201
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Rodrigues P, Patel SA, Harewood L, Olan I, Vojtasova E, Syafruddin SE, Zaini MN, Richardson EK, Burge J, Warren AY, Stewart GD, Saeb-Parsy K, Samarajiwa SA, Vanharanta S. NF-κB-Dependent Lymphoid Enhancer Co-option Promotes Renal Carcinoma Metastasis. Cancer Discov 2018; 8:850-865. [PMID: 29875134 PMCID: PMC6031301 DOI: 10.1158/2159-8290.cd-17-1211] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 03/26/2018] [Accepted: 05/01/2018] [Indexed: 01/10/2023]
Abstract
Metastases, the spread of cancer cells to distant organs, cause the majority of cancer-related deaths. Few metastasis-specific driver mutations have been identified, suggesting aberrant gene regulation as a source of metastatic traits. However, how metastatic gene expression programs arise is poorly understood. Here, using human-derived metastasis models of renal cancer, we identify transcriptional enhancers that promote metastatic carcinoma progression. Specific enhancers and enhancer clusters are activated in metastatic cancer cell populations, and the associated gene expression patterns are predictive of poor patient outcome in clinical samples. We find that the renal cancer metastasis-associated enhancer complement consists of multiple coactivated tissue-specific enhancer modules. Specifically, we identify and functionally characterize a coregulatory enhancer cluster, activated by the renal cancer driver HIF2A and an NF-κB-driven lymphoid element, as a mediator of metastasis in vivo We conclude that oncogenic pathways can acquire metastatic phenotypes through cross-lineage co-option of physiologic epigenetic enhancer states.Significance: Renal cancer is associated with significant mortality due to metastasis. We show that in metastatic renal cancer, functionally important metastasis genes are activated via co-option of gene regulatory enhancer modules from distant developmental lineages, thus providing clues to the origins of metastatic cancer. Cancer Discov; 8(7); 850-65. ©2018 AACR.This article is highlighted in the In This Issue feature, p. 781.
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Affiliation(s)
- Paulo Rodrigues
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge, United Kingdom
| | - Saroor A Patel
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge, United Kingdom
| | - Louise Harewood
- Cancer Research UK/Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, United Kingdom
| | - Ioana Olan
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge, United Kingdom
| | - Erika Vojtasova
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge, United Kingdom
| | - Saiful E Syafruddin
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge, United Kingdom
- UKM Medical Molecular Biology Institute, Universiti Kebangsaan Malaysia, Jalan Yaa'cob Latiff, Bandar Tun Razak, Kuala Lumpur, Malaysia
| | - M Nazhif Zaini
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge, United Kingdom
| | - Emma K Richardson
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge, United Kingdom
| | - Johanna Burge
- Academic Urology Group, Department of Surgery, University of Cambridge, Addenbrooke's Hospital, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Anne Y Warren
- Department of Histopathology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | - Grant D Stewart
- Academic Urology Group, Department of Surgery, University of Cambridge, Addenbrooke's Hospital, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Kourosh Saeb-Parsy
- Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Cambridge, United Kingdom
| | - Shamith A Samarajiwa
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge, United Kingdom
| | - Sakari Vanharanta
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge, United Kingdom.
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202
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Fagnocchi L, Poli V, Zippo A. Enhancer reprogramming in tumor progression: a new route towards cancer cell plasticity. Cell Mol Life Sci 2018; 75:2537-2555. [PMID: 29691590 PMCID: PMC11105402 DOI: 10.1007/s00018-018-2820-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 04/11/2018] [Accepted: 04/17/2018] [Indexed: 12/13/2022]
Abstract
Cancer heterogeneity arises during tumor progression as a consequence of genetic insults, environmental cues, and reversible changes in the epigenetic state, favoring tumor cell plasticity. The role of enhancer reprogramming is emerging as a relevant field in cancer biology as it supports adaptation of cancer cells to those environmental changes encountered during tumor progression and metastasis seeding. In this review, we describe the cancer-related alterations that drive oncogenic enhancer activity, leading to dysregulated transcriptional programs. We discuss the molecular mechanisms of both cis- and trans-factors in overriding the regulatory circuits that maintain cell-type specificity and imposing an alternative, de-regulated enhancer activity in cancer cells. We further comment on the increasing evidence which implicates stress response and aging-signaling pathways in the enhancer landscape reprogramming during tumorigenesis. Finally, we focus on the potential therapeutic implications of these enhancer-mediated subverted transcriptional programs, putting particular emphasis on the lack of information regarding tumor progression and the metastatic outgrowth, which still remain the major cause of mortality related to cancer.
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Affiliation(s)
- Luca Fagnocchi
- Laboratory of Chromatin Biology and Epigenetics, Center for Integrative Biology (CIBIO), University of Trento, 38123, Trento, Italy.
| | - Vittoria Poli
- Laboratory of Chromatin Biology and Epigenetics, Center for Integrative Biology (CIBIO), University of Trento, 38123, Trento, Italy
| | - Alessio Zippo
- Laboratory of Chromatin Biology and Epigenetics, Center for Integrative Biology (CIBIO), University of Trento, 38123, Trento, Italy.
- Department of Epigenetics, Fondazione Istituto Nazionale di Genetica Molecolare "Romeo ed Enrica Invernizzi", Via F. Sforza 35, 20122, Milan, Italy.
- Division of Pathology, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy.
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203
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Single-Cell RNA-Seq Analysis of Infiltrating Neoplastic Cells at the Migrating Front of Human Glioblastoma. Cell Rep 2018; 21:1399-1410. [PMID: 29091775 DOI: 10.1016/j.celrep.2017.10.030] [Citation(s) in RCA: 577] [Impact Index Per Article: 96.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Revised: 07/19/2017] [Accepted: 10/08/2017] [Indexed: 12/20/2022] Open
Abstract
Glioblastoma (GBM) is the most common primary brain cancer in adults and is notoriously difficult to treat because of its diffuse nature. We performed single-cell RNA sequencing (RNA-seq) on 3,589 cells in a cohort of four patients. We obtained cells from the tumor core as well as surrounding peripheral tissue. Our analysis revealed cellular variation in the tumor's genome and transcriptome. We were also able to identify infiltrating neoplastic cells in regions peripheral to the core lesions. Despite the existence of significant heterogeneity among neoplastic cells, we found that infiltrating GBM cells share a consistent gene signature between patients, suggesting a common mechanism of infiltration. Additionally, in investigating the immunological response to the tumors, we found transcriptionally distinct myeloid cell populations residing in the tumor core and the surrounding peritumoral space. Our data provide a detailed dissection of GBM cell types, revealing an abundance of information about tumor formation and migration.
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204
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Sanosaka T, Imamura T, Hamazaki N, Chai M, Igarashi K, Ideta-Otsuka M, Miura F, Ito T, Fujii N, Ikeo K, Nakashima K. DNA Methylome Analysis Identifies Transcription Factor-Based Epigenomic Signatures of Multilineage Competence in Neural Stem/Progenitor Cells. Cell Rep 2018; 20:2992-3003. [PMID: 28930691 DOI: 10.1016/j.celrep.2017.08.086] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Revised: 07/10/2017] [Accepted: 08/25/2017] [Indexed: 12/17/2022] Open
Abstract
Regulation of the epigenome during in vivo specification of brain stem cells is still poorly understood. Here, we report DNA methylome analyses of directly sampled cortical neural stem and progenitor cells (NS/PCs) at different development stages, as well as those of terminally differentiated cortical neurons, astrocytes, and oligodendrocytes. We found that sequential specification of cortical NS/PCs is regulated by two successive waves of demethylation at early and late development stages, which are responsible for the establishment of neuron- and glia-specific low-methylated regions (LMRs), respectively. The regulatory role of demethylation of the gliogenic genes was substantiated by the enrichment of nuclear factor I (NFI)-binding sites. We provide evidence that de novo DNA methylation of neuron-specific LMRs establishes glia-specific epigenotypes, essentially by silencing neuronal genes. Our data highlight the in vivo implications of DNA methylation dynamics in shaping epigenomic features that confer the differentiation potential of NS/PCs sequentially during development.
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Affiliation(s)
- Tsukasa Sanosaka
- Department of Stem Cell Biology and Medicine, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan; Department of Physiology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan.
| | - Takuya Imamura
- Department of Stem Cell Biology and Medicine, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan.
| | - Nobuhiko Hamazaki
- Department of Stem Cell Biology and Medicine, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - MuhChyi Chai
- Department of Physiology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Katsuhide Igarashi
- Life Science Tokyo Advanced Research Center (L-StaR), Hoshi University School of Pharmacy and Pharmaceutical Sciences, 2-4-41 Ebara, Shinagawa-ku, Tokyo 142-5801, Japan
| | - Maky Ideta-Otsuka
- Life Science Tokyo Advanced Research Center (L-StaR), Hoshi University School of Pharmacy and Pharmaceutical Sciences, 2-4-41 Ebara, Shinagawa-ku, Tokyo 142-5801, Japan
| | - Fumihito Miura
- Department of Biochemistry, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Takashi Ito
- Department of Biochemistry, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Nobuyuki Fujii
- Center for Information Biology, National Institute of Genetics, Research Organization of Information and Systems, Yata 1111, Mishima, Shizuoka 411-8540, Japan
| | - Kazuho Ikeo
- Center for Information Biology, National Institute of Genetics, Research Organization of Information and Systems, Yata 1111, Mishima, Shizuoka 411-8540, Japan
| | - Kinichi Nakashima
- Department of Stem Cell Biology and Medicine, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan.
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205
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Fane ME, Chhabra Y, Smith AG, Sturm RA. BRN2, a POUerful driver of melanoma phenotype switching and metastasis. Pigment Cell Melanoma Res 2018; 32:9-24. [PMID: 29781575 DOI: 10.1111/pcmr.12710] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 04/18/2018] [Accepted: 04/25/2018] [Indexed: 12/30/2022]
Abstract
The POU domain family of transcription factors play a central role in embryogenesis and are highly expressed in neural crest cells and the developing brain. BRN2 is a class III POU domain protein that is a key mediator of neuroendocrine and melanocytic development and differentiation. While BRN2 is a central regulator in numerous developmental programs, it has also emerged as a major player in the biology of tumourigenesis. In melanoma, BRN2 has been implicated as one of the master regulators of the acquisition of invasive behaviour within the phenotype switching model of progression. As a mediator of melanoma cell phenotype switching, it coordinates the transition to a dedifferentiated, slow cycling and highly motile cell type. Its inverse expression relationship with MITF is believed to mediate tumour progression and metastasis within this model. Recent evidence has now outlined a potential epigenetic switching mechanism in melanoma cells driven by BRN2 expression that induces melanoma cell invasion. We summarize the role of BRN2 in tumour cell dissemination and metastasis in melanoma, while also examining it as a potential metastatic regulator in other tumour models.
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Affiliation(s)
- Mitchell E Fane
- School of Biomedical Sciences, Institute of Health and Biomedical Innovation at the Translational Research Institute, Queensland University of Technology, Brisbane, QLD, Australia.,Dermatology Research Centre, UQ Diamantina Institute, Translational Research Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Yash Chhabra
- School of Biomedical Sciences, Institute of Health and Biomedical Innovation at the Translational Research Institute, Queensland University of Technology, Brisbane, QLD, Australia.,Dermatology Research Centre, UQ Diamantina Institute, Translational Research Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Aaron G Smith
- School of Biomedical Sciences, Institute of Health and Biomedical Innovation at the Translational Research Institute, Queensland University of Technology, Brisbane, QLD, Australia
| | - Richard A Sturm
- Dermatology Research Centre, UQ Diamantina Institute, Translational Research Institute, The University of Queensland, Brisbane, QLD, Australia
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206
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Genome-scale identification of transcription factors that mediate an inflammatory network during breast cellular transformation. Nat Commun 2018; 9:2068. [PMID: 29802342 PMCID: PMC5970197 DOI: 10.1038/s41467-018-04406-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 04/26/2018] [Indexed: 01/05/2023] Open
Abstract
Transient activation of Src oncoprotein in non-transformed, breast epithelial cells can initiate an epigenetic switch to the stably transformed state via a positive feedback loop that involves the inflammatory transcription factors STAT3 and NF-κB. Here, we develop an experimental and computational pipeline that includes 1) a Bayesian network model (AccessTF) that accurately predicts protein-bound DNA sequence motifs based on chromatin accessibility, and 2) a scoring system (TFScore) that rank-orders transcription factors as candidates for being important for a biological process. Genetic experiments validate TFScore and suggest that more than 40 transcription factors contribute to the oncogenic state in this model. Interestingly, individual depletion of several of these factors results in similar transcriptional profiles, indicating that a complex and interconnected transcriptional network promotes a stable oncogenic state. The combined experimental and computational pipeline represents a general approach to comprehensively identify transcriptional regulators important for a biological process.
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207
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Madrigal P, Alasoo K. AP-1 Takes Centre Stage in Enhancer Chromatin Dynamics. Trends Cell Biol 2018; 28:509-511. [PMID: 29778529 DOI: 10.1016/j.tcb.2018.04.009] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 04/18/2018] [Accepted: 04/24/2018] [Indexed: 01/24/2023]
Abstract
Recent studies involving induced pluripotent stem cell (iPSC) reprogramming in mice and monocyte-to-macrophage differentiation in humans have revealed a role for the transcription factor (TF) activator protein 1 (AP-1) in chromatin accessibility. Enhancer selection may be determined not only by cell type-specific sets of TFs but also by broadly expressed ones like AP-1.
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Affiliation(s)
- Pedro Madrigal
- Wellcome Sanger Institute, Hinxton CB10 1SA, UK; Current address: Centre for Trophoblast Research, Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EG, UK.
| | - Kaur Alasoo
- Institute of Computer Science, University of Tartu, 50409 Tartu, Estonia
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208
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Parry AJ, Hoare M, Bihary D, Hänsel-Hertsch R, Smith S, Tomimatsu K, Mannion E, Smith A, D'Santos P, Russell IA, Balasubramanian S, Kimura H, Samarajiwa SA, Narita M. NOTCH-mediated non-cell autonomous regulation of chromatin structure during senescence. Nat Commun 2018; 9:1840. [PMID: 29743479 PMCID: PMC5943456 DOI: 10.1038/s41467-018-04283-9] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2017] [Accepted: 04/16/2018] [Indexed: 12/16/2022] Open
Abstract
Senescent cells interact with the surrounding microenvironment achieving diverse functional outcomes. We have recently identified that NOTCH1 can drive 'lateral induction' of a unique senescence phenotype in adjacent cells by specifically upregulating the NOTCH ligand JAG1. Here we show that NOTCH signalling can modulate chromatin structure autonomously and non-autonomously. In addition to senescence-associated heterochromatic foci (SAHF), oncogenic RAS-induced senescent (RIS) cells exhibit a massive increase in chromatin accessibility. NOTCH signalling suppresses SAHF and increased chromatin accessibility in this context. Strikingly, NOTCH-induced senescent cells, or cancer cells with high JAG1 expression, drive similar chromatin architectural changes in adjacent cells through cell-cell contact. Mechanistically, we show that NOTCH signalling represses the chromatin architectural protein HMGA1, an association found in multiple human cancers. Thus, HMGA1 is involved not only in SAHFs but also in RIS-driven chromatin accessibility. In conclusion, this study identifies that the JAG1-NOTCH-HMGA1 axis mediates the juxtacrine regulation of chromatin architecture.
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Affiliation(s)
- Aled J Parry
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
| | - Matthew Hoare
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
- Department of Medicine, Addenbrooke's Hospital, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Dóra Bihary
- MRC Cancer Unit, Hutchison/MRC Research Centre, University of Cambridge, Cambridge Biomedical Campus, Cambridge, CB2 0XZ, UK
| | - Robert Hänsel-Hertsch
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
| | - Stephen Smith
- Department of Pathology, Addenbrooke's Hospital, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Kosuke Tomimatsu
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
| | - Elizabeth Mannion
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
| | - Amy Smith
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
| | - Paula D'Santos
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
| | - I Alasdair Russell
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
| | - Shankar Balasubramanian
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Hiroshi Kimura
- Cell Biology Centre, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, 226-8503, Japan
| | - Shamith A Samarajiwa
- MRC Cancer Unit, Hutchison/MRC Research Centre, University of Cambridge, Cambridge Biomedical Campus, Cambridge, CB2 0XZ, UK.
| | - Masashi Narita
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK.
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209
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Pascual G, Domínguez D, Benitah SA. The contributions of cancer cell metabolism to metastasis. Dis Model Mech 2018; 11:11/8/dmm032920. [PMID: 29739810 PMCID: PMC6124557 DOI: 10.1242/dmm.032920] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Metastasis remains the leading cause of cancer-related deaths worldwide, and our inability to identify the tumour cells that colonize distant sites hampers the development of effective anti-metastatic therapies. However, with recent research advances we are beginning to distinguish metastasis-initiating cells from their non-metastatic counterparts. Importantly, advances in genome sequencing indicate that the acquisition of metastatic competency does not involve the progressive accumulation of driver mutations; moreover, in the early stages of tumorigenesis, cancer cells harbour combinations of driver mutations that endow them with metastatic competency. Novel findings highlight that cells can disseminate to distant sites early during primary tumour growth, remaining dormant and untreatable for long periods before metastasizing. Thus, metastatic cells must require local and systemic influences to generate metastases. This hypothesis suggests that factors derived from our lifestyle, such as our diet, exert a strong influence on tumour progression, and that such factors could be modulated if understood. Here, we summarize the recent findings on how specific metabolic cues modulate the behaviour of metastatic cells and how they influence the genome and epigenome of metastatic cells. We also discuss how crosstalk between metabolism and the epigenome can be harnessed to develop new anti-metastatic therapies.
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Affiliation(s)
- Gloria Pascual
- Institute for Research in Biomedicine (IRB Barcelona), Oncology Department, The Barcelona Institute of Science and Technology (BIST), 08028, Barcelona, Spain
| | - Diana Domínguez
- Institute for Research in Biomedicine (IRB Barcelona), Oncology Department, The Barcelona Institute of Science and Technology (BIST), 08028, Barcelona, Spain
| | - Salvador Aznar Benitah
- Institute for Research in Biomedicine (IRB Barcelona), Oncology Department, The Barcelona Institute of Science and Technology (BIST), 08028, Barcelona, Spain .,Catalan Institution for Research and Advanced Studies (ICREA), 08010, Barcelona, Spain
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210
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Sathyan S, Barzilai N, Atzmon G, Milman S, Ayers E, Verghese J. Genetic Insights Into Frailty: Association of 9p21-23 Locus With Frailty. Front Med (Lausanne) 2018; 5:105. [PMID: 29765957 PMCID: PMC5938407 DOI: 10.3389/fmed.2018.00105] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 03/29/2018] [Indexed: 12/16/2022] Open
Abstract
Frailty is a complex aging phenotype associated with increased vulnerability to disability and death. Understanding the biological antecedents of frailty may provide clues to healthy aging. The genome-wide association study hotspot, 9p21-23 region, is a risk locus for a number of age-related complex disorders associated with frailty. Hence, we conducted an association study to examine whether variations in 9p21-23 locus plays a role in the pathogenesis of frailty in 637 community-dwelling Ashkenazi Jewish adults aged 65 and older enrolled in the LonGenity study. The strongest association with frailty (adjusted for age and gender) was found with the SNP rs518054 (odds ratio: 1.635, 95% CI = 1.241-2.154; p-value: 4.81 × 10-04) intergenic and located between LOC105375977 and C9orf146. The prevalence of four SNPs (rs1324192, rs7019262, rs518054, and rs571221) risk alleles haplotype in this region was significantly higher (compared with other haplotypes) in frail older adults compared with non-frail older adults (29.7 vs. 20.8%, p = 0.0005, respectively). Functional analyses using in silico approaches placed rs518054 in the CTCF binding site as well as DNase hypersensitive region. Furthermore, rs518054 was found to be in an enhancer site of NFIB gene located downstream. NFIB is a transcription factor that promotes cell differentiation during development, has antiapoptotic effect, maintains stem cell populations in adult tissues, and also acts as epigenetic regulators. Our study found novel association of SNPs in the regulatory region in the 9p21-23 region with the frailty phenotype; signifying the importance of this locus in aging.
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Affiliation(s)
- Sanish Sathyan
- Department of Neurology, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Nir Barzilai
- Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, United States.,Department of Genetics, Institute for Aging Research, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Gil Atzmon
- Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, United States.,Department of Genetics, Institute for Aging Research, Albert Einstein College of Medicine, Bronx, NY, United States.,Department of Biology, Faculty of Natural Science, University of Haifa, Haifa, Israel
| | - Sofiya Milman
- Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Emmeline Ayers
- Department of Neurology, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Joe Verghese
- Department of Neurology, Albert Einstein College of Medicine, Bronx, NY, United States.,Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, United States
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211
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Kumar VHS, Chaker El Khoury J, Gronostajski R, Wang H, Nielsen L, Ryan RM. Nfib hemizygous mice are protected from hyperoxic lung injury and death. Physiol Rep 2018; 5:5/16/e13398. [PMID: 28830981 PMCID: PMC5582271 DOI: 10.14814/phy2.13398] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Revised: 07/22/2017] [Accepted: 07/28/2017] [Indexed: 12/17/2022] Open
Abstract
Nuclear Factor I (Nfi) genes encode transcription factors essential for the development of organ systems including the lung. Nfib null mice die at birth with immature lungs. Nfib hemizygous mice have reduced lung maturation with decreased survival. We therefore hypothesized that these mice would be more sensitive to lung injury and would have lower survival to hyperoxia. Adult Nfib hemizygous mice and their wild-type (Wt) littermates were exposed to 100% O2 for 89, 80, 72 and 66 h for survival studies with lung outcome measurements at 66 h. Nfib hemizygous and Wt controls were also studied in RA at 66 h. Cell counts and cytokines were measured in bronchoalveolar lavage (BAL); lung sections examined by histopathology; lung angiogenic and oxidative stress gene expression assessed by real-time PCR Unexpectedly, Nfib hemizygous mice (0/14-0%) had significantly lower mortality compared to Wt mice (10/22-45%) at 80 h of hyperoxia (P < 0.003). LD50 was 80 h in the Wt group versus 89 h in the hemizygous group. There were no differences in BAL cell counts between the groups. Among the cytokines studied, MIP-2 was significantly lower in hemizygous mice exposed to hyperoxia. New vessel formation, edema, congestion, and alveolar hemorrhage were noted on histopathology at 72 and 80 h in wild-type mice. Nfib hemizygous lungs had significant downregulation of genes involved in redox signaling and inflammatory pathways. Adult Nfib hemizygous mice are relatively resistant to hyperoxia compared to wild-type littermates. Mechanisms contributing to this resistance are not clear; however, transcription factors such as Nfib may regulate cell survival and play a role in modulating postnatal lung development.
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Affiliation(s)
| | | | - Richard Gronostajski
- Departments of Biochemistry and Developmental Genomics & Genetics, Genomics & Bioinformatics Program, University at Buffalo, Buffalo, New York
| | - Huamei Wang
- Department of Pediatrics, University at Buffalo, Buffalo, New York
| | - Lori Nielsen
- Department of Pediatrics, University at Buffalo, Buffalo, New York
| | - Rita M Ryan
- Department of Pediatrics, Medical University of South Carolina, Charleston, South Carolina
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212
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Dechassa ML, Tryndyak V, de Conti A, Xiao W, Beland FA, Pogribny IP. Identification of chromatin-accessible domains in non-alcoholic steatohepatitis-derived hepatocellular carcinoma. Mol Carcinog 2018; 57:978-987. [DOI: 10.1002/mc.22818] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2017] [Revised: 03/20/2018] [Accepted: 03/27/2018] [Indexed: 12/16/2022]
Affiliation(s)
- Mekonnen L. Dechassa
- Division of Biochemical Toxicology; National Center for Toxicological Research; U.S. Food Drug Administration; Jefferson Arkansas
| | - Volodymyr Tryndyak
- Division of Biochemical Toxicology; National Center for Toxicological Research; U.S. Food Drug Administration; Jefferson Arkansas
| | - Aline de Conti
- Division of Biochemical Toxicology; National Center for Toxicological Research; U.S. Food Drug Administration; Jefferson Arkansas
| | - Wenming Xiao
- Division of Bioinformatics and Biostatistics; National Center for Toxicological Research; U.S. Food and Drug Administration; Jefferson Arkansas
| | - Frederick A. Beland
- Division of Biochemical Toxicology; National Center for Toxicological Research; U.S. Food Drug Administration; Jefferson Arkansas
| | - Igor P. Pogribny
- Division of Biochemical Toxicology; National Center for Toxicological Research; U.S. Food Drug Administration; Jefferson Arkansas
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213
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Wang J, Zibetti C, Shang P, Sripathi SR, Zhang P, Cano M, Hoang T, Xia S, Ji H, Merbs SL, Zack DJ, Handa JT, Sinha D, Blackshaw S, Qian J. ATAC-Seq analysis reveals a widespread decrease of chromatin accessibility in age-related macular degeneration. Nat Commun 2018; 9:1364. [PMID: 29636475 PMCID: PMC5893535 DOI: 10.1038/s41467-018-03856-y] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 03/15/2018] [Indexed: 12/31/2022] Open
Abstract
Age-related macular degeneration (AMD) is a significant cause of vision loss in the elderly. The extent to which epigenetic changes regulate AMD progression is unclear. Here we globally profile chromatin accessibility using ATAC-Seq in the retina and retinal pigmented epithelium (RPE) from AMD and control patients. Global decreases in chromatin accessibility occur in the RPE with early AMD, and in the retina of advanced disease, suggesting that dysfunction in the RPE drives disease onset. Footprints of photoreceptor and RPE-specific transcription factors are enriched in differentially accessible regions (DARs). Genes associated with DARs show altered expression in AMD. Cigarette smoke treatment of RPE cells recapitulates chromatin accessibility changes seen in AMD, providing an epigenetic link between a known risk factor for AMD and AMD pathology. Finally, overexpression of HDAC11 is partially responsible for the observed reduction in chromatin accessibility, suggesting that HDAC11 may be a potential new therapeutic target for AMD.
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Affiliation(s)
- Jie Wang
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Cristina Zibetti
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Peng Shang
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Departments of Ophthalmology, Cell Biology and Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15224, USA
| | - Srinivasa R Sripathi
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Pingwu Zhang
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Marisol Cano
- 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
| | - Shuli Xia
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Hugo W Moser Research Institute at Kennedy Krieger, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Hongkai Ji
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA
| | - Shannath L Merbs
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Donald J Zack
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - James T Handa
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Debasish Sinha
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Departments of Ophthalmology, Cell Biology and Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15224, 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 Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
- Center for Human Systems Biology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
| | - Jiang Qian
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
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214
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Lee S, Liang F, Cai L, Xiao G. A two-stage approach of gene network analysis for high-dimensional heterogeneous data. Biostatistics 2018; 19:216-232. [PMID: 29036516 PMCID: PMC5862270 DOI: 10.1093/biostatistics/kxx033] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Revised: 04/18/2017] [Accepted: 05/07/2017] [Indexed: 11/13/2022] Open
Abstract
Gaussian graphical models have been widely used to construct gene regulatory networks from gene expression data. Most existing methods for Gaussian graphical models are designed to model homogeneous data, assuming a single Gaussian distribution. In practice, however, data may consist of gene expression studies with unknown confounding factors, such as study cohort, microarray platforms, experimental batches, which produce heterogeneous data, and hence lead to false positive edges or low detection power in resulting network, due to those unknown factors. To overcome this problem and improve the performance in constructing gene networks, we propose a two-stage approach to construct a gene network from heterogeneous data. The first stage is to perform a clustering analysis in order to assign samples to a few clusters where the samples in each cluster are approximately homogeneous, and the second stage is to conduct an integrative analysis of networks from each cluster. In particular, we first apply a model-based clustering method using the singular value decomposition for high-dimensional data, and then integrate the networks from each cluster using the integrative $\psi$-learning method. The proposed method is based on an equivalent measure of partial correlation coefficients in Gaussian graphical models, which is computed with a reduced conditional set and thus it is useful for high-dimensional data. We compare the proposed two-stage learning approach with some existing methods in various simulation settings, and demonstrate the robustness of the proposed method. Finally, it is applied to integrate multiple gene expression studies of lung adenocarcinoma to identify potential therapeutic targets and treatment biomarkers.
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Affiliation(s)
- Sangin Lee
- Department of Information and Statistics, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Korea
| | - Faming Liang
- Department of Biostatistics, University of Florida, FL 32610, USA
| | - Ling Cai
- Quantitative Biomedical Research Center, Department of Clinical Sciences, and Children's Research Institute, University of Texas Southwestern Medical Center, 6000 Harry Hines Blvd, Dallas, TX 75390, USA
| | - Guanghua Xiao
- Quantitative Biomedical Research Center, Department of Clinical Sciences, Department of Bioinformatics, Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, 6000 Harry Hines Blvd, Dallas, TX 75390, USA
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215
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Yang B, Zhou ZH, Chen L, Cui X, Hou JY, Fan KJ, Han SH, Li P, Yi SQ, Liu Y. Prognostic significance of NFIA and NFIB in esophageal squamous carcinoma and esophagogastric junction adenocarcinoma. Cancer Med 2018; 7:1756-1765. [PMID: 29577671 PMCID: PMC5943462 DOI: 10.1002/cam4.1434] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 02/09/2018] [Accepted: 02/17/2018] [Indexed: 12/12/2022] Open
Abstract
The nuclear factor I (NFI) family members, especially NFIA and NFIB, play essential roles in cancers. The roles of NFIA and NFIB in esophageal squamous cell carcinoma (ESCC) and esophagogastric junction adenocarcinoma (EJA) remain poorly known. This study aimed to determine the expression of NFIA and NFIB in ESCC and EJA and elucidate their prognostic significance. The expression of NFIA and NFIB was examined in 163 ESCC samples and 26 EJA samples by immunohistochemistry. The results showed that high NFIA expression correlated significantly with poor differentiation, lymph node metastasis, and advanced TNM stage in patients with ESCC. High NFIB expression only correlated with poor differentiation in patients with ESCC. Survival analysis showed that NFIA but not NFIB associated with short overall survival (OS) and disease‐free survival (DFS) of patients with ESCC. On the other hand, high NFIB expression correlated with lymph node metastasis, advanced TNM stage, and short OS and DFS in patients with EJA. Finally, multivariate analysis demonstrated that high NFIA expression was an independent prognostic factor for ESCC. Taken together, these results demonstrated that NFIA and NFIB could serve as prognostic indicators for ESCC and EJA, respectively.
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Affiliation(s)
- Bo Yang
- Department of General Thoracic Surgery, The General Hospital of PLA, Beijing, China
| | - Zhi-Hang Zhou
- Department of Digestive Disease, the Second affiliated hospital of Chongqing Medical University, Chongqing, China
| | - Li Chen
- Department of Emergency, The General Hospital of PLA, Beijing, China
| | - Xiang Cui
- Department of Orthopedics, The General Hospital of PLA, Beijing, China
| | - Jun-Yan Hou
- The Medico-technical Division, The General Hospital of PLA, Beijing, China
| | - Kai-Jie Fan
- Department of General Thoracic Surgery, The General Hospital of PLA, Beijing, China
| | - Si-Hao Han
- Harvard T.H.Chan School of Public Health, Boston, Massachusetts
| | - Peng Li
- Department of General Surgery, The General Hospital of PLA, Beijing, China
| | - Shao-Qiong Yi
- Department of General Thoracic Surgery, The General Hospital of PLA, Beijing, China
| | - Yang Liu
- Department of General Thoracic Surgery, The General Hospital of PLA, Beijing, China
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216
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Baek S, Goldstein I, Hager GL. Bivariate Genomic Footprinting Detects Changes in Transcription Factor Activity. Cell Rep 2018; 19:1710-1722. [PMID: 28538187 DOI: 10.1016/j.celrep.2017.05.003] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Revised: 04/04/2017] [Accepted: 04/26/2017] [Indexed: 02/06/2023] Open
Abstract
In response to activating signals, transcription factors (TFs) bind DNA and regulate gene expression. TF binding can be measured by protection of the bound sequence from DNase digestion (i.e., footprint). Here, we report that 80% of TF binding motifs do not show a measurable footprint, partly because of a variable cleavage pattern within the motif sequence. To more faithfully portray the effect of TFs on chromatin, we developed an algorithm that captures two TF-dependent effects on chromatin accessibility: footprinting and motif-flanking accessibility. The algorithm, termed bivariate genomic footprinting (BaGFoot), efficiently detects TF activity. BaGFoot is robust to different accessibility assays (DNase-seq, ATAC-seq), all examined peak-calling programs, and a variety of cut bias correction approaches. BaGFoot reliably predicts TF binding and provides valuable information regarding the TFs affecting chromatin accessibility in various biological systems and following various biological events, including in cases where an absolute footprint cannot be determined.
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Affiliation(s)
- Songjoon Baek
- Lab of Receptor Biology and Gene Expression, The National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Ido Goldstein
- Lab of Receptor Biology and Gene Expression, The National Cancer Institute, NIH, Bethesda, MD 20892, USA.
| | - Gordon L Hager
- Lab of Receptor Biology and Gene Expression, The National Cancer Institute, NIH, Bethesda, MD 20892, USA.
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217
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Wu N, Jia D, Ibrahim AH, Bachurski CJ, Gronostajski RM, MacPherson D. NFIB overexpression cooperates with Rb/p53 deletion to promote small cell lung cancer. Oncotarget 2018; 7:57514-57524. [PMID: 27613844 PMCID: PMC5295369 DOI: 10.18632/oncotarget.11583] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 08/20/2016] [Indexed: 11/25/2022] Open
Abstract
Small cell lung cancer (SCLC) is a highly aggressive neuroendocrine tumor type that is typically metastatic upon diagnosis. We have a poor understanding of the factors that control SCLC progression and metastasis. TheNFIB transcription factor is frequently amplified in mouse models of SCLC, but clear evidence that NFIB promotes SCLC in vivo is lacking. We report that in mouse models, Nfib amplifications are far more frequent in liver metastases over primary SCLC, suggesting roles in tumor progression/metastasis. Overexpression of Nfib in a sensitized mouse model led to acceleration of SCLC, indicating that Nfib functions as a bona fide oncogene. Suppression of Nfib expression in cell lines derived from the doxycycline-inducible Rb/p53/TET-Nfib model led to increased apoptosis and suppression of proliferation. Transcriptional analysis revealed that Nfib regulates the expression of genes related to axon guidance, focal adhesion and extracellular matrix-receptor interactions. These data indicate that Nfib is a potent oncogene in SCLC, and the enrichment of Nfib amplifications in liver metastases over primary SCLC points to Nfib as a candidate driver of SCLC metastasis.
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Affiliation(s)
- Nan Wu
- Divisions of Human Biology and Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Deshui Jia
- Divisions of Human Biology and Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Ali H Ibrahim
- Divisions of Human Biology and Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Cindy J Bachurski
- Division of Pulmonary Biology, Cincinnati Children's Hospital Research Foundation, Cincinnati, OH, USA
| | - Richard M Gronostajski
- Department of Biochemistry, Program in Genetics, Genomics & Bioinformatics, University at Buffalo, Buffalo, NY, USA
| | - David MacPherson
- Divisions of Human Biology and Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Department of Genome Sciences, University of Washington, Seattle, WA, USA
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218
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Gardner EE, Poirier JT, Rudin CM. Histone Code Aberrancies in Small Cell Lung Cancer. J Thorac Oncol 2018; 12:599-601. [PMID: 28343540 DOI: 10.1016/j.jtho.2017.02.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 02/10/2017] [Indexed: 01/12/2023]
Affiliation(s)
- Eric E Gardner
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - John T Poirier
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, New York; Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Charles M Rudin
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, New York; Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York; Weill Cornell Medical College, New York, New York.
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219
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Wu J, Dai W, Wu L, Wang J. SALP, a new single-stranded DNA library preparation method especially useful for the high-throughput characterization of chromatin openness states. BMC Genomics 2018; 19:143. [PMID: 29439663 PMCID: PMC5811972 DOI: 10.1186/s12864-018-4530-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 02/05/2018] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Next-generation sequencing (NGS) is fundamental to the current biological and biomedical research. Construction of sequencing library is a key step of NGS. Therefore, various library construction methods have been explored. However, the current methods are still limited by some shortcomings. RESULTS This study developed a new NGS library construction method, Single strand Adaptor Library Preparation (SALP), by using a novel single strand adaptor (SSA). SSA is a double-stranded oligonucleotide with a 3' overhang of 3 random nucleotides, which can be efficiently ligated to the 3' end of single strand DNA by T4 DNA ligase. SALP can be started with any denatured DNA fragments such as those sheared by Tn5 tagmentation, enzyme digestion and sonication. When started with Tn5-tagmented chromatin, SALP can overcome a key limitation of ATAC-seq and become a high-throughput NGS library construction method, SALP-seq, which can be used to comparatively characterize the chromatin openness state of multiple cells unbiasly. In this way, this study successfully characterized the comparative chromatin openness states of four different cell lines, including GM12878, HepG2, HeLa and 293T, with SALP-seq. Similarly, this study also successfully characterized the chromatin openness states of HepG2 cells with SALP-seq by using 105 to 500 cells. CONCLUSIONS This study developed a new NGS library construction method, SALP, by using a novel kind of single strand adaptor (SSA), which should has wide applications in the future due to its unique performance.
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Affiliation(s)
- Jian Wu
- State Key Laboratory of Bioelectronics, Southeast University, Sipailou 2, Nanjing, 210096, China
| | - Wei Dai
- State Key Laboratory of Bioelectronics, Southeast University, Sipailou 2, Nanjing, 210096, China
| | - Lin Wu
- State Key Laboratory of Bioelectronics, Southeast University, Sipailou 2, Nanjing, 210096, China
| | - Jinke Wang
- State Key Laboratory of Bioelectronics, Southeast University, Sipailou 2, Nanjing, 210096, China.
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220
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Koh AS, Miller EL, Buenrostro JD, Moskowitz DM, Wang J, Greenleaf WJ, Chang HY, Crabtree GR. Rapid chromatin repression by Aire provides precise control of immune tolerance. Nat Immunol 2018; 19:162-172. [PMID: 29335648 PMCID: PMC6049828 DOI: 10.1038/s41590-017-0032-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 12/07/2017] [Indexed: 01/23/2023]
Abstract
Aire mediates the expression of tissue-specific antigens in thymic epithelial cells to promote tolerance against self-reactive T lymphocytes. However, the mechanism that allows expression of tissue-specific genes at levels that prevent harm is unknown. Here we show that Brg1 generates accessibility at tissue-specific loci to impose central tolerance. We found that Aire has an intrinsic repressive function that restricts chromatin accessibility and opposes Brg1 across the genome. Aire exerted this repressive influence within minutes after recruitment to chromatin and restrained the amplitude of active transcription. Disease-causing mutations that impair Aire-induced activation also impair the protein's repressive function, which indicates dual roles for Aire. Together, Brg1 and Aire fine-tune the expression of tissue-specific genes at levels that prevent toxicity yet promote immune tolerance.
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Affiliation(s)
- Andrew S Koh
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
| | - Erik L Miller
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Jason D Buenrostro
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard Society of Fellows, Harvard University, Cambridge, MA, USA
| | - David M Moskowitz
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Jing Wang
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - William J Greenleaf
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Department of Applied Physics, Stanford University, Stanford, CA, USA
- Chan Zuckerburg Biohub, San Francisco, CA, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
| | - Gerald R Crabtree
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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221
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Kim DW, Kim KC, Kim KB, Dunn CT, Park KS. Transcriptional deregulation underlying the pathogenesis of small cell lung cancer. Transl Lung Cancer Res 2018. [PMID: 29535909 DOI: 10.21037/tlcr.2017.10.07] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The discovery of recurrent alterations in genes encoding transcription regulators and chromatin modifiers is one of the most important recent developments in the study of the small cell lung cancer (SCLC) genome. With advances in models and analytical methods, the field of SCLC biology has seen remarkable progress in understanding the deregulated transcription networks linked to the tumor development and malignant progression. This review will discuss recent discoveries on the roles of RB and P53 family of tumor suppressors and MYC family of oncogenes in tumor initiation and development. It will also describe the roles of lineage-specific factors in neuroendocrine (NE) cell differentiation and homeostasis and the roles of epigenetic alterations driven by changes in NFIB and chromatin modifiers in malignant progression and chemoresistance. These recent findings have led to a model of transcriptional network in which multiple pathways converge on regulatory regions of crucial genes linked to tumor development. Validation of this model and characterization of target genes will provide critical insights into the biology of SCLC and novel strategies for tumor intervention.
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Affiliation(s)
- Dong-Wook Kim
- Department of Microbiology, Immunology, and Cancer Biology, The University of Virginia Cancer Center, University of Virginia, Charlottesville, VA, USA
| | - Keun-Cheol Kim
- Department of Microbiology, Immunology, and Cancer Biology, The University of Virginia Cancer Center, University of Virginia, Charlottesville, VA, USA.,Department of Biological Sciences, Kangwon National University, Chuncheon, Korea
| | - Kee-Beom Kim
- Department of Microbiology, Immunology, and Cancer Biology, The University of Virginia Cancer Center, University of Virginia, Charlottesville, VA, USA
| | - Colin T Dunn
- Department of Microbiology, Immunology, and Cancer Biology, The University of Virginia Cancer Center, University of Virginia, Charlottesville, VA, USA
| | - Kwon-Sik Park
- Department of Microbiology, Immunology, and Cancer Biology, The University of Virginia Cancer Center, University of Virginia, Charlottesville, VA, USA
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222
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Zhang W, Girard L, Zhang YA, Haruki T, Papari-Zareei M, Stastny V, Ghayee HK, Pacak K, Oliver TG, Minna JD, Gazdar AF. Small cell lung cancer tumors and preclinical models display heterogeneity of neuroendocrine phenotypes. Transl Lung Cancer Res 2018. [PMID: 29535911 DOI: 10.21037/tlcr.2018.02.02] [Citation(s) in RCA: 154] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Background Small cell lung cancer (SCLC) is a deadly, high grade neuroendocrine (NE) tumor without recognized morphologic heterogeneity. However, over 30 years ago we described a SCLC subtype with "variant" morphology which did not express some NE markers and exhibited more aggressive growth. Methods To quantitate NE properties of SCLCs, we developed a 50-gene expression-based NE score that could be applied to human SCLC tumors and cell lines, and genetically engineered mouse (GEM) models. We identified high and low NE subtypes of SCLC in all of our sample types, and characterized their properties. Results We found that 16% of human SCLC tumors and 10% of SCLC cell lines were of the low NE subtype, as well as cell lines from the GEM model. High NE SCLC lines grew as non-adherent floating aggregates or spheroids while Low NE lines had morphologic features of the variant subtype and grew as loosely attached cells. While the high NE subtype expressed one of the NE lineage master transcription factors ASCL1 or NEUROD1, together with NKX2-1, the entire range of NE markers, and lacked expression of the neuronal and NE repressor REST, the low NE subtype had lost expression of most NE markers, ASCL1, NEUROD1 and NKX2-1 and expressed REST. The low NE subtype had undergone epithelial mesenchymal transition (EMT) and had activated the Notch, Hippo and TGFβ pathways and MYC oncogene . Importantly, the high and low NE group of SCLC lines had similar gene expression profiles as their SCLC tumor counterparts. Conclusions SCLC tumors and cell lines can exhibit distinct inter-tumor heterogeneity with respect to expression of NE features. Loss of NE expression results in major alterations in morphology, growth characteristics, and molecular properties. These findings have major clinical implications as the two subtypes are predicted to have very different responses to targeted therapies.
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Affiliation(s)
- Wei Zhang
- Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, Dallas, TX, USA
| | - Luc Girard
- Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, Dallas, TX, USA.,Department of Pharmacology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Yu-An Zhang
- Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, Dallas, TX, USA
| | - Tomohiro Haruki
- Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, Dallas, TX, USA
| | - Mahboubeh Papari-Zareei
- Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, Dallas, TX, USA
| | - Victor Stastny
- Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, Dallas, TX, USA
| | - Hans K Ghayee
- University of Florida Health and Malcom Randall VA Medical Center, Gainesville, FL, USA
| | - Karel Pacak
- National Institute of Child Health and Human Development, Bethesda, MD, USA
| | - Trudy G Oliver
- Huntsman Cancer Institute at University of Utah, Salk Lake City, UT, USA
| | - John D Minna
- Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, Dallas, TX, USA.,Department of Pharmacology, UT Southwestern Medical Center, Dallas, TX, USA.,Department of Internal Medicine, UT Southwestern Medical Center, Dallas, TX, USA
| | - Adi F Gazdar
- Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, Dallas, TX, USA.,Department of Pathology, UT Southwestern Medical Center, Dallas, TX, USA
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223
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Shue YT, Lim JS, Sage J. Tumor heterogeneity in small cell lung cancer defined and investigated in pre-clinical mouse models. Transl Lung Cancer Res 2018. [PMID: 29535910 DOI: 10.21037/tlcr.2018.01.15] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Small cell lung carcinoma (SCLC) is a fast-growing, highly metastatic form of lung cancer. A major difference between SCLC and other forms of lung cancer is that SCLC tumors often respond well to chemotherapy initially; unfortunately, resistant tumors rapidly recur. In addition, despite a large number of clinical trials with a variety of therapeutic agents, little progress has been achieved in the past three decades in improving the survival of SCLC patients. These clinical observations indicate that SCLC tumors have a high degree of plasticity and rapid adaptability to changes in growth conditions. Here we consider recent evidence pointing to several levels of heterogeneity in SCLC that may explain the ability of these tumors to adjust to different microenvironment and therapeutics. In particular, we review new data pointing to the existence of several subpopulations of tumor cells that interact with each other to promote tumor growth. We also discuss how SCLC tumors that look similar at the histopathological level may actually represent distinct subtypes of tumors and how these differences impact the response to specific therapeutic agents. A better understanding of genetic and cellular heterogeneity will guide the development of personalized approaches to help SCLC patients.
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Affiliation(s)
- Yan Ting Shue
- Department of Pediatrics, Stanford University, Stanford, CA, USA.,Department of Genetics, Stanford University, Stanford, CA, USA
| | - Jing Shan Lim
- Department of Pediatrics, Stanford University, Stanford, CA, USA.,Department of Genetics, Stanford University, Stanford, CA, USA
| | - Julien Sage
- Department of Pediatrics, Stanford University, Stanford, CA, USA.,Department of Genetics, Stanford University, Stanford, CA, USA
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224
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Morrow JJ, Bayles I, Funnell APW, Miller TE, Saiakhova A, Lizardo MM, Bartels CF, Kapteijn MY, Hung S, Mendoza A, Dhillon G, Chee DR, Myers JT, Allen F, Gambarotti M, Righi A, DiFeo A, Rubin BP, Huang AY, Meltzer PS, Helman LJ, Picci P, Versteeg H, Stamatoyannopolus J, Khanna C, Scacheri PC. Positively selected enhancer elements endow osteosarcoma cells with metastatic competence. Nat Med 2018; 24:176-185. [PMID: 29334376 PMCID: PMC5803371 DOI: 10.1038/nm.4475] [Citation(s) in RCA: 105] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 12/18/2017] [Indexed: 12/13/2022]
Abstract
Metastasis results from a complex set of traits acquired by tumor cells, distinct from those necessary for tumorigenesis. Here, we investigate the contribution of enhancer elements to the metastatic phenotype of osteosarcoma. Through epigenomic profiling, we identify substantial differences in enhancer activity between primary and metastatic human tumors and between near isogenic pairs of highly lung metastatic and nonmetastatic osteosarcoma cell lines. We term these regions metastatic variant enhancer loci (Met-VELs). Met-VELs drive coordinated waves of gene expression during metastatic colonization of the lung. Met-VELs cluster nonrandomly in the genome, indicating that activity of these enhancers and expression of their associated gene targets are positively selected. As evidence of this causal association, osteosarcoma lung metastasis is inhibited by global interruptions of Met-VEL-associated gene expression via pharmacologic BET inhibition, by knockdown of AP-1 transcription factors that occupy Met-VELs, and by knockdown or functional inhibition of individual genes activated by Met-VELs, such as that encoding coagulation factor III/tissue factor (F3). We further show that genetic deletion of a single Met-VEL at the F3 locus blocks metastatic cell outgrowth in the lung. These findings indicate that Met-VELs and the genes they regulate play a functional role in metastasis and may be suitable targets for antimetastatic therapies.
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Affiliation(s)
- James J. Morrow
- Department of Pathology, Case Western Reserve University, Cleveland, OH 44106, USA
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Ian Bayles
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44106, USA
| | | | - Tyler E. Miller
- Department of Pathology, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Alina Saiakhova
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Michael M. Lizardo
- Pediatric Oncology Branch, Center for Cancer Research, NCI, NIH, Bethesda, MD, 20892 USA
| | - Cynthia F. Bartels
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Maaike Y. Kapteijn
- Thrombosis and Hemostasis Division, Department of Internal Medicine, LUMC, Leiden, Netherlands
| | - Stevephen Hung
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Arnulfo Mendoza
- Pediatric Oncology Branch, Center for Cancer Research, NCI, NIH, Bethesda, MD, 20892 USA
| | - Gursimran Dhillon
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Daniel R. Chee
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Jay T. Myers
- Department of Pediatrics, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Frederick Allen
- Department of Pathology, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Marco Gambarotti
- Research Laboratory, Istituto Ortopedico Rizzoli, Via Pupilli 1, 40136, Bologna, Italy
| | - Alberto Righi
- Research Laboratory, Istituto Ortopedico Rizzoli, Via Pupilli 1, 40136, Bologna, Italy
| | - Analisa DiFeo
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Brian P. Rubin
- Departments of Anatomic Pathology and Molecular Genetics, Cleveland Clinic, Lerner Research Institute and Taussig Cancer Center, Cleveland, OH 44195, USA
| | - Alex Y. Huang
- Department of Pathology, Case Western Reserve University, Cleveland, OH 44106, USA
- Department of Pediatrics, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Paul S. Meltzer
- Genetics Branch, Center for Cancer Research, NCI, NIH, Bethesda, MD, 20892 USA
| | - Lee J. Helman
- Pediatric Oncology Branch, Center for Cancer Research, NCI, NIH, Bethesda, MD, 20892 USA
| | - Piero Picci
- Research Laboratory, Istituto Ortopedico Rizzoli, Via Pupilli 1, 40136, Bologna, Italy
| | - Henri Versteeg
- Thrombosis and Hemostasis Division, Department of Internal Medicine, LUMC, Leiden, Netherlands
| | | | - Chand Khanna
- Pediatric Oncology Branch, Center for Cancer Research, NCI, NIH, Bethesda, MD, 20892 USA
| | - Peter C. Scacheri
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44106, USA
- Research Laboratory, Istituto Ortopedico Rizzoli, Via Pupilli 1, 40136, Bologna, Italy
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225
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Gazdar AF, Bunn PA, Minna JD. Small-cell lung cancer: what we know, what we need to know and the path forward. Nat Rev Cancer 2017; 17:725-737. [PMID: 29077690 DOI: 10.1038/nrc.2017.87] [Citation(s) in RCA: 433] [Impact Index Per Article: 61.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Small-cell lung cancer (SCLC) is a deadly tumour accounting for approximately 15% of lung cancers and is pathologically, molecularly, biologically and clinically very different from other lung cancers. While the majority of tumours express a neuroendocrine programme (integrating neural and endocrine properties), an important subset of tumours have low or absent expression of this programme. The probable initiating molecular events are inactivation of TP53 and RB1, as well as frequent disruption of several signalling networks, including Notch signalling. SCLC, when diagnosed, is usually widely metastatic and initially responds to cytotoxic therapy but nearly always rapidly relapses with resistance to further therapies. There were no important therapeutic clinical advances for 30 years, leading SCLC to be designated a 'recalcitrant cancer'. Scientific studies are hampered by a lack of tissue availability. However, over the past 5 years, there has been a worldwide resurgence of studies on SCLC, including comprehensive molecular analyses, the development of relevant genetically engineered mouse models and the establishment of patient-derived xenografts. These studies have led to the discovery of new potential therapeutic vulnerabilities for SCLC and therefore to new clinical trials. Thus, while the past has been bleak, the future offers greater promise.
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Affiliation(s)
- Adi F Gazdar
- Hamon Center for Therapeutic Oncology Research, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75230-8593, USA
- Department of Pathology, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75230-8593, USA
| | - Paul A Bunn
- Division of Medical Oncology, University of Colorado Cancer Center, 12801 East 17th Avenue, Aurora, Colorado 80045, USA
| | - John D Minna
- Hamon Center for Therapeutic Oncology Research, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75230-8593, USA
- Departments of Internal Medicine and Pharmacology, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75230-8593, USA
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226
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Wang G, Bi L, Wang G, Huang F, Lu M, Zhu K. Microarray analysis to identify the similarities and differences of pathogenesis between aortic occlusive disease and abdominal aortic aneurysm. Vascular 2017; 26:301-314. [PMID: 29087237 DOI: 10.1177/1708538117736695] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Objectives Expression profile of GSE57691 was analyzed to identify the similarities and differences between aortic occlusive disease and abdominal aortic aneurysm. Methods The expression profile of GSE57691 was downloaded from Gene Expression Omnibus database, including 20 small abdominal aortic aneurysm samples, 29 large abdominal aortic aneurysm samples, 9 aortic occlusive disease samples, and 10 control samples. Using the limma package in R, the differentially expressed genes were screened. Followed by enrichment analysis was performed for the differentially expressed genes using database for annotation, visualization, and integrated discovery online tool. Based on string online tool and Cytoscape software, protein-protein interaction network and module analyses were carried out. Moreover, integrated TF platform database and Cytoscape software were used for constructing transcriptional regulatory networks. Results As a result, 1757, 354, and 396 differentially expressed genes separately were identified in aortic occlusive disease, large abdominal aortic aneurysm, and small abdominal aortic aneurysm samples. UBB was significantly enriched in proteolysis related pathways with a high degree in three groups. SPARCL1 was another gene shared by these groups and regulated by NFIA, which had a high degree in transcriptional regulatory network. ACTB, a significant upregulated gene in abdominal aortic aneurysm samples, could be regulated by CLIC4, which was significantly enriched in cell motions. ACLY and NFIB were separately identified in aortic occlusive disease and small abdominal aortic aneurysm samples, and separately enriched in lipid metabolism and negative regulation of cell proliferation. Conclusions The downregulated UBB, NFIA, and SPARCL1 might play key roles in both aortic occlusive disease and abdominal aortic aneurysm, while the upregulated ACTB might only involve in abdominal aortic aneurysm. ACLY and NFIB were specifically involved in aortic occlusive disease and small abdominal aortic aneurysm separately.
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Affiliation(s)
- Guofu Wang
- Department of Vascular Surgery, Shaoxing Hospital of China Medical University, Shaoxing, China
| | - Lechang Bi
- Department of Vascular Surgery, Shaoxing Hospital of China Medical University, Shaoxing, China
| | - Gaofeng Wang
- Department of Vascular Surgery, Shaoxing Hospital of China Medical University, Shaoxing, China
| | - Feilai Huang
- Department of Vascular Surgery, Shaoxing Hospital of China Medical University, Shaoxing, China
| | - Mingjing Lu
- Department of Vascular Surgery, Shaoxing Hospital of China Medical University, Shaoxing, China
| | - Kai Zhu
- Department of Vascular Surgery, Shaoxing Hospital of China Medical University, Shaoxing, China
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227
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Transcriptional regulation of Nfix by NFIB drives astrocytic maturation within the developing spinal cord. Dev Biol 2017; 432:286-297. [PMID: 29106906 DOI: 10.1016/j.ydbio.2017.10.019] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Revised: 10/23/2017] [Accepted: 10/23/2017] [Indexed: 01/15/2023]
Abstract
During mouse spinal cord development, ventricular zone progenitor cells transition from producing neurons to producing glia at approximately embryonic day 11.5, a process known as the gliogenic switch. The transcription factors Nuclear Factor I (NFI) A and B initiate this developmental transition, but the contribution of a third NFI member, NFIX, remains unknown. Here, we reveal that ventricular zone progenitor cells within the spinal cord express NFIX after the onset of NFIA and NFIB expression, and after the gliogenic switch has occurred. Mice lacking NFIX exhibit normal neurogenesis within the spinal cord, and, while early astrocytic differentiation proceeds normally, aspects of terminal astrocytic differentiation are impaired. Finally, we report that, in the absence of Nfia or Nfib, there is a marked reduction in the spinal cord expression of NFIX, and that NFIB can transcriptionally activate Nfix expression in vitro. These data demonstrate that NFIX is part of the downstream transcriptional program through which NFIA and NFIB coordinate gliogenesis within the spinal cord. This hierarchical organisation of NFI protein expression and function during spinal cord gliogenesis reveals a previously unrecognised auto-regulatory mechanism within this gene family.
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228
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SCENIC: single-cell regulatory network inference and clustering. Nat Methods 2017; 14:1083-1086. [PMID: 28991892 PMCID: PMC5937676 DOI: 10.1038/nmeth.4463] [Citation(s) in RCA: 2600] [Impact Index Per Article: 371.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 09/07/2017] [Indexed: 11/21/2022]
Abstract
Although single-cell RNA-seq is revolutionizing biology, data interpretation remains a challenge. We present SCENIC for the simultaneous reconstruction of gene regulatory networks and identification of cell states. We apply SCENIC to a compendium of single-cell data from tumors and brain, and demonstrate that the genomic regulatory code can be exploited to guide the identification of transcription factors and cell states. SCENIC provides critical biological insights into the mechanisms driving cellular heterogeneity.
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229
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The convergent roles of the nuclear factor I transcription factors in development and cancer. Cancer Lett 2017; 410:124-138. [PMID: 28962832 DOI: 10.1016/j.canlet.2017.09.015] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Revised: 09/11/2017] [Accepted: 09/16/2017] [Indexed: 02/07/2023]
Abstract
The nuclear factor I (NFI) transcription factors play important roles during normal development and have been associated with developmental abnormalities in humans. All four family members, NFIA, NFIB, NFIC and NFIX, have a homologous DNA binding domain and function by regulating cell proliferation and differentiation via the transcriptional control of their target genes. More recently, NFI genes have also been implicated in cancer based on genomic analyses and studies of animal models in a variety of tumours across multiple organ systems. However, the association between their functions in development and in cancer is not well described. In this review, we summarise the evidence suggesting a converging role for the NFI genes in development and cancer. Our review includes all cancer types in which the NFI genes are implicated, focusing predominantly on studies demonstrating their oncogenic or tumour-suppressive potential. We conclude by presenting the challenges impeding our understanding of NFI function in cancer biology, and demonstrate how a developmental perspective may contribute towards overcoming such hurdles.
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230
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Asselin-Labat ML, Rampersad R, Xu X, Ritchie ME, Michalski J, Huang L, Onaitis MW. High-LET Radiation Increases Tumor Progression in a K-Ras-Driven Model of Lung Adenocarcinoma. Radiat Res 2017; 188:562-570. [PMID: 28952911 DOI: 10.1667/rr14794.1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
High-linear energy transfer (LET) radiation encountered by astronauts in space generates clustered DNA damage that is potentially oncogenic. Analysis of the impact of exposure to space radiation on cancer formation is necessary to determine the best ways to prepare astronauts for space travel so they are protected for the duration of the space mission. A mouse model of lung adenocarcinoma driven by oncogenic K-Ras was used to ascertain the effect of low- and high-LET radiation on tumor formation. We observed increased tumor progression and tumor cell proliferation after single dose or fractionated high-LET doses, which was not observed in mice exposed to low-LET radiation. Location of the tumor nodules was not affected by radiation, indicating that the cell of origin of K-Ras-driven tumors was the same in irradiated or nonirradiated mice. Gene expression analysis revealed an upregulation of genes involved in cell proliferation and DNA damage repair. This study provides evidence that exposure to a single dose or fractionated doses of high-LET radiation induces molecular and cellular changes that accelerate lung tumor growth.
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Affiliation(s)
- Marie-Liesse Asselin-Labat
- a University California San Diego, Moores Cancer Center, La Jolla, California.,b ACRF Stem Cells and Cancer Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,d Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
| | - Rishi Rampersad
- f Department of Surgery, Duke University Medical Center, Durham, North Carolina
| | - Xia Xu
- f Department of Surgery, Duke University Medical Center, Durham, North Carolina
| | - Matthew E Ritchie
- c Molecular Medicine Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,e School of Mathematics and Statistics, The University of Melbourne, Parkville, Victoria, Australia
| | - Jacob Michalski
- f Department of Surgery, Duke University Medical Center, Durham, North Carolina
| | - Lingling Huang
- f Department of Surgery, Duke University Medical Center, Durham, North Carolina
| | - Mark W Onaitis
- a University California San Diego, Moores Cancer Center, La Jolla, California.,f Department of Surgery, Duke University Medical Center, Durham, North Carolina
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231
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Varga J, Greten FR. Cell plasticity in epithelial homeostasis and tumorigenesis. Nat Cell Biol 2017; 19:1133-1141. [PMID: 28945230 DOI: 10.1038/ncb3611] [Citation(s) in RCA: 146] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2016] [Accepted: 08/11/2017] [Indexed: 02/06/2023]
Abstract
The adult organism is characterized by remarkable plasticity, which enables efficient regeneration and restoration of homeostasis after damage. When aberrantly activated, this plasticity contributes to tumour initiation and progression. Here we review recent advances in this field with a focus on cell fate changes and the epithelial-mesenchymal transition-two distinct, yet closely related, forms of plasticity with fundamental roles in homeostasis and cancer.
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Affiliation(s)
- Julia Varga
- Institute for Tumor Biology and Experimental Therapy, Georg-Speyer-Haus, Paul-Ehrlich-Str. 42-44, 60596 Frankfurt/Main, Germany
| | - Florian R Greten
- Institute for Tumor Biology and Experimental Therapy, Georg-Speyer-Haus, Paul-Ehrlich-Str. 42-44, 60596 Frankfurt/Main, Germany.,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
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232
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Duruisseaux M, Esteller M. Lung cancer epigenetics: From knowledge to applications. Semin Cancer Biol 2017; 51:116-128. [PMID: 28919484 DOI: 10.1016/j.semcancer.2017.09.005] [Citation(s) in RCA: 183] [Impact Index Per Article: 26.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 09/12/2017] [Accepted: 09/13/2017] [Indexed: 12/17/2022]
Abstract
Lung cancer is the leading cause of cancer-related mortality worldwide. Advances in our understanding of the genomics of lung cancer have led to substantial progress in the treatment of specific molecular subsets. Immunotherapy also emerges as a major breakthrough in lung cancer treatment. However, challenges remain as a consensual approach for early lung cancer detection remains elusive while primary or secondary drug resistance eventually leads to treatment failure in all patients with advanced disease. Furthermore, a large portion of patients are still treated with conventional chemotherapy that is only modestly effective. The last two decades have seen exponential developments in the epigenetic understanding of lung cancer. Epigenetic alterations in DNA methylation, non-coding RNA expression, chromatin modeling and post transcriptional regulators are key events in each step of lung cancer pathogenesis. Here, we review the central role epigenetic disruptions play in lung cancer carcinogenesis and the acquisition of cancerous phenotype and aggressive behavior as well as in the resistance to therapy. Epigenetic disruptions could represent reliable biomarkers for lung cancer risk assessment, early diagnosis, prognosis stratification, molecular classification and prediction of treatment efficacy. The therapeutic potential of epigenetics targeted drugs in combination with chemotherapy, targeted therapy and/or immunotherapy is currently being intensively investigated. We suggest that integration of tissue-derived or circulating epigenetic biomarkers and epidrugs in clinical trial design will translate epigenetic knowledge of lung cancer into the clinic and improve lung cancer patient outcomes.
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Affiliation(s)
- Michaël Duruisseaux
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), 08908 L'Hospitalet de Llobregat, Barcelona, Catalonia, Spain and Centro de Investigación Biomédica en Red de Cáncer (CIBERONC); Department of Respiratory Medecine, Hôpital Louis-Pradel, Hospices civils de Lyon, 28 avenue du Doyen Lépine, 69677, Lyon cedex, France.
| | - Manel Esteller
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), 08908 L'Hospitalet de Llobregat, Barcelona, Catalonia, Spain and Centro de Investigación Biomédica en Red de Cáncer (CIBERONC); Instituciò Catalana de Recerca i Estudis Avançats (ICREA), 08010, Barcelona, Catalonia, Spain; Department of Physiological Sciences II, School of Medicine, University of Barcelona, 08036, Barcelona, Catalonia, Spain.
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233
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Farago AF, Piotrowska Z, Sequist LV. Unlocking the Mystery of Small-Cell Lung Cancer Transformations in EGFR Mutant Adenocarcinoma. J Clin Oncol 2017; 35:2987-2988. [DOI: 10.1200/jco.2017.73.5696] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Anna F. Farago
- Anna F. Farago, Zofia Piotrowska, and Lecia V. Sequist, Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, MA
| | - Zofia Piotrowska
- Anna F. Farago, Zofia Piotrowska, and Lecia V. Sequist, Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, MA
| | - Lecia V. Sequist
- Anna F. Farago, Zofia Piotrowska, and Lecia V. Sequist, Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, MA
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234
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Gianferante DM, Mirabello L, Savage SA. Germline and somatic genetics of osteosarcoma - connecting aetiology, biology and therapy. Nat Rev Endocrinol 2017; 13:480-491. [PMID: 28338660 DOI: 10.1038/nrendo.2017.16] [Citation(s) in RCA: 295] [Impact Index Per Article: 42.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Clinical outcomes and treatment modalities for osteosarcoma, the most common primary cancer of bone, have changed very little over the past 30 years. The peak incidence of osteosarcoma occurs during the adolescent growth spurt, which suggests that bone growth and pubertal hormones are important in the aetiology of the disease. Tall stature, high birth weight and certain inherited cancer predisposition syndromes are well-described risk factors for osteosarcoma. Common genetic variants are also associated with osteosarcoma. The somatic genome of osteosarcoma is highly aneuploid, exhibits extensive intratumoural heterogeneity and has a higher mutation rate than most other paediatric cancers. Complex pathways related to bone growth and development and tumorigenesis are also important in osteosarcoma biology. In this Review, we discuss the contributions of germline and somatic genetics, tumour biology and animal models in improving our understanding of osteosarcoma aetiology, and their potential to identify novel therapeutic targets and thus improve the lives of patients with osteosarcoma.
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Affiliation(s)
- D Matthew Gianferante
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, 9609 Medical Center Drive, Bethesda, Maryland 20892, USA
| | - Lisa Mirabello
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, 9609 Medical Center Drive, Bethesda, Maryland 20892, USA
| | - Sharon A Savage
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, 9609 Medical Center Drive, Bethesda, Maryland 20892, USA
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235
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Roe JS, Hwang CI, Somerville TDD, Milazzo JP, Lee EJ, Da Silva B, Maiorino L, Tiriac H, Young CM, Miyabayashi K, Filippini D, Creighton B, Burkhart RA, Buscaglia JM, Kim EJ, Grem JL, Lazenby AJ, Grunkemeyer JA, Hollingsworth MA, Grandgenett PM, Egeblad M, Park Y, Tuveson DA, Vakoc CR. Enhancer Reprogramming Promotes Pancreatic Cancer Metastasis. Cell 2017; 170:875-888.e20. [PMID: 28757253 DOI: 10.1016/j.cell.2017.07.007] [Citation(s) in RCA: 308] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 05/29/2017] [Accepted: 07/07/2017] [Indexed: 01/01/2023]
Abstract
Pancreatic ductal adenocarcinoma (PDA) is one of the most lethal human malignancies, owing in part to its propensity for metastasis. Here, we used an organoid culture system to investigate how transcription and the enhancer landscape become altered during discrete stages of disease progression in a PDA mouse model. This approach revealed that the metastatic transition is accompanied by massive and recurrent alterations in enhancer activity. We implicate the pioneer factor FOXA1 as a driver of enhancer activation in this system, a mechanism that renders PDA cells more invasive and less anchorage-dependent for growth in vitro, as well as more metastatic in vivo. In this context, FOXA1-dependent enhancer reprogramming activates a transcriptional program of embryonic foregut endoderm. Collectively, our study implicates enhancer reprogramming, FOXA1 upregulation, and a retrograde developmental transition in PDA metastasis.
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Affiliation(s)
- Jae-Seok Roe
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Chang-Il Hwang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA; Lustgarten Foundation Pancreatic Cancer Research Laboratory, Cold Spring Harbor, NY 11724, USA
| | | | - Joseph P Milazzo
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Eun Jung Lee
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA; Lustgarten Foundation Pancreatic Cancer Research Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Brandon Da Silva
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA; Lustgarten Foundation Pancreatic Cancer Research Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Laura Maiorino
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Hervé Tiriac
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA; Lustgarten Foundation Pancreatic Cancer Research Laboratory, Cold Spring Harbor, NY 11724, USA
| | - C Megan Young
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA; Lustgarten Foundation Pancreatic Cancer Research Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Koji Miyabayashi
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA; Lustgarten Foundation Pancreatic Cancer Research Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Dea Filippini
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA; Lustgarten Foundation Pancreatic Cancer Research Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Brianna Creighton
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA; Lustgarten Foundation Pancreatic Cancer Research Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Richard A Burkhart
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, Johns Hopkins Hospital, Baltimore, MD 21287, USA
| | - Jonathan M Buscaglia
- Division of Gastroenterology & Hepatology, Stony Brook University School of Medicine, Stony Brook, NY 11790, USA
| | - Edward J Kim
- Division of Hematology/Oncology, UC Davis Medical Center, Sacramento, CA 95817, USA
| | - Jean L Grem
- Department of Medicine, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Audrey J Lazenby
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - James A Grunkemeyer
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Michael A Hollingsworth
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Paul M Grandgenett
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Mikala Egeblad
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Youngkyu Park
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA; Lustgarten Foundation Pancreatic Cancer Research Laboratory, Cold Spring Harbor, NY 11724, USA
| | - David A Tuveson
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA; Lustgarten Foundation Pancreatic Cancer Research Laboratory, Cold Spring Harbor, NY 11724, USA.
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236
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Funata S, Matsusaka K, Yamanaka R, Yamamoto S, Okabe A, Fukuyo M, Aburatani H, Fukayama M, Kaneda A. Histone modification alteration coordinated with acquisition of promoter DNA methylation during Epstein-Barr virus infection. Oncotarget 2017; 8:55265-55279. [PMID: 28903418 PMCID: PMC5589657 DOI: 10.18632/oncotarget.19423] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 07/11/2017] [Indexed: 12/23/2022] Open
Abstract
Aberrant DNA hypermethylation is a major epigenetic mechanism to inactivate tumor suppressor genes in cancer. Epstein-Barr virus positive gastric cancer is the most frequently hypermethylated tumor among human malignancies. Herein, we performed comprehensive analysis of epigenomic alteration during EBV infection, by Infinium HumanMethylation 450K BeadChip for DNA methylation and ChIP-sequencing for histone modification alteration during EBV infection into gastric cancer cell line MKN7. Among 7,775 genes with increased DNA methylation in promoter regions, roughly half were “DNA methylation-sensitive” genes, which acquired DNA methylation in the whole promoter regions and thus were repressed. These included anti-oncogenic genes, e.g. CDKN2A. The other half were “DNA methylation-resistant” genes, where DNA methylation is acquired in the surrounding of promoter regions, but unmethylated status is protected in the vicinity of transcription start site. These genes thereby retained gene expression, and included DNA repair genes. Histone modification was altered dynamically and coordinately with DNA methylation alteration. DNA methylation-sensitive genes significantly correlated with loss of H3K27me3 pre-marks or decrease of active histone marks, H3K4me3 and H3K27ac. Apoptosis-related genes were significantly enriched in these epigenetically repressed genes. Gain of active histone marks significantly correlated with DNA methylation-resistant genes. Genes related to mitotic cell cycle and DNA repair were significantly enriched in these epigenetically activated genes. Our data show that orchestrated epigenetic alterations are important in gene regulation during EBV infection, and histone modification status in promoter regions significantly associated with acquisition of de novo DNA methylation or protection of unmethylated status at transcription start site.
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Affiliation(s)
- Sayaka Funata
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan.,Department of Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Keisuke Matsusaka
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Ryota Yamanaka
- Genome Science Division, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Shogo Yamamoto
- Genome Science Division, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Atsushi Okabe
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Masaki Fukuyo
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Hiroyuki Aburatani
- Genome Science Division, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Masashi Fukayama
- Department of Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Atsushi Kaneda
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
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237
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Vakoc CR, Tuveson DA. Untangling the genetics from the epigenetics in pancreatic cancer metastasis. Nat Genet 2017; 49:323-324. [PMID: 28232730 DOI: 10.1038/ng.3798] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Comparative genomic analyses of primary tumors and metastases within individuals with pancreatic cancer have exposed the complex clonal dynamics that underlie the dissemination of cancer cells to distant sites. Recent studies implicate non-genetic mechanisms in this process, particularly fluctuations in chromatin states and metabolism, which can endow rare cells within a primary tumor with metastatic potential.
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Affiliation(s)
| | - David A Tuveson
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
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238
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Qu K, Zaba LC, Satpathy AT, Giresi PG, Li R, Jin Y, Armstrong R, Jin C, Schmitt N, Rahbar Z, Ueno H, Greenleaf WJ, Kim YH, Chang HY. Chromatin Accessibility Landscape of Cutaneous T Cell Lymphoma and Dynamic Response to HDAC Inhibitors. Cancer Cell 2017; 32. [PMID: 28625481 PMCID: PMC5559384 DOI: 10.1016/j.ccell.2017.05.008] [Citation(s) in RCA: 109] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Here, we define the landscape and dynamics of active regulatory DNA in cutaneous T cell lymphoma (CTCL) by ATAC-seq. Analysis of 111 human CTCL and control samples revealed extensive chromatin signatures that distinguished leukemic, host, and normal CD4+ T cells. We identify three dominant patterns of transcription factor (TF) activation that drive leukemia regulomes, as well as TF deactivations that alter host T cells in CTCL patients. Clinical response to histone deacetylase inhibitors (HDACi) is strongly associated with a concurrent gain in chromatin accessibility. HDACi causes distinct chromatin responses in leukemic and host CD4+ T cells, reprogramming host T cells toward normalcy. These results provide a foundational framework to study personal regulomes in human cancer and epigenetic therapy.
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Affiliation(s)
- Kun Qu
- CAS Key Laboratory of Innate Immunity and Chronic Diseases, School of Life Sciences and Medical Center, University of Science and Technology of China, Hefei 230027, China; Center for Personal Dynamic Regulomes and Program in Epithelial Biology, Stanford University School of Medicine, CCSR 2155c, 269 Campus Drive, Stanford, CA 94305-5168, USA
| | - Lisa C Zaba
- Center for Personal Dynamic Regulomes and Program in Epithelial Biology, Stanford University School of Medicine, CCSR 2155c, 269 Campus Drive, Stanford, CA 94305-5168, USA; Department of Dermatology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ansuman T Satpathy
- Center for Personal Dynamic Regulomes and Program in Epithelial Biology, Stanford University School of Medicine, CCSR 2155c, 269 Campus Drive, Stanford, CA 94305-5168, USA; Department of Dermatology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | | | - Rui Li
- Center for Personal Dynamic Regulomes and Program in Epithelial Biology, Stanford University School of Medicine, CCSR 2155c, 269 Campus Drive, Stanford, CA 94305-5168, USA
| | - Yonghao Jin
- CAS Key Laboratory of Innate Immunity and Chronic Diseases, School of Life Sciences and Medical Center, University of Science and Technology of China, Hefei 230027, China
| | - Randall Armstrong
- Stanford Blood and Marrow Transplantation Cellular Therapy Facility, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Chen Jin
- CAS Key Laboratory of Innate Immunity and Chronic Diseases, School of Life Sciences and Medical Center, University of Science and Technology of China, Hefei 230027, China
| | | | - Ziba Rahbar
- Department of Dermatology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Hideki Ueno
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - William J Greenleaf
- Center for Personal Dynamic Regulomes and Program in Epithelial Biology, Stanford University School of Medicine, CCSR 2155c, 269 Campus Drive, Stanford, CA 94305-5168, USA; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Youn H Kim
- Department of Dermatology, Stanford University School of Medicine, Stanford, CA 94305, USA.
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes and Program in Epithelial Biology, Stanford University School of Medicine, CCSR 2155c, 269 Campus Drive, Stanford, CA 94305-5168, USA; Department of Dermatology, Stanford University School of Medicine, Stanford, CA 94305, USA.
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239
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Becker-Santos DD, Lonergan KM, Gronostajski RM, Lam WL. Nuclear Factor I/B: A Master Regulator of Cell Differentiation with Paradoxical Roles in Cancer. EBioMedicine 2017; 22:2-9. [PMID: 28596133 PMCID: PMC5552107 DOI: 10.1016/j.ebiom.2017.05.027] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2017] [Revised: 05/19/2017] [Accepted: 05/23/2017] [Indexed: 11/16/2022] Open
Abstract
Emerging evidence indicates that nuclear factor I/B (NFIB), a transcription factor required for proper development and regulation of cellular differentiation in several tissues, also plays critical roles in cancer. Despite being a metastatic driver in small cell lung cancer and melanoma, it has become apparent that NFIB also exhibits tumour suppressive functions in many malignancies. The contradictory contributions of NFIB to both the inhibition and promotion of tumour development and progression, corroborates its diverse and context-dependent roles in many tissues and cell types. Considering the frequent involvement of NFIB in cancer, a better understanding of its multifaceted nature may ultimately benefit the development of novel strategies for the management of a broad spectrum of malignancies. Here we discuss recent findings which bring to light NFIB as a crucial and paradoxical player in cancer. NFIB, a versatile regulator of cell differentiation, is emerging as a crucial driver of cancer metastasis. Paradoxically, NFIB also exhibits tumour suppressive functions in several cancer types. A deeper understanding of the multifaceted and context-dependent nature of NFIB has the potential to improve the clinical management of a variety of cancers.
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Affiliation(s)
- Daiana D Becker-Santos
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, BC, Canada; Interdisciplinary Oncology Program, University of British Columbia, Vancouver, BC, Canada.
| | - Kim M Lonergan
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, BC, Canada
| | - Richard M Gronostajski
- Department of Biochemistry, Program in Genetics, Genomics and Bioinformatics, Center of Excellence in Bioinformatics and Life Sciences, State University of New York at Buffalo, Buffalo, NY, USA
| | - Wan L Lam
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, BC, Canada; Interdisciplinary Oncology Program, University of British Columbia, Vancouver, BC, Canada
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240
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Lim JS, Ibaseta A, Fischer MM, Cancilla B, O'Young G, Cristea S, Luca VC, Yang D, Jahchan NS, Hamard C, Antoine M, Wislez M, Kong C, Cain J, Liu YW, Kapoun AM, Garcia KC, Hoey T, Murriel CL, Sage J. Intratumoural heterogeneity generated by Notch signalling promotes small-cell lung cancer. Nature 2017; 545:360-364. [PMID: 28489825 PMCID: PMC5776014 DOI: 10.1038/nature22323] [Citation(s) in RCA: 283] [Impact Index Per Article: 40.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 03/30/2017] [Indexed: 12/14/2022]
Abstract
The Notch signaling pathway mediates cell fate decisions1,2 and is tumor suppressive or oncogenic depending on the context2,3. During lung development, Notch pathway activation inhibits the differentiation of precursor cells to a neuroendocrine (NE) fate4–6. In small cell lung cancer (SCLC), an aggressive NE lung cancer7, loss-of-function NOTCH mutations and the inhibitory effects of ectopic Notch activation indicate that Notch signaling is tumor suppressive8,9. Here, we show that Notch signaling can be both tumor suppressive and pro-tumorigenic in SCLC. Endogenous activation of the Notch pathway results in a NE to non-NE fate switch in 10-50% of tumor cells in a mouse model of SCLC and in human tumors. This switch is mediated in part by Rest/Nrsf, a transcriptional repressor that inhibits NE gene expression. Non-NE Notch-active SCLC cells are slow growing, consistent with a tumor suppressive role for Notch, but these cells are also relatively chemoresistant and provide trophic support to NE tumor cells, consistent with a pro-tumorigenic role. Importantly, Notch blockade in combination with chemotherapy suppresses tumor growth and delays relapse. Thus, SCLC tumors generate their own microenvironment via activation of Notch signaling in a subset of tumor cells, and the presence of these cells may serve as a biomarker for the use of Notch pathway inhibitors in combination with chemotherapy in select SCLC patients.
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Affiliation(s)
- Jing Shan Lim
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California 94305, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Alvaro Ibaseta
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California 94305, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Marcus M Fischer
- OncoMed Pharmaceuticals, Inc., Redwood City, California 94063, USA
| | - Belinda Cancilla
- OncoMed Pharmaceuticals, Inc., Redwood City, California 94063, USA
| | - Gilbert O'Young
- OncoMed Pharmaceuticals, Inc., Redwood City, California 94063, USA
| | - Sandra Cristea
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California 94305, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Vincent C Luca
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, California 94305, USA.,Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305, USA.,Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Dian Yang
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California 94305, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Nadine S Jahchan
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California 94305, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Cécile Hamard
- Sorbonne Universités, UPMC Univ Paris 06, GRC n°04, Theranoscan, F-75252, Paris, France.,AP-HP, Hôpital Tenon, Service de Pneumologie, F-75970, Paris, France
| | - Martine Antoine
- Sorbonne Universités, UPMC Univ Paris 06, GRC n°04, Theranoscan, F-75252, Paris, France.,AP-HP, Hôpital Tenon, Service de Pneumologie, F-75970, Paris, France
| | - Marie Wislez
- Sorbonne Universités, UPMC Univ Paris 06, GRC n°04, Theranoscan, F-75252, Paris, France.,AP-HP, Hôpital Tenon, Service de Pneumologie, F-75970, Paris, France
| | - Christina Kong
- Department of Pathology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Jennifer Cain
- OncoMed Pharmaceuticals, Inc., Redwood City, California 94063, USA
| | - Yu-Wang Liu
- OncoMed Pharmaceuticals, Inc., Redwood City, California 94063, USA
| | - Ann M Kapoun
- OncoMed Pharmaceuticals, Inc., Redwood City, California 94063, USA
| | - K Christopher Garcia
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, California 94305, USA.,Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305, USA.,Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Timothy Hoey
- OncoMed Pharmaceuticals, Inc., Redwood City, California 94063, USA
| | | | - Julien Sage
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California 94305, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
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241
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Chuang CH, Greenside PG, Rogers ZN, Brady JJ, Yang D, Ma RK, Caswell DR, Chiou SH, Winters AF, Grüner BM, Ramaswami G, Spencley AL, Kopecky KE, Sayles LC, Sweet-Cordero EA, Li JB, Kundaje A, Winslow MM. Molecular definition of a metastatic lung cancer state reveals a targetable CD109-Janus kinase-Stat axis. Nat Med 2017; 23:291-300. [PMID: 28191885 DOI: 10.1038/nm.4285] [Citation(s) in RCA: 105] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 01/18/2017] [Indexed: 12/14/2022]
Abstract
Lung cancer is the leading cause of cancer deaths worldwide, with the majority of mortality resulting from metastatic spread. However, the molecular mechanism by which cancer cells acquire the ability to disseminate from primary tumors, seed distant organs, and grow into tissue-destructive metastases remains incompletely understood. We combined tumor barcoding in a mouse model of human lung adenocarcinoma with unbiased genomic approaches to identify a transcriptional program that confers metastatic ability and predicts patient survival. Small-scale in vivo screening identified several genes, including Cd109, that encode novel pro-metastatic factors. We uncovered signaling mediated by Janus kinases (Jaks) and the transcription factor Stat3 as a critical, pharmacologically targetable effector of CD109-driven lung cancer metastasis. In summary, by coupling the systematic genomic analysis of purified cancer cells in distinct malignant states from mouse models with extensive human validation, we uncovered several key regulators of metastatic ability, including an actionable pro-metastatic CD109-Jak-Stat3 axis.
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Affiliation(s)
- Chen-Hua Chuang
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Peyton G Greenside
- Biomedical Informatics Training Program, Stanford University School of Medicine, Stanford, California, USA
| | - Zoë N Rogers
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Jennifer J Brady
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Dian Yang
- Cancer Biology Program, Stanford University School of Medicine, Stanford, California, USA
| | - Rosanna K Ma
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Deborah R Caswell
- Cancer Biology Program, Stanford University School of Medicine, Stanford, California, USA
| | - Shin-Heng Chiou
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Aidan F Winters
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Barbara M Grüner
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Gokul Ramaswami
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Andrew L Spencley
- Cancer Biology Program, Stanford University School of Medicine, Stanford, California, USA
| | - Kimberly E Kopecky
- Department of Surgery, Stanford University School of Medicine, Stanford, California, USA
| | - Leanne C Sayles
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California, USA
| | - E Alejandro Sweet-Cordero
- Cancer Biology Program, Stanford University School of Medicine, Stanford, California, USA.,Department of Pediatrics, Stanford University School of Medicine, Stanford, California, USA
| | - Jin Billy Li
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Anshul Kundaje
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA.,Department of Computer Science, Stanford University, Stanford, California, USA
| | - Monte M Winslow
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA.,Cancer Biology Program, Stanford University School of Medicine, Stanford, California, USA.,Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
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242
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Mollaoglu G, Guthrie MR, Böhm S, Brägelmann J, Can I, Ballieu PM, Marx A, George J, Heinen C, Chalishazar MD, Cheng H, Ireland AS, Denning KE, Mukhopadhyay A, Vahrenkamp JM, Berrett KC, Mosbruger TL, Wang J, Kohan JL, Salama ME, Witt BL, Peifer M, Thomas RK, Gertz J, Johnson JE, Gazdar AF, Wechsler-Reya RJ, Sos ML, Oliver TG. MYC Drives Progression of Small Cell Lung Cancer to a Variant Neuroendocrine Subtype with Vulnerability to Aurora Kinase Inhibition. Cancer Cell 2017; 31:270-285. [PMID: 28089889 PMCID: PMC5310991 DOI: 10.1016/j.ccell.2016.12.005] [Citation(s) in RCA: 380] [Impact Index Per Article: 54.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 09/15/2016] [Accepted: 12/13/2016] [Indexed: 01/19/2023]
Abstract
Loss of the tumor suppressors RB1 and TP53 and MYC amplification are frequent oncogenic events in small cell lung cancer (SCLC). We show that Myc expression cooperates with Rb1 and Trp53 loss in the mouse lung to promote aggressive, highly metastatic tumors, that are initially sensitive to chemotherapy followed by relapse, similar to human SCLC. Importantly, MYC drives a neuroendocrine-low "variant" subset of SCLC with high NEUROD1 expression corresponding to transcriptional profiles of human SCLC. Targeted drug screening reveals that SCLC with high MYC expression is vulnerable to Aurora kinase inhibition, which, combined with chemotherapy, strongly suppresses tumor progression and increases survival. These data identify molecular features for patient stratification and uncover a potential targeted treatment approach for MYC-driven SCLC.
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Affiliation(s)
- Gurkan Mollaoglu
- Department of Oncological Sciences, University of Utah, Huntsman Cancer Institute, Salt Lake City, UT 84112, USA
| | - Matthew R Guthrie
- Department of Oncological Sciences, University of Utah, Huntsman Cancer Institute, Salt Lake City, UT 84112, USA
| | - Stefanie Böhm
- Molecular Pathology, Institute for Pathology, Medical Faculty, University of Cologne, 50937 Cologne, Germany; Department of Translational Genomics, Center of Integrated Oncology Cologne-Bonn, Medical Faculty, University of Cologne, 50931 Cologne, Germany
| | - Johannes Brägelmann
- Molecular Pathology, Institute for Pathology, Medical Faculty, University of Cologne, 50937 Cologne, Germany; Department of Translational Genomics, Center of Integrated Oncology Cologne-Bonn, Medical Faculty, University of Cologne, 50931 Cologne, Germany
| | - Ismail Can
- Department of Oncological Sciences, University of Utah, Huntsman Cancer Institute, Salt Lake City, UT 84112, USA
| | - Paul M Ballieu
- Department of Oncological Sciences, University of Utah, Huntsman Cancer Institute, Salt Lake City, UT 84112, USA
| | - Annika Marx
- Molecular Pathology, Institute for Pathology, Medical Faculty, University of Cologne, 50937 Cologne, Germany; Department of Translational Genomics, Center of Integrated Oncology Cologne-Bonn, Medical Faculty, University of Cologne, 50931 Cologne, Germany
| | - Julie George
- Department of Translational Genomics, Center of Integrated Oncology Cologne-Bonn, Medical Faculty, University of Cologne, 50931 Cologne, Germany
| | - Christine Heinen
- Department of Translational Genomics, Center of Integrated Oncology Cologne-Bonn, Medical Faculty, University of Cologne, 50931 Cologne, Germany
| | - Milind D Chalishazar
- Department of Oncological Sciences, University of Utah, Huntsman Cancer Institute, Salt Lake City, UT 84112, USA
| | - Haixia Cheng
- Department of Oncological Sciences, University of Utah, Huntsman Cancer Institute, Salt Lake City, UT 84112, USA
| | - Abbie S Ireland
- Department of Oncological Sciences, University of Utah, Huntsman Cancer Institute, Salt Lake City, UT 84112, USA
| | - Kendall E Denning
- Department of Oncological Sciences, University of Utah, Huntsman Cancer Institute, Salt Lake City, UT 84112, USA
| | - Anandaroop Mukhopadhyay
- Department of Oncological Sciences, University of Utah, Huntsman Cancer Institute, Salt Lake City, UT 84112, USA
| | - Jeffery M Vahrenkamp
- Department of Oncological Sciences, University of Utah, Huntsman Cancer Institute, Salt Lake City, UT 84112, USA
| | - Kristofer C Berrett
- Department of Oncological Sciences, University of Utah, Huntsman Cancer Institute, Salt Lake City, UT 84112, USA
| | - Timothy L Mosbruger
- Huntsman Cancer Institute, Bioinformatics Shared Resource, Salt Lake City, UT 84112, USA
| | - Jun Wang
- Tumor Initiation and Maintenance Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Jessica L Kohan
- Department of Pathology, University of Utah and ARUP Laboratories, Salt Lake City, UT 84112, USA
| | - Mohamed E Salama
- Department of Pathology, University of Utah and ARUP Laboratories, Salt Lake City, UT 84112, USA
| | - Benjamin L Witt
- Department of Pathology, University of Utah and ARUP Laboratories, Salt Lake City, UT 84112, USA
| | - Martin Peifer
- Department of Translational Genomics, Center of Integrated Oncology Cologne-Bonn, Medical Faculty, University of Cologne, 50931 Cologne, Germany; Center for Molecular Medicine Cologne, University of Cologne, 50931 Cologne, Germany
| | - Roman K Thomas
- Department of Translational Genomics, Center of Integrated Oncology Cologne-Bonn, Medical Faculty, University of Cologne, 50931 Cologne, Germany; Department of Pathology, University Hospital Cologne, 50937 Cologne, Germany; German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Jason Gertz
- Department of Oncological Sciences, University of Utah, Huntsman Cancer Institute, Salt Lake City, UT 84112, USA
| | - Jane E Johnson
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Adi F Gazdar
- Department of Pathology, Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, Dallas, TX 75235, USA
| | - Robert J Wechsler-Reya
- Tumor Initiation and Maintenance Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Martin L Sos
- Molecular Pathology, Institute for Pathology, Medical Faculty, University of Cologne, 50937 Cologne, Germany; Department of Translational Genomics, Center of Integrated Oncology Cologne-Bonn, Medical Faculty, University of Cologne, 50931 Cologne, Germany.
| | - Trudy G Oliver
- Department of Oncological Sciences, University of Utah, Huntsman Cancer Institute, Salt Lake City, UT 84112, USA.
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243
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Abstract
Metastases account for the great majority of cancer-associated deaths, yet this complex process remains the least understood aspect of cancer biology. As the body of research concerning metastasis continues to grow at a rapid rate, the biological programs that underlie the dissemination and metastatic outgrowth of cancer cells are beginning to come into view. In this review we summarize the cellular and molecular mechanisms involved in metastasis, with a focus on carcinomas where the most is known, and we highlight the general principles of metastasis that have begun to emerge.
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Affiliation(s)
- Arthur W Lambert
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA
| | - Diwakar R Pattabiraman
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA
| | - Robert A Weinberg
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology and the MIT Ludwig Center for Molecular Oncology, Cambridge, MA 02142, USA.
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244
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Fane M, Harris L, Smith AG, Piper M. Nuclear factor one transcription factors as epigenetic regulators in cancer. Int J Cancer 2017; 140:2634-2641. [PMID: 28076901 DOI: 10.1002/ijc.30603] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 12/12/2016] [Accepted: 12/29/2016] [Indexed: 12/23/2022]
Abstract
Tumour heterogeneity poses a distinct obstacle to therapeutic intervention. While the initiation of tumours across various physiological systems is frequently associated with signature mutations in genes that drive proliferation and bypass senescence, increasing evidence suggests that tumour progression and clonal diversity is driven at an epigenetic level. The tumour microenvironment plays a key role in driving diversity as cells adapt to demands imposed during tumour growth, and is thought to drive certain subpopulations back to a stem cell-like state. This stem cell-like phenotype primes tumour cells to react to external cues via the use of developmental pathways that facilitate changes in proliferation, migration and invasion. Because the dynamism of this stem cell-like state requires constant chromatin remodelling and rapid alterations at regulatory elements, it is of great therapeutic interest to identify the cell-intrinsic factors that confer these epigenetic changes that drive tumour progression. The nuclear factor one (NFI) family are transcription factors that play an important role in the development of many mammalian organ systems. While all four family members have been shown to act as either oncogenes or tumour suppressors across various cancer models, evidence has emerged implicating them as key epigenetic regulators during development and within tumours. Notably, NFIs have also been shown to regulate chromatin accessibility at distal regulatory elements that drive tumour cell dissemination and metastasis. Here we summarize the role of the NFIs in cancer, focusing largely on the potential mechanisms associated with chromatin remodelling and epigenetic modulation of gene expression.
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Affiliation(s)
- Mitchell Fane
- The School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, Australia.,School of Biomedical Sciences, Institute of Health and Biomedical Innovation at the Translational Research Institute, Queensland University of Technology, Woolloongabba, QLD, Australia
| | - Lachlan Harris
- The School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Aaron G Smith
- School of Biomedical Sciences, Institute of Health and Biomedical Innovation at the Translational Research Institute, Queensland University of Technology, Woolloongabba, QLD, Australia.,Dermatology Research Centre, The University of Queensland, School of Medicine, Translational Research Institute, Brisbane, QLD, Australia
| | - Michael Piper
- The School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, Australia
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Moskowitz DM, Zhang DW, Hu B, Le Saux S, Yanes RE, Ye Z, Buenrostro JD, Weyand CM, Greenleaf WJ, Goronzy JJ. Epigenomics of human CD8 T cell differentiation and aging. Sci Immunol 2017; 2:eaag0192. [PMID: 28439570 PMCID: PMC5399889 DOI: 10.1126/sciimmunol.aag0192] [Citation(s) in RCA: 151] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The efficacy of the adaptive immune response declines dramatically with age, but the cell-intrinsic mechanisms driving immune aging in humans remain poorly understood. Immune aging is characterized by a loss of self-renewing naïve cells and the accumulation of differentiated but dysfunctional cells within the CD8 T cell compartment. Using ATAC-seq, we inferred the transcription factor binding activities correlated with naive and central and effector memory CD8 T cell states in young adults. Integrating our results with RNA-seq, we identified transcription networks associated with CD8 T cell differentiation, with prominent roles implicated for BATF, ETS1, Eomes, and Sp1. Extending our analysis to aged humans, we found that the differences between the memory and naive subsets were largely preserved across age, but that naive and central memory cells from older individuals exhibited a shift toward more differentiated patterns of chromatin openness. Additionally, aged naive cells displayed a loss in chromatin accessibility at gene promoters, largely associated with a decrease in NRF1 binding. This shift was implicated in a marked drop-off in the ability of the aged naive cells to transcribe respiratory chain genes, which may explain the reduced capacity of oxidative phosphorylation in older naïve cells. Our findings identify BATF- and NRF1-driven gene regulation as potential targets for delaying CD8 T cell aging and restoring function.
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Affiliation(s)
- David M Moskowitz
- Department of Genetics, Stanford University School of Medicine, Stanford, California
- Biomedical Informatics Training Program, Stanford University School of Medicine, Stanford, California
| | - David W Zhang
- Department of Genetics, Stanford University School of Medicine, Stanford, California
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University, Stanford, CA 94305; and Department of Medicine, Veterans Affairs Palo Alto Health Care, System, Palo Alto, CA 94306
| | - Bin Hu
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University, Stanford, CA 94305; and Department of Medicine, Veterans Affairs Palo Alto Health Care, System, Palo Alto, CA 94306
| | - Sabine Le Saux
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University, Stanford, CA 94305; and Department of Medicine, Veterans Affairs Palo Alto Health Care, System, Palo Alto, CA 94306
| | - Rolando E Yanes
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University, Stanford, CA 94305; and Department of Medicine, Veterans Affairs Palo Alto Health Care, System, Palo Alto, CA 94306
| | - Zhongde Ye
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University, Stanford, CA 94305; and Department of Medicine, Veterans Affairs Palo Alto Health Care, System, Palo Alto, CA 94306
| | - Jason D Buenrostro
- Department of Genetics, Stanford University School of Medicine, Stanford, California
- Program in Epithelial Biology and the Howard Hughes Medical Institute, Stanford University, School of Medicine, Stanford, California
| | - Cornelia M Weyand
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University, Stanford, CA 94305; and Department of Medicine, Veterans Affairs Palo Alto Health Care, System, Palo Alto, CA 94306
| | - William J Greenleaf
- Department of Genetics, Stanford University School of Medicine, Stanford, California
| | - Jörg J Goronzy
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University, Stanford, CA 94305; and Department of Medicine, Veterans Affairs Palo Alto Health Care, System, Palo Alto, CA 94306
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246
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Wouters J, Kalender Atak Z, Aerts S. Decoding transcriptional states in cancer. Curr Opin Genet Dev 2017; 43:82-92. [PMID: 28129557 DOI: 10.1016/j.gde.2017.01.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 01/05/2017] [Accepted: 01/09/2017] [Indexed: 12/27/2022]
Abstract
Gene regulatory networks determine cellular identity. In cancer, aberrations of gene networks are caused by driver mutations that often affect transcription factors and chromatin modifiers. Nevertheless, gene transcription in cancer follows the same cis-regulatory rules as normal cells, and cancer cells have served as convenient model systems to study transcriptional regulation. Tumours often show regulatory heterogeneity, with subpopulations of cells in different transcriptional states, which has important therapeutic implications. Here, we review recent experimental and computational techniques to reverse engineer cancer gene networks using transcriptome and epigenome data. New algorithms, data integration strategies, and increasing amounts of single cell genomics data provide exciting opportunities to model dynamic regulatory states at unprecedented resolution.
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Affiliation(s)
- Jasper Wouters
- Laboratory of Computational Biology, VIB Center for Brain & Disease Research, Leuven, Belgium; Department of Human Genetics, KU Leuven (University of Leuven), Leuven, Belgium
| | - Zeynep Kalender Atak
- Laboratory of Computational Biology, VIB Center for Brain & Disease Research, Leuven, Belgium; Department of Human Genetics, KU Leuven (University of Leuven), Leuven, Belgium
| | - Stein Aerts
- Laboratory of Computational Biology, VIB Center for Brain & Disease Research, Leuven, Belgium; Department of Human Genetics, KU Leuven (University of Leuven), Leuven, Belgium.
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247
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NFIB Mediates BRN2 Driven Melanoma Cell Migration and Invasion Through Regulation of EZH2 and MITF. EBioMedicine 2017; 16:63-75. [PMID: 28119061 PMCID: PMC5474438 DOI: 10.1016/j.ebiom.2017.01.013] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Revised: 12/23/2016] [Accepted: 01/09/2017] [Indexed: 11/21/2022] Open
Abstract
While invasion and metastasis of tumour cells are the principle factor responsible for cancer related deaths, the mechanisms governing the process remain poorly defined. Moreover, phenotypic divergence of sub-populations of tumour cells is known to underpin alternative behaviors linked to tumour progression such as proliferation, survival and invasion. In the context of melanoma, heterogeneity between two transcription factors, BRN2 and MITF, has been associated with phenotypic switching between predominantly invasive and proliferative behaviors respectively. Epigenetic changes, in response to external cues, have been proposed to underpin this process, however the mechanism by which the phenotypic switch occurs is unclear. Here we report the identification of the NFIB transcription factor as a novel downstream effector of BRN2 function in melanoma cells linked to the migratory and invasive characteristics of these cells. Furthermore, the function of NFIB appears to drive an invasive phenotype through an epigenetic mechanism achieved via the upregulation of the polycomb group protein EZH2. A notable target of NFIB mediated up-regulation of EZH2 is decreased MITF expression, which further promotes a less proliferative, more invasive phenotype. Together our data reveal that NFIB has the ability to promote dynamic changes in the chromatin state of melanoma cells to facilitate migration, invasion and metastasis. NFIB mediates a slow cycling, highly invasive/migratory melanoma cell phenotype downstream of BRN2. NFIB increases EZH2 expression downstream of BRN2, which further decreases MITF levels. NFIB expression is defined by an invasive gene signature and colocalises with BRN2 in primary and metastatic human melanoma tumours.
Melanoma is a heterogeneous cancer, made up of many cellular populations that differ in their ability to induce tumour growth or invasion throughout the body (metastasis). These populations have been found to switch back and forth to drive invasion and progression. This process appears to be controlled by an inverse axis between two genes, MITF and BRN2. BRN2 drives metastatic spread, but the process by which it acts is not well characterized and cannot be targeted clinically. This study has uncovered a role for the gene NFIB in driving invasion downstream of BRN2. Importantly, it appears to drive this process through EZH2, which can be targeted therapeutically to reduce metastasis.
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248
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Patel SA, Vanharanta S. Epigenetic determinants of metastasis. Mol Oncol 2017; 11:79-96. [PMID: 27756687 PMCID: PMC5423227 DOI: 10.1016/j.molonc.2016.09.008] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 09/12/2016] [Accepted: 09/30/2016] [Indexed: 02/06/2023] Open
Abstract
Genetic analyses of cancer progression in patient samples and model systems have thus far failed to identify specific mutational drivers of metastasis. Yet, at least in experimental systems, metastatic cancer clones display stable traits that can facilitate progression through the many steps of metastasis. How cancer cells establish and maintain the transcriptional programmes required for metastasis remains mostly unknown. Emerging evidence suggests that metastatic traits may arise from epigenetically altered transcriptional output of the oncogenic signals that drive tumour initiation and early progression. Molecular dissection of such mechanisms remains a central challenge for a comprehensive understanding of the origins of metastasis.
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Affiliation(s)
- Saroor A Patel
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge, CB2 0XZ, United Kingdom
| | - Sakari Vanharanta
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge, CB2 0XZ, United Kingdom.
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Willi M, Yoo KH, Wang C, Trajanoski Z, Hennighausen L. Differential cytokine sensitivities of STAT5-dependent enhancers rely on Stat5 autoregulation. Nucleic Acids Res 2016; 44:10277-10291. [PMID: 27694626 PMCID: PMC5137441 DOI: 10.1093/nar/gkw844] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 08/22/2016] [Accepted: 09/11/2016] [Indexed: 12/28/2022] Open
Abstract
Cytokines utilize the transcription factor STAT5 to control cell-specific genes at a larger scale than universal genes, with a mechanistic explanation yet to be supplied. Genome-wide studies have identified putative STAT5-based mammary-specific and universal enhancers, an opportunity to investigate mechanisms underlying their differential response to cytokines. We have now interrogated the integrity and function of both categories of regulatory elements using biological and genetic approaches. During lactation, STAT5 occupies mammary-specific and universal cytokine-responsive elements. Following lactation, prolactin levels decline and mammary-specific STAT5-dependent enhancers are decommissioned within 24 h, while universal regulatory complexes remain intact. These differential sensitivities are linked to STAT5 concentrations and the mammary-specific Stat5 autoregulatory enhancer. In its absence, mammary-specific enhancers, but not universal elements, fail to be fully established. Upon termination of lactation STAT5 binding to a subset of mammary enhancers is substituted by STAT3. No STAT3 binding was observed at the most sensitive STAT5 enhancers suggesting that upon hormone withdrawal their chromatin becomes inaccessible. Lastly, we demonstrate that the mammary-enriched transcription factors GR, ELF5 and NFIB associate with STAT5 at sites lacking bona fide binding motifs. This study provides, for the first time, molecular insight into the differential sensitivities of mammary-specific and universal cytokine-sensing enhancers.
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Affiliation(s)
- Michaela Willi
- Laboratory of Genetics and Physiology, National Institute of Diabetes and Digestive and Kidney Diseases, US National Institutes of Health, Bethesda, MD 20892, USA.,Division of Bioinformatics, Biocenter, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Kyung Hyun Yoo
- Laboratory of Genetics and Physiology, National Institute of Diabetes and Digestive and Kidney Diseases, US National Institutes of Health, Bethesda, MD 20892, USA.,Department of Life Systems, Sookmyung Women's University, Seoul 140-742, Republic of Korea
| | - Chaochen Wang
- Laboratory of Genetics and Physiology, National Institute of Diabetes and Digestive and Kidney Diseases, US National Institutes of Health, Bethesda, MD 20892, USA
| | - Zlatko Trajanoski
- Division of Bioinformatics, Biocenter, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Lothar Hennighausen
- Laboratory of Genetics and Physiology, National Institute of Diabetes and Digestive and Kidney Diseases, US National Institutes of Health, Bethesda, MD 20892, USA
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