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Hasan MK, Jeannine Brady L. Nucleic acid-binding KH domain proteins influence a spectrum of biological pathways including as part of membrane-localized complexes. J Struct Biol X 2024; 10:100106. [PMID: 39040530 PMCID: PMC11261784 DOI: 10.1016/j.yjsbx.2024.100106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 06/18/2024] [Accepted: 06/24/2024] [Indexed: 07/24/2024] Open
Abstract
K-Homology domain (KH domain) proteins bind single-stranded nucleic acids, influence protein-protein interactions of proteins that harbor them, and are found in all kingdoms of life. In concert with other functional protein domains KH domains contribute to a variety of critical biological activities, often within higher order machineries including membrane-localized protein complexes. Eukaryotic KH domain proteins are linked to developmental processes, morphogenesis, and growth regulation, and their aberrant expression is often associated with cancer. Prokaryotic KH domain proteins are involved in integral cellular activities including cell division and protein translocation. Eukaryotic and prokaryotic KH domains share structural features, but are differentiated based on their structural organizations. In this review, we explore the structure/function relationships of known examples of KH domain proteins, and highlight cases in which they function within or at membrane surfaces. We also summarize examples of KH domain proteins that influence bacterial virulence and pathogenesis. We conclude the article by discussing prospective research avenues that could be pursued to better investigate this largely understudied protein category.
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Affiliation(s)
- Md Kamrul Hasan
- Department of Oral Biology, University of Florida, Gainesville, FL 32610, USA
- Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| | - L. Jeannine Brady
- Department of Oral Biology, University of Florida, Gainesville, FL 32610, USA
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2
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Harioudh MK, Perez J, So L, Maheshwari M, Ebert TS, Hornung V, Savan R, Rouf Banday A, Diamond MS, Rathinam VA, Sarkar SN. The canonical antiviral protein oligoadenylate synthetase 1 elicits antibacterial functions by enhancing IRF1 translation. Immunity 2024; 57:1812-1827.e7. [PMID: 38955184 PMCID: PMC11324410 DOI: 10.1016/j.immuni.2024.06.003] [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: 11/21/2023] [Revised: 04/11/2024] [Accepted: 06/07/2024] [Indexed: 07/04/2024]
Abstract
An important property of the host innate immune response during microbial infection is its ability to control the expression of antimicrobial effector proteins, but how this occurs post-transcriptionally is not well defined. Here, we describe a critical antibacterial role for the classic antiviral gene 2'-5'-oligoadenylate synthetase 1 (OAS1). Human OAS1 and its mouse ortholog, Oas1b, are induced by interferon-γ and protect against cytosolic bacterial pathogens such as Francisella novicida and Listeria monocytogenes in vitro and in vivo. Proteomic and transcriptomic analysis showed reduced IRF1 protein expression in OAS1-deficient cells. Mechanistically, OAS1 binds and localizes IRF1 mRNA to the rough endoplasmic reticulum (ER)-Golgi endomembranes, licensing effective translation of IRF1 mRNA without affecting its transcription or decay. OAS1-dependent translation of IRF1 leads to the enhanced expression of antibacterial effectors, such as GBPs, which restrict intracellular bacteria. These findings uncover a noncanonical function of OAS1 in antibacterial innate immunity.
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Affiliation(s)
- Munesh K Harioudh
- Cancer Virology Program, UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA; Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Joseph Perez
- Cancer Virology Program, UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA; Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Lomon So
- Department of Immunology, School of Medicine, University of Washington, Seattle, WA, USA
| | - Mayank Maheshwari
- Cancer Virology Program, UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA; Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Thomas S Ebert
- Department of Biochemistry, Ludwig Maximilians Universität, Munich, Germany
| | - Veit Hornung
- Department of Biochemistry, Ludwig Maximilians Universität, Munich, Germany
| | - Ram Savan
- Department of Immunology, School of Medicine, University of Washington, Seattle, WA, USA
| | - A Rouf Banday
- Genitourinary Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Michael S Diamond
- Departments of Medicine, Molecular Microbiology, Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Vijay A Rathinam
- Department of Immunology, UConn Health School of Medicine, Farmington, CT, USA
| | - Saumendra N Sarkar
- Cancer Virology Program, UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA; Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA; Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
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3
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Wedler A, Bley N, Glaß M, Müller S, Rausch A, Lederer M, Urbainski J, Schian L, Obika KB, Simon T, Peters L, Misiak C, Fuchs T, Köhn M, Jacob R, Gutschner T, Ihling C, Sinz A, Hüttelmaier S. RAVER1 hinders lethal EMT and modulates miR/RISC activity by the control of alternative splicing. Nucleic Acids Res 2024; 52:3971-3988. [PMID: 38300787 PMCID: PMC11039986 DOI: 10.1093/nar/gkae046] [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: 06/15/2023] [Revised: 12/24/2023] [Accepted: 01/12/2024] [Indexed: 02/03/2024] Open
Abstract
The RAVER1 protein serves as a co-factor in guiding the polypyrimidine tract-binding protein (PTBP)-dependent control of alternative splicing (AS). Whether RAVER1 solely acts in concert with PTBPs and how it affects cancer cell fate remained elusive. Here, we provide the first comprehensive investigation of RAVER1-controlled AS in cancer cell models. This reveals a pro-oncogenic role of RAVER1 in modulating tumor growth and epithelial-mesenchymal-transition (EMT). Splicing analyses and protein-association studies indicate that RAVER1 guides AS in association with other splicing regulators, including PTBPs and SRSFs. In cancer cells, one major function of RAVER1 is the stimulation of proliferation and restriction of apoptosis. This involves the modulation of AS events within the miR/RISC pathway. Disturbance of RAVER1 impairs miR/RISC activity resulting in severely deregulated gene expression, which promotes lethal TGFB-driven EMT. Among others, RAVER1-modulated splicing events affect the insertion of protein interaction modules in factors guiding miR/RISC-dependent gene silencing. Most prominently, in all three human TNRC6 proteins, RAVER1 controls AS of GW-enriched motifs, which are essential for AGO2-binding and the formation of active miR/RISC complexes. We propose, that RAVER1 is a key modulator of AS events in the miR/RISC pathway ensuring proper abundance and composition of miR/RISC effectors. This ensures balanced expression of TGFB signaling effectors and limits TGFB induced lethal EMT.
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Affiliation(s)
- Alice Wedler
- Institute of Molecular Medicine, Section for Molecular Cell Biology, Faculty of Medicine, Martin Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Nadine Bley
- Institute of Molecular Medicine, Section for Molecular Cell Biology, Faculty of Medicine, Martin Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Markus Glaß
- Institute of Molecular Medicine, Section for Molecular Cell Biology, Faculty of Medicine, Martin Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Simon Müller
- Institute of Molecular Medicine, Section for Molecular Cell Biology, Faculty of Medicine, Martin Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany
- New York Genome Center, New York, NY, USA
- Department of Biology, New York University, New York, NY, USA
| | - Alexander Rausch
- Institute of Molecular Medicine, Section for Molecular Cell Biology, Faculty of Medicine, Martin Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Marcell Lederer
- Institute of Molecular Medicine, Section for Molecular Cell Biology, Faculty of Medicine, Martin Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Julia Urbainski
- Institute of Molecular Medicine, Section for Molecular Cell Biology, Faculty of Medicine, Martin Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Laura Schian
- Institute of Molecular Medicine, Section for Molecular Cell Biology, Faculty of Medicine, Martin Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Kingsley-Benjamin Obika
- Institute of Molecular Medicine, Section for Molecular Cell Biology, Faculty of Medicine, Martin Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Theresa Simon
- Institute of Molecular Medicine, Section for Molecular Cell Biology, Faculty of Medicine, Martin Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Lara Meret Peters
- Institute of Molecular Medicine, Section for Molecular Cell Biology, Faculty of Medicine, Martin Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Claudia Misiak
- Institute of Molecular Medicine, Section for Molecular Cell Biology, Faculty of Medicine, Martin Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Tommy Fuchs
- Institute of Molecular Medicine, Section for Molecular Cell Biology, Faculty of Medicine, Martin Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Marcel Köhn
- Institute of Molecular Medicine, Section for Molecular Cell Biology, Faculty of Medicine, Martin Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Roland Jacob
- Institute of Molecular Medicine, Section for Molecular Cell Biology, Faculty of Medicine, Martin Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Tony Gutschner
- Institute of Molecular Medicine, Section for Molecular Cell Biology, Faculty of Medicine, Martin Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Christian Ihling
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Andrea Sinz
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Stefan Hüttelmaier
- Institute of Molecular Medicine, Section for Molecular Cell Biology, Faculty of Medicine, Martin Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany
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Álvarez-Campos P, García-Castro H, Emili E, Pérez-Posada A, Del Olmo I, Peron S, Salamanca-Díaz DA, Mason V, Metzger B, Bely AE, Kenny NJ, Özpolat BD, Solana J. Annelid adult cell type diversity and their pluripotent cellular origins. Nat Commun 2024; 15:3194. [PMID: 38609365 PMCID: PMC11014941 DOI: 10.1038/s41467-024-47401-6] [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: 07/28/2023] [Accepted: 03/27/2024] [Indexed: 04/14/2024] Open
Abstract
Many annelids can regenerate missing body parts or reproduce asexually, generating all cell types in adult stages. However, the putative adult stem cell populations involved in these processes, and the diversity of cell types generated by them, are still unknown. To address this, we recover 75,218 single cell transcriptomes of the highly regenerative and asexually-reproducing annelid Pristina leidyi. Our results uncover a rich cell type diversity including annelid specific types as well as novel types. Moreover, we characterise transcription factors and gene networks that are expressed specifically in these populations. Finally, we uncover a broadly abundant cluster of putative stem cells with a pluripotent signature. This population expresses well-known stem cell markers such as vasa, piwi and nanos homologues, but also shows heterogeneous expression of differentiated cell markers and their transcription factors. We find conserved expression of pluripotency regulators, including multiple chromatin remodelling and epigenetic factors, in piwi+ cells. Finally, lineage reconstruction analyses reveal computational differentiation trajectories from piwi+ cells to diverse adult types. Our data reveal the cell type diversity of adult annelids by single cell transcriptomics and suggest that a piwi+ cell population with a pluripotent stem cell signature is associated with adult cell type differentiation.
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Affiliation(s)
- Patricia Álvarez-Campos
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK.
- Centro de Investigación en Biodiversidad y Cambio Global (CIBC-UAM) & Departamento de Biología (Zoología), Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain.
| | - Helena García-Castro
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK
- Living Systems Institute, University of Exeter, Exeter, UK
| | - Elena Emili
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK
| | - Alberto Pérez-Posada
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK
- Living Systems Institute, University of Exeter, Exeter, UK
| | - Irene Del Olmo
- Centro de Investigación en Biodiversidad y Cambio Global (CIBC-UAM) & Departamento de Biología (Zoología), Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
| | - Sophie Peron
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK
- Living Systems Institute, University of Exeter, Exeter, UK
| | - David A Salamanca-Díaz
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK
- Living Systems Institute, University of Exeter, Exeter, UK
| | - Vincent Mason
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK
| | - Bria Metzger
- Eugene Bell Center for Regenerative Biology and Tissue Engineering, Marine Biological Laboratory, 7 MBL Street, Woods Hole, MA, 05432, USA
- Department of Biology, Washington University in St. Louis. 1 Brookings Dr. Saint Louis, Saint Louis, MO, 63130, USA
| | - Alexandra E Bely
- Department of Biology, University of Maryland, College Park, MD, 20742, USA
| | - Nathan J Kenny
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK
- Department of Biochemistry, University of Otago, P.O. Box 56, Dunedin, Aotearoa, New Zealand
| | - B Duygu Özpolat
- Eugene Bell Center for Regenerative Biology and Tissue Engineering, Marine Biological Laboratory, 7 MBL Street, Woods Hole, MA, 05432, USA.
- Department of Biology, Washington University in St. Louis. 1 Brookings Dr. Saint Louis, Saint Louis, MO, 63130, USA.
| | - Jordi Solana
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK.
- Living Systems Institute, University of Exeter, Exeter, UK.
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5
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Feicht J, Jansen RP. The high-density lipoprotein binding protein HDLBP is an unusual RNA-binding protein with multiple roles in cancer and disease. RNA Biol 2024; 21:1-10. [PMID: 38477883 PMCID: PMC10939154 DOI: 10.1080/15476286.2024.2313881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/29/2024] [Indexed: 03/14/2024] Open
Abstract
The high-density lipoprotein binding protein (HDLBP) is the human member of an evolutionarily conserved family of RNA-binding proteins, the vigilin protein family. These proteins are characterized by 14 or 15 RNA-interacting KH (heterologous nuclear ribonucleoprotein K homology) domains. While mainly present at the cytoplasmic face of the endoplasmic reticulum, HDLBP and its homologs are also found in the cytosol and nucleus. HDLBP is involved in various processes, including translation, chromosome segregation, cholesterol transport and carcinogenesis. Especially, its association with the latter two has attracted specific interest in the HDLBP's molecular role. In this review, we give an overview of some of the functions of the protein as well as introduce its impact on different kinds of cancer, its connection to lipid metabolism and its role in viral infection. We also aim at addressing the possible use of HDLBP as a drug target or biomarker and discuss its future implications.
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Affiliation(s)
- Jonathan Feicht
- Interfaculty Institute of Biochemistry, University of Tuebingen, Tuebingen, Germany
| | - Ralf-Peter Jansen
- Interfaculty Institute of Biochemistry, University of Tuebingen, Tuebingen, Germany
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6
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Suryo Rahmanto A, Blum CJ, Scalera C, Heidelberger JB, Mesitov M, Horn-Ghetko D, Gräf JF, Mikicic I, Hobrecht R, Orekhova A, Ostermaier M, Ebersberger S, Möckel MM, Krapoth N, Da Silva Fernandes N, Mizi A, Zhu Y, Chen JX, Choudhary C, Papantonis A, Ulrich HD, Schulman BA, König J, Beli P. K6-linked ubiquitylation marks formaldehyde-induced RNA-protein crosslinks for resolution. Mol Cell 2023; 83:4272-4289.e10. [PMID: 37951215 DOI: 10.1016/j.molcel.2023.10.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 08/17/2023] [Accepted: 10/13/2023] [Indexed: 11/13/2023]
Abstract
Reactive aldehydes are produced by normal cellular metabolism or after alcohol consumption, and they accumulate in human tissues if aldehyde clearance mechanisms are impaired. Their toxicity has been attributed to the damage they cause to genomic DNA and the subsequent inhibition of transcription and replication. However, whether interference with other cellular processes contributes to aldehyde toxicity has not been investigated. We demonstrate that formaldehyde induces RNA-protein crosslinks (RPCs) that stall the ribosome and inhibit translation in human cells. RPCs in the messenger RNA (mRNA) are recognized by the translating ribosomes, marked by atypical K6-linked ubiquitylation catalyzed by the RING-in-between-RING (RBR) E3 ligase RNF14, and subsequently resolved by the ubiquitin- and ATP-dependent unfoldase VCP. Our findings uncover an evolutionary conserved formaldehyde-induced stress response pathway that protects cells against RPC accumulation in the cytoplasm, and they suggest that RPCs contribute to the cellular and tissue toxicity of reactive aldehydes.
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Affiliation(s)
- Aldwin Suryo Rahmanto
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany; Institute of Developmental Biology and Neurobiology (IDN), Johannes Gutenberg-Universität, 55128 Mainz, Germany
| | | | | | | | | | - Daniel Horn-Ghetko
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Justus F Gräf
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany; Department of Proteomics, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Ivan Mikicic
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany
| | | | - Anna Orekhova
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany
| | | | | | | | - Nils Krapoth
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany
| | | | - Athanasia Mizi
- Institute of Pathology, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Yajie Zhu
- Institute of Pathology, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Jia-Xuan Chen
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany
| | - Chunaram Choudhary
- Department of Proteomics, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Argyris Papantonis
- Institute of Pathology, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Helle D Ulrich
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany
| | - Brenda A Schulman
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Julian König
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany
| | - Petra Beli
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany; Institute of Developmental Biology and Neurobiology (IDN), Johannes Gutenberg-Universität, 55128 Mainz, Germany.
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Seker-Cin H, Tay TKY, Kazdal D, Kluck K, Ball M, Neumann O, Winter H, Herth F, Heußel CP, Savai R, Schirmacher P, Thomas M, Budczies J, Allgäuer M, Christopoulos P, Stenzinger A, Volckmar AL. Analysis of rare fusions in NSCLC: Genomic architecture and clinical implications. Lung Cancer 2023; 184:107317. [PMID: 37586177 DOI: 10.1016/j.lungcan.2023.107317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 07/12/2023] [Accepted: 07/24/2023] [Indexed: 08/18/2023]
Abstract
OBJECTIVES Molecular diagnosis for targeted therapies has been improved significantly in non-small-cell lung cancer (NSCLC) patients in recent years. Here we report on the prevalence of rare fusions in NSCLC and dissect their genomic architecture and potential clinical implications. MATERIALS AND METHODS Overall, n = 5554 NSCLC patients underwent next-generation sequencing (NGS) for combined detection of oncogenic mutations and fusions either at primary diagnosis (n = 5246) or after therapy resistance (n = 308). Panels of different sizes were employed with closed amplicon-based, or open assays, i.e. anchored multiplex PCR (AMP) and hybrid capture-based, for detection of translocations, including "rare" fusions, defined as those beyond ALK, ROS1, RET and <0.5 % frequency in NSCLC. RESULTS Rare fusions involving EGFR, MET, HER2, BRAF and other potentially actionable oncogenes were detected in 0.5% (n = 26) of therapy-naive and 2% (n = 6) TKI-treated tumors. Detection was increased using open assays and/or larger panels, especially those covering >25 genes, by approximately 1-2% (p = 0.001 for both). Patient characteristics (age, gender, smoking, TP53 co-mutations (56%), or mean tumor mutational burden (TMB) (4.8 mut/Mb)) showed no association with presence of rare fusions. Non-functional alterations, i.e. out-of-frame or lacking kinase domains, comprised one-third of detected rare fusions and were significantly associated with simultaneous presence of classical oncogenic drivers, e.g. EGFR or KRAS mutations (p < 0.001), or use of larger panels (frequency of non-functional among the detected rare fusions 57% for 25+ gene- vs. 12% for smaller panels, p < 0.001). As many rare fusions were identified before availability of targeted therapy, mean survival for therapy-naïve patients was 23.8 months, comparable with wild-type tumors. CONCLUSION Approximately 1-2% of advanced NSCLC harbor rare fusions, which are potentially actionable and may support diagnosis. Routine adoption of broad NGS assays capable to identify exact fusion points and potentially retained protein domains can increase the yield of therapeutically relevant molecular information in advanced NSCLC.
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Affiliation(s)
- Huriye Seker-Cin
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Timothy Kwang Yong Tay
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany; Department of Anatomical Pathology, Department of Molecular Pathology, Singapore General Hospital, Singapore
| | - Daniel Kazdal
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany; Translational Lung Research Center (TLRC) Heidelberg, German Center for Lung Research (DZL), Germany
| | - Klaus Kluck
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Markus Ball
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Olaf Neumann
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Hauke Winter
- Translational Lung Research Center (TLRC) Heidelberg, German Center for Lung Research (DZL), Germany; Department of Thoracic Oncology, Thoraxklinik at University Hospital Heidelberg, Heidelberg, Germany
| | - Felix Herth
- Translational Lung Research Center (TLRC) Heidelberg, German Center for Lung Research (DZL), Germany; Department of Pulmonology, Thoraxklinik at University Hospital Heidelberg, Heidelberg, Germany
| | - Claus-Peter Heußel
- Translational Lung Research Center (TLRC) Heidelberg, German Center for Lung Research (DZL), Germany; Diagnostic and Interventional Radiology with Nuclear Medicine, Thoraxklinik at University Hospital Heidelberg, Heidelberg, Germany
| | - Rajkumar Savai
- Department of Lung Development and Remodelling, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany; Institute for Lung Health (ILH), Justus Liebig University, 35392 Giessen, Germany
| | - Peter Schirmacher
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany; Center for Personalized Medicine Heidelberg (ZPM), Heidelberg, Germany
| | - Michael Thomas
- Translational Lung Research Center (TLRC) Heidelberg, German Center for Lung Research (DZL), Germany; Department of Thoracic Oncology, Thoraxklinik at University Hospital Heidelberg, Heidelberg, Germany
| | - Jan Budczies
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany; Translational Lung Research Center (TLRC) Heidelberg, German Center for Lung Research (DZL), Germany; Center for Personalized Medicine Heidelberg (ZPM), Heidelberg, Germany
| | - Michael Allgäuer
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Petros Christopoulos
- Translational Lung Research Center (TLRC) Heidelberg, German Center for Lung Research (DZL), Germany; Department of Thoracic Oncology, Thoraxklinik at University Hospital Heidelberg, Heidelberg, Germany
| | - Albrecht Stenzinger
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany; Translational Lung Research Center (TLRC) Heidelberg, German Center for Lung Research (DZL), Germany.
| | - Anna-Lena Volckmar
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany.
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8
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Miller SC, MacDonald CC, Kellogg MK, Karamysheva ZN, Karamyshev AL. Specialized Ribosomes in Health and Disease. Int J Mol Sci 2023; 24:ijms24076334. [PMID: 37047306 PMCID: PMC10093926 DOI: 10.3390/ijms24076334] [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: 02/28/2023] [Revised: 03/21/2023] [Accepted: 03/23/2023] [Indexed: 03/30/2023] Open
Abstract
Ribosomal heterogeneity exists within cells and between different cell types, at specific developmental stages, and occurs in response to environmental stimuli. Mounting evidence supports the existence of specialized ribosomes, or specific changes to the ribosome that regulate the translation of a specific group of transcripts. These alterations have been shown to affect the affinity of ribosomes for certain mRNAs or change the cotranslational folding of nascent polypeptides at the exit tunnel. The identification of specialized ribosomes requires evidence of the incorporation of different ribosomal proteins or of modifications to rRNA and/or protein that lead(s) to physiologically relevant changes in translation. In this review, we summarize ribosomal heterogeneity and specialization in mammals and discuss their relevance to several human diseases.
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Affiliation(s)
- Sarah C. Miller
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
| | - Clinton C. MacDonald
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
| | - Morgana K. Kellogg
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
| | | | - Andrey L. Karamyshev
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
- Correspondence: ; Tel.: +1-806-743-4102
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9
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Yuan J, Lv T, Yang J, Wu Z, Yan L, Yang J, Shi Y, Jiang L. The lipid transporter HDLBP promotes hepatocellular carcinoma metastasis through BRAF-dependent epithelial-mesenchymal transition. Cancer Lett 2022; 549:215921. [PMID: 36122630 DOI: 10.1016/j.canlet.2022.215921] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 09/09/2022] [Accepted: 09/12/2022] [Indexed: 11/30/2022]
Abstract
Tumor metastasis is a major cause of cancer mortality. However, little is known regarding the regulation of abnormal cholesterol metabolism in hepatocellular carcinoma (HCC) metastasis. Here, we show that the expression of high-density lipoprotein binding protein (HDLBP), a lipid transporter, is clinically correlated with tumor metastasis in HCC patients. Moreover, HDLBP was required for cholesterol-induced HCC metastasis. We revealed that knockdown and overexpression of HDLBP significantly inhibited and enhanced, respectively, the metastasis, invasion and epithelial-mesenchymal transition (EMT) of HCC cells in vitro and in vivo. Mechanistically, coimmunoprecipitation and mass spectrometry screening uncovered BRAF as a protein target of HDLBP. HDLBP was found to promote EMT signaling in a BRAF-dependent manner. Furthermore, HDLBP interacts with BRAF and inhibits its ubiquitinated degradation by abrogating BRAF-ITCH interactions. Notably, further studies suggest that dabrafenib exhibited a greater metastasis-suppressive effect in HDLBP knockout HCC than isolated treatment. Overall, our findings imply that cholesterol-induced HDLBP contributes to the metastasis and invasion of HCC through BRAF-dependent EMT signaling and that HDLBP may be applied as a biomarker and therapeutic target for HCC.
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Affiliation(s)
- Jingsheng Yuan
- Department of Liver Surgery and Liver Transplantation Center, West China Hospital of Sichuan University, Chengdu, 610041, China; Laboratory of Liver Transplantation, Frontiers Science Center for Disease-related Molecular Network, West China Hospital of Sichuan University, Chengdu, 610041, China
| | - Tao Lv
- Department of Liver Surgery and Liver Transplantation Center, West China Hospital of Sichuan University, Chengdu, 610041, China; Laboratory of Liver Transplantation, Frontiers Science Center for Disease-related Molecular Network, West China Hospital of Sichuan University, Chengdu, 610041, China
| | - Jian Yang
- Department of Liver Surgery and Liver Transplantation Center, West China Hospital of Sichuan University, Chengdu, 610041, China; Laboratory of Liver Transplantation, Frontiers Science Center for Disease-related Molecular Network, West China Hospital of Sichuan University, Chengdu, 610041, China
| | - Zhenru Wu
- Laboratory of Pathology, Key Laboratory of Transplant Engineering and Immunology, NHC, West China Hospital of Sichuan University, Chengdu, 610041, China
| | - Lvnan Yan
- Department of Liver Surgery and Liver Transplantation Center, West China Hospital of Sichuan University, Chengdu, 610041, China; Laboratory of Liver Transplantation, Frontiers Science Center for Disease-related Molecular Network, West China Hospital of Sichuan University, Chengdu, 610041, China
| | - Jiayin Yang
- Department of Liver Surgery and Liver Transplantation Center, West China Hospital of Sichuan University, Chengdu, 610041, China; Laboratory of Liver Transplantation, Frontiers Science Center for Disease-related Molecular Network, West China Hospital of Sichuan University, Chengdu, 610041, China.
| | - Yujun Shi
- Laboratory of Liver Transplantation, Frontiers Science Center for Disease-related Molecular Network, West China Hospital of Sichuan University, Chengdu, 610041, China; Laboratory of Pathology, Key Laboratory of Transplant Engineering and Immunology, NHC, West China Hospital of Sichuan University, Chengdu, 610041, China.
| | - Li Jiang
- Department of Liver Surgery and Liver Transplantation Center, West China Hospital of Sichuan University, Chengdu, 610041, China; Laboratory of Liver Transplantation, Frontiers Science Center for Disease-related Molecular Network, West China Hospital of Sichuan University, Chengdu, 610041, China.
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Identification of Novel Loci Involved in Adalimumab Response in Crohn’s Disease Patients Using Integration of Genome Profiling and Isoform-Level Immune-Cell Deconvoluted Transcriptome Profiling of Colon Tissue. Pharmaceutics 2022; 14:pharmaceutics14091893. [PMID: 36145641 PMCID: PMC9500628 DOI: 10.3390/pharmaceutics14091893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 08/25/2022] [Accepted: 09/02/2022] [Indexed: 11/17/2022] Open
Abstract
Crohn’s disease is a consequence of dysregulated inflammatory response to the host’s microbiota. Although anti-TNF treatment improves the quality of the patient’s life, a large proportion of patients lose response to the treatment. The past decade of research has led to a continuum of studies showcasing the heterogeneity of anti-TNF response; thus, the aim of the present study was to dissect transcriptome-wide findings to transcript isoform specific levels and combine the analyses with refined information of immune cell landscapes in colon tissue, and subsequently select promising candidates using gene ontology and genomic integration. We enrolled Slovenian Crohn’s disease patients who were naïve with respect to adalimumab treatment. We performed colon tissue RNA sequencing and peripheral blood mononuclear cell DNA genotyping with a subsequent contemporary integrative approach to combine immune cell deconvoluted isoform transcript specific transcriptome analysis, gene ontology layering and genomic data. We identified nine genes (MACF1, CTSE, HDLBP, HSPA9, HLA-DMB, TAP2, LGMN, ANAPC11, ACP5) with 15 transcripts and 16 variants involved in the adalimumab response. Our study identified loci, some of which were previously shown to contribute to inflammatory bowel disease susceptibility, as novel loci involved in adalimumab response in Crohn’s disease patients.
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