1
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Schmidt C, Cohen S, Gudenas BL, Husain S, Carlson A, Westelman S, Wang L, Phillips JJ, Northcott PA, Weiss WA, Schwer B. PRDM6 promotes medulloblastoma by repressing chromatin accessibility and altering gene expression. bioRxiv 2023:2023.08.29.555389. [PMID: 37693484 PMCID: PMC10491178 DOI: 10.1101/2023.08.29.555389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
SNCAIP duplication may promote Group 4 medulloblastoma via induction of PRDM6, a poorly characterized member of the PRDF1 and RIZ1 homology domain-containing (PRDM) family of transcription factors. Here, we investigated the function of PRDM6 in human hindbrain neuroepithelial stem cells and tested PRDM6 as a driver of Group 4 medulloblastoma. We report that human PRDM6 localizes predominantly to the nucleus, where it causes widespread repression of chromatin accessibility and complex alterations of gene expression patterns. Genome-wide mapping of PRDM6 binding reveals that PRDM6 binds to chromatin regions marked by histone H3 lysine 27 trimethylation that are located within, or proximal to, genes. Moreover, we show that PRDM6 expression in neuroepithelial stem cells promotes medulloblastoma. Surprisingly, medulloblastomas derived from PRDM6-expressing neuroepithelial stem cells match human Group 3, but not Group 4, medulloblastoma. We conclude that PRDM6 expression has oncogenic potential but is insufficient to drive Group 4 medulloblastoma from neuroepithelial stem cells. We propose that both PRDM6 and additional factors, such as specific cell-of-origin features, are required for Group 4 medulloblastoma. Given the lack of PRDM6 expression in normal tissues and its oncogenic potential shown here, we suggest that PRDM6 inhibition may have therapeutic value in PRDM6-expressing medulloblastomas.
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2
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Smith KS, Bihannic L, Gudenas BL, Haldipur P, Tao R, Gao Q, Li Y, Aldinger KA, Iskusnykh IY, Chizhikov VV, Scoggins M, Zhang S, Edwards A, Deng M, Glass IA, Overman LM, Millman J, Sjoboen AH, Hadley J, Golser J, Mankad K, Sheppard H, Onar-Thomas A, Gajjar A, Robinson GW, Hovestadt V, Orr BA, Patay Z, Millen KJ, Northcott PA. Unified rhombic lip origins of group 3 and group 4 medulloblastoma. Nature 2022; 609:1012-1020. [PMID: 36131015 PMCID: PMC9748853 DOI: 10.1038/s41586-022-05208-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 08/08/2022] [Indexed: 02/01/2023]
Abstract
Medulloblastoma, a malignant childhood cerebellar tumour, segregates molecularly into biologically distinct subgroups, suggesting that a personalized approach to therapy would be beneficial1. Mouse modelling and cross-species genomics have provided increasing evidence of discrete, subgroup-specific developmental origins2. However, the anatomical and cellular complexity of developing human tissues3-particularly within the rhombic lip germinal zone, which produces all glutamatergic neuronal lineages before internalization into the cerebellar nodulus-makes it difficult to validate previous inferences that were derived from studies in mice. Here we use multi-omics to resolve the origins of medulloblastoma subgroups in the developing human cerebellum. Molecular signatures encoded within a human rhombic-lip-derived lineage trajectory aligned with photoreceptor and unipolar brush cell expression profiles that are maintained in group 3 and group 4 medulloblastoma, suggesting a convergent basis. A systematic diagnostic-imaging review of a prospective institutional cohort localized the putative anatomical origins of group 3 and group 4 tumours to the nodulus. Our results connect the molecular and phenotypic features of clinically challenging medulloblastoma subgroups to their unified beginnings in the rhombic lip in the early stages of human development.
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Affiliation(s)
- Kyle S Smith
- Department of Developmental Neurobiology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Laure Bihannic
- Department of Developmental Neurobiology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Brian L Gudenas
- Department of Developmental Neurobiology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Parthiv Haldipur
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Ran Tao
- Department of Developmental Neurobiology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Qingsong Gao
- Department of Developmental Neurobiology, St Jude Children's Research Hospital, Memphis, TN, USA
- Department of Pathology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Yiran Li
- Department of Developmental Neurobiology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Kimberly A Aldinger
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Igor Y Iskusnykh
- Department of Anatomy and Neurobiology, University of Tennessee, Memphis, TN, USA
| | - Victor V Chizhikov
- Department of Anatomy and Neurobiology, University of Tennessee, Memphis, TN, USA
| | - Matthew Scoggins
- Department of Diagnostic Imaging, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Silu Zhang
- Department of Diagnostic Imaging, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Angela Edwards
- Department of Diagnostic Imaging, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Mei Deng
- Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Ian A Glass
- Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Lynne M Overman
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Jake Millman
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Alexandria H Sjoboen
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Jennifer Hadley
- Department of Developmental Neurobiology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Joseph Golser
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Kshitij Mankad
- Department of Radiology, Great Ormond Street Hospital for Children, London, UK
| | - Heather Sheppard
- Department of Pathology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Arzu Onar-Thomas
- Department of Biostatistics, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Amar Gajjar
- Department of Oncology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Giles W Robinson
- Department of Oncology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Volker Hovestadt
- Department of Pediatric Oncology, Dana Farber Cancer Institute, Boston, MA, USA
| | - Brent A Orr
- Department of Pathology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Zoltán Patay
- Department of Diagnostic Imaging, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Kathleen J Millen
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Paul A Northcott
- Department of Developmental Neurobiology, St Jude Children's Research Hospital, Memphis, TN, USA.
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3
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Inoue A, Janke LJ, Gudenas BL, Jin H, Fan Y, Paré J, Clay MR, Northcott PA, Hirbe AC, Cao X. A genetic mouse model with postnatal Nf1 and p53 loss recapitulates the histology and transcriptome of human malignant peripheral nerve sheath tumor. Neurooncol Adv 2021; 3:vdab129. [PMID: 34647023 PMCID: PMC8500687 DOI: 10.1093/noajnl/vdab129] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Malignant peripheral nerve sheath tumors (MPNST) are aggressive sarcomas. Somatic inactivation of NF1 and cooperating tumor suppressors, including CDKN2A/B, PRC2, and p53, is found in most MPNST. Inactivation of LATS1/2 of the Hippo pathway was recently shown to cause tumors resembling MPNST histologically, although Hippo pathway mutations are rarely found in MPNST. Because existing genetically engineered mouse (GEM) models of MPNST do not recapitulate some of the key genetic features of human MPNST, we aimed to establish a GEM-MPNST model that recapitulated the human disease genetically, histologically, and molecularly. METHODS We combined 2 genetically modified alleles, an Nf1;Trp53 cis-conditional allele and an inducible Plp-CreER allele (NP-Plp), to model the somatic, possibly postnatal, mutational events in human MPNST. We also generated conditional Lats1;Lats2 knockout mice. We performed histopathologic analyses of mouse MPNST models and transcriptomic comparison of mouse models and human nerve sheath tumors. RESULTS Postnatal Nf1;Trp53 cis-deletion resulted in GEM-MPNST that were histologically more similar to human MPNST than the widely used germline Nf1;Trp53 cis-heterozygous (NPcis) model and showed partial loss of H3K27me3. At the transcriptome level, Nf1;p53-driven GEM-MPNST were distinct from Lats-driven GEM-MPNST and resembled human MPNST more closely than do Lats-driven tumors. CONCLUSIONS The NP-Plp model recapitulates human MPNST genetically, histologically, and molecularly.
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Affiliation(s)
- Akira Inoue
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Laura J Janke
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Brian L Gudenas
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Hongjian Jin
- Center for Applied Bioinformatics, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Yiping Fan
- Center for Applied Bioinformatics, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Joshua Paré
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Michael R Clay
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Paul A Northcott
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Angela C Hirbe
- Division of Medical Oncology, Washington University, St. Louis, Missouri, USA
| | - Xinwei Cao
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
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4
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Robinson GW, Waszak SM, Gudenas BL, Smith KS, Forget A, Kojic M, Jesus GL, Hadley J, Hamilton KV, Indersie E, Buchhalter I, Jager N, Sharma T, Rausch T, Kool M, Sturm D, Jones DTW, Tatevossian R, Lombard B, Loew D, Bowers D, Bendel A, Partap S, Chintagumpala M, Crawford J, Gottardo NG, Smith A, Dufour C, Rutkowski S, Grotzer M, Remke M, Puget S, Pajtler KW, Milde T, Witt O, Ryzhova M, Korshunov A, Orr BA, Ellison DW, Brugieres L, Lichter P, Nichols KE, Gajjar A, Wainwright BJ, Ayrault O, Korbel JO, Northcott PA, Pfister SM. MBCL-21. GERMLINE ELONGATOR MUTATIONS IN SONIC HEDGEHOG MEDULLOBLASTOMA. Neuro Oncol 2020. [PMCID: PMC7715847 DOI: 10.1093/neuonc/noaa222.497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Our previous analysis of established cancer predisposition genes in medulloblastoma (MB) identified pathogenic germline variants in ~5% of all patients. Here, we extended our analysis to include all protein-coding genes. METHODS Case-control analysis performed on 795 MB patients against >118,000 cancer-free children and adults was performed to identify an association between rare germline variants and MB. RESULTS Germline loss-of-function variants of Elongator Complex Protein 1 (ELP1; 9q31.3) were strongly associated with SHH subgroup (MBSHH). ELP1-associated-MBs accounted for ~15% (29/202) of pediatric MBSHH cases and were restricted to the SHHα subtype. ELP1-associated-MBs demonstrated biallelic inactivation of ELP1 due to somatic chromosome 9q loss and most tumors exhibited co-occurring somatic PTCH1 (9q22.32) alterations. Inheritance was verified by parent-offspring sequencing (n=3) and pedigree analysis identified two families with a history of pediatric MB. ELP1-associated-MBSHH were characterized by desmoplastic/nodular histology (76%; 13/17) and demonstrated a favorable clinical outcome when compared to TP53-associated-MBSHH (5-yr OS 92% vs 20%; p-value=1.3e-6) despite both belonging to the SHHα subtype. ELP1 is a subunit of the Elongator complex, that promotes efficient translational elongation through tRNA modifications at the wobble (U34) position. Biochemical, transcriptional, and proteomic analyses revealed ELP1-associated-MBs exhibit destabilization of the core Elongator complex, loss of tRNA wobble modifications, codon-dependent translational reprogramming, and induction of the unfolded protein response. CONCLUSIONS We identified ELP1 as the most common MB predisposition gene, increasing the total genetic predisposition for pediatric MBSHH to 40%. These results mark MBSHH as an overwhelmingly genetically-predisposed disease and implicate disruption of protein homeostasis in MBSHH development.
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Affiliation(s)
| | | | - Brian L Gudenas
- St. Jude Children’s Research Hospital (SJCRH), Memphis, TN, USA
| | - Kyle S Smith
- St. Jude Children’s Research Hospital (SJCRH), Memphis, TN, USA
| | | | - Marija Kojic
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
| | | | - Jennifer Hadley
- St. Jude Children’s Research Hospital (SJCRH), Memphis, TN, USA
| | | | | | - Ivo Buchhalter
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Natalie Jager
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
| | - Tanvi Sharma
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
| | - Tobias Rausch
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Marcel Kool
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Princess Maxima Center for Pediatric Oncology, Utrecht, Netherlands
| | - Dominic Sturm
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
| | - David T W Jones
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
| | | | | | - Damarys Loew
- Institut Curie, PSL Research University, Paris, France
| | - Daniel Bowers
- University of Texas Southwestern Medical School, Dallas, TX, USA
| | | | | | | | - John Crawford
- Rady Children’s Hospital, University of California San Diego, San Diego, CA, USA
| | | | - Amy Smith
- Arnold Palmer Hospital Center for Children’s Cancer, Orlando, FL, USA
| | | | | | - Michael Grotzer
- University Children’s Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Mark Remke
- University Hospital Dusseldorf, Dusseldorf, Germany
| | | | | | - Till Milde
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
| | - Olaf Witt
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
| | - Marina Ryzhova
- Burdenko Neurosurgical Institute, Moscow, Russian Federation
| | | | - Brent A Orr
- St. Jude Children’s Research Hospital (SJCRH), Memphis, TN, USA
| | - David W Ellison
- St. Jude Children’s Research Hospital (SJCRH), Memphis, TN, USA
| | | | - Peter Lichter
- German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
| | - Kim E Nichols
- St. Jude Children’s Research Hospital (SJCRH), Memphis, TN, USA
| | - Amar Gajjar
- St. Jude Children’s Research Hospital (SJCRH), Memphis, TN, USA
| | - Brandon J Wainwright
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
| | | | - Jan O Korbel
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | | | - Stefan M Pfister
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
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5
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Kutscher LM, Okonechnikov K, Batora NV, Clark J, Silva PBG, Vouri M, van Rijn S, Sieber L, Statz B, Gearhart MD, Shiraishi R, Mack N, Orr BA, Korshunov A, Gudenas BL, Smith KS, Mercier AL, Ayrault O, Hoshino M, Kool M, von Hoff K, Graf N, Fleischhack G, Bardwell VJ, Pfister SM, Northcott PA, Kawauchi D. Functional loss of a noncanonical BCOR-PRC1.1 complex accelerates SHH-driven medulloblastoma formation. Genes Dev 2020; 34:1161-1176. [PMID: 32820036 PMCID: PMC7462063 DOI: 10.1101/gad.337584.120] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 07/10/2020] [Indexed: 12/17/2022]
Abstract
In this study, Kutscher et al. investigated the transcriptional corepressor BCOR as a putative tumor suppressor and used a genetically engineered mouse model to delete exons 9/10 of Bcor in GNPs during development. Their data suggest that BCOR–PRC1.1 disruption leads to Igf2 overexpression, which transforms preneoplastic cells to malignant tumors. Medulloblastoma is a malignant childhood brain tumor arising from the developing cerebellum. In Sonic Hedgehog (SHH) subgroup medulloblastoma, aberrant activation of SHH signaling causes increased proliferation of granule neuron progenitors (GNPs), and predisposes these cells to tumorigenesis. A second, cooperating genetic hit is often required to push these hyperplastic cells to malignancy and confer mutation-specific characteristics associated with oncogenic signaling. Somatic loss-of-function mutations of the transcriptional corepressor BCOR are recurrent and enriched in SHH medulloblastoma. To investigate BCOR as a putative tumor suppressor, we used a genetically engineered mouse model to delete exons 9/10 of Bcor (BcorΔE9–10) in GNPs during development. This mutation leads to reduced expression of C-terminally truncated BCOR (BCORΔE9–10). While BcorΔE9–10 alone did not promote tumorigenesis or affect GNP differentiation, BcorΔE9–10 combined with loss of the SHH receptor gene Ptch1 resulted in fully penetrant medulloblastomas. In Ptch1+/−;BcorΔE9–10 tumors, the growth factor gene Igf2 was aberrantly up-regulated, and ectopic Igf2 overexpression was sufficient to drive tumorigenesis in Ptch1+/− GNPs. BCOR directly regulates Igf2, likely through the PRC1.1 complex; the repressive histone mark H2AK119Ub is decreased at the Igf2 promoter in Ptch1+/−;BcorΔE9–10 tumors. Overall, our data suggests that BCOR–PRC1.1 disruption leads to Igf2 overexpression, which transforms preneoplastic cells to malignant tumors.
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Affiliation(s)
- Lena M Kutscher
- Hopp-Children's Cancer Center Heidelberg (KiTZ), 69120 Heidelberg, Germany.,Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Konstantin Okonechnikov
- Hopp-Children's Cancer Center Heidelberg (KiTZ), 69120 Heidelberg, Germany.,Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Nadja V Batora
- Hopp-Children's Cancer Center Heidelberg (KiTZ), 69120 Heidelberg, Germany.,Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Jessica Clark
- Hopp-Children's Cancer Center Heidelberg (KiTZ), 69120 Heidelberg, Germany.,Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Patricia B G Silva
- Hopp-Children's Cancer Center Heidelberg (KiTZ), 69120 Heidelberg, Germany.,Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Mikaella Vouri
- Hopp-Children's Cancer Center Heidelberg (KiTZ), 69120 Heidelberg, Germany.,Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Sjoerd van Rijn
- Hopp-Children's Cancer Center Heidelberg (KiTZ), 69120 Heidelberg, Germany.,Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Laura Sieber
- Hopp-Children's Cancer Center Heidelberg (KiTZ), 69120 Heidelberg, Germany.,Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Britta Statz
- Hopp-Children's Cancer Center Heidelberg (KiTZ), 69120 Heidelberg, Germany.,Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Micah D Gearhart
- Department of Genetics, Cell Biology, and Development, Masonic Cancer Center, Developmental Biology Center, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Ryo Shiraishi
- Department of Biochemistry and Cellular Biology, National Institute of Neuroscience, National Center of Neurology and Psychiatry (NCNP), Tokyo 187-0031, Japan
| | - Norman Mack
- Hopp-Children's Cancer Center Heidelberg (KiTZ), 69120 Heidelberg, Germany.,Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Brent A Orr
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Andrey Korshunov
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.,Department of Neuropathology, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Brian L Gudenas
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Kyle S Smith
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Audrey L Mercier
- Institut Curie, PSL Research University, UMR 3347, Centre National de la Recherche Scientifique (CNRS), U1021, Institut National de la Santé et de la Recherche Médicale (INSERM), Orsay 91405, France.,Université Paris Sud, Université, UMR 3347, CNRS, U1021, INSERM, Orsay 91405, France
| | - Olivier Ayrault
- Institut Curie, PSL Research University, UMR 3347, Centre National de la Recherche Scientifique (CNRS), U1021, Institut National de la Santé et de la Recherche Médicale (INSERM), Orsay 91405, France.,Université Paris Sud, Université, UMR 3347, CNRS, U1021, INSERM, Orsay 91405, France
| | - Mikio Hoshino
- Department of Biochemistry and Cellular Biology, National Institute of Neuroscience, National Center of Neurology and Psychiatry (NCNP), Tokyo 187-0031, Japan
| | - Marcel Kool
- Hopp-Children's Cancer Center Heidelberg (KiTZ), 69120 Heidelberg, Germany.,Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), 69120 Heidelberg, Germany.,Princess Maxima Center for Pediatric Oncology, 3584 CS Utrecht, The Netherlands
| | - Katja von Hoff
- Department for Paediatric Oncology and Haematology, Charité University Medicine, 13354 Berlin, Germany
| | - Norbert Graf
- Department for Pediatric Oncology and Hematology, Universitätsklinikum des Saarlandes, 66421 Homburg, Germany
| | - Gudrun Fleischhack
- Pediatric Haematology and Oncology, Pediatrics III, University Hospital of Essen, 45147 Essen, Germany
| | - Vivian J Bardwell
- Department of Genetics, Cell Biology, and Development, Masonic Cancer Center, Developmental Biology Center, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Stefan M Pfister
- Hopp-Children's Cancer Center Heidelberg (KiTZ), 69120 Heidelberg, Germany.,Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), 69120 Heidelberg, Germany.,Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Paul A Northcott
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Daisuke Kawauchi
- Hopp-Children's Cancer Center Heidelberg (KiTZ), 69120 Heidelberg, Germany.,Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
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6
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Waszak SM, Robinson GW, Gudenas BL, Smith KS, Forget A, Kojic M, Garcia-Lopez J, Hadley J, Hamilton KV, Indersie E, Buchhalter I, Kerssemakers J, Jäger N, Sharma T, Rausch T, Kool M, Sturm D, Jones DTW, Vasilyeva A, Tatevossian RG, Neale G, Lombard B, Loew D, Nakitandwe J, Rusch M, Bowers DC, Bendel A, Partap S, Chintagumpala M, Crawford J, Gottardo NG, Smith A, Dufour C, Rutkowski S, Eggen T, Wesenberg F, Kjaerheim K, Feychting M, Lannering B, Schüz J, Johansen C, Andersen TV, Röösli M, Kuehni CE, Grotzer M, Remke M, Puget S, Pajtler KW, Milde T, Witt O, Ryzhova M, Korshunov A, Orr BA, Ellison DW, Brugieres L, Lichter P, Nichols KE, Gajjar A, Wainwright BJ, Ayrault O, Korbel JO, Northcott PA, Pfister SM. Germline Elongator mutations in Sonic Hedgehog medulloblastoma. Nature 2020; 580:396-401. [PMID: 32296180 PMCID: PMC7430762 DOI: 10.1038/s41586-020-2164-5] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 01/30/2020] [Indexed: 12/13/2022]
Abstract
Cancer genomics has revealed many genes and core molecular processes that contribute to human malignancies, but the genetic and molecular bases of many rare cancers remains unclear. Genetic predisposition accounts for 5 to 10% of cancer diagnoses in children1,2, and genetic events that cooperate with known somatic driver events are poorly understood. Pathogenic germline variants in established cancer predisposition genes have been recently identified in 5% of patients with the malignant brain tumour medulloblastoma3. Here, by analysing all protein-coding genes, we identify and replicate rare germline loss-of-function variants across ELP1 in 14% of paediatric patients with the medulloblastoma subgroup Sonic Hedgehog (MBSHH). ELP1 was the most common medulloblastoma predisposition gene and increased the prevalence of genetic predisposition to 40% among paediatric patients with MBSHH. Parent-offspring and pedigree analyses identified two families with a history of paediatric medulloblastoma. ELP1-associated medulloblastomas were restricted to the molecular SHHα subtype4 and characterized by universal biallelic inactivation of ELP1 owing to somatic loss of chromosome arm 9q. Most ELP1-associated medulloblastomas also exhibited somatic alterations in PTCH1, which suggests that germline ELP1 loss-of-function variants predispose individuals to tumour development in combination with constitutive activation of SHH signalling. ELP1 is the largest subunit of the evolutionarily conserved Elongator complex, which catalyses translational elongation through tRNA modifications at the wobble (U34) position5,6. Tumours from patients with ELP1-associated MBSHH were characterized by a destabilized Elongator complex, loss of Elongator-dependent tRNA modifications, codon-dependent translational reprogramming, and induction of the unfolded protein response, consistent with loss of protein homeostasis due to Elongator deficiency in model systems7-9. Thus, genetic predisposition to proteome instability may be a determinant in the pathogenesis of paediatric brain cancers. These results support investigation of the role of protein homeostasis in other cancer types and potential for therapeutic interference.
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Affiliation(s)
- Sebastian M Waszak
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Giles W Robinson
- Department of Oncology, Division of Neuro-Oncology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Brian L Gudenas
- Department of Developmental Neurobiology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Kyle S Smith
- Department of Developmental Neurobiology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Antoine Forget
- Université Paris Sud, Université Paris-Saclay, CNRS UMR 3347, INSERM U1021, Orsay, France
| | - Marija Kojic
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
| | - Jesus Garcia-Lopez
- Department of Developmental Neurobiology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Jennifer Hadley
- Department of Developmental Neurobiology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Kayla V Hamilton
- Department of Oncology, Division of Cancer Predisposition, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Emilie Indersie
- Université Paris Sud, Université Paris-Saclay, CNRS UMR 3347, INSERM U1021, Orsay, France
| | - Ivo Buchhalter
- Omics IT and Data Management Core Facility (W610), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jules Kerssemakers
- Omics IT and Data Management Core Facility (W610), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Natalie Jäger
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Tanvi Sharma
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Tobias Rausch
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Marcel Kool
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Dominik Sturm
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Pediatric Glioma Research Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - David T W Jones
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Pediatric Glioma Research Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Aksana Vasilyeva
- Cancer Center Administration, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Ruth G Tatevossian
- Department of Pathology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Geoffrey Neale
- Hartwell Center, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Bérangère Lombard
- Institut Curie, PSL Research University, Centre de Recherche, Laboratoire de Spectrométrie de Masse Protéomique, Paris, France
| | - Damarys Loew
- Institut Curie, PSL Research University, Centre de Recherche, Laboratoire de Spectrométrie de Masse Protéomique, Paris, France
| | - Joy Nakitandwe
- Department of Pathology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Michael Rusch
- Department of Computational Biology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Daniel C Bowers
- Division of Pediatric Hematology-Oncology, University of Texas Southwestern Medical School, Dallas, TX, USA
| | - Anne Bendel
- Department of Pediatric Hematology and Oncology, Children's Hospitals and Clinics of Minnesota, Minnesota, MN, USA
| | - Sonia Partap
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| | | | - John Crawford
- Department of Neurosciences, University of California San Diego and Rady Children's Hospital, San Diego, CA, USA
- Department of Pediatrics, University of California San Diego and Rady Children's Hospital, San Diego, CA, USA
| | - Nicholas G Gottardo
- Department of Paediatric and Adolescent Oncology/Haematology, Perth Children's Hospital and Brain Tumour Research Programme, Telethon Kids Institute, Perth, Western Australia, Australia
| | - Amy Smith
- Arnold Palmer Hospital Center for Children's Cancer, Orlando, FL, USA
| | - Christelle Dufour
- Gustave Roussy, Université Paris-Saclay, Department of Pediatric and Adolescent Oncology, Villejuif, France
| | - Stefan Rutkowski
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Tone Eggen
- The Cancer Registry of Norway, Majorstuen, Oslo, Norway
| | - Finn Wesenberg
- Department of Research, Cancer Registry of Norway, Institute of Population-Based Cancer Research, Oslo, Norway
| | - Kristina Kjaerheim
- Department of Research, Cancer Registry of Norway, Institute of Population-Based Cancer Research, Oslo, Norway
| | - Maria Feychting
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Birgitta Lannering
- Department of Pediatrics, University of Gothenburg, The Queen Silvia Children's Hospital, Gothenburg, Sweden
| | - Joachim Schüz
- Section of Environment and Radiation, International Agency for Research on Cancer (IARC), Lyon, France
| | - Christoffer Johansen
- Oncology Clinic, Finsen Centre, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
- Danish Cancer Society Research Center, Danish Cancer Society, Copenhagen, Denmark
| | - Tina V Andersen
- Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, University of Basel, Basel, Switzerland
| | - Martin Röösli
- Swiss Childhood Cancer Registry, Institute of Social and Preventive Medicine University of Bern, Bern, Switzerland
| | - Claudia E Kuehni
- Swiss Childhood Cancer Registry, Institute of Social and Preventive Medicine University of Bern, Bern, Switzerland
- Department of Paediatric Haematology and Oncology, University Children's Hospital, Bern, Switzerland
| | - Michael Grotzer
- University Children's Hospital of Zurich, Zurich, Switzerland
| | - Marc Remke
- Department of Pediatric Oncology, Hematology, and Clinical Immunology, Medical Faculty, University Hospital Düsseldorf, Düsseldorf, Germany
| | - Stéphanie Puget
- Department of Pediatric Neurosurgery, Necker Hospital, Université de Paris, Paris, France
| | - Kristian W Pajtler
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Till Milde
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Olaf Witt
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Marina Ryzhova
- Department of Neuropathology, Burdenko Neurosurgical Institute, Moscow, Russia
| | - Andrey Korshunov
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Neuropathology, University Hospital, Heidelberg, Germany
| | - Brent A Orr
- Department of Pathology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - David W Ellison
- Department of Pathology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Laurence Brugieres
- Gustave Roussy, Université Paris-Saclay, Department of Pediatric and Adolescent Oncology, Villejuif, France
| | - Peter Lichter
- Division of Molecular Genetics, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center Heidelberg (DKFZ), Heidelberg, Germany
| | - Kim E Nichols
- Department of Oncology, Division of Cancer Predisposition, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Amar Gajjar
- Department of Oncology, Division of Neuro-Oncology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Brandon J Wainwright
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
| | - Olivier Ayrault
- Université Paris Sud, Université Paris-Saclay, CNRS UMR 3347, INSERM U1021, Orsay, France
| | - Jan O Korbel
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany.
| | - Paul A Northcott
- Department of Developmental Neurobiology, St Jude Children's Research Hospital, Memphis, TN, USA.
| | - Stefan M Pfister
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.
- Division of Pediatric Neurooncology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany.
- Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany.
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Gudenas BL, Wang J, Kuang SZ, Wei AQ, Cogill SB, Wang LJ. Genomic data mining for functional annotation of human long noncoding RNAs. J Zhejiang Univ Sci B 2019; 20:476-487. [PMID: 31090273 DOI: 10.1631/jzus.b1900162] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Life may have begun in an RNA world, which is supported by increasing evidence of the vital role that RNAs perform in biological systems. In the human genome, most genes actually do not encode proteins; they are noncoding RNA genes. The largest class of noncoding genes is known as long noncoding RNAs (lncRNAs), which are transcripts greater in length than 200 nucleotides, but with no protein-coding capacity. While some lncRNAs have been demonstrated to be key regulators of gene expression and 3D genome organization, most lncRNAs are still uncharacterized. We thus propose several data mining and machine learning approaches for the functional annotation of human lncRNAs by leveraging the vast amount of data from genetic and genomic studies. Recent results from our studies and those of other groups indicate that genomic data mining can give insights into lncRNA functions and provide valuable information for experimental studies of candidate lncRNAs associated with human disease.
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Affiliation(s)
- Brian L Gudenas
- Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina 29634, USA
| | - Jun Wang
- Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina 29634, USA
| | - Shu-Zhen Kuang
- Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina 29634, USA
| | - An-Qi Wei
- Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina 29634, USA
| | - Steven B Cogill
- Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina 29634, USA
| | - Liang-Jiang Wang
- Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina 29634, USA
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Abstract
Long non-coding RNAs are involved in biological processes throughout the cell including the nucleus, chromatin and cytosol. However, most lncRNAs remain unannotated and functional annotation of lncRNAs is difficult due to their low conservation and their tissue and developmentally specific expression. LncRNA subcellular localization is highly informative regarding its biological function, although it is difficult to discover because few prediction methods currently exist. While protein subcellular localization prediction is a well-established research field, lncRNA localization prediction is a novel research problem. We developed DeepLncRNA, a deep learning algorithm which predicts lncRNA subcellular localization directly from lncRNA transcript sequences. We analyzed 93 strand-specific RNA-seq samples of nuclear and cytosolic fractions from multiple cell types to identify differentially localized lncRNAs. We then extracted sequence-based features from the lncRNAs to construct our DeepLncRNA model, which achieved an accuracy of 72.4%, sensitivity of 83%, specificity of 62.4% and area under the receiver operating characteristic curve of 0.787. Our results suggest that primary sequence motifs are a major driving force in the subcellular localization of lncRNAs.
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Affiliation(s)
- Brian L Gudenas
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC, USA
| | - Liangjiang Wang
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC, USA.
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9
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Gudenas BL, Srivastava AK, Wang L. Integrative genomic analyses for identification and prioritization of long non-coding RNAs associated with autism. PLoS One 2017; 12:e0178532. [PMID: 28562671 PMCID: PMC5451068 DOI: 10.1371/journal.pone.0178532] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 05/15/2017] [Indexed: 12/20/2022] Open
Abstract
Genetic studies have identified many risk loci for autism spectrum disorder (ASD) although causal factors in the majority of cases are still unknown. Currently, known ASD risk genes are all protein-coding genes; however, the vast majority of transcripts in humans are non-coding RNAs (ncRNAs) which do not encode proteins. Recently, long non-coding RNAs (lncRNAs) were shown to be highly expressed in the human brain and crucial for normal brain development. We have constructed a computational pipeline for the integration of various genomic datasets to identify lncRNAs associated with ASD. This pipeline utilizes differential gene expression patterns in affected tissues in conjunction with gene co-expression networks in tissue-matched non-affected samples. We analyzed RNA-seq data from the cortical brain tissues from ASD cases and controls to identify lncRNAs differentially expressed in ASD. We derived a gene co-expression network from an independent human brain developmental transcriptome and detected a convergence of the differentially expressed lncRNAs and known ASD risk genes into specific co-expression modules. Co-expression network analysis facilitates the discovery of associations between previously uncharacterized lncRNAs with known ASD risk genes, affected molecular pathways and at-risk developmental time points. In addition, we show that some of these lncRNAs have a high degree of overlap with major CNVs detected in ASD genetic studies. By utilizing this integrative approach comprised of differential expression analysis in affected tissues and connectivity metrics from a developmental co-expression network, we have prioritized a set of candidate ASD-associated lncRNAs. The identification of lncRNAs as novel ASD susceptibility genes could help explain the genetic pathogenesis of ASD.
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Affiliation(s)
- Brian L. Gudenas
- Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina, United States of America
| | - Anand K. Srivastava
- J.C. Self Research Institute of Human Genetics, Greenwood Genetic Center, Greenwood, South Carolina, United States of America
| | - Liangjiang Wang
- Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina, United States of America
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10
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Gudenas BL, Wang L. Gene Coexpression Networks in Human Brain Developmental Transcriptomes Implicate the Association of Long Noncoding RNAs with Intellectual Disability. Bioinform Biol Insights 2015; 9:21-7. [PMID: 26523118 PMCID: PMC4624004 DOI: 10.4137/bbi.s29435] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Revised: 09/07/2015] [Accepted: 09/09/2015] [Indexed: 01/12/2023] Open
Abstract
The advent of next-generation sequencing for genetic diagnoses of complex developmental disorders, such as intellectual disability (ID), has facilitated the identification of hundreds of predisposing genetic variants. However, there still exists a vast gap in our knowledge of causal genetic factors for ID as evidenced by low diagnostic yield of genetic screening, in which identifiable genetic causes are not found for the majority of ID cases. Most methods of genetic screening focus on protein-coding genes; however, noncoding RNAs may outnumber protein-coding genes and play important roles in brain development. Long noncoding RNAs (lncRNAs) specifically have been shown to be enriched in the brain and have diverse roles in gene regulation at the transcriptional and posttranscriptional levels. LncRNAs are a vastly uncharacterized group of noncoding genes, which could function in brain development and harbor ID-predisposing genetic variants. We analyzed lncRNAs for coexpression with known ID genes and affected biological pathways within a weighted gene coexpression network derived from RNA-sequencing data spanning human brain development. Several ID-associated gene modules were found to be enriched for lncRNAs, known ID genes, and affected biological pathways. Utilizing a list of de novo and pathogenic copy number variants detected in ID probands, we identified lncRNAs overlapping these genetic structural variants. By integrating our results, we have made a prioritized list of potential ID-associated lncRNAs based on the developing brain gene coexpression network and genetic structural variants found in ID probands.
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Affiliation(s)
- Brian L Gudenas
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC, USA
| | - Liangjiang Wang
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC, USA
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