Institute of Medical Research, 27-31 Wright Street, Clayton, VIC, 3168, Australia.,Department of Molecular and Translational Science, Monash University, 27-31 Wright Street, Clayton, VIC, 3168, Australia
| | - Anette Szczepny
- Centre for Cancer Research, Hudson Institute of Medical Research, 27-31 Wright Street, Clayton, VIC, 3168, Australia.,Department of Molecular and Translational Science, Monash University, 27-31 Wright Street, Clayton, VIC, 3168, Australia
| | - Daniel J Garama
- Centre for Cancer Research, Hudson Institute of Medical Research, 27-31 Wright Street, Clayton, VIC, 3168, Australia.,Department of Molecular and Translational Science, Monash University, 27-31 Wright Street, Clayton, VIC, 3168, Australia
| | - Prudence A Russell
- Department of Anatomical Pathology, St Vincent's Hospital, Fitzroy, Melbourne, VIC, Australia
| | - Vinod Ganju
- Centre for Cancer Research, Hudson Institute of Medical Research, 27-31 Wright Street, Clayton, VIC, 3168, Australia.,Department of Molecular and Translational Science, Monash University, 27-31 Wright Street, Clayton, VIC, 3168, Australia
| | - Jason E Cain
- Centre for Cancer Research, Hudson Institute of Medical Research, 27-31 Wright Street, Clayton, VIC, 3168, Australia.,Department of Molecular and Translational Science, Monash University, 27-31 Wright Street, Clayton, VIC, 3168, Australia
| | - D Neil Watkins
- Research Institute in Oncology and Hematology, Cancer Care Manitoba, Winnipeg, MB, R3E 0V9, Canada.,Department of Internal Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada
| | - Daniel J Gough
- Centre for Cancer Research, Hudson Institute of Medical Research, 27-31 Wright Street, Clayton, VIC, 3168, Australia. .,Department of Molecular and Translational Science, Monash University, 27-31 Wright Street, Clayton, VIC, 3168, Australia.
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87
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Huang L, Yi X, Yu X, Wang Y, Zhang C, Qin L, Guo D, Zhou S, Zhang G, Deng Y, Bao X, Wang D. High-Throughput Strategies for the Discovery of Anticancer Drugs by Targeting Transcriptional Reprogramming. Front Oncol 2021; 11:762023. [PMID: 34660328 PMCID: PMC8518531 DOI: 10.3389/fonc.2021.762023] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 09/15/2021] [Indexed: 12/28/2022] Open
Abstract
Transcriptional reprogramming contributes to the progression and recurrence of cancer. However, the poorly elucidated mechanisms of transcriptional reprogramming in tumors make the development of effective drugs difficult, and gene expression signature is helpful for connecting genetic information and pharmacologic treatment. So far, there are two gene-expression signature-based high-throughput drug discovery approaches: L1000, which measures the mRNA transcript abundance of 978 "landmark" genes, and high-throughput sequencing-based high-throughput screening (HTS2); they are suitable for anticancer drug discovery by targeting transcriptional reprogramming. L1000 uses ligation-mediated amplification and hybridization to Luminex beads and highlights gene expression changes by detecting bead colors and fluorescence intensity of phycoerythrin signal. HTS2 takes advantage of RNA-mediated oligonucleotide annealing, selection, and ligation, high throughput sequencing, to quantify gene expression changes by directly measuring gene sequences. This article summarizes technological principles and applications of L1000 and HTS2, and discusses their advantages and limitations in anticancer drug discovery.
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Affiliation(s)
- Lijun Huang
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Xiaohong Yi
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Xiankuo Yu
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Yumei Wang
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Chen Zhang
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Lixia Qin
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Dale Guo
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Shiyi Zhou
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Guanbin Zhang
- Department of Infectious Diseases, 404 Hospital of Mianyang, Mianyang, China.,National Engineering Research Center for Beijing Biochip Technology, Beijing, China
| | - Yun Deng
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Xilinqiqige Bao
- Medical Innovation Center for Nationalities, Inner Mongolia Medical University, Hohhot, China
| | - Dong Wang
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, China
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88
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Tasdogan A, Ubellacker JM, Morrison SJ. Redox Regulation in Cancer Cells during Metastasis. Cancer Discov 2021; 11:2682-2692. [PMID: 34649956 DOI: 10.1158/2159-8290.cd-21-0558] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 06/15/2021] [Accepted: 07/07/2021] [Indexed: 12/19/2022]
Abstract
Metastasis is an inefficient process in which the vast majority of cancer cells are fated to die, partly because they experience oxidative stress. Metastasizing cancer cells migrate through diverse environments that differ dramatically from their tumor of origin, leading to redox imbalances. The rare metastasizing cells that survive undergo reversible metabolic changes that confer oxidative stress resistance. We review the changes in redox regulation that cancer cells undergo during metastasis. By better understanding these mechanisms, it may be possible to develop pro-oxidant therapies that block disease progression by exacerbating oxidative stress in cancer cells. SIGNIFICANCE: Oxidative stress often limits cancer cell survival during metastasis, raising the possibility of inhibiting cancer progression with pro-oxidant therapies. This is the opposite strategy of treating patients with antioxidants, an approach that worsened outcomes in large clinical trials.
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Affiliation(s)
- Alpaslan Tasdogan
- Children's Research Institute and Department of Pediatrics, The University of Texas Southwestern Medical Center, Dallas, Texas
| | - Jessalyn M Ubellacker
- Children's Research Institute and Department of Pediatrics, The University of Texas Southwestern Medical Center, Dallas, Texas
| | - Sean J Morrison
- Children's Research Institute and Department of Pediatrics, The University of Texas Southwestern Medical Center, Dallas, Texas. .,Howard Hughes Medical Institute, The University of Texas Southwestern Medical Center, Dallas, Texas
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89
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An Epigenetic Perspective on Intra-Tumour Heterogeneity: Novel Insights and New Challenges from Multiple Fields. Cancers (Basel) 2021; 13:cancers13194969. [PMID: 34638453 PMCID: PMC8508087 DOI: 10.3390/cancers13194969] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 09/29/2021] [Accepted: 10/01/2021] [Indexed: 12/14/2022] Open
Abstract
Simple Summary Although research on cancer biology in recent decades has unveiled the main genetic perturbations driving the onset of tumorigenesis, we are still far from properly treating this disease without the occurrence of drug resistance and metastatic burden. This achievement is hampered by the onset of intra-tumour heterogeneity (ITH), which increases cancer cell fitness and plasticity, thereby fostering cell adaptation to foreign environments and stimuli. In this review, we discuss the contribution of the epigenetic factors in sustaining ITH and their interplay with the tumour microenvironment. We also highlight the recent technological advancements that are contributing to defining the epigenetic mechanisms governing tumour heterogeneity at the single-cell level. Abstract Cancer is a group of heterogeneous diseases that results from the occurrence of genetic alterations combined with epigenetic changes and environmental stimuli that increase cancer cell plasticity. Indeed, multiple cancer cell populations coexist within the same tumour, favouring cancer progression and metastatic dissemination as well as drug resistance, thereby representing a major obstacle for treatment. Epigenetic changes contribute to the onset of intra-tumour heterogeneity (ITH) as they facilitate cell adaptation to perturbation of the tumour microenvironment. Despite being its central role, the intrinsic multi-layered and reversible epigenetic pattern limits the possibility to uniquely determine its contribution to ITH. In this review, we first describe the major epigenetic mechanisms involved in tumourigenesis and then discuss how single-cell-based approaches contribute to dissecting the key role of epigenetic changes in tumour heterogeneity. Furthermore, we highlight the importance of dissecting the interplay between genetics, epigenetics, and tumour microenvironments to decipher the molecular mechanisms governing tumour progression and drug resistance.
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90
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Cejas P, Xie Y, Font-Tello A, Lim K, Syamala S, Qiu X, Tewari AK, Shah N, Nguyen HM, Patel RA, Brown L, Coleman I, Hackeng WM, Brosens L, Dreijerink KMA, Ellis L, Alaiwi SA, Seo JH, Baca S, Beltran H, Khani F, Pomerantz M, Dall'Agnese A, Crowdis J, Van Allen EM, Bellmunt J, Morrisey C, Nelson PS, DeCaprio J, Farago A, Dyson N, Drapkin B, Liu XS, Freedman M, Haffner MC, Corey E, Brown M, Long HW. Subtype heterogeneity and epigenetic convergence in neuroendocrine prostate cancer. Nat Commun 2021; 12:5775. [PMID: 34599169 PMCID: PMC8486778 DOI: 10.1038/s41467-021-26042-z] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 09/07/2021] [Indexed: 12/30/2022] Open
Abstract
Neuroendocrine carcinomas (NEC) are tumors expressing markers of neuronal differentiation that can arise at different anatomic sites but have strong histological and clinical similarities. Here we report the chromatin landscapes of a range of human NECs and show convergence to the activation of a common epigenetic program. With a particular focus on treatment emergent neuroendocrine prostate cancer (NEPC), we analyze cell lines, patient-derived xenograft (PDX) models and human clinical samples to show the existence of two distinct NEPC subtypes based on the expression of the neuronal transcription factors ASCL1 and NEUROD1. While in cell lines and PDX models these subtypes are mutually exclusive, single-cell analysis of human clinical samples exhibits a more complex tumor structure with subtypes coexisting as separate sub-populations within the same tumor. These tumor sub-populations differ genetically and epigenetically contributing to intra- and inter-tumoral heterogeneity in human metastases. Overall, our results provide a deeper understanding of the shared clinicopathological characteristics shown by NECs. Furthermore, the intratumoral heterogeneity of human NEPCs suggests the requirement of simultaneous targeting of coexisting tumor populations as a therapeutic strategy. Neuroendocrine carcinomas (NECs) arise from different anatomic sites, but have similar histological and clinical features. Here, the authors show that the epigenetic landscape of a range of NECs converges towards a common epigenetic state, while distinct subtypes occur within neuroendocrine prostate cancer contributing to intratumor heterogeneity in clinical samples.
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Affiliation(s)
- Paloma Cejas
- Department of Medical Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA. .,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA. .,Translational Oncology Laboratory, Hospital La Paz Institute for Health Research (IdiPAZ) and CIBERONC, La Paz University Hospital, Madrid, Spain.
| | - Yingtian Xie
- Department of Medical Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Alba Font-Tello
- Department of Medical Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Klothilda Lim
- Department of Medical Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Sudeepa Syamala
- Department of Medical Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Xintao Qiu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Alok K Tewari
- Department of Medical Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Neel Shah
- Department of Medical Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Holly M Nguyen
- Department of Urology, University of Washington, Seattle, WA, USA
| | - Radhika A Patel
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Lisha Brown
- Department of Urology, University of Washington, Seattle, WA, USA
| | - Ilsa Coleman
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Wenzel M Hackeng
- Department of Pathology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Lodewijk Brosens
- Department of Pathology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | | | - Leigh Ellis
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Oncologic Pathology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Sarah Abou Alaiwi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA
| | - Ji-Heui Seo
- Department of Medical Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA
| | - Sylvan Baca
- Department of Medical Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA
| | - Himisha Beltran
- Department of Medical Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA
| | - Francesca Khani
- Weill Cornell Medical Center, Department of Pathology and Laboratory Medicine, New York Presbyterian Hospital, New York, NY, USA
| | - Mark Pomerantz
- Department of Medical Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA
| | | | - Jett Crowdis
- Department of Medical Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Eliezer M Van Allen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Joaquim Bellmunt
- Beth Israel Deaconess Medical Center and PSMAR-IMIM Lab. Harvard Medical School, Boston, Massachusetts, USA
| | - Colm Morrisey
- Department of Urology, University of Washington, Seattle, WA, USA
| | - Peter S Nelson
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - James DeCaprio
- Department of Medical Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA
| | - Anna Farago
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Nicholas Dyson
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Benjamin Drapkin
- Nancy B. and Jake L. Hamon Center for Therapeutic Oncology Research, Dallas, TX, USA.,Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA.,Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - X Shirley Liu
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Data Science, Dana-Farber Cancer Institute, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Matthew Freedman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Michael C Haffner
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Division of Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Department of Pathology, University of Washington, Seattle, WA, USA
| | - Eva Corey
- Department of Urology, University of Washington, Seattle, WA, USA
| | - Myles Brown
- Department of Medical Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA. .,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA.
| | - Henry W Long
- Department of Medical Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA. .,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA.
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91
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Shen Y, Chen LL, Gao J. CharPlant: A De Novo Open Chromatin Region Prediction Tool for Plant Genomes. GENOMICS, PROTEOMICS & BIOINFORMATICS 2021; 19:860-871. [PMID: 33662624 PMCID: PMC9170768 DOI: 10.1016/j.gpb.2020.06.021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 05/17/2020] [Accepted: 10/28/2020] [Indexed: 11/01/2022]
Abstract
Chromatin accessibility is a highly informative structural feature for understanding gene transcription regulation, because it indicates the degree to which nuclear macromolecules such as proteins and RNAs can access chromosomal DNA. Studies have shown that chromatin accessibility is highly dynamic during stress response, stimulus response, and developmental transition. Moreover, physical access to chromosomal DNA in eukaryotes is highly cell-specific. Therefore, current technologies such as DNase-seq, ATAC-seq, and FAIRE-seq reveal only a portion of the open chromatin regions (OCRs) present in a given species. Thus, the genome-wide distribution of OCRs remains unknown. In this study, we developed a bioinformatics tool called CharPlant for the de novo prediction of OCRs in plant genomes. To develop this tool, we constructed a three-layer convolutional neural network (CNN) and subsequently trained the CNN using DNase-seq and ATAC-seq datasets of four plant species. The model simultaneously learns the sequence motifs and regulatory logics, which are jointly used to determine DNA accessibility. All of these steps are integrated into CharPlant, which can be run using a simple command line. The results of data analysis using CharPlant in this study demonstrate its prediction power and computational efficiency. To our knowledge, CharPlant is the first de novo prediction tool that can identify potential OCRs in the whole genome. The source code of CharPlant and supporting files are freely available from https://github.com/Yin-Shen/CharPlant.
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Affiliation(s)
- Yin Shen
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Ling-Ling Chen
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China; National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Junxiang Gao
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China.
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Gokey JJ, Snowball J, Sridharan A, Sudha P, Kitzmiller JA, Xu Y, Whitsett JA. YAP regulates alveolar epithelial cell differentiation and AGER via NFIB/KLF5/NKX2-1. iScience 2021; 24:102967. [PMID: 34466790 PMCID: PMC8383002 DOI: 10.1016/j.isci.2021.102967] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 02/26/2021] [Accepted: 08/06/2021] [Indexed: 01/04/2023] Open
Abstract
Ventilation is dependent upon pulmonary alveoli lined by two major epithelial cell types, alveolar type-1 (AT1) and 2 (AT2) cells. AT1 cells mediate gas exchange while AT2 cells synthesize and secrete pulmonary surfactants and serve as progenitor cells which repair the alveoli. We developed transgenic mice in which YAP was activated or deleted to determine its roles in alveolar epithelial cell differentiation. Postnatal YAP activation increased epithelial cell proliferation, increased AT1 cell numbers, and caused indeterminate differentiation of subsets of alveolar cells expressing atypical genes normally restricted to airway epithelial cells. YAP deletion increased expression of genes associated with mature AT2 cells. YAP activation enhanced DNA accessibility in promoters of transcription factors and motif enrichment analysis predicted target genes associated with alveolar cell differentiation. YAP participated with KLF5, NFIB, and NKX2-1 to regulate AGER. YAP plays a central role in a transcriptional network that regulates alveolar epithelial differentiation.
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Affiliation(s)
- Jason J. Gokey
- Department of Medicine, Division of Allergy, Pulmonary, and Critical Care Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - John Snowball
- Division of Neonatology, Perinatal and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, Perinatal Institute, Cincinnati, OH 45229, USA
| | - Anusha Sridharan
- Division of Neonatology, Perinatal and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, Perinatal Institute, Cincinnati, OH 45229, USA
| | - Parvathi Sudha
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Joseph A. Kitzmiller
- Division of Neonatology, Perinatal and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, Perinatal Institute, Cincinnati, OH 45229, USA
| | - Yan Xu
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
- The Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Jeffrey A. Whitsett
- Division of Neonatology, Perinatal and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, Perinatal Institute, Cincinnati, OH 45229, USA
- The Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
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93
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ASCL1, NKX2-1, and PROX1 co-regulate subtype-specific genes in small-cell lung cancer. iScience 2021; 24:102953. [PMID: 34466783 PMCID: PMC8384902 DOI: 10.1016/j.isci.2021.102953] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 07/05/2021] [Accepted: 08/02/2021] [Indexed: 12/20/2022] Open
Abstract
Lineage-defining transcription factors (LTFs) play key roles in small-cell lung cancer (SCLC) pathophysiology. Delineating the LTF-regulated genes operative in SCLC could provide a road map to identify SCLC dependencies. We integrated chromatin landscape and transcriptome analyses of patient-derived SCLC preclinical models to identify super-enhancers (SEs) and their associated genes in the ASCL1-, NEUROD1-, and POU2F3-high SCLC subtypes. We find SE signatures predict LTF-based classification of SCLC, and the SE-associated genes are enriched with those defined as common essential genes in DepMap. In addition, in ASCL1-high SCLC, we show ASCL1 complexes with NKX2-1 and PROX1 to co-regulate genes functioning in NOTCH signaling, catecholamine biosynthesis, and cell-cycle processes. Depletion of ASCL1 demonstrates it is a key dependency factor in preclinical SCLC models and directly regulates multiple DepMap-defined essential genes. We provide LTF/SE-based subtype-specific gene sets for SCLC for further therapeutic investigation. Super-enhancers support lineage-defining transcription factor SCLC classification SCLC super-enhancer-associated genes represent essential and lineage-identity genes ASCL1, NKX2-1, and PROX1 proteins interact in a complex in SCLC-A ASCL1, NKX2-1, and PROX1 regulate Notch-signaling, NE-specific, and cell-cycle genes
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94
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Zboril E, Yoo H, Chen L, Liu Z. Dynamic Interactions of Transcription Factors and Enhancer Reprogramming in Cancer Progression. Front Oncol 2021; 11:753051. [PMID: 34616687 PMCID: PMC8488287 DOI: 10.3389/fonc.2021.753051] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 09/03/2021] [Indexed: 01/01/2023] Open
Abstract
While improved tumor treatment has significantly reduced the overall mortality rates, invasive progression including recurrence, therapy resistance and metastasis contributes to the majority of deaths caused by cancer. Enhancers are essential distal DNA regulatory elements that control temporal- or spatial-specific gene expression patterns during development and other biological processes. Genome-wide sequencing has revealed frequent alterations of enhancers in cancers and reprogramming of distal enhancers has emerged as one of the important features for tumors. In this review, we will discuss tumor progression-associated enhancer dynamics, its transcription factor (TF) drivers and how enhancer reprogramming modulates gene expression during cancer invasive progression. Additionally, we will explore recent advancements in contemporary technology including single-cell sequencing, spatial transcriptomics and CUT&RUN, which have permitted integrated studies of enhancer reprogramming in vivo. Given the essential roles of enhancer dynamics and its drivers in controlling cancer progression and treatment outcome, understanding these changes will be paramount in mitigating invasive events and discovering novel therapeutic targets.
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Affiliation(s)
- Emily Zboril
- Department of Molecular Medicine, Mays Cancer Center, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
| | - Hannah Yoo
- Department of Molecular Medicine, Mays Cancer Center, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
| | - Lizhen Chen
- Department of Molecular Medicine, Mays Cancer Center, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
- Department of Cell Systems and Anatomy, Barshop Institute for Longevity and Aging Studies, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
| | - Zhijie Liu
- Department of Molecular Medicine, Mays Cancer Center, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
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95
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The roles of epigenetics in cancer progression and metastasis. Biochem J 2021; 478:3373-3393. [PMID: 34520519 DOI: 10.1042/bcj20210084] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 08/25/2021] [Accepted: 08/26/2021] [Indexed: 01/12/2023]
Abstract
Cancer metastasis remains a major clinical challenge for cancer treatment. It is therefore crucial to understand how cancer cells establish and maintain their metastatic traits. However, metastasis-specific genetic mutations have not been identified in most exome or genome sequencing studies. Emerging evidence suggests that key steps of metastasis are controlled by reversible epigenetic mechanisms, which can be targeted to prevent and treat the metastatic disease. A variety of epigenetic mechanisms were identified to regulate metastasis, including the well-studied DNA methylation and histone modifications. In the past few years, large scale chromatin structure alterations including reprogramming of the enhancers and chromatin accessibility to the transcription factors were shown to be potential driving force of cancer metastasis. To dissect the molecular mechanisms and functional output of these epigenetic changes, it is critical to use advanced techniques and alternative animal models for interdisciplinary and translational research on this topic. Here we summarize our current understanding of epigenetic aberrations in cancer progression and metastasis, and their implications in developing new effective metastasis-specific therapies.
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96
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Wei Y, Wang T, Ma L, Zhang Y, Zhao Y, Lye K, Xiao L, Chen C, Wang Z, Ma Y, Zhou X, Sun F, Li W, Dunk C, Li S, Nagy A, Yu Y, Pan G, Lye SJ, Shan Y. Efficient derivation of human trophoblast stem cells from primed pluripotent stem cells. SCIENCE ADVANCES 2021; 7:eabf4416. [PMID: 34380613 PMCID: PMC8357231 DOI: 10.1126/sciadv.abf4416] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 06/22/2021] [Indexed: 05/04/2023]
Abstract
Human trophoblast stem cells (hTSCs) provide a valuable model to study placental development and function. While primary hTSCs have been derived from embryos/early placenta, and transdifferentiated hTSCs from naïve human pluripotent stem cells (hPSCs), the generation of hTSCs from primed PSCs is problematic. We report the successful generation of TSCs from primed hPSCs and show that BMP4 substantially enhances this process. TSCs derived from primed hPSCs are similar to blastocyst-derived hTSCs in terms of morphology, proliferation, differentiation potential, and gene expression. We define the chromatin accessibility dynamics and histone modifications (H3K4me3/H3K27me3) that specify hPSC-derived TSCs. Consistent with low density of H3K27me3 in primed hPSC-derived hTSCs, we show that knockout of H3K27 methyltransferases (EZH1/2) increases the efficiency of hTSC derivation from primed hPSCs. Efficient derivation of hTSCs from primed hPSCs provides a simple and powerful model to understand human trophoblast development, including the pathogenesis of trophoblast-related disorders, by generating disease-specific hTSCs.
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Affiliation(s)
- Yanxing Wei
- Placenta Research Group, Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
- Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto M5T3H7, Canada
| | - Tianyu Wang
- CAS Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lishi Ma
- Placenta Research Group, Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
- Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Yanqi Zhang
- CAS Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Yuan Zhao
- CAS Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Kathryn Lye
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto M5T3H7, Canada
- Institute of Medical Science, University of Toronto, Toronto M5G1L4, Canada
| | - Lu Xiao
- Placenta Research Group, Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
- Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Chunlin Chen
- Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Zhijian Wang
- Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Yanlin Ma
- Hainan Provincial Key Laboratory for Human Reproductive Medicine and Genetic Research, The Key Laboratory of Tropical Diseases and Translational Medicine of the Ministry of Education, Affiliated Hospital of Hainan Medical University, Hainan Medical University, Haikou, Hainan 570102, China
| | - Xiaohua Zhou
- Placenta Research Group, Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
- Department of Obstetrics and Gynecology, The Second People's Hospital of Shenzhen, The First Hospital Affiliated to Shenzhen University, Shenzhen 518029, China
| | - Fei Sun
- Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Weili Li
- Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Caroline Dunk
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto M5T3H7, Canada
| | - Siliang Li
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto M5T3H7, Canada
- China National Gene Bank-Shenzhen, Shenzhen 518083, China
| | - Andras Nagy
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto M5T3H7, Canada
- Department of Obstetrics & Gynecology, University of Toronto, Toronto M5G1L4, Canada
- Institute of Medical Science, University of Toronto, Toronto M5S 1A8, Canada
- Australian Regenerative Medicine Institute, Monash University, Melbourne, Victoria, Australia
| | - Yanhong Yu
- Placenta Research Group, Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
- Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Guangjin Pan
- CAS Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.
| | - Stephen J Lye
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto M5T3H7, Canada.
- Department of Obstetrics & Gynecology, University of Toronto, Toronto M5G1L4, Canada
- Department of Physiology, University of Toronto, Toronto M5G1L4, Canada
- Department of Medicine, University of Toronto, Toronto M5G1L4, Canada
| | - Yongli Shan
- Placenta Research Group, Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China.
- Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
- CAS Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
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97
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Wang X, Yan J, Shen B, Wei G. Integrated Chromatin Accessibility and Transcriptome Landscapes of Doxorubicin-Resistant Breast Cancer Cells. Front Cell Dev Biol 2021; 9:708066. [PMID: 34395436 PMCID: PMC8363264 DOI: 10.3389/fcell.2021.708066] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 07/12/2021] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Doxorubicin is one of the most effective chemotherapeutic drugs for breast cancer while its common drug resistance leads to poor patient prognosis and survival. Growing evidence indicate dynamically reorganized chromatin allows rapid access of the gene regulatory machinery to open genomic regions facilitating subsequent gene expression through direct transcription factor (TF) activation and regulatory element binding. METHODS To better understand the regulatory network underlying doxorubicin resistance in breast cancer cells, we explored the systematic alterations of chromatin accessibility and gene expression by the assay for transposase-accessible chromatin using sequencing (ATAC-seq) in combination with RNA sequencing, followed by integrative analysis to identify potential regulators and their targets associated with differentially accessible regions (DARs) in doxorubicin-resistant MCF7 (MCF7-DR) cells. RESULTS A total of 3,963 differentially expressed genes (DEGs) related to doxorubicin resistance were identified, including dramatically up-regulated MT1E, GSTP1, LDHB, significantly down-regulated TFF1, UBB, DSCAM-AS1, and histone-modifying enzyme coding genes HDAC2, EZH2, PRMT5, etc. By integrating with transcriptomic datasets, we identified 18,228 DARs in MCF7-DR cells compared to control, which were positively correlated with their nearest DEGs (r = 0.6). There were 11,686 increased chromatin-accessible regions, which were enriched in up-regulated genes related to diverse KEGG pathways, such as the cell cycle, regulation of actin cytoskeleton, signaling pathways of MAPK, PI3K/Akt and Hippo, which play essential roles in regulating cell apoptosis, proliferation, metabolism, and inflammatory responses. The 6,542 decreased chromatin-accessible regions were identified for the declined doxorubicin-associated biological processes, for instance, endocrine and insulin resistance, central carbon metabolism, signaling pathways of TGF-beta and P53. Combining data from TCGA, analyses of the DAR sequences associated with the DNA-binding motifs of significantly enriched TF families including AP-1, TEAD and FOX, indicated that the loss-function of FOXA1 might play a critical role in doxorubicin-resistant breast cancer cells (DOX-R BCCs). CONCLUSION These data exhibit the non-genetic landscape of chromatin accessibility and transcript levels in the DOX-R BCCs, and provide clear insights and resources for the detection of critical TFs and potential cis-regulatory elements-based putative therapeutic targets.
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Affiliation(s)
- Xuelong Wang
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, China
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
- Research Institute of Pancreatic Diseases, Shanghai JiaoTong University School of Medicine, Shanghai, China
| | - Jizhou Yan
- Department of Developmental Biology, Institute for Marine Biosystem and Neurosciences, Shanghai Ocean University, Shanghai, China
| | - Baiyong Shen
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, China
- Research Institute of Pancreatic Diseases, Shanghai JiaoTong University School of Medicine, Shanghai, China
- Institute of Translational Medicine, Shanghai JiaoTong University, Shanghai, China
| | - Gang Wei
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
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Epigenetic Alterations in Pancreatic Cancer Metastasis. Biomolecules 2021; 11:biom11081082. [PMID: 34439749 PMCID: PMC8394313 DOI: 10.3390/biom11081082] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 07/16/2021] [Accepted: 07/19/2021] [Indexed: 12/11/2022] Open
Abstract
Pancreatic cancer is the third leading cause of cancer-related deaths in the United States. Pancreatic ductal adenocarcinoma (PDA) is the most common (90%) and aggressive type of pancreatic cancer. Genomic analyses of PDA specimens have identified the recurrent genetic mutations that drive PDA initiation and progression. However, the underlying mechanisms that further drive PDA metastasis remain elusive. Despite many attempts, no recurrent genetic mutation driving PDA metastasis has been found, suggesting that PDA metastasis is driven by epigenetic fluctuations rather than genetic factors. Therefore, establishing epigenetic mechanisms of PDA metastasis would facilitate the development of successful therapeutic interventions. In this review, we provide a comprehensive overview on the role of epigenetic mechanisms in PDA as a critical contributor on PDA progression and metastasis. In particular, we explore the recent advancements elucidating the role of nucleosome remodeling, histone modification, and DNA methylation in the process of cancer metastasis.
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Lang F, Contreras-Gerenas MF, Gelléri M, Neumann J, Kröger O, Sadlo F, Berniak K, Marx A, Cremer C, Wagenknecht HA, Allgayer H. Tackling Tumour Cell Heterogeneity at the Super-Resolution Level in Human Colorectal Cancer Tissue. Cancers (Basel) 2021; 13:cancers13153692. [PMID: 34359592 PMCID: PMC8345115 DOI: 10.3390/cancers13153692] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 07/19/2021] [Accepted: 07/20/2021] [Indexed: 12/12/2022] Open
Abstract
Simple Summary Tumour cell heterogeneity is the most fundamental problem in cancer diagnosis and therapy. Micro-diagnostic technologies able to differentiate the heterogeneous molecular, especially metastatic, potential of single cells or cell clones already within early primary tumours of carcinoma patients would be of utmost importance. Single molecule localisation microscopy (SMLM) has recently allowed the imaging of subcellular features at the nanoscale. However, the technology has mostly been limited to cultured cell lines only. We introduce a first-in-field approach for quantitative SMLM-analysis of chromatin nanostructure in individual cells in resected, routine-pathology colorectal carcinoma patient tissue sections, illustrating, as a first example, changes in nuclear chromatin nanostructure and microRNA intracellular distribution within carcinoma cells as opposed to normal cells, chromatin accessibility and microRNAs having been shown to be critical in gene regulation and metastasis. We believe this technology to have an enormous potential for future differential diagnosis between individual cells in the tissue context. Abstract Tumour cell heterogeneity, and its early individual diagnosis, is one of the most fundamental problems in cancer diagnosis and therapy. Single molecule localisation microscopy (SMLM) resolves subcellular features but has been limited to cultured cell lines only. Since nuclear chromatin architecture and microRNAs are critical in metastasis, we introduce a first-in-field approach for quantitative SMLM-analysis of chromatin nanostructure in individual cells in resected, routine-pathology colorectal carcinoma (CRC) patient tissue sections. Chromatin density profiles proved to differ for cells in normal and carcinoma colorectal tissues. In tumour sections, nuclear size and chromatin compaction percentages were significantly different in carcinoma versus normal epithelial and other cells of colorectal tissue. SMLM analysis in nuclei from normal colorectal tissue revealed abrupt changes in chromatin density profiles at the nanoscale, features not detected by conventional widefield microscopy. SMLM for microRNAs relevant for metastasis was achieved in colorectal cancer tissue at the nuclear level. Super-resolution microscopy with quantitative image evaluation algorithms provide powerful tools to analyse chromatin nanostructure and microRNAs of individual cells from normal and tumour tissue at the nanoscale. Our new perspectives improve the differential diagnosis of normal and (metastatically relevant) tumour cells at the single-cell level within the heterogeneity of primary tumours of patients.
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Affiliation(s)
- Fabian Lang
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, Campus Süd, 76131 Karlsruhe, Germany; (F.L.); (H.-A.W.)
| | - María F. Contreras-Gerenas
- Department of Experimental Surgery—Cancer Metastasis, Mannheim Medical Faculty, Ruprecht-Karls University of Heidelberg, Ludolf-Krehl-Straße 13-17, 68167 Mannheim, Germany;
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128 Mainz, Germany; (M.G.); (J.N.); (C.C.)
| | - Márton Gelléri
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128 Mainz, Germany; (M.G.); (J.N.); (C.C.)
| | - Jan Neumann
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128 Mainz, Germany; (M.G.); (J.N.); (C.C.)
| | - Ole Kröger
- Interdisciplinary Centre for Scientific Computing (IWR), University Heidelberg, Mathematikon B, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany; (O.K.); (F.S.)
| | - Filip Sadlo
- Interdisciplinary Centre for Scientific Computing (IWR), University Heidelberg, Mathematikon B, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany; (O.K.); (F.S.)
| | - Krzysztof Berniak
- Department of Cell Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7 Street, 30-387 Krakow, Poland;
| | - Alexander Marx
- Institute of Pathology, Mannheim Medical Faculty, Ruprecht-Karls University of Heidelberg, Theodor-Kutzer-Ufer 1, 68167 Mannheim, Germany;
| | - Christoph Cremer
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128 Mainz, Germany; (M.G.); (J.N.); (C.C.)
- Interdisciplinary Centre for Scientific Computing (IWR), University Heidelberg, Mathematikon B, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany; (O.K.); (F.S.)
- Institute of Pharmacy & Molecular Biotechnology, Ruprecht-Karls University of Heidelberg, Im Neuenheimer Feld 364, 69120 Heidelberg, Germany
| | - Hans-Achim Wagenknecht
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, Campus Süd, 76131 Karlsruhe, Germany; (F.L.); (H.-A.W.)
| | - Heike Allgayer
- Department of Experimental Surgery—Cancer Metastasis, Mannheim Medical Faculty, Ruprecht-Karls University of Heidelberg, Ludolf-Krehl-Straße 13-17, 68167 Mannheim, Germany;
- Correspondence: ; Tel.: +49-(0)621-383-71630/-1406/-71635; Fax: +49-(0)621-383-71631
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Jin Y, Xiao T, Feng Y, Yang J, Guo C, Hu L, Ji H. A mesenchymal-like subpopulation in non-neuroendocrine SCLC contributes to metastasis. J Genet Genomics 2021; 48:571-581. [PMID: 34373217 DOI: 10.1016/j.jgg.2021.05.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 05/24/2021] [Accepted: 05/30/2021] [Indexed: 11/28/2022]
Abstract
Small cell lung cancer (SCLC) is the most aggressive lung cancer with high heterogeneity. Mouse SCLC cells derived from the Rb1L/L/Trp53L/L (RP) autochthonous mouse model grew as adhesion or suspension in cell culture, and the adhesion cells are defined as non-neuroendocrine (non-NE) SCLC cells. Here, we uncover the heterogenous subpopulations within the non-NE cells and referred to them as mesenchymal-like (Mes) and epithelial-like (Epi) SCLC cells. The Mes cells have increased capability to form colonies in soft agar and harbored stronger metastatic capability in vivo when compared with the Epi cells. Gene Set Enrichment Analysis reveals that the transforming growth factor (TGF)-β signaling is enriched in the Mes cells. Importantly, inhibition of the TGF-β signaling through ectopic expression of dominant-negative Tgfbr2 (Tgfbr2-DN) or treatment with Tgfbr1 inhibitor SD-208 consistently abrogates tumor metastasis in nude mouse allograft assays. Moreover, genetic deletion of Tgfbr2 or Smad4, the key components of the TGF-β signaling pathway, dramatically attenuates SCLC metastasis in the RP autochthonous mouse model. Collectively, our results uncover the high heterogeneity in non-NE SCLC cells and highlight an important role of TGF-β signaling in promoting SCLC metastasis.
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Affiliation(s)
- Yujuan Jin
- State Key Laboratory of Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China; Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China; Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Tian Xiao
- Shenzhen Key Laboratory of Translational Medicine of Tumor, Department of Cell Biology and Genetics, Shenzhen University Health Sciences Center, Shenzhen, Guangdong 518060, China
| | - Yan Feng
- State Key Laboratory of Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China; Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China; Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Jinhua Yang
- State Key Laboratory of Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China; Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China; Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chenchen Guo
- State Key Laboratory of Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China; Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China; Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Liang Hu
- State Key Laboratory of Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China; Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China; Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Hongbin Ji
- State Key Laboratory of Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China; Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China; Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China; University of Chinese Academy of Sciences, Beijing 100049, China; School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China.
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