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Shekhar R, O'Grady T, Keil N, Feswick A, Amador DM, Tibbetts S, Flemington E, Renne R. High-density resolution of the Kaposi's sarcoma associated herpesvirus transcriptome identifies novel transcript isoforms generated by long-range transcription and alternative splicing. Nucleic Acids Res 2024; 52:7720-7739. [PMID: 38922687 PMCID: PMC11260491 DOI: 10.1093/nar/gkae540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 05/14/2024] [Accepted: 06/11/2024] [Indexed: 06/28/2024] Open
Abstract
Kaposi's sarcoma-associated herpesvirus is the etiologic agent of Kaposi's sarcoma and two B-cell malignancies. Recent advancements in sequencing technologies have led to high resolution transcriptomes for several human herpesviruses that densely encode genes on both strands. However, for KSHV progress remained limited due to the overall low percentage of KSHV transcripts, even during lytic replication. To address this challenge, we have developed a target enrichment method to increase the KSHV-specific reads for both short- and long-read sequencing platforms. Furthermore, we combined this approach with the Transcriptome Resolution through Integration of Multi-platform Data (TRIMD) pipeline developed previously to annotate transcript structures. TRIMD first builds a scaffold based on long-read sequencing and validates each transcript feature with supporting evidence from Illumina RNA-Seq and deepCAGE sequencing data. Our stringent innovative approach identified 994 unique KSHV transcripts, thus providing the first high-density KSHV lytic transcriptome. We describe a plethora of novel coding and non-coding KSHV transcript isoforms with alternative untranslated regions, splice junctions and open-reading frames, thus providing deeper insights on gene expression regulation of KSHV. Interestingly, as described for Epstein-Barr virus, we identified transcription start sites that augment long-range transcription and may increase the number of latency-associated genes potentially expressed in KS tumors.
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Affiliation(s)
- Ritu Shekhar
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL, USA
| | - Tina O'Grady
- Department of Pathology, Tulane University, New Orleans, LA, USA
| | - Netanya Keil
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL, USA
- UF Genetics Institute, University of Florida, Gainesville, FL, USA
| | - April Feswick
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL, USA
| | - David A Moraga Amador
- UF Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL, USA
| | - Scott A Tibbetts
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL, USA
- UF Health Cancer Center, University of Florida, Gainesville, FL, USA
- UF Genetics Institute, University of Florida, Gainesville, FL, USA
| | | | - Rolf Renne
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL, USA
- UF Health Cancer Center, University of Florida, Gainesville, FL, USA
- UF Genetics Institute, University of Florida, Gainesville, FL, USA
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Sin SH, Eason AB, Kim Y, Schneider JW, Damania B, Dittmer DP. The complete Kaposi sarcoma-associated herpesvirus genome induces early-onset, metastatic angiosarcoma in transgenic mice. Cell Host Microbe 2024; 32:755-767.e4. [PMID: 38653242 PMCID: PMC11305081 DOI: 10.1016/j.chom.2024.03.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 01/16/2024] [Accepted: 03/27/2024] [Indexed: 04/25/2024]
Abstract
Kaposi sarcoma (KS) is the most common cancer in persons living with HIV. It is caused by KS-associated herpesvirus (KSHV). There exists no animal model for KS. Pronuclear injection of the 170,000-bp viral genome induces early-onset, aggressive angiosarcoma in transgenic mice. The tumors are histopathologically indistinguishable from human KS. As in human KS, all tumor cells express the viral latency-associated nuclear antigen (LANA). The tumors transcribe most viral genes, whereas endothelial cells in other organs only transcribe the viral latent genes. The tumor cells are of endothelial lineage and exhibit the same molecular pattern of pathway activation as KS, namely phosphatidylinositol 3-kinase (PI3K)/Akt/mTOR, interleukin-10 (IL-10), and vascular endothelial growth factor (VEGF). The KSHV-induced tumors are more aggressive than Ha-ras-induced angiosarcomas. Overall survival is increased by prophylactic ganciclovir. Thus, whole-virus KSHV-transgenic mice represent an accurate model for KS and open the door for the genetic dissection of KS pathogenesis and evaluation of therapies, including vaccines.
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Affiliation(s)
- Sang-Hoon Sin
- Lineberger Comprehensive Cancer Center and Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Anthony B Eason
- Lineberger Comprehensive Cancer Center and Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Yongbaek Kim
- Laboratory of Veterinary Clinical Pathology, College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea
| | - Johann W Schneider
- National Health Laboratory Service, Division of Anatomical Pathology, Faculty of Medicine and Health Sciences, Tygerberg Hospital, Stellenbosch University, Cape Town, South Africa
| | - Blossom Damania
- Lineberger Comprehensive Cancer Center and Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Dirk P Dittmer
- Lineberger Comprehensive Cancer Center and Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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Rauch DA, Ramos PV, Khanfar M, Harding J, Joseph A, Griffith O, Griffith M, Ratner L. Single-Cell Transcriptomic Analysis of Kaposi Sarcoma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.01.592010. [PMID: 38746135 PMCID: PMC11092626 DOI: 10.1101/2024.05.01.592010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Kaposi Sarcoma (KS) is a complex tumor caused by KS-associated herpesvirus 8 (KSHV). Histological analysis reveals a mixture of "spindle cells", vascular-like spaces, extravasated erythrocytes, and immune cells. In order to elucidate the infected and uninfected cell types in KS tumors, we examined skin and blood samples from twelve subjects by single cell RNA sequence analyses. Two populations of KSHV-infected cells were identified, one of which represented a proliferative fraction of lymphatic endothelial cells, and the second represented an angiogenic population of vascular endothelial tip cells. Both infected clusters contained cells expressing lytic and latent KSHV genes. Novel cellular biomarkers were identified in the KSHV infected cells, including the sodium channel SCN9A. The number of KSHV positive tumor cells was found to be in the 6% range in HIV-associated KS, correlated inversely with tumor-infiltrating immune cells, and was reduced in biopsies from HIV-negative individuals. T-cell receptor clones were expanded in KS tumors and blood, although in differing magnitudes. Changes in cellular composition in KS tumors were identified in subjects treated with antiretroviral therapy alone, or immunotherapy. These studies demonstrate the feasibility of single cell analyses to identify prognostic and predictive biomarkers. Author Summary Kaposi sarcoma (KS) is a malignancy caused by the KS-associated herpesvirus (KSHV) that causes skin lesions, and may also be found in lymph nodes, lungs, gastrointestinal tract, and other organs in immunosuppressed individuals more commonly than immunocompetent subjects. The current study examined gene expression in single cells from the tumor and blood of these subjects, and identified the characteristics of the complex mixtures of cells in the tumor. This method also identified differences in KSHV gene expression in different cell types and associated cellular genes expressed in KSHV infected cells. In addition, changes in the cellular composition could be elucidated with therapeutic interventions.
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Suneja G, Kimani SM, Gill H, Painschab MS, Knettel BA, Watt MH. Addressing the Intersectional Stigma of Kaposi Sarcoma and HIV: A Call to Action. JCO Glob Oncol 2024; 10:e2300264. [PMID: 38301182 PMCID: PMC10846783 DOI: 10.1200/go.23.00264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 11/17/2023] [Accepted: 12/05/2023] [Indexed: 02/03/2024] Open
Affiliation(s)
- Gita Suneja
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT
- Department of Radiation Oncology, Spencer Fox Eccles School of Medicine, University of Utah, Salt Lake City, UT
| | - Stephen M. Kimani
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT
- Division of Oncology, Department of Medicine, Spencer Fox Eccles School of Medicine, University of Utah, Salt Lake City, UT
| | - Hailie Gill
- Spencer Fox Eccles School of Medicine, University of Utah, Salt Lake City, UT
| | - Matthew S. Painschab
- Division of Hematology, Department of Medicine, School of Medicine, University of North Carolina, Chapel Hill, NC
- UNC Project Malawi, Lilongwe, Malawi
| | - Brandon A. Knettel
- School of Nursing, Duke University, Durham, NC
- Duke Global Health Institute, Duke University, Durham, NC
| | - Melissa H. Watt
- Department of Population Health Sciences, Spencer Fox Eccles School of Medicine, University of Utah, Salt Lake City, UT
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Brownlee AJ, Dewey M, Chagomerana MB, Tomoka T, Mulenga M, Khan S, Kampani C, Chimzimu F, Gastier-Foster JM, Westmoreland KD, Ozuah NW, Krysiak R, Malamba-Banda C, Painschab MS, Gopal S, Fedoriw Y. Update on pathology laboratory development and research in advancing regional cancer care in Malawi. Front Med (Lausanne) 2024; 11:1336861. [PMID: 38298817 PMCID: PMC10829605 DOI: 10.3389/fmed.2024.1336861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Accepted: 01/02/2024] [Indexed: 02/02/2024] Open
Abstract
The pathology laboratory at Kamuzu Central Hospital (KCH) in Lilongwe, Malawi was established in 2011. We published our initial experiences in laboratory development and telepathology in 2013 and 2016, respectively. The purpose of this paper is to provide an update on our work by highlighting the positive role laboratory development has played in improving regional cancer care and research. In addition, we provide a summary of the adult pathology data from specimens received between July 1, 2011, and May 31, 2019, with an emphasis on malignant diagnoses. We compare these summaries to estimates of cancer incidence in this region to identify gaps and future needs.
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Affiliation(s)
- Amy J. Brownlee
- Department of Pathology and Laboratory Medicine, School of Medicine, University of North Carolina, Chapel Hill, NC, United States
| | - Morgan Dewey
- School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Maganizo B. Chagomerana
- University of North Carolina (UNC) Project-Malawi, Lilongwe, Malawi
- Division of Infectious Diseases, School of Medicine, University of North Carolina, Chapel Hill, NC, United States
| | - Tamiwe Tomoka
- University of North Carolina (UNC) Project-Malawi, Lilongwe, Malawi
| | - Maurice Mulenga
- Kamuzu Central Hospital, Malawi Ministry of Health, Lilongwe, Malawi
| | - Shiraz Khan
- University of North Carolina (UNC) Project-Malawi, Lilongwe, Malawi
- Kamuzu Central Hospital, Malawi Ministry of Health, Lilongwe, Malawi
| | - Coxcilly Kampani
- University of North Carolina (UNC) Project-Malawi, Lilongwe, Malawi
| | - Fred Chimzimu
- University of North Carolina (UNC) Project-Malawi, Lilongwe, Malawi
| | - Julie M. Gastier-Foster
- Departments of Pediatrics and Pathology & Immunology, Baylor College of Medicine, Texas Children's Hospital, Houston, TX, United States
| | - Kate D. Westmoreland
- University of North Carolina (UNC) Project-Malawi, Lilongwe, Malawi
- Division of Pediatric Hematology Oncology, Department of Medicine, University of North Carolina, Chapel Hill, NC, United States
- Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina, Chapel Hill, NC, United States
| | - Nmazuo W. Ozuah
- Section of Hematology and Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, TX, United States
| | - Robert Krysiak
- University of North Carolina (UNC) Project-Malawi, Lilongwe, Malawi
| | - Chikondi Malamba-Banda
- University of North Carolina (UNC) Project-Malawi, Lilongwe, Malawi
- Malawi University of Science and Technology, Limbe, Malawi
- Malawi-Liverpool-Wellcome Trust Clinical Research Program, Blantyre, Malawi
| | - Matthew S. Painschab
- University of North Carolina (UNC) Project-Malawi, Lilongwe, Malawi
- Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina, Chapel Hill, NC, United States
- Division of Hematology, Department of Medicine, University of North Carolina, Chapel Hill, NC, United States
| | - Satish Gopal
- Center for Global Health, National Cancer Institute (NIH), Bethesda, MD, United States
| | - Yuri Fedoriw
- Department of Pathology and Laboratory Medicine, School of Medicine, University of North Carolina, Chapel Hill, NC, United States
- University of North Carolina (UNC) Project-Malawi, Lilongwe, Malawi
- Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina, Chapel Hill, NC, United States
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