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Ma RK, Tsai PY, Farghli AR, Shumway A, Kanke M, Gordan JD, Gujral TS, Vakili K, Nukaya M, Noetzli L, Ronnekleiv-Kelly S, Broom W, Barrow J, Sethupathy P. DNAJB1-PRKACA fusion protein-regulated LINC00473 promotes tumor growth and alters mitochondrial fitness in fibrolamellar carcinoma. PLoS Genet 2024; 20:e1011216. [PMID: 38512964 PMCID: PMC11020935 DOI: 10.1371/journal.pgen.1011216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 09/14/2023] [Revised: 04/16/2024] [Accepted: 03/08/2024] [Indexed: 03/23/2024] Open
Abstract
Fibrolamellar carcinoma (FLC) is a rare liver cancer that disproportionately affects adolescents and young adults. Currently, no standard of care is available and there remains a dire need for new therapeutics. Most patients harbor the fusion oncogene DNAJB1-PRKACA (DP fusion), but clinical inhibitors are not yet developed and it is critical to identify downstream mediators of FLC pathogenesis. Here, we identify long noncoding RNA LINC00473 among the most highly upregulated genes in FLC tumors and determine that it is strongly suppressed by RNAi-mediated inhibition of the DP fusion in FLC tumor epithelial cells. We show by loss- and gain-of-function studies that LINC00473 suppresses apoptosis, increases the expression of FLC marker genes, and promotes FLC growth in cell-based and in vivo disease models. Mechanistically, LINC00473 plays an important role in promoting glycolysis and altering mitochondrial activity. Specifically, LINC00473 knockdown leads to increased spare respiratory capacity, which indicates mitochondrial fitness. Overall, we propose that LINC00473 could be a viable target for this devastating disease.
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Affiliation(s)
- Rosanna K. Ma
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
| | - Pei-Yin Tsai
- Division of Nutritional Sciences, Cornell University, Ithaca, New York, United States of America
| | - Alaa R. Farghli
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
| | - Alexandria Shumway
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
| | - Matt Kanke
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
| | - John D. Gordan
- Division of Hematology/Oncology, Helen Diller Family Comprehensive Cancer Center, UCSF, San Francisco, California, United States of America
| | - Taranjit S. Gujral
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - Khashayar Vakili
- Department of Surgery, Boston Children’s Hospital, Boston, Massachusetts, United States of America
| | - Manabu Nukaya
- Department of Surgery, Division of Surgical Oncology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, United States of America
| | - Leila Noetzli
- Alnylam Pharmaceuticals, Cambridge, Massachusetts, United States of America
| | - Sean Ronnekleiv-Kelly
- Department of Surgery, Division of Surgical Oncology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, United States of America
| | - Wendy Broom
- Alnylam Pharmaceuticals, Cambridge, Massachusetts, United States of America
| | - Joeva Barrow
- Division of Nutritional Sciences, Cornell University, Ithaca, New York, United States of America
| | - Praveen Sethupathy
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
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Chen KA, Nishiyama NC, Kennedy Ng MM, Shumway A, Joisa CU, Schaner MR, Lian G, Beasley C, Zhu LC, Bantumilli S, Kapadia MR, Gomez SM, Furey TS, Sheikh SZ. Linking gene expression to clinical outcomes in pediatric Crohn's disease using machine learning. Sci Rep 2024; 14:2667. [PMID: 38302662 PMCID: PMC10834600 DOI: 10.1038/s41598-024-52678-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 07/13/2023] [Accepted: 01/21/2024] [Indexed: 02/03/2024] Open
Abstract
Pediatric Crohn's disease (CD) is characterized by a severe disease course with frequent complications. We sought to apply machine learning-based models to predict risk of developing future complications in pediatric CD using ileal and colonic gene expression. Gene expression data was generated from 101 formalin-fixed, paraffin-embedded (FFPE) ileal and colonic biopsies obtained from treatment-naïve CD patients and controls. Clinical outcomes including development of strictures or fistulas and progression to surgery were analyzed using differential expression and modeled using machine learning. Differential expression analysis revealed downregulation of pathways related to inflammation and extra-cellular matrix production in patients with strictures. Machine learning-based models were able to incorporate colonic gene expression and clinical characteristics to predict outcomes with high accuracy. Models showed an area under the receiver operating characteristic curve (AUROC) of 0.84 for strictures, 0.83 for remission, and 0.75 for surgery. Genes with potential prognostic importance for strictures (REG1A, MMP3, and DUOX2) were not identified in single gene differential analysis but were found to have strong contributions to predictive models. Our findings in FFPE tissue support the importance of colonic gene expression and the potential for machine learning-based models in predicting outcomes for pediatric CD.
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Affiliation(s)
- Kevin A Chen
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, 7314 Medical Biomolecular Research Building, 111 Mason Farm Road, Chapel Hill, NC, 27599, USA
- Department of Surgery, University of North Carolina at Chapel Hill, Chapel Hill, USA
| | - Nina C Nishiyama
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, 7314 Medical Biomolecular Research Building, 111 Mason Farm Road, Chapel Hill, NC, 27599, USA
- Departments of Genetics and Biology, Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, 5022 Genetic Medicine Building, 120 Mason Farm Road, Chapel Hill, NC, 27599, USA
| | - Meaghan M Kennedy Ng
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, 7314 Medical Biomolecular Research Building, 111 Mason Farm Road, Chapel Hill, NC, 27599, USA
- Departments of Genetics and Biology, Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, 5022 Genetic Medicine Building, 120 Mason Farm Road, Chapel Hill, NC, 27599, USA
| | - Alexandria Shumway
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill, Chapel Hill, USA
| | - Chinmaya U Joisa
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, USA
| | - Matthew R Schaner
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, 7314 Medical Biomolecular Research Building, 111 Mason Farm Road, Chapel Hill, NC, 27599, USA
| | - Grace Lian
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, 7314 Medical Biomolecular Research Building, 111 Mason Farm Road, Chapel Hill, NC, 27599, USA
| | - Caroline Beasley
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, 7314 Medical Biomolecular Research Building, 111 Mason Farm Road, Chapel Hill, NC, 27599, USA
| | - Lee-Ching Zhu
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, USA
| | - Surekha Bantumilli
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, USA
| | - Muneera R Kapadia
- Department of Surgery, University of North Carolina at Chapel Hill, Chapel Hill, USA
| | - Shawn M Gomez
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, USA
| | - Terrence S Furey
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, 7314 Medical Biomolecular Research Building, 111 Mason Farm Road, Chapel Hill, NC, 27599, USA.
- Departments of Genetics and Biology, Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, 5022 Genetic Medicine Building, 120 Mason Farm Road, Chapel Hill, NC, 27599, USA.
| | - Shehzad Z Sheikh
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, 7314 Medical Biomolecular Research Building, 111 Mason Farm Road, Chapel Hill, NC, 27599, USA.
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Carlston C, Huntington A, Dahl M, Shumway A, Albertine K, Moyer-Mileur L. Total Protein and Zinc Content are Increased in Milk of Preterm Ewes. J Investig Med 2006. [DOI: 10.1177/108155890605401s127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
| | | | - M.J. Dahl
- University of Utah, Salt Lake City, UT
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Albertine K, Null D, Dahl M, Shumway A, Lane R. Lung Parenchymal Development is Improved in Preterm Lambs Managed by Nasal Continuous Positive Airway Pressure for 21 Days. J Investig Med 2006. [DOI: 10.1177/108155890605401s48] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
| | - D.M. Null
- University of Utah, Salt Lake City, UT
| | - M.J. Dahl
- University of Utah, Salt Lake City, UT
| | | | - R.H. Lane
- University of Utah, Salt Lake City, UT
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Alvord J, Dong L, Dahl M, Shumway A, Null D, Lane R, Albertine K. Neuronal Death Occurs in the Brain of Preterm Lambs Managed by Conventional Ventilation for 3 Days. J Investig Med 2006. [DOI: 10.1177/108155890605401s120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- J. Alvord
- Pediatrics, University of Utah, Salt Lake City, UT
| | - L. Dong
- Pediatrics, University of Utah, Salt Lake City, UT
| | - M.J. Dahl
- Pediatrics, University of Utah, Salt Lake City, UT
| | - A. Shumway
- Pediatrics, University of Utah, Salt Lake City, UT
| | - D.M. Null
- Pediatrics, University of Utah, Salt Lake City, UT
| | - R.H. Lane
- Pediatrics, University of Utah, Salt Lake City, UT
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