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Townley BA, Buerer L, Tsao N, Bacolla A, Mansoori F, Rusanov T, Clark N, Goodarzi N, Schmidt N, Srivatsan SN, Sun H, Sample RA, Brickner JR, McDonald D, Tsai MS, Walter MJ, Wozniak DF, Holehouse AS, Pena V, Tainer JA, Fairbrother WG, Mosammaparast N. A functional link between lariat debranching enzyme and the intron-binding complex is defective in non-photosensitive trichothiodystrophy. Mol Cell 2023; 83:2258-2275.e11. [PMID: 37369199 PMCID: PMC10483886 DOI: 10.1016/j.molcel.2023.06.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 03/25/2023] [Accepted: 06/06/2023] [Indexed: 06/29/2023]
Abstract
The pre-mRNA life cycle requires intron processing; yet, how intron-processing defects influence splicing and gene expression is unclear. Here, we find that TTDN1/MPLKIP, which is encoded by a gene implicated in non-photosensitive trichothiodystrophy (NP-TTD), functionally links intron lariat processing to spliceosomal function. The conserved TTDN1 C-terminal region directly binds lariat debranching enzyme DBR1, whereas its N-terminal intrinsically disordered region (IDR) binds the intron-binding complex (IBC). TTDN1 loss, or a mutated IDR, causes significant intron lariat accumulation, as well as splicing and gene expression defects, mirroring phenotypes observed in NP-TTD patient cells. A Ttdn1-deficient mouse model recapitulates intron-processing defects and certain neurodevelopmental phenotypes seen in NP-TTD. Fusing DBR1 to the TTDN1 IDR is sufficient to recruit DBR1 to the IBC and circumvents the functional requirement for TTDN1. Collectively, our findings link RNA lariat processing with splicing outcomes by revealing the molecular function of TTDN1.
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Affiliation(s)
- Brittany A Townley
- Department of Pathology & Immunology, Center for Genome Integrity, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Luke Buerer
- Center for Computational Molecular Biology, Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI 02912, USA
| | - Ning Tsao
- Department of Pathology & Immunology, Center for Genome Integrity, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Albino Bacolla
- Department of Molecular and Cellular Oncology, University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA
| | - Fadhel Mansoori
- Department of Pathology & Immunology, Center for Genome Integrity, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Timur Rusanov
- Department of Pathology & Immunology, Center for Genome Integrity, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Nathanial Clark
- Center for Computational Molecular Biology, Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI 02912, USA
| | - Negar Goodarzi
- Mechanisms and Regulation of Splicing Research Group, The Institute of Cancer Research, London, UK
| | - Nicolas Schmidt
- Department of Pathology & Immunology, Center for Genome Integrity, Washington University School of Medicine, St. Louis, MO 63110, USA
| | | | - Hua Sun
- Department of Pathology & Immunology, Center for Genome Integrity, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Reilly A Sample
- Department of Pathology & Immunology, Center for Genome Integrity, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Joshua R Brickner
- Department of Pathology & Immunology, Center for Genome Integrity, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Drew McDonald
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Miaw-Sheue Tsai
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Matthew J Walter
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - David F Wozniak
- Department of Psychiatry, Intellectual and Developmental Disabilities Research Center, Washington University School of Medicine, St. Louis, MO 63110-1093, USA
| | - Alex S Holehouse
- Department of Biochemistry & Molecular Biophysics, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA; Center for Science and Engineering of Living Systems, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Vladimir Pena
- Mechanisms and Regulation of Splicing Research Group, The Institute of Cancer Research, London, UK
| | - John A Tainer
- Department of Molecular and Cellular Oncology, University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA; Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - William G Fairbrother
- Center for Computational Molecular Biology, Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI 02912, USA; Hassenfeld Child Health Innovation Institute of Brown University, Providence, RI 02912, USA.
| | - Nima Mosammaparast
- Department of Pathology & Immunology, Center for Genome Integrity, Washington University School of Medicine, St. Louis, MO 63110, USA.
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Sample RA, Nogueira MF, Mitra RD, Puram SV. Epigenetic regulation of hybrid epithelial-mesenchymal cell states in cancer. Oncogene 2023; 42:2237-2248. [PMID: 37344626 PMCID: PMC10578205 DOI: 10.1038/s41388-023-02749-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [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: 03/02/2023] [Revised: 05/09/2023] [Accepted: 06/08/2023] [Indexed: 06/23/2023]
Abstract
Epithelial-to-mesenchymal transition (EMT) is a process by which cells lose their epithelial characteristics and gain mesenchymal phenotypes. In cancer, EMT is thought to drive tumor invasion and metastasis. Recent efforts to understand EMT biology have uncovered that cells undergoing EMT attain a spectrum of intermediate "hybrid E/M" states, which exist along an epithelial-mesenchymal continuum. Here, we summarize recent studies characterizing the epigenetic drivers of hybrid E/M states. We focus on the histone-modification writers, erasers, and readers that assist or oppose the canonical hybrid E/M transcription factors that modulate hybrid E/M state transitions. We also examine the role of chromatin remodelers and DNA methylation in hybrid E/M states. Finally, we highlight the challenges of targeting hybrid E/M pharmacologically, and we propose future directions that might reveal the specific and targetable mechanisms by which hybrid E/M drives metastasis in patients.
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Affiliation(s)
- Reilly A Sample
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
- Department of Otolaryngology-Head and Neck Surgery, Washington University School of Medicine, St. Louis, MO, USA
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Marina F Nogueira
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
- Department of Otolaryngology-Head and Neck Surgery, Washington University School of Medicine, St. Louis, MO, USA
| | - Robi D Mitra
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA.
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA.
| | - Sidharth V Puram
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Otolaryngology-Head and Neck Surgery, Washington University School of Medicine, St. Louis, MO, USA.
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA.
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Day AT, Sample RA, Salley JR, Oliver D, Dahlstrom KR, Sturgis EM, Tiro JA. Stepped Behavioral and Biological Screening for Oral Oncogenic HPV DNA in Middle-aged and Elderly Adults: A Feasibility Study. Cancer Prev Res (Phila) 2023; 16:127-132. [PMID: 36596658 DOI: 10.1158/1940-6207.capr-22-0371] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Revised: 11/07/2022] [Accepted: 12/30/2022] [Indexed: 01/05/2023]
Abstract
Novel preventive interventions are needed to address the rising incidence of human papillomavirus (HPV)-mediated oropharyngeal cancer (HPV+ OPC). This pilot study evaluated the feasibility of a stepped, behavioral and biological screening program for oral oncogenic HPV infection, an intermediate HPV+ OPC outcome. This was a cross-sectional, feasibility study. Eligible 45-74 years old adults identified from three clinical research registries were administered a behavioral risk survey (step 1). Participant tobacco use and sexual behavior history were translated into a quantifiable risk of oral oncogenic HPV DNA, according to prior National Health and Nutrition Examination Survey analyses. Females with >2% risk and males with >7% risk were offered biological screening for oral oncogenic HPV DNA (step 2) via an oral rinse and gargle specimen. A total of 292 individuals were contacted, but only 144 (49%) were reached. Among these, 56 individuals (19%) were uninterested and 18 (13%) were ineligible. Seventy individuals began the survey and 66 completed it (step 1), among whom 46 were classified as low-risk. Among the remaining 20 participants classified as high-risk for an oral oncogenic HPV infection, 5% were current smokers and the median participant had performed oral sex on 10 unique partners. During step 2 (biological screening), 45% (9/20) completed testing, all of whom tested negative for oral oncogenic HPV DNA. In this pilot of a stepped, oral oncogenic HPV screening program, enrollment and study completion were suboptimal. These barriers to screening should be characterized and addressed before reevaluating the feasibility of this program. PREVENTION RELEVANCE Novel preventive interventions are needed to address the rising incidence of HPV+ OPC. In this feasibility study, we characterized barriers to a two-step, behavioral and biological screening program for oral oncogenic HPV infection, an intermediate outcome for HPV+ OPC.
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Affiliation(s)
- Andrew T Day
- Department of Otolaryngology-Head and Neck Surgery, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Reilly A Sample
- Department of Otolaryngology-Head and Neck Surgery, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Jordan R Salley
- Department of Otolaryngology-Head and Neck Surgery, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Dwight Oliver
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Kristina R Dahlstrom
- Department of Medicine, Section: Epidemiology and Population Science, Baylor College of Medicine, Houston, Texas
| | - Erich M Sturgis
- Department of Otolaryngology-Head and Neck Surgery, Baylor College of Medicine, Houston, Texas
| | - Jasmin A Tiro
- Department of Public Health Sciences, University of Chicago, Chicago, Illinois
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Sample RA, Wood CB, Mazul AL, Barrett TF, Paniello RC, Rich JT, Kang SY, Zevallos J, Daly MD, Thorstad WL, Chen SY, Pipkorn P, Jackson RS, Puram SV. Low-risk human papilloma virus positive oropharyngeal cancer with one positive lymph node: Equivalent outcomes in patients treated with surgery and radiation therapy versus surgery alone. Head Neck 2021; 43:1759-1768. [PMID: 33586842 DOI: 10.1002/hed.26642] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 11/20/2020] [Accepted: 02/01/2021] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND For human papilloma virus positive (HPV+) oropharyngeal squamous cell carcinoma (OPSCC), management recommendations for patients with a single metastatic lymph node <6 cm in diameter remain nebulous, leading to treatment heterogeneity in this common subgroup of patients. METHODS We utilized the National Cancer Database to perform survival and multivariable analyses of patients with HPV+ OPSCC with one positive lymph node <6 cm and negative surgical margins. RESULTS We found that 5-year survival is comparable between patients who receive surgery and adjuvant radiation versus surgery alone. In multivariable analyses, we found no significant difference in the hazard ratio of overall survival after adjusting for various potential confounders. CONCLUSIONS These data suggest that patients with margin-negative HPV+ OPSCC with a single positive lymph node <6 cm have comparable survival with or without adjuvant radiation. Future studies exploring outcomes for this specific group in randomized-controlled trials will be critical for further evaluating these initial observations.
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Affiliation(s)
- Reilly A Sample
- Department of Otolaryngology - Head and Neck Surgery, Washington University School of Medicine, St Louis, Missouri, USA.,Clinical Research Training Center, Institute of Clinical and Translational Sciences, Washington University School of Medicine, St Louis, Missouri, USA
| | - Carey Burton Wood
- Department of Otolaryngology - Head and Neck Surgery, Washington University School of Medicine, St Louis, Missouri, USA
| | - Angela L Mazul
- Department of Otolaryngology - Head and Neck Surgery, Washington University School of Medicine, St Louis, Missouri, USA.,Division of Public Health Sciences, Department of Surgery, Washington University, St Louis, Missouri, USA
| | - Thomas F Barrett
- Department of Otolaryngology - Head and Neck Surgery, Washington University School of Medicine, St Louis, Missouri, USA
| | - Randal C Paniello
- Department of Otolaryngology - Head and Neck Surgery, Washington University School of Medicine, St Louis, Missouri, USA
| | - Jason T Rich
- Department of Otolaryngology - Head and Neck Surgery, Washington University School of Medicine, St Louis, Missouri, USA
| | - Stephen Y Kang
- Department of Otolaryngology - Head and Neck Surgery, The James Cancer Hospital, Solove Research Institute, The Ohio State University, Columbus, Ohio, USA
| | - Jose Zevallos
- Department of Otolaryngology - Head and Neck Surgery, Washington University School of Medicine, St Louis, Missouri, USA
| | - Mackenzie D Daly
- Department of Radiation Oncology, Washington University School of Medicine, St Louis, Missouri, USA
| | - Wade L Thorstad
- Department of Radiation Oncology, Washington University School of Medicine, St Louis, Missouri, USA
| | - Stephanie Y Chen
- Department of Otolaryngology - Head and Neck Surgery, Washington University School of Medicine, St Louis, Missouri, USA
| | - Patrik Pipkorn
- Department of Otolaryngology - Head and Neck Surgery, Washington University School of Medicine, St Louis, Missouri, USA
| | - Ryan S Jackson
- Department of Otolaryngology - Head and Neck Surgery, Washington University School of Medicine, St Louis, Missouri, USA
| | - Sidharth V Puram
- Department of Otolaryngology - Head and Neck Surgery, Washington University School of Medicine, St Louis, Missouri, USA.,Department of Genetics, Washington University School of Medicine, St Louis, Missouri, USA
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