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Ozarslan N, Mong C, Ategeka J, Li L, Buarpung S, Robinson JF, Kizza J, Kakuru A, Kamya MR, Dorsey G, Rosenthal PJ, Gaw SL. Placental Malaria Induces a Unique Placental Methylation Profile Associated with Fetal Growth Restriction. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.09.593431. [PMID: 38798500 PMCID: PMC11118523 DOI: 10.1101/2024.05.09.593431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Background Fetal growth restriction (FGR) is associated with perinatal death and other adverse birth outcomes, as well as long term complications including increased childhood morbidity, abnormal neurodevelopment, and cardio-metabolic diseases in adulthood. FGR has been associated with placental epigenetic reprogramming, which may mediate these long term outcomes. Placental malaria (PM) is the leading cause of FGR globally, but the impact on placental epigenetics is unknown. We hypothesized that methylomic profiling of placentas from non-malarial and malarial FGR would reveal common and distinct mechanistic pathways associated with FGR. Results We used a methylation array to compare the CpG profiles between FGR from a cohort with no malaria exposure and a cohort of pregnancies complicated by both PM and FGR. Non-malarial FGR was associated with 65 differentially methylated CpGs, whereas PM-FGR was associated with 133 DMCs, compared to their corresponding controls. One DMC (cg16389901) was commonly hypomethylated in both groups, corresponding to the promoter region of BMP4 . Comparison of FGR vs. PM-FGR identified 522 DMCs between these two groups, which was not attributable to geographic location or different cellular compositions of these two groups. Conclusion Placentas from pregnancies with PM-associated FGR showed distinct methylation profiles as compared to non-malarial FGR, suggesting novel epigenetic reprogramming in response to malaria. There may be distinct long-term health outcomes in FGR pregnancies also complicated by PM.
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2
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Stathopoulou A, Wang P, Thellier C, Kelly RG, Zheng D, Scambler PJ. CHARGE syndrome-associated CHD7 acts at ISL1-regulated enhancers to modulate second heart field gene expression. Cardiovasc Res 2023; 119:2089-2105. [PMID: 37052590 PMCID: PMC10478754 DOI: 10.1093/cvr/cvad059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 01/20/2022] [Accepted: 04/12/2023] [Indexed: 04/14/2023] Open
Abstract
AIMS Haploinsufficiency of the chromo-domain protein CHD7 underlies most cases of CHARGE syndrome, a multisystem birth defect including congenital heart malformation. Context specific roles for CHD7 in various stem, progenitor, and differentiated cell lineages have been reported. Previously, we showed severe defects when Chd7 is absent from cardiopharyngeal mesoderm (CPM). Here, we investigate altered gene expression in the CPM and identify specific CHD7-bound target genes with known roles in the morphogenesis of affected structures. METHODS AND RESULTS We generated conditional KO of Chd7 in CPM and analysed cardiac progenitor cells using transcriptomic and epigenomic analyses, in vivo expression analysis, and bioinformatic comparisons with existing datasets. We show CHD7 is required for correct expression of several genes established as major players in cardiac development, especially within the second heart field (SHF). We identified CHD7 binding sites in cardiac progenitor cells and found strong association with histone marks suggestive of dynamically regulated enhancers during the mesodermal to cardiac progenitor transition of mESC differentiation. Moreover, CHD7 shares a subset of its target sites with ISL1, a pioneer transcription factor in the cardiogenic gene regulatory network, including one enhancer modulating Fgf10 expression in SHF progenitor cells vs. differentiating cardiomyocytes. CONCLUSION We show that CHD7 interacts with ISL1, binds ISL1-regulated cardiac enhancers, and modulates gene expression across the mesodermal heart fields during cardiac morphogenesis.
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Affiliation(s)
- Athanasia Stathopoulou
- Developmental Biology of Birth Defects, UCL Great Ormond Street Institute of Child Health, 30 Guilford Street, London WC1N 1EH, UK
| | - Ping Wang
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
- School of Medical Imaging, Tianjin Medical University, Tianjin, China
| | | | - Robert G Kelly
- Aix-Marseille University, CNRS UMR 7288, IBDM, Marseille, France
| | - Deyou Zheng
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
- Departments of Neurology and Neurosciences, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Peter J Scambler
- Developmental Biology of Birth Defects, UCL Great Ormond Street Institute of Child Health, 30 Guilford Street, London WC1N 1EH, UK
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3
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Chohra I, Chung K, Giri S, Malgrange B. ATP-Dependent Chromatin Remodellers in Inner Ear Development. Cells 2023; 12:cells12040532. [PMID: 36831199 PMCID: PMC9954591 DOI: 10.3390/cells12040532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 01/30/2023] [Accepted: 02/01/2023] [Indexed: 02/11/2023] Open
Abstract
During transcription, DNA replication and repair, chromatin structure is constantly modified to reveal specific genetic regions and allow access to DNA-interacting enzymes. ATP-dependent chromatin remodelling complexes use the energy of ATP hydrolysis to modify chromatin architecture by repositioning and rearranging nucleosomes. These complexes are defined by a conserved SNF2-like, catalytic ATPase subunit and are divided into four families: CHD, SWI/SNF, ISWI and INO80. ATP-dependent chromatin remodellers are crucial in regulating development and stem cell biology in numerous organs, including the inner ear. In addition, mutations in genes coding for proteins that are part of chromatin remodellers have been implicated in numerous cases of neurosensory deafness. In this review, we describe the composition, structure and functional activity of these complexes and discuss how they contribute to hearing and neurosensory deafness.
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4
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Bélanger C, Cardinal T, Leduc E, Viger RS, Pilon N. CHARGE syndrome-associated proteins FAM172A and CHD7 influence male sex determination and differentiation through transcriptional and alternative splicing mechanisms. FASEB J 2022; 36:e22176. [PMID: 35129866 PMCID: PMC9304217 DOI: 10.1096/fj.202100837rr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 01/05/2022] [Accepted: 01/10/2022] [Indexed: 11/11/2022]
Abstract
To gain further insight into chromatin‐mediated regulation of mammalian sex determination, we analyzed the role of the CHARGE syndrome‐associated proteins FAM172A and CHD7. This study is based on our prior discoveries that a subset of corresponding mutant mice display complete male‐to‐female sex reversal, and that both of these proteins regulate co‐transcriptional alternative splicing in neural crest cells. Here, we report that FAM172A and CHD7 are present in the developing gonads when sex determination normally occurs in mice. The interactome of FAM172A in pre‐Sertoli cells again suggests a role at the chromatin‐spliceosome interface, like in neural crest cells. Accordingly, analysis of Fam172a‐mutant pre‐Sertoli cells revealed transcriptional and splicing dysregulation of hundreds of genes. Many of these genes are similarly affected in Chd7‐mutant pre‐Sertoli cells, including several known key regulators of sex determination and subsequent formation of testis cords. Among them, we notably identified Sry as a direct transcriptional target and WNT pathway‐associated Lef1 and Tcf7l2 as direct splicing targets. The identified molecular defects are also associated with the abnormal morphology of seminiferous tubules in mutant postnatal testes. Altogether, our results thus identify FAM172A and CHD7 as new players in the regulation of male sex determination and differentiation in mice, and further highlight the importance of chromatin‐mediated regulatory mechanisms in these processes.
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Affiliation(s)
- Catherine Bélanger
- Molecular Genetics of Development Laboratory, Département des Sciences Biologiques, Université du Québec à Montréal (UQAM), Montréal, Québec, Canada.,Centre d'Excellence en Recherche sur les Maladies Orphelines - Fondation Courtois (CERMO-FC), Université du Québec à Montréal, Montréal, Québec, Canada
| | - Tatiana Cardinal
- Molecular Genetics of Development Laboratory, Département des Sciences Biologiques, Université du Québec à Montréal (UQAM), Montréal, Québec, Canada.,Centre d'Excellence en Recherche sur les Maladies Orphelines - Fondation Courtois (CERMO-FC), Université du Québec à Montréal, Montréal, Québec, Canada
| | - Elizabeth Leduc
- Molecular Genetics of Development Laboratory, Département des Sciences Biologiques, Université du Québec à Montréal (UQAM), Montréal, Québec, Canada.,Centre d'Excellence en Recherche sur les Maladies Orphelines - Fondation Courtois (CERMO-FC), Université du Québec à Montréal, Montréal, Québec, Canada
| | - Robert S Viger
- Reproduction, Mother and Child Health, Centre de recherche en reproduction, développement et santé intergénérationnelle (CRDSI), Centre de recherche du CHU de Québec-Université Laval, Quebec City, Québec, Canada.,Department of Obstetrics, Gynecology, and Reproduction, Faculty of Medicine, Université Laval, Quebec City, Québec, Canada
| | - Nicolas Pilon
- Molecular Genetics of Development Laboratory, Département des Sciences Biologiques, Université du Québec à Montréal (UQAM), Montréal, Québec, Canada.,Centre d'Excellence en Recherche sur les Maladies Orphelines - Fondation Courtois (CERMO-FC), Université du Québec à Montréal, Montréal, Québec, Canada.,Département de pédiatrie, Université de Montréal, Montréal, Québec, Canada
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5
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Weissberg O, Elliott E. The Mechanisms of CHD8 in Neurodevelopment and Autism Spectrum Disorders. Genes (Basel) 2021; 12:genes12081133. [PMID: 34440307 PMCID: PMC8393912 DOI: 10.3390/genes12081133] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 07/23/2021] [Accepted: 07/23/2021] [Indexed: 11/16/2022] Open
Abstract
Chromodomain-helicase-DNA-binding protein 8 (CHD8) has been identified as one of the genes with the strongest association with autism. The CHD8 protein is a transcriptional regulator that is expressed in nearly all cell types and has been implicated in multiple cellular processes, including cell cycle, cell adhesion, neuronal development, myelination, and synaptogenesis. Considering the central role of CHD8 in the genetics of autism, a deeper understanding of the physiological functions of CHD8 is important to understand the development of the autism phenotype and potential therapeutic targets. Different CHD8 mutant mouse models were developed to determine autism-like phenotypes and to fully understand their mechanisms. Here, we review the current knowledge on CHD8, with an emphasis on mechanistic lessons gained from animal models that have been studied.
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6
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Kaur G, Iyer LM, Burroughs AM, Aravind L. Bacterial death and TRADD-N domains help define novel apoptosis and immunity mechanisms shared by prokaryotes and metazoans. eLife 2021; 10:70394. [PMID: 34061031 PMCID: PMC8195603 DOI: 10.7554/elife.70394] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Accepted: 05/23/2021] [Indexed: 12/12/2022] Open
Abstract
Several homologous domains are shared by eukaryotic immunity and programmed cell-death systems and poorly understood bacterial proteins. Recent studies show these to be components of a network of highly regulated systems connecting apoptotic processes to counter-invader immunity, in prokaryotes with a multicellular habit. However, the provenance of key adaptor domains, namely those of the Death-like and TRADD-N superfamilies, a quintessential feature of metazoan apoptotic systems, remained murky. Here, we use sensitive sequence analysis and comparative genomics methods to identify unambiguous bacterial homologs of the Death-like and TRADD-N superfamilies. We show the former to have arisen as part of a radiation of effector-associated α-helical adaptor domains that likely mediate homotypic interactions bringing together diverse effector and signaling domains in predicted bacterial apoptosis- and counter-invader systems. Similarly, we show that the TRADD-N domain defines a key, widespread signaling bridge that links effector deployment to invader-sensing in multicellular bacterial and metazoan counter-invader systems. TRADD-N domains are expanded in aggregating marine invertebrates and point to distinctive diversifying immune strategies probably directed both at RNA and retroviruses and cellular pathogens that might infect such communities. These TRADD-N and Death-like domains helped identify several new bacterial and metazoan counter-invader systems featuring underappreciated, common functional principles: the use of intracellular invader-sensing lectin-like (NPCBM and FGS), transcription elongation GreA/B-C, glycosyltransferase-4 family, inactive NTPase (serving as nucleic acid receptors), and invader-sensing GTPase switch domains. Finally, these findings point to the possibility of multicellular bacteria-stem metazoan symbiosis in the emergence of the immune/apoptotic systems of the latter.
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Affiliation(s)
- Gurmeet Kaur
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, United States
| | - Lakshminarayan M Iyer
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, United States
| | - A Maxwell Burroughs
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, United States
| | - L Aravind
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, United States
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7
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Neve B, Jonckheere N, Vincent A, Van Seuningen I. Long non-coding RNAs: the tentacles of chromatin remodeler complexes. Cell Mol Life Sci 2021; 78:1139-1161. [PMID: 33001247 PMCID: PMC11072783 DOI: 10.1007/s00018-020-03646-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 09/01/2020] [Accepted: 09/12/2020] [Indexed: 02/07/2023]
Abstract
Chromatin remodeler complexes regulate gene transcription, DNA replication and DNA repair by changing both nucleosome position and post-translational modifications. The chromatin remodeler complexes are categorized into four families: the SWI/SNF, INO80/SWR1, ISWI and CHD family. In this review, we describe the subunits of these chromatin remodeler complexes, in particular, the recently identified members of the ISWI family and novelties of the CHD family. Long non-coding (lnc) RNAs regulate gene expression through different epigenetic mechanisms, including interaction with chromatin remodelers. For example, interaction of lncBRM with BRM inhibits the SWI/SNF complex associated with a differentiated phenotype and favors assembly of a stem cell-related SWI/SNF complex. Today, over 50 lncRNAs have been shown to affect chromatin remodeler complexes and we here discuss the mechanisms involved.
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Affiliation(s)
- Bernadette Neve
- UMR9020-U1277 - CANTHER - Cancer Heterogeneity, Plasticity and Resistance to Therapies, Univ. Lille, CNRS, Inserm, CHU Lille, 59000, Lille, France.
| | - Nicolas Jonckheere
- UMR9020-U1277 - CANTHER - Cancer Heterogeneity, Plasticity and Resistance to Therapies, Univ. Lille, CNRS, Inserm, CHU Lille, 59000, Lille, France
| | - Audrey Vincent
- UMR9020-U1277 - CANTHER - Cancer Heterogeneity, Plasticity and Resistance to Therapies, Univ. Lille, CNRS, Inserm, CHU Lille, 59000, Lille, France
| | - Isabelle Van Seuningen
- UMR9020-U1277 - CANTHER - Cancer Heterogeneity, Plasticity and Resistance to Therapies, Univ. Lille, CNRS, Inserm, CHU Lille, 59000, Lille, France
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8
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Wilson MM, Henshall DC, Byrne SM, Brennan GP. CHD2-Related CNS Pathologies. Int J Mol Sci 2021; 22:E588. [PMID: 33435571 PMCID: PMC7827033 DOI: 10.3390/ijms22020588] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 01/04/2021] [Accepted: 01/05/2021] [Indexed: 02/08/2023] Open
Abstract
Epileptic encephalopathies (EE) are severe epilepsy syndromes characterized by multiple seizure types, developmental delay and even regression. This class of disorders are increasingly being identified as resulting from de novo genetic mutations including many identified mutations in the family of chromodomain helicase DNA binding (CHD) proteins. In particular, several de novo pathogenic mutations have been identified in the gene encoding chromodomain helicase DNA binding protein 2 (CHD2), a member of the sucrose nonfermenting (SNF-2) protein family of epigenetic regulators. These mutations in the CHD2 gene are causative of early onset epileptic encephalopathy, abnormal brain function, and intellectual disability. Our understanding of the mechanisms by which modification or loss of CHD2 cause this condition remains poorly understood. Here, we review what is known and still to be elucidated as regards the structure and function of CHD2 and how its dysregulation leads to a highly variable range of phenotypic presentations.
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Affiliation(s)
- Marc-Michel Wilson
- Department of Physiology and Medical Physics, RCSI, University of Medicine and Health Sciences, Dublin 02, Ireland; (M.-M.W.); (D.C.H.)
- FutureNeuro SFI Research Centre, RCSI, University of Medicine and Health Sciences, Dublin D02 YN77, Ireland;
| | - David C. Henshall
- Department of Physiology and Medical Physics, RCSI, University of Medicine and Health Sciences, Dublin 02, Ireland; (M.-M.W.); (D.C.H.)
- FutureNeuro SFI Research Centre, RCSI, University of Medicine and Health Sciences, Dublin D02 YN77, Ireland;
| | - Susan M. Byrne
- FutureNeuro SFI Research Centre, RCSI, University of Medicine and Health Sciences, Dublin D02 YN77, Ireland;
- Department of Paediatrics, RCSI, University of Medicine and Health Sciences, Dublin 02, Ireland
- Department of Paediatric Neurology, Our Ladies Children’s Hospital Crumlin, Dublin 12, Ireland
| | - Gary P. Brennan
- FutureNeuro SFI Research Centre, RCSI, University of Medicine and Health Sciences, Dublin D02 YN77, Ireland;
- UCD School of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin, Belfield, Dublin 04, Ireland
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9
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Kasah S, Oddy C, Basson MA. Autism-linked CHD gene expression patterns during development predict multi-organ disease phenotypes. J Anat 2018; 233:755-769. [PMID: 30277262 DOI: 10.1111/joa.12889] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/23/2018] [Indexed: 12/24/2022] Open
Abstract
Recent large-scale exome sequencing studies have identified mutations in several members of the CHD (Chromodomain Helicase DNA-binding protein) gene family in neurodevelopmental disorders. Mutations in the CHD2 gene have been linked to developmental delay, intellectual disability, autism and seizures, CHD8 mutations to autism and intellectual disability, whereas haploinsufficiency of CHD7 is associated with executive dysfunction and intellectual disability. In addition to these neurodevelopmental features, a wide range of other developmental defects are associated with mutants of these genes, especially with regards to CHD7 haploinsufficiency, which is the primary cause of CHARGE syndrome. Whilst the developmental expression of CHD7 has been reported previously, limited information on the expression of CHD2 and CHD8 during development is available. Here, we compare the expression patterns of all three genes during mouse development directly. We find high, widespread expression of these genes at early stages of development that gradually becomes restricted during later developmental stages. Chd2 and Chd8 are widely expressed in the developing central nervous system (CNS) at all stages of development, with moderate expression remaining in the neocortex, hippocampus, olfactory bulb and cerebellum of the postnatal brain. Similarly, Chd7 expression is seen throughout the CNS during late embryogenesis and early postnatal development, with strong enrichment in the cerebellum, but displays low expression in the cortex and neurogenic niches in early life. In addition to expression in the brain, novel sites of Chd2 and Chd8 expression are reported. These findings suggest additional roles for these genes in organogenesis and predict that mutation of these genes may predispose individuals to a range of other, non-neurological developmental defects.
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Affiliation(s)
- Sahrunizam Kasah
- Centre for Craniofacial and Regenerative Biology, King's College London, London, UK
| | - Christopher Oddy
- Centre for Craniofacial and Regenerative Biology, King's College London, London, UK
| | - M Albert Basson
- Centre for Craniofacial and Regenerative Biology, King's College London, London, UK.,MRC Centre for Neurodevelopmental Disorders, King's College London, London, UK
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10
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Oligodendrocyte precursor survival and differentiation requires chromatin remodeling by Chd7 and Chd8. Proc Natl Acad Sci U S A 2018; 115:E8246-E8255. [PMID: 30108144 PMCID: PMC6126750 DOI: 10.1073/pnas.1802620115] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Oligodendrocyte precursor cells (OPCs) constitute the main proliferative cells in the adult brain and deregulation of OPC proliferation-differentiation balance results in either glioma formation or defective (re)myelination. Mutations in chromatin remodelers CHD7 and CHD8 are the cause of CHARGE syndrome and some autism spectrum disorders (ASD). Here we show that Chd7 protects OPCs from apoptosis by chromatin closing and gene repression of p53, while Chd7 induces chromatin opening and gene activation of OPC-differentiation regulators. Chd7 is, however, dispensable for oligodendrocyte stage progression, consistent with Chd8 compensatory function, as suggested by their common chromatin-binding profiles, including ASD-risk–associated genes. Our results thus involve oligodendroglia in ASD and CHARGE and offer new avenues to understand and modulate CHD7/CHD8 functions in normal and pathological brain development. Oligodendrocyte precursor cells (OPCs) constitute the main proliferative cells in the adult brain, and deregulation of OPC proliferation-differentiation balance results in either glioma formation or defective adaptive (re)myelination. OPC differentiation requires significant genetic reprogramming, implicating chromatin remodeling. Mounting evidence indicates that chromatin remodelers play important roles during normal development and their mutations are associated with neurodevelopmental defects, with CHD7 haploinsuficiency being the cause of CHARGE syndrome and CHD8 being one of the strongest autism spectrum disorder (ASD) high-risk–associated genes. Herein, we report on uncharacterized functions of the chromatin remodelers Chd7 and Chd8 in OPCs. Their OPC-chromatin binding profile, combined with transcriptome and chromatin accessibility analyses of Chd7-deleted OPCs, demonstrates that Chd7 protects nonproliferative OPCs from apoptosis by chromatin closing and transcriptional repression of p53. Furthermore, Chd7 controls OPC differentiation through chromatin opening and transcriptional activation of key regulators, including Sox10, Nkx2.2, and Gpr17. However, Chd7 is dispensable for oligodendrocyte stage progression, consistent with Chd8 compensatory function, as suggested by their common chromatin-binding profiles and genetic interaction. Finally, CHD7 and CHD8 bind in OPCs to a majority of ASD risk-associated genes, suggesting an implication of oligodendrocyte lineage cells in ASD neurological defects. Our results thus offer new avenues to understand and modulate the CHD7 and CHD8 functions in normal development and disease.
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11
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Yao H, Hill SF, Skidmore JM, Sperry ED, Swiderski DL, Sanchez GJ, Bartels CF, Raphael Y, Scacheri PC, Iwase S, Martin DM. CHD7 represses the retinoic acid synthesis enzyme ALDH1A3 during inner ear development. JCI Insight 2018; 3:97440. [PMID: 29467333 DOI: 10.1172/jci.insight.97440] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 01/23/2018] [Indexed: 12/13/2022] Open
Abstract
CHD7, an ATP-dependent chromatin remodeler, is disrupted in CHARGE syndrome, an autosomal dominant disorder characterized by variably penetrant abnormalities in craniofacial, cardiac, and nervous system tissues. The inner ear is uniquely sensitive to CHD7 levels and is the most commonly affected organ in individuals with CHARGE. Interestingly, upregulation or downregulation of retinoic acid (RA) signaling during embryogenesis also leads to developmental defects similar to those in CHARGE syndrome, suggesting that CHD7 and RA may have common target genes or signaling pathways. Here, we tested three separate potential mechanisms for CHD7 and RA interaction: (a) direct binding of CHD7 with RA receptors, (b) regulation of CHD7 levels by RA, and (c) CHD7 binding and regulation of RA-related genes. We show that CHD7 directly regulates expression of Aldh1a3, the gene encoding the RA synthetic enzyme ALDH1A3 and that loss of Aldh1a3 partially rescues Chd7 mutant mouse inner ear defects. Together, these studies indicate that ALDH1A3 acts with CHD7 in a common genetic pathway to regulate inner ear development, providing insights into how CHD7 and RA regulate gene expression and morphogenesis in the developing embryo.
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Affiliation(s)
- Hui Yao
- Department of Pediatrics and Communicable Diseases
| | | | | | - Ethan D Sperry
- Department of Human Genetics.,Medical Scientist Training Program, and
| | - Donald L Swiderski
- Department of Otolaryngology, University of Michigan, Ann Arbor, Michigan, USA
| | | | - Cynthia F Bartels
- Department of Genetics, Case Western Reserve University, Cleveland, Ohio, USA
| | - Yehoash Raphael
- Department of Otolaryngology, University of Michigan, Ann Arbor, Michigan, USA
| | - Peter C Scacheri
- Department of Genetics, Case Western Reserve University, Cleveland, Ohio, USA
| | | | - Donna M Martin
- Department of Pediatrics and Communicable Diseases.,Department of Human Genetics.,Medical Scientist Training Program, and
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12
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Huang R, Liao X, Li Q. Identification and validation of potential prognostic gene biomarkers for predicting survival in patients with acute myeloid leukemia. Onco Targets Ther 2017; 10:5243-5254. [PMID: 29138577 PMCID: PMC5679677 DOI: 10.2147/ott.s147717] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Background Molecular analysis is a promising source of clinically useful prognostic biomarkers. The aim of this investigation was to identify prognostic biomarkers for patients with acute myeloid leukemia (AML) by using the gene expression profile dataset from public database. Methods The gene expression profile dataset and corresponding overall survival (OS) information of three cohorts of AML patients from GSE12417 and The Cancer Genome Atlas AML project (TCGA-LAML) were included in the present study. Prognostic gene screening was performed by using a survival package, whereas time-dependent receiver operating characteristic (ROC) curve analysis was performed using the survivalROC package. Results In the three cohorts, 11 genes were identified that were significantly associated with AML OS. A linear prognostic model of the 11 genes was constructed and weighted by regression coefficient (β) from the multivariate Cox regression analyses of GSE12417 HG-U133A cohort to divide patients into high- and low-risk groups. GSE12417 HG-U133 plus 2.0 and TCGA-LAML were validation cohorts. Patients assigned to the high-risk group exhibited poor OS compared to patients in the low-risk group. The 11-gene signature is a prognostic marker of AML and demonstrates good performance for predicting 1-, 3-, and 5-year OS as evaluated by survivalROC in the three cohorts. Conclusion Our study has identified an mRNA signature including 11 genes, which may serve as a potential prognostic marker of AML.
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Affiliation(s)
| | - Xiwen Liao
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, People's Republic of China
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13
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Wilop S, Chou WC, Jost E, Crysandt M, Panse J, Chuang MK, Brümmendorf TH, Wagner W, Tien HF, Kharabi Masouleh B. A three-gene expression-based risk score can refine the European LeukemiaNet AML classification. J Hematol Oncol 2016; 9:78. [PMID: 27585840 PMCID: PMC5009640 DOI: 10.1186/s13045-016-0308-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 08/24/2016] [Indexed: 12/18/2022] Open
Abstract
Background Risk stratification based on cytogenetics of acute myeloid leukemia (AML) remains imprecise. The introduction of novel genetic and epigenetic markers has helped to close this gap and increased the specificity of risk stratification, although most studies have been conducted in specific AML subpopulations. In order to overcome this limitation, we used a genome-wide approach in multiple AML populations to develop a robust prediction model for AML survival. Methods We conducted a genome-wide expression analysis of two data sets from AML patients enrolled into the AMLCG-1999 trial and from the Tumor Cancer Genome Atlas (TCGA) to develop a prognostic score to refine current risk classification and performed a validation on two data sets of the National Taiwan University Hospital (NTUH) and an independent AMLCG cohort. Results In our training set, using a stringent multi-step approach, we identified a small three-gene prognostic scoring system, named Tri-AML score (TriAS) which highly correlated with overall survival (OS). Multivariate analysis revealed TriAS to be an independent prognostic factor in all tested training and additional validation sets, even including age, current cytogenetic-based risk stratification, and three other recently developed expression-based scoring models for AML. Conclusions The Tri-AML score allows robust and clinically practical risk stratification for the outcome of AML patients. TriAS substantially refined current ELN risk stratification assigning 44.5 % of the patients into a different risk category. Electronic supplementary material The online version of this article (doi:10.1186/s13045-016-0308-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Stefan Wilop
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Wen-Chien Chou
- Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan.,Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Edgar Jost
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Martina Crysandt
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Jens Panse
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Ming-Kai Chuang
- Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Tim H Brümmendorf
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Wolfgang Wagner
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular, Engineering, University Hospital of the RWTH Aachen, Aachen, Germany.,Institute for Biomedical Engineering - Cell Biology, University Hospital of the RWTH, Aachen, Germany
| | - Hwei-Fang Tien
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Behzad Kharabi Masouleh
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, Medical Faculty, RWTH Aachen University, Aachen, Germany.
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14
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Seldon CS, Colbert LE, Hall WA, Fisher SB, Yu DS, Landry JC. Chromodomain-helicase-DNA binding protein 5, 7 and pronecrotic mixed lineage kinase domain-like protein serve as potential prognostic biomarkers in patients with resected pancreatic adenocarcinomas. World J Gastrointest Oncol 2016; 8:358-365. [PMID: 27096031 PMCID: PMC4824714 DOI: 10.4251/wjgo.v8.i4.358] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Revised: 12/05/2015] [Accepted: 01/11/2016] [Indexed: 02/05/2023] Open
Abstract
Pancreatic cancer is one of the deadliest cancers with a very poor prognosis. Recently, there has been a significant increase in research directed towards identifying potential biomarkers that can be used to diagnose and provide prognostic information for pancreatic cancer. These markers can be used clinically to optimize and personalize therapy for individual patients. In this review, we focused on 3 biomarkers involved in the DNA damage response pathway and the necroptosis pathway: Chromodomain-helicase-DNA binding protein 5, chromodomain-helicase-DNA binding protein 7, and mixed lineage kinase domain-like protein. The aim of this article is to review present literature provided for these biomarkers and current studies in which their effectiveness as prognostic biomarkers are analyzed in order to determine their future use as biomarkers in clinical medicine. Based on the data presented, these biomarkers warrant further investigation, and should be validated in future studies.
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15
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Dynamic network-based relevance score reveals essential proteins and functional modules in directed differentiation. Stem Cells Int 2015; 2015:792843. [PMID: 25977693 PMCID: PMC4419265 DOI: 10.1155/2015/792843] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Revised: 03/19/2015] [Accepted: 03/27/2015] [Indexed: 01/17/2023] Open
Abstract
The induction of stem cells toward a desired differentiation direction is required for the advancement of stem cell-based therapies. Despite successful demonstrations of the control of differentiation direction, the effective use of stem cell-based therapies suffers from a lack of systematic knowledge regarding the mechanisms underlying directed differentiation. Using dynamic modeling and the temporal microarray data of three differentiation stages, three dynamic protein-protein interaction networks were constructed. The interaction difference networks derived from the constructed networks systematically delineated the evolution of interaction variations and the underlying mechanisms. A proposed relevance score identified the essential components in the directed differentiation. Inspection of well-known proteins and functional modules in the directed differentiation showed the plausibility of the proposed relevance score, with the higher scores of several proteins and function modules indicating their essential roles in the directed differentiation. During the differentiation process, the proteins and functional modules with higher relevance scores also became more specific to the neuronal identity. Ultimately, the essential components revealed by the relevance scores may play a role in controlling the direction of differentiation. In addition, these components may serve as a starting point for understanding the systematic mechanisms of directed differentiation and for increasing the efficiency of stem cell-based therapies.
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16
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Abstract
Epigenetic events including chromatin remodeling and histone modifications have recently emerged as important contributors to a variety of neurodevelopmental disorders. This review focuses on CHARGE syndrome, a multiple anomaly condition caused by mutations in the gene encoding CHD7, an ATP-dependent chromatin remodeling protein. CHD7 exhibits pleiotropic effects during embryonic development, consistent with highly variable clinical features in CHARGE syndrome. In this review, a historical description of CHARGE is provided, followed by establishment of diagnostic criteria, gene discovery, and development of animal models. Current understanding of epigenetic CHD7 functions and interacting proteins in cells and tissues is also presented, and final emphasis is placed on challenges and major questions to be answered with ongoing research efforts.
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Affiliation(s)
- Donna M Martin
- Department of Human Genetics at The University of Michigan Medical School, Ann Arbor, MI, 48109 ; Department of Pediatrics and Communicable Diseases at The University of Michigan Medical School, Ann Arbor, MI, 48109
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17
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Schulz Y, Freese L, Mänz J, Zoll B, Völter C, Brockmann K, Bögershausen N, Becker J, Wollnik B, Pauli S. CHARGE and Kabuki syndromes: a phenotypic and molecular link. Hum Mol Genet 2014; 23:4396-405. [PMID: 24705355 DOI: 10.1093/hmg/ddu156] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
CHARGE syndrome is a complex developmental disorder caused by mutations in the chromodomain helicase DNA-binding gene CHD7. Kabuki syndrome, another developmental disorder, is characterized by typical facial features in combination with developmental delay, short stature, prominent digit pads and visceral abnormalities. Mutations in the KMT2D gene, which encodes a H3K4 histone methyltransferase, are the major cause of Kabuki syndrome. Here, we report a patient, who was initially diagnosed with CHARGE syndrome based on the spectrum of inner organ malformations like choanal hypoplasia, heart defect, anal atresia, vision problems and conductive hearing impairment. While sequencing and MLPA analysis of all coding exons of CHD7 revealed no pathogenic mutation, sequence analysis of the KMT2D gene identified the heterozygous de novo nonsense mutation c.5263C > T (p.Gln1755*). Thus, our patient was diagnosed with Kabuki syndrome. By using co-immunoprecipitation, immunohistochemistry and direct yeast two hybrid assays, we could show that, like KMT2D, CHD7 interacts with members of the WAR complex, namely WDR5, ASH2L and RbBP5. We therefore propose that CHD7 and KMT2D function in the same chromatin modification machinery, thus pointing out a mechanistic connection, and presenting a probable explanation for the phenotypic overlap between Kabuki and CHARGE syndromes.
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Affiliation(s)
- Yvonne Schulz
- Institute of Human Genetics, University Medical Center Göttingen, 37073 Göttingen, Germany
| | - Luisa Freese
- Institute of Human Genetics, University Medical Center Göttingen, 37073 Göttingen, Germany
| | - Johanna Mänz
- Institute of Human Genetics, University Medical Center Göttingen, 37073 Göttingen, Germany
| | - Barbara Zoll
- Institute of Human Genetics, University Medical Center Göttingen, 37073 Göttingen, Germany
| | - Christiane Völter
- Phoniatrics and Pedaudiology, Department of Otorhinolaryngology, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Knut Brockmann
- Interdisciplinary Pediatric Center for Children with Developmental Disabilities and Severe Chronic Disorders, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Nina Bögershausen
- Institute of Human Genetics, University of Cologne, 50931 Cologne, Germany Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50931 Cologne, Germany
| | - Jutta Becker
- Institute of Human Genetics, University of Cologne, 50931 Cologne, Germany
| | - Bernd Wollnik
- Institute of Human Genetics, University of Cologne, 50931 Cologne, Germany Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50931 Cologne, Germany
| | - Silke Pauli
- Institute of Human Genetics, University Medical Center Göttingen, 37073 Göttingen, Germany
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18
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Colbert LE, Petrova AV, Fisher SB, Pantazides BG, Madden MZ, Hardy CW, Warren MD, Pan Y, Nagaraju GP, Liu EA, Saka B, Hall WA, Shelton JW, Gandhi K, Pauly R, Kowalski J, Kooby DA, El-Rayes BF, Staley CA, Adsay NV, Curran WJ, Landry JC, Maithel SK, Yu DS. CHD7 expression predicts survival outcomes in patients with resected pancreatic cancer. Cancer Res 2014; 74:2677-87. [PMID: 24626090 DOI: 10.1158/0008-5472.can-13-1996] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a devastating disease with poor outcomes with current therapies. Gemcitabine is the primary adjuvant drug used clinically, but its effectiveness is limited. In this study, our objective was to use a rationale-driven approach to identify novel biomarkers for outcome in patients with early-stage resected PDAC treated with adjuvant gemcitabine. Using a synthetic lethal screen in human PDAC cells, we identified 93 genes, including 55 genes linked to DNA damage responses (DDR), that demonstrated gemcitabine sensitization when silenced, including CHD7, which functions in chromatin remodeling. CHD7 depletion sensitized PDAC cells to gemcitabine and delayed their growth in tumor xenografts. Moreover, CHD7 silencing impaired ATR-dependent phosphorylation of CHK1 and increased DNA damage induced by gemcitabine. CHD7 was dysregulated, ranking above the 90th percentile in differential expression in a panel of PDAC clinical specimens, highlighting its potential as a biomarker. Immunohistochemical analysis of specimens from 59 patients with resected PDAC receiving adjuvant gemcitabine revealed that low CHD7 expression was associated with increased recurrence-free survival (RFS) and overall survival (OS), in univariate and multivariate analyses. Notably, CHD7 expression was not associated with RFS or OS for patients not receiving gemcitabine. Thus, low CHD7 expression was correlated selectively with gemcitabine sensitivity in this patient population. These results supported our rationale-driven strategy to exploit dysregulated DDR pathways in PDAC to identify genetic determinants of gemcitabine sensitivity, identifying CHD7 as a novel biomarker candidate to evaluate further for individualizing PDAC treatment.
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MESH Headings
- Animals
- Antimetabolites, Antineoplastic/pharmacology
- Antimetabolites, Antineoplastic/therapeutic use
- Biomarkers, Tumor/biosynthesis
- Biomarkers, Tumor/genetics
- Carcinoma, Pancreatic Ductal/drug therapy
- Carcinoma, Pancreatic Ductal/enzymology
- Carcinoma, Pancreatic Ductal/genetics
- Carcinoma, Pancreatic Ductal/surgery
- Cell Line, Tumor
- DNA Helicases/biosynthesis
- DNA Helicases/genetics
- DNA-Binding Proteins/biosynthesis
- DNA-Binding Proteins/genetics
- Deoxycytidine/analogs & derivatives
- Deoxycytidine/pharmacology
- Deoxycytidine/therapeutic use
- Drug Screening Assays, Antitumor
- Gene Expression Regulation, Enzymologic
- Gene Expression Regulation, Neoplastic
- Gene Knockdown Techniques
- Humans
- Male
- Mice
- Pancreatic Neoplasms/drug therapy
- Pancreatic Neoplasms/enzymology
- Pancreatic Neoplasms/genetics
- Pancreatic Neoplasms/surgery
- Proportional Hazards Models
- Random Allocation
- Survival Analysis
- Xenograft Model Antitumor Assays
- Gemcitabine
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Affiliation(s)
- Lauren E Colbert
- Authors' Affiliations: Departments of Radiation Oncology, Medical Oncology, and Pathology; Division of Surgical Oncology, Department of Surgery; Biostatistics and Bioinformatics Shared Resource, Winship Cancer Institute, Emory University; and Atlanta Veterans Affairs Medical Center, Atlanta, Georgia
| | - Aleksandra V Petrova
- Authors' Affiliations: Departments of Radiation Oncology, Medical Oncology, and Pathology; Division of Surgical Oncology, Department of Surgery; Biostatistics and Bioinformatics Shared Resource, Winship Cancer Institute, Emory University; and Atlanta Veterans Affairs Medical Center, Atlanta, Georgia
| | - Sarah B Fisher
- Authors' Affiliations: Departments of Radiation Oncology, Medical Oncology, and Pathology; Division of Surgical Oncology, Department of Surgery; Biostatistics and Bioinformatics Shared Resource, Winship Cancer Institute, Emory University; and Atlanta Veterans Affairs Medical Center, Atlanta, Georgia
| | - Brooke G Pantazides
- Authors' Affiliations: Departments of Radiation Oncology, Medical Oncology, and Pathology; Division of Surgical Oncology, Department of Surgery; Biostatistics and Bioinformatics Shared Resource, Winship Cancer Institute, Emory University; and Atlanta Veterans Affairs Medical Center, Atlanta, Georgia
| | - Matthew Z Madden
- Authors' Affiliations: Departments of Radiation Oncology, Medical Oncology, and Pathology; Division of Surgical Oncology, Department of Surgery; Biostatistics and Bioinformatics Shared Resource, Winship Cancer Institute, Emory University; and Atlanta Veterans Affairs Medical Center, Atlanta, Georgia
| | - Claire W Hardy
- Authors' Affiliations: Departments of Radiation Oncology, Medical Oncology, and Pathology; Division of Surgical Oncology, Department of Surgery; Biostatistics and Bioinformatics Shared Resource, Winship Cancer Institute, Emory University; and Atlanta Veterans Affairs Medical Center, Atlanta, Georgia
| | - Matthew D Warren
- Authors' Affiliations: Departments of Radiation Oncology, Medical Oncology, and Pathology; Division of Surgical Oncology, Department of Surgery; Biostatistics and Bioinformatics Shared Resource, Winship Cancer Institute, Emory University; and Atlanta Veterans Affairs Medical Center, Atlanta, Georgia
| | - Yunfeng Pan
- Authors' Affiliations: Departments of Radiation Oncology, Medical Oncology, and Pathology; Division of Surgical Oncology, Department of Surgery; Biostatistics and Bioinformatics Shared Resource, Winship Cancer Institute, Emory University; and Atlanta Veterans Affairs Medical Center, Atlanta, Georgia
| | - Ganji P Nagaraju
- Authors' Affiliations: Departments of Radiation Oncology, Medical Oncology, and Pathology; Division of Surgical Oncology, Department of Surgery; Biostatistics and Bioinformatics Shared Resource, Winship Cancer Institute, Emory University; and Atlanta Veterans Affairs Medical Center, Atlanta, Georgia
| | - Elaine A Liu
- Authors' Affiliations: Departments of Radiation Oncology, Medical Oncology, and Pathology; Division of Surgical Oncology, Department of Surgery; Biostatistics and Bioinformatics Shared Resource, Winship Cancer Institute, Emory University; and Atlanta Veterans Affairs Medical Center, Atlanta, Georgia
| | - Burcu Saka
- Authors' Affiliations: Departments of Radiation Oncology, Medical Oncology, and Pathology; Division of Surgical Oncology, Department of Surgery; Biostatistics and Bioinformatics Shared Resource, Winship Cancer Institute, Emory University; and Atlanta Veterans Affairs Medical Center, Atlanta, Georgia
| | - William A Hall
- Authors' Affiliations: Departments of Radiation Oncology, Medical Oncology, and Pathology; Division of Surgical Oncology, Department of Surgery; Biostatistics and Bioinformatics Shared Resource, Winship Cancer Institute, Emory University; and Atlanta Veterans Affairs Medical Center, Atlanta, Georgia
| | - Joseph W Shelton
- Authors' Affiliations: Departments of Radiation Oncology, Medical Oncology, and Pathology; Division of Surgical Oncology, Department of Surgery; Biostatistics and Bioinformatics Shared Resource, Winship Cancer Institute, Emory University; and Atlanta Veterans Affairs Medical Center, Atlanta, Georgia
| | - Khanjan Gandhi
- Authors' Affiliations: Departments of Radiation Oncology, Medical Oncology, and Pathology; Division of Surgical Oncology, Department of Surgery; Biostatistics and Bioinformatics Shared Resource, Winship Cancer Institute, Emory University; and Atlanta Veterans Affairs Medical Center, Atlanta, Georgia
| | - Rini Pauly
- Authors' Affiliations: Departments of Radiation Oncology, Medical Oncology, and Pathology; Division of Surgical Oncology, Department of Surgery; Biostatistics and Bioinformatics Shared Resource, Winship Cancer Institute, Emory University; and Atlanta Veterans Affairs Medical Center, Atlanta, Georgia
| | - Jeanne Kowalski
- Authors' Affiliations: Departments of Radiation Oncology, Medical Oncology, and Pathology; Division of Surgical Oncology, Department of Surgery; Biostatistics and Bioinformatics Shared Resource, Winship Cancer Institute, Emory University; and Atlanta Veterans Affairs Medical Center, Atlanta, Georgia
| | - David A Kooby
- Authors' Affiliations: Departments of Radiation Oncology, Medical Oncology, and Pathology; Division of Surgical Oncology, Department of Surgery; Biostatistics and Bioinformatics Shared Resource, Winship Cancer Institute, Emory University; and Atlanta Veterans Affairs Medical Center, Atlanta, GeorgiaAuthors' Affiliations: Departments of Radiation Oncology, Medical Oncology, and Pathology; Division of Surgical Oncology, Department of Surgery; Biostatistics and Bioinformatics Shared Resource, Winship Cancer Institute, Emory University; and Atlanta Veterans Affairs Medical Center, Atlanta, Georgia
| | - Bassel F El-Rayes
- Authors' Affiliations: Departments of Radiation Oncology, Medical Oncology, and Pathology; Division of Surgical Oncology, Department of Surgery; Biostatistics and Bioinformatics Shared Resource, Winship Cancer Institute, Emory University; and Atlanta Veterans Affairs Medical Center, Atlanta, Georgia
| | - Charles A Staley
- Authors' Affiliations: Departments of Radiation Oncology, Medical Oncology, and Pathology; Division of Surgical Oncology, Department of Surgery; Biostatistics and Bioinformatics Shared Resource, Winship Cancer Institute, Emory University; and Atlanta Veterans Affairs Medical Center, Atlanta, Georgia
| | - N Volkan Adsay
- Authors' Affiliations: Departments of Radiation Oncology, Medical Oncology, and Pathology; Division of Surgical Oncology, Department of Surgery; Biostatistics and Bioinformatics Shared Resource, Winship Cancer Institute, Emory University; and Atlanta Veterans Affairs Medical Center, Atlanta, Georgia
| | - Walter J Curran
- Authors' Affiliations: Departments of Radiation Oncology, Medical Oncology, and Pathology; Division of Surgical Oncology, Department of Surgery; Biostatistics and Bioinformatics Shared Resource, Winship Cancer Institute, Emory University; and Atlanta Veterans Affairs Medical Center, Atlanta, Georgia
| | - Jerome C Landry
- Authors' Affiliations: Departments of Radiation Oncology, Medical Oncology, and Pathology; Division of Surgical Oncology, Department of Surgery; Biostatistics and Bioinformatics Shared Resource, Winship Cancer Institute, Emory University; and Atlanta Veterans Affairs Medical Center, Atlanta, Georgia
| | - Shishir K Maithel
- Authors' Affiliations: Departments of Radiation Oncology, Medical Oncology, and Pathology; Division of Surgical Oncology, Department of Surgery; Biostatistics and Bioinformatics Shared Resource, Winship Cancer Institute, Emory University; and Atlanta Veterans Affairs Medical Center, Atlanta, Georgia
| | - David S Yu
- Authors' Affiliations: Departments of Radiation Oncology, Medical Oncology, and Pathology; Division of Surgical Oncology, Department of Surgery; Biostatistics and Bioinformatics Shared Resource, Winship Cancer Institute, Emory University; and Atlanta Veterans Affairs Medical Center, Atlanta, Georgia
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