The Genomics Core has the privilege of working with many outstanding investigators that cross a wide range of research topics. Listed here are just a few of the projects that the Genomics Core has recently contributed to.
Remember to acknowledge the valuable services provided by the Genomics Core in your research papers and publications:
"This research was supported by the Genomics Core Facility of the CWRU School of Medicine."
Cohn EF, Clayton BLL, Madhavan M, et al. Pervasive environmental chemicals impair oligodendrocyte development. Nat Neurosci. 2024;27(5):836-845. doi:10.1038/s41593-024-01599-2
Leir, SH., Tkachenko, S., Paranjapye, A. et al. Stellate cells are in utero markers of pancreatic disease in cystic fibrosis. Mol Med 30, 115 (2024). https://doi.org/10.1186/s10020-024-00871-2
Benjamin L.L. Clayton, Lilianne Barbar, Maria Sapar, Kriti Kalpana, Chandrika Rao, Bianca Migliori, Tomasz Rusielewicz, Daniel Paull, Katie Brenner, Dorota Moroziewicz, Ilana Katz Sand, Patrizia Casaccia, Paul J. Tesar, Valentina Fossati. Patient iPSC models reveal glia-intrinsic phenotypes in multiple sclerosis. Cell Stem Cell 31,11 (2024). https://doi.org/10.1016/j.stem.2024.08.002.
Clayton BLL, Kristell JD, Allan KC, et al. A phenotypic screening platform for identifying chemical modulators of astrocyte reactivity. Nat Neurosci. 2024;27(4):656-665. doi:10.1038/s41593-024-01580-z
Vaidyanathan S, Kerschner JL, Paranjapye A, et al. Investigating adverse genomic and regulatory changes caused by replacement of the full-length CFTR cDNA using Cas9 and AAV. Mol Ther Nucleic Acids. 2024;35(1):102134. Published 2024 Feb 2. doi:10.1016/j.omtn.2024.102134
Kerschner JL, Paranjapye A, Vaghela N, Wilson MD, Harris A. An ectopic enhancer restores CFTR expression through de novo chromatin looping. Gene Ther. 2023;30(6):478-486. doi:10.1038/s41434-022-00378-7
Fu C, Ngo J, Zhang S, et al. Novel correlative analysis identifies multiple genomic variations impacting ASD with macrocephaly. Hum Mol Genet. 2023;32(10):1589-1606. doi:10.1093/hmg/ddac300
Bayik D, Bartels CF, Lovrenert K, et al. Distinct Cell Adhesion Signature Defines Glioblastoma Myeloid-Derived Suppressor Cell Subsets [published correction appears in Cancer Res. 2023 May 15;83(10):1757. doi: 10.1158/0008-5472.CAN-23-0773.]. Cancer Res. 2022;82(22):4274-4287. doi:10.1158/0008-5472.CAN-21-3840
Pontius WD, Hong ES, Faber ZJ, et al. Temporal chromatin accessibility changes define transcriptional states essential for osteosarcoma metastasis. Nat Commun. 2023;14(1):7209. Published 2023 Nov 8. doi:10.1038/s41467-023-42656-x
Martin S, Allan KC, Pinkard O, Sweet T, Tesar PJ, Coller J. Oligodendrocyte differentiation alters tRNA modifications and codon optimality-mediated mRNA decay. Nat Commun. 2022;13(1):5003. Published 2022 Aug 25. doi:10.1038/s41467-022-32766-3
Farrokhian N, Maltas J, Dinh M, et al. Measuring competitive exclusion in non-small cell lung cancer. Sci Adv. 2022;8(26):eabm7212. doi:10.1126/sciadv.abm7212
LaForce GR, Farr JS, Liu J, et al. Suppression of premature transcription termination leads to reduced mRNA isoform diversity and neurodegeneration. Neuron. 2022;110(8):1340-1357.e7. doi:10.1016/j.neuron.2022.01.018
Krokowski D, Jobava R, Szkop KJ, et al. Stress-induced perturbations in intracellular amino acids reprogram mRNA translation in osmoadaptation independently of the ISR. Cell Rep. 2022;40(3):111092. doi:10.1016/j.celrep.2022.111092
Kitt MM, Tabuchi N, Spencer WC, et al. An adult-stage transcriptional program for survival of serotonergic connectivity. Cell Rep. 2022;39(3):110711. doi:10.1016/j.celrep.2022.110711
Mucha B, Qie S, Bajpai S, et al. Tumor suppressor mediated ubiquitylation of hnRNPK is a barrier to oncogenic translation. Nat Commun. 2022;13(1):6614. Published 2022 Nov 3. doi:10.1038/s41467-022-34402-6
Paranjapye A, NandyMazumdar M, Harris A. Krüppel-Like Factor 5 Regulates CFTR Expression Through Repression by Maintaining Chromatin Architecture Coupled with Direct Enhancer Activation. J Mol Biol. 2022;434(10):167561. doi:10.1016/j.jmb.2022.167561
Allan KC, Hu LR, Scavuzzo MA, et al. Non-canonical Targets of HIF1a Impair Oligodendrocyte Progenitor Cell Function. Cell Stem Cell. 2021;28(2):257-272.e11. doi:10.1016/j.stem.2020.09.019
Adrian Gomez-Nguyen, Abigail R. Basson, Luc Dark-Fleury, Kristen Hsu, Abdullah Osme, Paola Menghini, Theresa T. Pizarro, Fabio Cominelli. Parabacteroides distasonis induces depressive-like behavior in a mouse model of Crohn’s disease. Brain, Behavior, and Immunity. 2021;98:245-250. https://doi.org/10.1016/j.bbi.2021.08.218.
Sharma D, Zagore LL, Brister MM, et al. The kinetic landscape of an RNA-binding protein in cells. Nature. 2021;591(7848):152-156. doi:10.1038/s41586-021-03222-x
Jobava R, Mao Y, Guan BJ, et al. Adaptive translational pausing is a hallmark of the cellular response to severe environmental stress. Mol Cell. 2021;81(20):4191-4208.e8. doi:10.1016/j.molcel.2021.09.029
Taftaf R, Liu X, Singh S, et al. ICAM1 initiates CTC cluster formation and trans-endothelial migration in lung metastasis of breast cancer. Nat Commun. 2021;12(1):4867. Published 2021 Aug 11. doi:10.1038/s41467-021-25189-z
Tzeng A, Sangwan N, Jia M, et al. Human breast microbiome correlates with prognostic features and immunological signatures in breast cancer. Genome Med. 2021;13(1):60. Published 2021 Apr 16. doi:10.1186/s13073-021-00874-2
Factor DC, Barbeau AM, Allan KC, et al. Cell Type-Specific Intralocus Interactions Reveal Oligodendrocyte Mechanisms in MS. Cell. 2020;181(2):382-395.e21. doi:10.1016/j.cell.2020.03.002
Elitt MS, Barbar L, Shick HE, et al. Suppression of proteolipid protein rescues Pelizaeus-Merzbacher disease. Nature. 2020;585(7825):397-403. doi:10.1038/s41586-020-2494-3
Pinkard O, McFarland S, Sweet T, Coller J. Quantitative tRNA-sequencing uncovers metazoan tissue-specific tRNA regulation. Nat Commun. 2020;11(1):4104. Published 2020 Aug 14. doi:10.1038/s41467-020-17879-x
Basson AR, Gomez-Nguyen A, Menghini P, et al. Human Gut Microbiome Transplantation in Ileitis Prone Mice: A Tool for the Functional Characterization of the Microbiota in Inflammatory Bowel Disease Patients. Inflamm Bowel Dis. 2020;26(3):347-359. doi:10.1093/ibd/izz242
Verma S, Shankar E, Chan ER, Gupta S. Metabolic Reprogramming and Predominance of Solute Carrier Genes during Acquired Enzalutamide Resistance in Prostate Cancer. Cells. 2020;9(12):2535. Published 2020 Nov 24. doi:10.3390/cells9122535
Verma S, Shankar E, Kalayci FNC, et al. Androgen Deprivation Induces Transcriptional Reprogramming in Prostate Cancer Cells to Develop Stem Cell-Like Characteristics. Int J Mol Sci. 2020;21(24):9568. Published 2020 Dec 16. doi:10.3390/ijms21249568
Samsa WE, Mamidi MK, Bashur LA, et al. The crucial p53-dependent oncogenic role of JAB1 in osteosarcoma in vivo. Oncogene. 2020;39(23):4581-4591. doi:10.1038/s41388-020-1320-6
Seachrist DD, Hannigan MM, Ingles NN, et al. The transcriptional repressor BCL11A promotes breast cancer metastasis. J Biol Chem. 2020;295(33):11707-11719. doi:10.1074/jbc.RA120.014018
Hao S, Roesch EA, Perez A, et al. Inactivation of CFTR by CRISPR/Cas9 alters transcriptional regulation of inflammatory pathways and other networks. J Cyst Fibros. 2020;19(1):34-39. doi:10.1016/j.jcf.2019.05.003
Meserve EE, Strickland KC, Miron A, et al. Evidence of a Monoclonal Origin for Bilateral Serous Tubal Intraepithelial Neoplasia. Int J Gynecol Pathol. 2019;38(5):443-448. doi:10.1097/PGP.0000000000000534
Patel R, Zhang L, Desai A, et al. Mlh1 deficiency increases the risk of hematopoietic malignancy after simulated space radiation exposure. Leukemia. 2019;33(5):1135-1147. doi:10.1038/s41375-018-0269-8
Hung S, Saiakhova A, Faber ZJ, et al. Mismatch repair-signature mutations activate gene enhancers across human colorectal cancer epigenomes. Elife. 2019;8:e40760. Published 2019 Feb 13. doi:10.7554/eLife.40760
Papp-Wallace KM, Zeiser ET, Becka SA, et al. Ceftazidime-Avibactam in Combination With Fosfomycin: A Novel Therapeutic Strategy Against Multidrug-Resistant Pseudomonas aeruginosa. J Infect Dis. 2019;220(4):666-676. doi:10.1093/infdis/jiz149
Lager AM, Corradin OG, Cregg JM, et al. Rapid functional genetics of the oligodendrocyte lineage using pluripotent stem cells. Nat Commun. 2018;9(1):3708. Published 2018 Sep 13. doi:10.1038/s41467-018-06102-7
Madhavan M, Nevin ZS, Shick HE, et al. Induction of myelinating oligodendrocytes in human cortical spheroids. Nat Methods. 2018;15(9):700-706. doi:10.1038/s41592-018-0081-4
Elitt MS, Shick HE, Madhavan M, et al. Chemical Screening Identifies Enhancers of Mutant Oligodendrocyte Survival and Unmasks a Distinct Pathological Phase in Pelizaeus-Merzbacher Disease. Stem Cell Reports. 2018;11(3):711-726. doi:10.1016/j.stemcr.2018.07.015
Smolko AE, Shapiro-Kulnane L, Salz HK. The H3K9 methyltransferase SETDB1 maintains female identity in Drosophila germ cells. Nat Commun. 2018;9(1):4155. Published 2018 Oct 8. doi:10.1038/s41467-018-06697-x
Zagore LL, Sweet TJ, Hannigan MM, et al. DAZL Regulates Germ Cell Survival through a Network of PolyA-Proximal mRNA Interactions. Cell Rep. 2018;25(5):1225-1240.e6. doi:10.1016/j.celrep.2018.10.012
Hanson G, Alhusaini N, Morris N, Sweet T, Coller J. Translation elongation and mRNA stability are coupled through the ribosomal A-site. RNA. 2018;24(10):1377-1389. doi:10.1261/rna.066787.118
Soong TR, Howitt BE, Miron A, et al. Evidence for lineage continuity between early serous proliferations (ESPs) in the Fallopian tube and disseminated high-grade serous carcinomas. J Pathol. 2018;246(3):344-351. doi:10.1002/path.5145
McHugh DR, Steele MS, Valerio DM, et al. A G542X cystic fibrosis mouse model for examining nonsense mutation directed therapies. PLoS One. 2018;13(6):e0199573. Published 2018 Jun 20. doi:10.1371/journal.pone.0199573