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Zhang JY, Zhu X, Liu Y, Wu X. The Prognostic Biomarker RAB7A Promotes Growth and Metastasis of Liver Cancer Cells by Regulating Glycolysis and YAP1 Activation. J Cell Biochem 2024; 125:e30621. [PMID: 38924128 DOI: 10.1002/jcb.30621] [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: 12/21/2023] [Revised: 05/27/2024] [Accepted: 06/12/2024] [Indexed: 06/28/2024]
Abstract
Activating transcription factor 6 (ATF6) and its downstream genes are involved in progression of hepatocellular carcinoma (HCC). Herein, we demonstrated that sulfhydration of Ras-related protein Rab-7a (RAB7A) was regulated by ATF6. High expression of RAB7A indicated poor prognosis of HCC patients. RAB7A overexpression contributed to proliferation, colony formation, migration, and invasion of HepG2 and Hep3B cells. Furthermore, we found that RAB7A enhanced aerobic glycolysis in HepG2 cells, indicating a higher degree of tumor malignancy. Mechanistically, RAB7A suppressed Yes-associated protein 1 (YAP1) binding to 14-3-3 and conduced to YAP1 nuclear translocation and activation, promoting its downstream gene expression, thereby promoting growth and metastasis of liver cancer cells. In addition, knocking down RAB7A attenuated the progression of orthotopic liver tumors in mice. These findings illustrate the important role of RAB7A in regulating HCC progression. Thus, RAB7A may be a potential innovative target for HCC treatment.
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MESH Headings
- Humans
- Liver Neoplasms/metabolism
- Liver Neoplasms/pathology
- Liver Neoplasms/genetics
- YAP-Signaling Proteins/metabolism
- Animals
- Adaptor Proteins, Signal Transducing/metabolism
- Adaptor Proteins, Signal Transducing/genetics
- Glycolysis
- Mice
- Cell Proliferation
- rab7 GTP-Binding Proteins
- Carcinoma, Hepatocellular/metabolism
- Carcinoma, Hepatocellular/pathology
- Carcinoma, Hepatocellular/genetics
- Prognosis
- Transcription Factors/metabolism
- Transcription Factors/genetics
- Gene Expression Regulation, Neoplastic
- rab GTP-Binding Proteins/metabolism
- rab GTP-Binding Proteins/genetics
- Biomarkers, Tumor/metabolism
- Biomarkers, Tumor/genetics
- Mice, Nude
- Hep G2 Cells
- Cell Movement
- Neoplasm Metastasis
- Mice, Inbred BALB C
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Affiliation(s)
- Jun-Yuan Zhang
- Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, People's Republic of China
| | - Xilin Zhu
- Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, People's Republic of China
| | - Ying Liu
- Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, People's Republic of China
| | - Xiaopan Wu
- Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, People's Republic of China
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2
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Langley A, Abeling-Wang S, Wagner E, Salogiannis J. Movement of the endoplasmic reticulum is driven by multiple classes of vesicles marked by Rab-GTPases. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.14.592021. [PMID: 38798686 PMCID: PMC11118391 DOI: 10.1101/2024.05.14.592021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Peripheral endoplasmic reticulum (ER) tubules move along microtubules to interact with various organelles through membrane contact sites (MCS). Traditionally, ER moves by either sliding along stable microtubules via molecular motors or attaching to the plus ends of dynamic microtubules through tip attachment complexes (TAC). A recently discovered third process, hitchhiking, involves motile vesicles pulling ER tubules along microtubules. Previous research showed that ER hitchhikes on Rab5- and Rab7-marked endosomes, but it is uncertain if other Rab-vesicles can do the same. In U2OS cells, we screened Rabs for their ability to cotransport with ER tubules and found that ER hitchhikes on post-Golgi vesicles marked by Rab6 (isoforms a and b). Rab6-ER hitchhiking occurs independently of ER-endolysosome contacts and TAC-mediated ER movement. Disrupting either Rab6 or the motility of Rab6-vesicles reduces overall ER movement. Conversely, relocating these vesicles to the cell periphery causes peripheral ER accumulation, indicating that Rab6-vesicle motility is crucial for a subset of ER movements. Proximal post-Golgi vesicles marked by TGN46 are involved in Rab6-ER hitchhiking, while other post-Golgi vesicles (Rabs 8/10/11/13/14) are not essential for ER movement. Our further analysis finds that ER to Golgi vesicles marked by Rab1 are also capable of driving a subset of ER movements. Taken together, our findings suggest that ER hitchhiking on Rab-vesicles is a significant mode of ER movement. SIGNIFICANCE STATEMENT Peripheral endoplasmic reticulum tubules move on microtubules by either attaching to motors (cargo adaptor-mediated), dynamic microtubule-plus ends (tip attachment complexes) or motile vesicles (hitchhiking) but the prevalence of each mode is not clearPost-Golgi vesicles marked by Rab6/TGN46 and ER to Golgi vesicles marked by Rab1 drive ER movementsER hitchhiking on multiple classes of vesicles (endolysosomal, post-Golgi and ER to Golgi) marked by Rabs plays a prominent role in ER movement.
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3
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Gaur P, Rajendran Y, Srivastava B, Markandey M, Fishbain-Yoskovitz V, Mohapatra G, Suhail A, Chaudhary S, Tyagi S, Yadav SC, Pandey AK, Merbl Y, Bajaj A, Ahuja V, Srikanth C. Rab7-dependent regulation of goblet cell protein CLCA1 modulates gastrointestinal homeostasis. eLife 2024; 12:RP89776. [PMID: 38593125 PMCID: PMC11003743 DOI: 10.7554/elife.89776] [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] [Indexed: 04/11/2024] Open
Abstract
Inflammation in ulcerative colitis is typically restricted to the mucosal layer of distal gut. Disrupted mucus barrier, coupled with microbial dysbiosis, has been reported to occur prior to the onset of inflammation. Here, we show the involvement of vesicular trafficking protein Rab7 in regulating the colonic mucus system. We identified a lowered Rab7 expression in goblet cells of colon during human and murine colitis. In vivo Rab7 knocked down mice (Rab7KD) displayed a compromised mucus layer, increased microbial permeability, and depleted gut microbiota with enhanced susceptibility to dextran sodium-sulfate induced colitis. These abnormalities emerged owing to altered mucus composition, as revealed by mucus proteomics, with increased expression of mucin protease chloride channel accessory 1 (CLCA1). Mechanistically, Rab7 maintained optimal CLCA1 levels by controlling its lysosomal degradation, a process that was dysregulated during colitis. Overall, our work establishes a role for Rab7-dependent control of CLCA1 secretion required for maintaining mucosal homeostasis.
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Affiliation(s)
- Preksha Gaur
- Laboratory of Gut Inflammation and Infection Biology, Regional Centre for BiotechnologyFaridabadIndia
| | - Yesheswini Rajendran
- Laboratory of Gut Inflammation and Infection Biology, Regional Centre for BiotechnologyFaridabadIndia
| | | | - Manasvini Markandey
- Department of Gastroenterology, All India Institute of Medical SciencesDelhiIndia
| | | | | | - Aamir Suhail
- Gene Lay Institute of Immunology and Inflammation, Brigham and Women’s Hospital, Massachusetts General Hospital and Harvard Medical SchoolBostonUnited States
| | - Shikha Chaudhary
- Department of Anatomy, All India Institute of Medical SciencesNew DelhiIndia
| | - Shaifali Tyagi
- Vaccine and Infectious Disease Research Center, Translational Health Science and Technology InstituteFaridabadIndia
| | | | - Amit Kumar Pandey
- Vaccine and Infectious Disease Research Center, Translational Health Science and Technology InstituteFaridabadIndia
| | - Yifat Merbl
- Department of Immunology, Weizmann Institute of ScienceRehovotIsrael
| | - Avinash Bajaj
- Laboratory of Gut Inflammation and Infection Biology, Regional Centre for BiotechnologyFaridabadIndia
| | - Vineet Ahuja
- Department of Gastroenterology, All India Institute of Medical SciencesDelhiIndia
| | - Chittur Srikanth
- Laboratory of Gut Inflammation and Infection Biology, Regional Centre for BiotechnologyFaridabadIndia
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4
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Bare Y, Matusek T, Vriz S, Deffieu MS, Thérond PP, Gaudin R. TMED10 mediates the loading of neosynthesised Sonic Hedgehog in COPII vesicles for efficient secretion and signalling. Cell Mol Life Sci 2023; 80:266. [PMID: 37624561 PMCID: PMC11072717 DOI: 10.1007/s00018-023-04918-1] [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: 04/18/2023] [Revised: 07/24/2023] [Accepted: 08/09/2023] [Indexed: 08/26/2023]
Abstract
The morphogen Sonic Hedgehog (SHH) plays an important role in coordinating embryonic development. Short- and long-range SHH signalling occurs through a variety of membrane-associated and membrane-free forms. However, the molecular mechanisms that govern the early events of the trafficking of neosynthesised SHH in mammalian cells are still poorly understood. Here, we employed the retention using selective hooks (RUSH) system to show that newly-synthesised SHH is trafficked through the classical biosynthetic secretory pathway, using TMED10 as an endoplasmic reticulum (ER) cargo receptor for efficient ER-to-Golgi transport and Rab6 vesicles for Golgi-to-cell surface trafficking. TMED10 and SHH colocalized at ER exit sites (ERES), and TMED10 depletion significantly delays SHH loading onto ERES and subsequent exit leading to significant SHH release defects. Finally, we utilised the Drosophila wing imaginal disc model to demonstrate that the homologue of TMED10, Baiser (Bai), participates in Hedgehog (Hh) secretion and signalling in vivo. In conclusion, our work highlights the role of TMED10 in cargo-specific egress from the ER and sheds light on novel important partners of neosynthesised SHH secretion with potential impact on embryonic development.
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Affiliation(s)
- Yonis Bare
- Institut de Recherche en Infectiologie de Montpellier (IRIM) CNRS, 1919 Route de Mende, 34293, Montpellier, France
- Université de Montpellier, 34090, Montpellier, France
| | - Tamás Matusek
- Université Côte d'Azur, UMR7277 CNRS, Inserm 1091, Institut de Biologie de Valrose (iBV), Parc Valrose, Nice, France
| | - Sophie Vriz
- Laboratoire des Biomolécules (LBM), Département de Chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005, Paris, France
- Faculty of Science, Université de Paris, Paris, France
| | - Maika S Deffieu
- Institut de Recherche en Infectiologie de Montpellier (IRIM) CNRS, 1919 Route de Mende, 34293, Montpellier, France
- Université de Montpellier, 34090, Montpellier, France
| | - Pascal P Thérond
- Université Côte d'Azur, UMR7277 CNRS, Inserm 1091, Institut de Biologie de Valrose (iBV), Parc Valrose, Nice, France
| | - Raphael Gaudin
- Institut de Recherche en Infectiologie de Montpellier (IRIM) CNRS, 1919 Route de Mende, 34293, Montpellier, France.
- Université de Montpellier, 34090, Montpellier, France.
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5
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Liang W, Sagar S, Ravindran R, Najor RH, Quiles JM, Chi L, Diao RY, Woodall BP, Leon LJ, Zumaya E, Duran J, Cauvi DM, De Maio A, Adler ED, Gustafsson ÅB. Mitochondria are secreted in extracellular vesicles when lysosomal function is impaired. Nat Commun 2023; 14:5031. [PMID: 37596294 PMCID: PMC10439183 DOI: 10.1038/s41467-023-40680-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 08/04/2023] [Indexed: 08/20/2023] Open
Abstract
Mitochondrial quality control is critical for cardiac homeostasis as these organelles are responsible for generating most of the energy needed to sustain contraction. Dysfunctional mitochondria are normally degraded via intracellular degradation pathways that converge on the lysosome. Here, we identified an alternative mechanism to eliminate mitochondria when lysosomal function is compromised. We show that lysosomal inhibition leads to increased secretion of mitochondria in large extracellular vesicles (EVs). The EVs are produced in multivesicular bodies, and their release is independent of autophagy. Deletion of the small GTPase Rab7 in cells or adult mouse heart leads to increased secretion of EVs containing ubiquitinated cargos, including intact mitochondria. The secreted EVs are captured by macrophages without activating inflammation. Hearts from aged mice or Danon disease patients have increased levels of secreted EVs containing mitochondria indicating activation of vesicular release during cardiac pathophysiology. Overall, these findings establish that mitochondria are eliminated in large EVs through the endosomal pathway when lysosomal degradation is inhibited.
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Affiliation(s)
- Wenjing Liang
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Shakti Sagar
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Rishith Ravindran
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Rita H Najor
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Justin M Quiles
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Liguo Chi
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Rachel Y Diao
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Benjamin P Woodall
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Leonardo J Leon
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Erika Zumaya
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Jason Duran
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - David M Cauvi
- Department of Surgery, University of California San Diego, La Jolla, CA, USA
| | - Antonio De Maio
- Department of Surgery, University of California San Diego, La Jolla, CA, USA
| | - Eric D Adler
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Åsa B Gustafsson
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.
- Department of Pharmacology, University of California San Diego, La Jolla, CA, USA.
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6
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Coulet M, Lachkar S, Leduc M, Trombe M, Gouveia Z, Perez F, Kepp O, Kroemer G, Basmaciogullari S. Identification of Small Molecules Affecting the Secretion of Therapeutic Antibodies with the Retention Using Selective Hook (RUSH) System. Cells 2023; 12:1642. [PMID: 37371112 DOI: 10.3390/cells12121642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 06/12/2023] [Accepted: 06/13/2023] [Indexed: 06/29/2023] Open
Abstract
Unlocking cell secretion capacity is of paramount interest for the pharmaceutical industry focused on biologics. Here, we leveraged retention using a selective hook (RUSH) system for the identification of human osteosarcoma U2OS cell secretion modulators, through automated, high-throughput screening of small compound libraries. We created a U2OS cell line which co-expresses a variant of streptavidin addressed to the lumen-facing membrane of the endoplasmic reticulum (ER) and a recombinant anti-PD-L1 antibody. The heavy chain of the antibody was modified at its C-terminus, to which a furin cleavage site, a green fluorescent protein (GFP), and a streptavidin binding peptide (SBP) were added. We show that the U2OS cell line stably expresses the streptavidin hook and the recombinant antibody bait, which is retained in the ER through the streptavidin-SBP interaction. We further document that the addition of biotin to the culture medium triggers the antibody release from the ER, its trafficking through the Golgi where the GFP-SBP moiety is clipped off, and eventually its release in the extra cellular space, with specific antigen-binding properties. The use of this clone in screening campaigns led to the identification of lycorine as a secretion enhancer, and nigericin and tyrphostin AG-879 as secretion inhibitors. Altogether, our data support the utility of this approach for the identification of agents that could be used to improve recombinant production yields and also for a better understanding of the regulatory mechanism at work in the conventional secretion pathway.
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Affiliation(s)
- Mathilde Coulet
- Sanofi R&D, 94400 Vitry-sur-Seine, France
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Center, 94800 Villejuif, France
- Centre de Recherche des Cordeliers, Equipe Labellisée par la Ligue Contre le Cancer, Université de Paris Cité, Sorbonne Université, Inserm U1138, Institut Universitaire de France, 75006 Paris, France
| | - Sylvie Lachkar
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Center, 94800 Villejuif, France
- Centre de Recherche des Cordeliers, Equipe Labellisée par la Ligue Contre le Cancer, Université de Paris Cité, Sorbonne Université, Inserm U1138, Institut Universitaire de France, 75006 Paris, France
| | - Marion Leduc
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Center, 94800 Villejuif, France
- Centre de Recherche des Cordeliers, Equipe Labellisée par la Ligue Contre le Cancer, Université de Paris Cité, Sorbonne Université, Inserm U1138, Institut Universitaire de France, 75006 Paris, France
| | | | - Zelia Gouveia
- Institut Curie, PSL Research University, Sorbonne Université, CNRS, UMR 144, 26 rue d'Ulm, 75005 Paris, France
| | - Franck Perez
- Institut Curie, PSL Research University, Sorbonne Université, CNRS, UMR 144, 26 rue d'Ulm, 75005 Paris, France
| | - Oliver Kepp
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Center, 94800 Villejuif, France
- Centre de Recherche des Cordeliers, Equipe Labellisée par la Ligue Contre le Cancer, Université de Paris Cité, Sorbonne Université, Inserm U1138, Institut Universitaire de France, 75006 Paris, France
| | - Guido Kroemer
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Center, 94800 Villejuif, France
- Centre de Recherche des Cordeliers, Equipe Labellisée par la Ligue Contre le Cancer, Université de Paris Cité, Sorbonne Université, Inserm U1138, Institut Universitaire de France, 75006 Paris, France
- Department of Biology, Institut du Cancer Paris CARPEM, Hôpital Européen Georges Pompidou, AP-HP, 75015 Paris, France
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7
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Lučanský V, Holubeková V, Kolková Z, Halašová E, Samec M, Golubnitschaja O. Multi-faceted CRISPR/Cas technological innovation aspects in the framework of 3P medicine. EPMA J 2023; 14:201-217. [PMID: 37275547 PMCID: PMC10201107 DOI: 10.1007/s13167-023-00324-6] [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: 05/02/2023] [Accepted: 05/10/2023] [Indexed: 06/07/2023]
Abstract
Since 2009, the European Association for Predictive, Preventive and Personalised Medicine (EPMA, Brussels) promotes the paradigm change from reactive approach to predictive, preventive, and personalized medicine (PPPM/3PM) to protect individuals in sub-optimal health conditions from the health-to-disease transition, to increase life-quality of the affected patient cohorts improving, therefore, ethical standards and cost-efficacy of healthcare to great benefits of the society at large. The gene-editing technology utilizing CRISPR/Cas gene-editing approach has demonstrated its enormous value as a powerful tool in a broad spectrum of bio/medical research areas. Further, CRISPR/Cas gene-editing system is considered applicable to primary and secondary healthcare, in order to prevent disease spread and to treat clinically manifested disorders, involving diagnostics of SARS-Cov-2 infection and experimental treatment of COVID-19. Although the principle of the proposed gene editing is simple and elegant, there are a lot of technological challenges and ethical considerations to be solved prior to its broadly scaled clinical implementation. This article highlights technological innovation beyond the state of the art, exemplifies current achievements, discusses unsolved technological and ethical problems, and provides clinically relevant outlook in the framework of 3PM.
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Affiliation(s)
- Vincent Lučanský
- Jessenius Faculty of Medicine in Martin (JFMED CU), Biomedical Center, Comenius University in Bratislava, Martin, Slovakia
| | - Veronika Holubeková
- Jessenius Faculty of Medicine in Martin (JFMED CU), Biomedical Center, Comenius University in Bratislava, Martin, Slovakia
| | - Zuzana Kolková
- Jessenius Faculty of Medicine in Martin (JFMED CU), Biomedical Center, Comenius University in Bratislava, Martin, Slovakia
| | - Erika Halašová
- Jessenius Faculty of Medicine in Martin (JFMED CU), Biomedical Center, Comenius University in Bratislava, Martin, Slovakia
| | - Marek Samec
- Department of Pathophysiology, Jessenius Faculty of Medicine, Comenius University in Bratislava, Martin, Slovakia
| | - Olga Golubnitschaja
- Predictive, Preventive, Personalised (3P) Medicine, Department of Radiation Oncology, University Hospital Bonn, Rheinische Friedrich-Wilhelms-Universität Bonn, 53127 Bonn, Germany
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Carlson RJ, Leiken MD, Guna A, Hacohen N, Blainey PC. A genome-wide optical pooled screen reveals regulators of cellular antiviral responses. Proc Natl Acad Sci U S A 2023; 120:e2210623120. [PMID: 37043539 PMCID: PMC10120039 DOI: 10.1073/pnas.2210623120] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 02/06/2023] [Indexed: 04/13/2023] Open
Abstract
The infection of mammalian cells by viruses and innate immune responses to infection are spatiotemporally organized processes. Cytosolic RNA sensors trigger nuclear translocation of the transcription factor interferon regulatory factor 3 (IRF3) and consequent induction of host immune responses to RNA viruses. Previous genetic screens for factors involved in viral sensing did not resolve changes in the subcellular localization of host or viral proteins. Here, we increased the throughput of our optical pooled screening technology by over fourfold. This allowed us to carry out a genome-wide CRISPR knockout screen using high-resolution multiparameter imaging of cellular responses to Sendai virus infection coupled with in situ cDNA sequencing by synthesis (SBS) to identify 80,408 single guide RNAs (sgRNAs) in 10,366,390 cells-over an order of magnitude more genomic perturbations than demonstrated previously using an in situ SBS readout. By ranking perturbations using human-designed and deep learning image feature scores, we identified regulators of IRF3 translocation, Sendai virus localization, and peroxisomal biogenesis. Among the hits, we found that ATP13A1, an ER-localized P5A-type ATPase, is essential for viral sensing and is required for targeting of mitochondrial antiviral signaling protein (MAVS) to mitochondrial membranes where MAVS must be localized for effective signaling through retinoic acid-inducible gene I (RIG-I). The ability to carry out genome-wide pooled screens with complex high-resolution image-based phenotyping dramatically expands the scope of functional genomics approaches.
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Affiliation(s)
- Rebecca J. Carlson
- Department of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA02139
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA02142
| | - Michael D. Leiken
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA02142
| | | | - Nir Hacohen
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA02142
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA02114
| | - Paul C. Blainey
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA02142
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA02139
- Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA02139
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9
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Liu Y, Ma J, Wang X, Liu P, Cai C, Han Y, Zeng S, Feng Z, Shen H. Lipophagy-related gene RAB7A is involved in immune regulation and malignant progression in hepatocellular carcinoma. Comput Biol Med 2023; 158:106862. [PMID: 37044053 DOI: 10.1016/j.compbiomed.2023.106862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 02/05/2023] [Accepted: 03/30/2023] [Indexed: 04/08/2023]
Abstract
BACKGROUND RAB7A (RAS-related in Brain 7A) is an important member of the RAS oncogene family. However, the correlation between RAB7A and the development and immune infiltration of hepatocellular carcinoma (HCC) has rarely been studied. Here, we studied the role of RAB7A in HCC through bioinformatics analysis, real-world cohort validation, and in vitro experimental exploration. MATERIALS AND METHODS The RAB7A expression level was analyzed through TCGA, HPA and TISIDB databases. TIMER and TISCH were used to analyze the correlation between RAB7A and tumor immune microenvironment. The expression of RAB7A was detected through real-time PCR and western blotting. The cell proliferation was detected by EdU and CCK8. Wound-healing and transwell assays were used to test the invasion and migration ability. Cell cycle distribution and reactive oxygen species (ROS) content were analyzed by flow cytometry. Identification of epithelial-mesenchymal transition (EMT) was performed by immunofluorescence double staining. Immunohistochemistry (IHC) was used to evaluate the correlation between RAB7A and immune checkpoints. RESULTS RAB7A is upregulated in most of the tumor types, and the upregulation of RAB7A is associated with a poorer prognosis in many cancers. The results showed that RAB7A was significantly positively correlated with the infiltration of macrophages and cancer-associated fibroblasts (CAFs), but negatively correlated with M2-type macrophages in most tumors. The single-cell atlas also revealed the distribution and proportion of RAB7A in immune cells of HCC. The in vitro experiments suggested that RAB7A was increased in HCC tissue and cell lines. The knockdown of RAB7A inhibited the activation of the PIK3CA-AKT pathway and suppressed the expression of CDK4, CDK6 and CCNA2. Knockdown of RAB7A induced G0/G1 arrest and ROS accumulation in HCC. In addition, overexpression of RAB7A enhanced migration and invasion by inducing EMT. The real-world cohort showed that the expression level of RAB7A was positively correlated with the expression levels of TGFBR1 and PD-L1. CONCLUSIONS RAB7A may serve as a potential tumor prognostic and immune infiltration-related biomarker, predicting immunotherapy efficacy in certain cancer types, especially in HCC. Besides, RAB7A was a multi-pathway target involved in the malignant progression of HCC.
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Affiliation(s)
- Yongting Liu
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China.
| | - Jiayao Ma
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China.
| | - Xinwen Wang
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China.
| | - Ping Liu
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China.
| | - Changjing Cai
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China.
| | - Ying Han
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China.
| | - Shan Zeng
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China.
| | - Ziyang Feng
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China.
| | - Hong Shen
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China.
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10
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Nielsen SSE, Holst MR, Langthaler K, Bruun EH, Brodin B, Nielsen MS. Apicobasal transferrin receptor localization and trafficking in brain capillary endothelial cells. Fluids Barriers CNS 2023; 20:2. [PMID: 36624498 PMCID: PMC9830855 DOI: 10.1186/s12987-022-00404-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 12/28/2022] [Indexed: 01/11/2023] Open
Abstract
The detailed mechanisms by which the transferrin receptor (TfR) and associated ligands traffic across brain capillary endothelial cells (BECs) of the CNS-protective blood-brain barrier constitute an important knowledge gap within maintenance and regulation of brain iron homeostasis. This knowledge gap also presents a major obstacle in research aiming to develop strategies for efficient receptor-mediated drug delivery to the brain. While TfR-mediated trafficking from blood to brain have been widely studied, investigation of TfR-mediated trafficking from brain to blood has been limited. In this study we investigated TfR distribution on the apical and basal plasma membranes of BECs using expansion microscopy, enabling sufficient resolution to separate the cellular plasma membranes of these morphological flat cells, and verifying both apical and basal TfR membrane domain localization. Using immunofluorescence-based transcellular transport studies, we delineated endosomal sorting of TfR endocytosed from the apical and basal membrane, respectively, as well as bi-directional TfR transcellular transport capability. The findings indicate different intracellular sorting mechanisms of TfR, depending on the apicobasal trafficking direction across the BBB, with the highest transcytosis capacity in the brain-to-blood direction. These results are of high importance for the current understanding of brain iron homeostasis. Also, the high level of TfR trafficking from the basal to apical membrane of BECs potentially explains the low transcytosis which are observed for the TfR-targeted therapeutics to the brain parenchyma.
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Affiliation(s)
- Simone S. E. Nielsen
- grid.7048.b0000 0001 1956 2722Department of Biomedicine, Faculty of Health, Aarhus University, 8000 Aarhus C, Denmark
| | - Mikkel R. Holst
- grid.7048.b0000 0001 1956 2722Department of Biomedicine, Faculty of Health, Aarhus University, 8000 Aarhus C, Denmark
| | - Kristine Langthaler
- grid.5254.60000 0001 0674 042XCNS Drug Delivery and Barrier Modelling, University of Copenhagen, Copenhagen, Denmark ,grid.424580.f0000 0004 0476 7612Translational DMPK, H. Lundbeck A/S, Copenhagen, Denmark
| | - Elisabeth Helena Bruun
- grid.7048.b0000 0001 1956 2722Department of Biomedicine, Faculty of Health, Aarhus University, 8000 Aarhus C, Denmark
| | - Birger Brodin
- grid.5254.60000 0001 0674 042XDepartment of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Morten S. Nielsen
- grid.7048.b0000 0001 1956 2722Department of Biomedicine, Faculty of Health, Aarhus University, 8000 Aarhus C, Denmark
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11
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Deffieu MS, Clément CMH, Dorobantu CM, Partiot E, Bare Y, Faklaris O, Rivière B, Ayala-Nunez NV, Baumert TF, Rondé P, Mély Y, Lucansky V, Gaudin R. Occludin stalls HCV particle dynamics apart from hepatocyte tight junctions, promoting virion internalization. Hepatology 2022; 76:1164-1179. [PMID: 35388524 DOI: 10.1002/hep.32514] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 03/28/2022] [Accepted: 04/03/2022] [Indexed: 12/08/2022]
Abstract
BACKGROUND AND AIMS Numerous HCV entry factors have been identified, and yet information regarding their spatiotemporal dynamics is still limited. Specifically, one of the main entry factors of HCV is occludin (OCLN), a protein clustered at tight junctions (TJs), away from the HCV landing site. Thus, whether HCV particles slide toward TJs or, conversely, OCLN is recruited away from TJs remain debated. APPROACH AND RESULTS Here, we generated CRISPR/CRISPR-associated protein 9 edited Huh7.5.1 cells expressing endogenous levels of enhanced green fluorescent protein/OCLN and showed that incoming HCV particles recruit OCLN outside TJs, independently of claudin 1 (CLDN1) expression, another important HCV entry factor located at TJs. Using ex vivo organotypic culture of hepatic slices obtained from human liver explants, a physiologically relevant model that preserves the overall tissue architecture, we confirmed that HCV associates with OCLN away from TJs. Furthermore, we showed, by live cell imaging, that increased OCLN recruitment beneath HCV particles correlated with lower HCV motility. To decipher the mechanism underlying virus slow-down upon OCLN recruitment, we performed CRISPR knockout (KO) of CLDN1, an HCV entry factor proposed to act upstream of OCLN. Although CLDN1 KO potently inhibits HCV infection, OCLN kept accumulating underneath the particle, indicating that OCLN recruitment is CLDN1 independent. Moreover, inhibition of the phosphorylation of Ezrin, a protein involved in HCV entry that links receptors to the actin cytoskeleton, increased OCLN accumulation and correlated with more efficient HCV internalization. CONCLUSIONS Together, our data provide robust evidence that HCV particles interact with OCLN away from TJs and shed mechanistic insights regarding the manipulation of transmembrane receptor localization by extracellular virus particles.
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Affiliation(s)
- Maika S Deffieu
- Institut de Recherche en infectiologie de Montpellier (IRIM), CNRS, Montpellier, France.,Université de Montpellier, Montpellier, France
| | - Camille M H Clément
- Institut de Recherche en infectiologie de Montpellier (IRIM), CNRS, Montpellier, France.,Université de Montpellier, Montpellier, France.,Université de Strasbourg, Strasbourg, France.,INSERM, Institut de Recherche sur les Maladies Virales et Hépatiques, Strasbourg, France
| | - Cristina M Dorobantu
- Université de Strasbourg, Strasbourg, France.,INSERM, Institut de Recherche sur les Maladies Virales et Hépatiques, Strasbourg, France
| | - Emma Partiot
- Institut de Recherche en infectiologie de Montpellier (IRIM), CNRS, Montpellier, France.,Université de Montpellier, Montpellier, France
| | - Yonis Bare
- Institut de Recherche en infectiologie de Montpellier (IRIM), CNRS, Montpellier, France.,Université de Montpellier, Montpellier, France
| | - Orestis Faklaris
- BCM, University of Montpellier, CNRS, INSERM, Montpellier, France
| | - Benjamin Rivière
- CHU Montpellier, Laboratoire d'Anatomie et Cytologie Pathologiques-CRB, Montpellier, France
| | - Nilda Vanesa Ayala-Nunez
- Institut de Recherche en infectiologie de Montpellier (IRIM), CNRS, Montpellier, France.,Université de Montpellier, Montpellier, France
| | - Thomas F Baumert
- Université de Strasbourg, Strasbourg, France.,INSERM, Institut de Recherche sur les Maladies Virales et Hépatiques, Strasbourg, France
| | - Philippe Rondé
- Université de Strasbourg, Strasbourg, France.,UMR 7021 CNRS, Laboratoire de Bioimagerie et Pathologies, Université de Strasbourg, Faculté de pharmacie, Illkirch, France
| | - Yves Mély
- Université de Strasbourg, Strasbourg, France.,UMR 7021 CNRS, Laboratoire de Bioimagerie et Pathologies, Université de Strasbourg, Faculté de pharmacie, Illkirch, France
| | - Vincent Lucansky
- Université de Strasbourg, Strasbourg, France.,INSERM, Institut de Recherche sur les Maladies Virales et Hépatiques, Strasbourg, France
| | - Raphael Gaudin
- Institut de Recherche en infectiologie de Montpellier (IRIM), CNRS, Montpellier, France.,Université de Montpellier, Montpellier, France
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12
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Samelson AJ, Tran QD, Robinot R, Carrau L, Rezelj VV, Kain AM, Chen M, Ramadoss GN, Guo X, Lim SA, Lui I, Nuñez JK, Rockwood SJ, Wang J, Liu N, Carlson-Stevermer J, Oki J, Maures T, Holden K, Weissman JS, Wells JA, Conklin BR, TenOever BR, Chakrabarti LA, Vignuzzi M, Tian R, Kampmann M. BRD2 inhibition blocks SARS-CoV-2 infection by reducing transcription of the host cell receptor ACE2. Nat Cell Biol 2022; 24:24-34. [PMID: 35027731 PMCID: PMC8820466 DOI: 10.1038/s41556-021-00821-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 11/24/2021] [Indexed: 12/11/2022]
Abstract
SARS-CoV-2 infection of human cells is initiated by the binding of the viral Spike protein to its cell-surface receptor ACE2. We conducted a targeted CRISPRi screen to uncover druggable pathways controlling Spike protein binding to human cells. Here we show that the protein BRD2 is required for ACE2 transcription in human lung epithelial cells and cardiomyocytes, and BRD2 inhibitors currently evaluated in clinical trials potently block endogenous ACE2 expression and SARS-CoV-2 infection of human cells, including those of human nasal epithelia. Moreover, pharmacological BRD2 inhibition with the drug ABBV-744 inhibited SARS-CoV-2 replication in Syrian hamsters. We also found that BRD2 controls transcription of several other genes induced upon SARS-CoV-2 infection, including the interferon response, which in turn regulates the antiviral response. Together, our results pinpoint BRD2 as a potent and essential regulator of the host response to SARS-CoV-2 infection and highlight the potential of BRD2 as a therapeutic target for COVID-19.
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Affiliation(s)
- Avi J Samelson
- Institute for Neurodegenerative Diseases, University of California San Francisco, San Francisco, CA, USA
- Chan-Zuckerberg Biohub, San Francisco, CA, USA
| | - Quang Dinh Tran
- Viral Populations and Pathogenesis Unit, Institut Pasteur, Paris, France
- École Doctorale BioSPC, Université de Paris, Sorbonne Paris Cité, Paris, France
| | - Rémy Robinot
- Institut Pasteur, CIVIC Group, Virus and Immunity Unit, Université de Paris, Paris, France
| | - Lucia Carrau
- Microbiology Department, NYU-Langone, New York, NY, USA
| | - Veronica V Rezelj
- Viral Populations and Pathogenesis Unit, Institut Pasteur, Paris, France
| | - Alice Mac Kain
- Viral Populations and Pathogenesis Unit, Institut Pasteur, Paris, France
- École Doctorale BioSPC, Université de Paris, Sorbonne Paris Cité, Paris, France
| | - Merissa Chen
- Institute for Neurodegenerative Diseases, University of California San Francisco, San Francisco, CA, USA
- Chan-Zuckerberg Biohub, San Francisco, CA, USA
| | - Gokul N Ramadoss
- Gladstone Institutes, San Francisco, CA, USA
- Biomedical Sciences PhD Program, University of California San Francisco, San Francisco, CA, USA
| | - Xiaoyan Guo
- Institute for Neurodegenerative Diseases, University of California San Francisco, San Francisco, CA, USA
- Chan-Zuckerberg Biohub, San Francisco, CA, USA
| | - Shion A Lim
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
- Department of Antibody Engineering, Genentech Inc., San Francisco, CA, USA
| | - Irene Lui
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - James K Nuñez
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA, USA
| | | | - Jianhui Wang
- School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Na Liu
- School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | | | | | | | | | - Jonathan S Weissman
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA, USA
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, USA
| | - James A Wells
- Chan-Zuckerberg Biohub, San Francisco, CA, USA
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Bruce R Conklin
- Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
- Department of Ophthalmology, University of California San Francisco, San Francisco, CA, USA
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | | | - Lisa A Chakrabarti
- Institut Pasteur, CIVIC Group, Virus and Immunity Unit, Université de Paris, Paris, France
| | - Marco Vignuzzi
- Viral Populations and Pathogenesis Unit, Institut Pasteur, Paris, France
| | - Ruilin Tian
- Institute for Neurodegenerative Diseases, University of California San Francisco, San Francisco, CA, USA.
- Chan-Zuckerberg Biohub, San Francisco, CA, USA.
- School of Medicine, Southern University of Science and Technology, Shenzhen, China.
| | - Martin Kampmann
- Institute for Neurodegenerative Diseases, University of California San Francisco, San Francisco, CA, USA.
- Chan-Zuckerberg Biohub, San Francisco, CA, USA.
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA.
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