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Bradburn DA, Reis JC, Arthanari H, Cyert MS. A novel motif in calcimembrin/C16orf74 dictates multimeric dephosphorylation by calcineurin. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.12.593783. [PMID: 38798520 PMCID: PMC11118366 DOI: 10.1101/2024.05.12.593783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Calcineurin (CN), the only Ca 2+ -calmodulin activated protein phosphatase, dephosphorylates substrates within membrane-associated Ca 2+ microdomains. CN binds to substrates and regulators via short linear motifs (SLIMs), PxIxIT and LxVP. PxIxIT binding to CN is Ca 2+ independent and affects its distribution, while LxVP associates only with the active enzyme and promotes catalysis. 31 human proteins contain one or more composite 'LxVPxIxIT' motifs, whose functional properties have not been examined. Here we report studies of calcimembrin/C16orf74 (CLMB), a largely uncharacterized protein containing a composite motif that binds and directs CN to membranes. We demonstrate that CLMB associates with membranes via N-myristoylation and dynamic S-acylation and is dephosphorylated by CN on Thr44. The LxVP and PxIxIT portions of the CLMB composite sequence, together with Thr44 phosphorylation, confer high affinity PxIxIT-mediated binding to CN (KD∼8.9 nM) via an extended, 33 LxVPxIxITxx(p)T 44 sequence. This binding promotes CLMB-based targeting of CN to membranes, but also protects Thr44 from dephosphorylation. Thus, we propose that CN dephosphorylates CLMB in multimeric complexes, where one CLMB molecule recruits CN to membranes via PxIxIT binding, allowing others to engage through their LxVP motif for dephosphorylation. This unique mechanism makes dephosphorylation sensitive to CLMB:CN ratios and is supported by in vivo and in vitro analyses. CLMB overexpression is associated with poor prognoses for several cancers, suggesting that it promotes oncogenesis by shaping CN signaling.
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Takeuchi Y, Wang Y, Sasaki K, Sato O, Tsuchikawa T, Wang L, Amaishi Y, Okamoto S, Mineno J, Hirokawa Y, Hatanaka KC, Hatanaka Y, Kato T, Shiku H, Hirano S. Exhaustion, rather than lack of infiltration and persistence, of CAR-T cells hampers the efficacy of CAR-T therapy in an orthotopic PDAC xenograft model. Biomed Pharmacother 2024; 170:116052. [PMID: 38141280 DOI: 10.1016/j.biopha.2023.116052] [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: 09/14/2023] [Revised: 12/15/2023] [Accepted: 12/15/2023] [Indexed: 12/25/2023] Open
Abstract
Chimeric antigen receptor T-cell (CAR-T) therapy has demonstrated impressive success in the treatment of patients with hematologic tumors yet achieved very limited efficacy for solid tumors due to hurdles unique to solid tumors. It is also noted that the tumor microenvironment composition varies between tumor type, which again imposes unique set of hurdles in each solid tumor. Therefore, elucidation of individual hurdles is key to achieving successful CAR-T therapy for solid tumors. In the present study, we employed an orthotopic human PDAC xenograft model, in which quantitative, spatial and functional dynamics of CAR-T cells in tumor tissues were analyzed to obtain insights into ways of overcoming PDAC related hurdles. Contrary to previous studies that demonstrated a limited persistency and infiltration of CAR-T cells in many solid tumors, they persist and accumulated in PDAC tumor tissues. Ex vivo analysis revealed that CAR-T cells that had been recovered at different time points from mice bearing an orthotopic PDAC tumor exhibited a gradual loss of tumor reactivity. This loss of tumor reactivity of CAR-T cells was associated with the increased expression of AMP-activated protein kinase and Mitofusin 1/ Dynamin-related protein 1 ratio.
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Affiliation(s)
- Yuta Takeuchi
- Department of Gastroenterological Surgery II, Hokkaido University Faculty of Medicine, Sapporo, Hokkaido, Japan
| | - Yizheng Wang
- Department of Personalized Cancer Immunotherapy, Mie University Graduate School of Medicine, Tsu, Mie, Japan
| | - Katsunori Sasaki
- Department of Gastroenterological Surgery II, Hokkaido University Faculty of Medicine, Sapporo, Hokkaido, Japan
| | - Osamu Sato
- Department of Gastroenterological Surgery II, Hokkaido University Faculty of Medicine, Sapporo, Hokkaido, Japan
| | - Takahiro Tsuchikawa
- Department of Gastroenterological Surgery II, Hokkaido University Faculty of Medicine, Sapporo, Hokkaido, Japan.
| | - Linan Wang
- Department of Immuno-Gene Therapy, Mie University Graduate School of Medicine, Tsu, Mie, Japan
| | | | | | | | - Yoshifumi Hirokawa
- Department of Oncologic Pathology, Mie University Graduate School of Medicine, Tsu, Mie, Japan
| | - Kanako C Hatanaka
- Center for Development of Advanced Diagnostics, Hokkaido University Hospital, Sapporo, Hokkaido, Japan
| | - Yutaka Hatanaka
- Center for Development of Advanced Diagnostics, Hokkaido University Hospital, Sapporo, Hokkaido, Japan
| | - Takuma Kato
- Department of Cellular and Molecular Immunology, Mie University Graduate School of Medicine, Tsu, Mie, Japan; Department of Immunology, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan.
| | - Hiroshi Shiku
- Department of Immuno-Gene Therapy, Mie University Graduate School of Medicine, Tsu, Mie, Japan; Center for Comprehensive Cancer Immunotherapy, Mie University, Tsu, Mie, Japan
| | - Satoshi Hirano
- Department of Gastroenterological Surgery II, Hokkaido University Faculty of Medicine, Sapporo, Hokkaido, Japan
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Ershov P, Yablokov E, Mezentsev Y, Ivanov A. Uncharacterized Proteins CxORFx: Subinteractome Analysis and Prognostic Significance in Cancers. Int J Mol Sci 2023; 24:10190. [PMID: 37373333 DOI: 10.3390/ijms241210190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 05/25/2023] [Accepted: 05/26/2023] [Indexed: 06/29/2023] Open
Abstract
Functions of about 10% of all the proteins and their associations with diseases are poorly annotated or not annotated at all. Among these proteins, there is a group of uncharacterized chromosome-specific open-reading frame genes (CxORFx) from the 'Tdark' category. The aim of the work was to reveal associations of CxORFx gene expression and ORF proteins' subinteractomes with cancer-driven cellular processes and molecular pathways. We performed systems biology and bioinformatic analysis of 219 differentially expressed CxORFx genes in cancers, an estimation of prognostic significance of novel transcriptomic signatures and analysis of subinteractome composition using several web servers (GEPIA2, KMplotter, ROC-plotter, TIMER, cBioPortal, DepMap, EnrichR, PepPSy, cProSite, WebGestalt, CancerGeneNet, PathwAX II and FunCoup). The subinteractome of each ORF protein was revealed using ten different data sources on physical protein-protein interactions (PPIs) to obtain representative datasets for the exploration of possible cellular functions of ORF proteins through a spectrum of neighboring annotated protein partners. A total of 42 out of 219 presumably cancer-associated ORF proteins and 30 cancer-dependent binary PPIs were found. Additionally, a bibliometric analysis of 204 publications allowed us to retrieve biomedical terms related to ORF genes. In spite of recent progress in functional studies of ORF genes, the current investigations aim at finding out the prognostic value of CxORFx expression patterns in cancers. The results obtained expand the understanding of the possible functions of the poorly annotated CxORFx in the cancer context.
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Affiliation(s)
- Pavel Ershov
- Institute of Biomedical Chemistry, Moscow 119121, Russia
| | | | - Yuri Mezentsev
- Institute of Biomedical Chemistry, Moscow 119121, Russia
| | - Alexis Ivanov
- Institute of Biomedical Chemistry, Moscow 119121, Russia
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Grodzki M, Bluhm AP, Schaefer M, Tagmount A, Russo M, Sobh A, Rafiee R, Vulpe CD, Karst SM, Norris MH. Genome-scale CRISPR screens identify host factors that promote human coronavirus infection. Genome Med 2022; 14:10. [PMID: 35086559 PMCID: PMC8792531 DOI: 10.1186/s13073-022-01013-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 01/10/2022] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND The COVID-19 pandemic has resulted in 275 million infections and 5.4 million deaths as of December 2021. While effective vaccines are being administered globally, there is still a great need for antiviral therapies as antigenically novel SARS-CoV-2 variants continue to emerge across the globe. Viruses require host factors at every step in their life cycle, representing a rich pool of candidate targets for antiviral drug design. METHODS To identify host factors that promote SARS-CoV-2 infection with potential for broad-spectrum activity across the coronavirus family, we performed genome-scale CRISPR knockout screens in two cell lines (Vero E6 and HEK293T ectopically expressing ACE2) with SARS-CoV-2 and the common cold-causing human coronavirus OC43. Gene knockdown, CRISPR knockout, and small molecule testing in Vero, HEK293, and human small airway epithelial cells were used to verify our findings. RESULTS While we identified multiple genes and functional pathways that have been previously reported to promote human coronavirus replication, we also identified a substantial number of novel genes and pathways. The website https://sarscrisprscreens.epi.ufl.edu/ was created to allow visualization and comparison of SARS-CoV2 CRISPR screens in a uniformly analyzed way. Of note, host factors involved in cell cycle regulation were enriched in our screens as were several key components of the programmed mRNA decay pathway. The role of EDC4 and XRN1 in coronavirus replication in human small airway epithelial cells was verified. Finally, we identified novel candidate antiviral compounds targeting a number of factors revealed by our screens. CONCLUSIONS Overall, our studies substantiate and expand the growing body of literature focused on understanding key human coronavirus-host cell interactions and exploit that knowledge for rational antiviral drug development.
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Affiliation(s)
- Marco Grodzki
- Department of Molecular Genetics and Microbiology, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Andrew P Bluhm
- Department of Geography, College of Liberal Arts and Sciences, University of Florida, Gainesville, FL, USA
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
| | - Moritz Schaefer
- Department of Physiological Sciences, College of Veterinary Medicine, University of Florida, Gainesville, FL, USA
| | - Abderrahmane Tagmount
- Department of Physiological Sciences, College of Veterinary Medicine, University of Florida, Gainesville, FL, USA
| | - Max Russo
- Department of Physiological Sciences, College of Veterinary Medicine, University of Florida, Gainesville, FL, USA
- Present address: Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Amin Sobh
- Univeristy of Florida Heath Cancer Center, University of Florida, Gainesville, FL, USA
| | - Roya Rafiee
- Department of Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Gainesville, FL, USA
| | - Chris D Vulpe
- Department of Physiological Sciences, College of Veterinary Medicine, University of Florida, Gainesville, FL, USA
| | - Stephanie M Karst
- Department of Molecular Genetics and Microbiology, College of Medicine, University of Florida, Gainesville, FL, USA.
| | - Michael H Norris
- Department of Geography, College of Liberal Arts and Sciences, University of Florida, Gainesville, FL, USA.
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA.
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Lin J, Yang J, Xu X, Wang Y, Yu M, Zhu Y. A robust 11-genes prognostic model can predict overall survival in bladder cancer patients based on five cohorts. Cancer Cell Int 2020; 20:402. [PMID: 32843852 PMCID: PMC7441568 DOI: 10.1186/s12935-020-01491-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 08/10/2020] [Indexed: 12/25/2022] Open
Abstract
Background Bladder cancer is the tenth most common cancer globally, but existing biomarkers and prognostic models are limited. Method In this study, we used four bladder cancer cohorts from The Cancer Genome Atlas and Gene Expression Omnibus databases to perform univariate Cox regression analysis to identify common prognostic genes. We used the least absolute shrinkage and selection operator regression to construct a prognostic Cox model. Kaplan-Meier analysis, receiver operating characteristic curve, and univariate/multivariate Cox analysis were used to evaluate the prognostic model. Finally, a co-expression network, CIBERSORT, and ESTIMATE algorithm were used to explore the mechanism related to the model. Results A total of 11 genes were identified from the four cohorts to construct the prognostic model, including eight risk genes (SERPINE2, PRR11, DSEL, DNM1, COMP, ELOVL4, RTKN, and MAPK12) and three protective genes (FABP6, C16orf74, and TNK1). The 11-genes model could stratify the risk of patients in all five cohorts, and the prognosis was worse in the group with a high-risk score. The area under the curve values of the five cohorts in the first year are all greater than 0.65. Furthermore, this model's predictive ability is stronger than that of age, gender, grade, and T stage. Through the weighted co-expression network analysis, the gene module related to the model was found, and the key genes in this module were mainly enriched in the tumor microenvironment. B cell memory showed low infiltration in high-risk patients. Furthermore, in the case of low B cell memory infiltration and high-risk score, the prognosis of the patients was the worst. Conclusion The proposed 11-genes model is a promising biomarker for estimating overall survival in bladder cancer. This model can be used to stratify the risk of bladder cancer patients, which is beneficial to the realization of individualized treatment.
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Affiliation(s)
- Jiaxing Lin
- Department of Urology, The First Hospital of China Medical University, Shenyang, 110001 Liaoning China
| | - Jieping Yang
- Department of Urology, The First Hospital of China Medical University, Shenyang, 110001 Liaoning China
| | - Xiao Xu
- Department of Pediatric Intensive Care Unit, The Shengjing Hospital of China Medical University, Shenyang, 110001 Liaoning China
| | - Yutao Wang
- Department of Urology, The First Hospital of China Medical University, Shenyang, 110001 Liaoning China
| | - Meng Yu
- Department of Reproductive Biology and Transgenic Animal, China Medical University, Shenyang, 110001 Liaoning China
| | - Yuyan Zhu
- Department of Urology, The First Hospital of China Medical University, Shenyang, 110001 Liaoning China
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Gong J, Fan H, Deng J, Zhang Q. LncRNA HAND2-AS1 represses cervical cancer progression by interaction with transcription factor E2F4 at the promoter of C16orf74. J Cell Mol Med 2020; 24:6015-6027. [PMID: 32314545 PMCID: PMC7294116 DOI: 10.1111/jcmm.15117] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 02/08/2020] [Accepted: 02/15/2020] [Indexed: 12/30/2022] Open
Abstract
Cervical cancer is one of the major malignancies, the pathophysiology and progression of which remain to be scarcely understood. Long non-coding RNAs (lncRNAs) have been previously implicated in the progression of cervical cancer. Here, the purpose of this study was to identify whether lncRNA heart- and neural crest derivative-expressed 2-antisense RNA 1 (HAND2-AS1) affect the development of cervical cancer through regulation of chromosome 16 open reading frame 74 (C16orf74) by mediating a transcription factor E2F4. RT-qPCR was performed to determine the expression of HAND2-AS1 in cervical cancer cells. Then, cervical cancer cells were treated with HAND2-AS1 or si-E2F4 RNA, or C16orf74, after which the proliferation, colony formation, migration and invasion were detected. Moreover, the binding between HAND2-AS1 and E2F4 or between E2F4 and C16orf74 was explored. Finally, the tumorigenesis of cervical cancer cells was measured in nude mice with altered HAND2-AS1/E2F4/C16orf74 expression. HAND2-AS1 exhibited poor expression in cervical cancer, and HAND2-AS1 overexpression suppressed the proliferation, colony formation, migration and invasion of cervical cancer cells. In addition, HAND2-AS1 was found to recruit transcription factor E2F4 to C16orf74 promoter region and down-regulate C16orf74 expression. Lastly, HAND2-AS1/E2F4/C16orf74 modulated the tumorigenesis of cervical cancer in nude mice. In conclusion, this study provided evidence on the inhibitory effect of HAND2-AS1 on the development of cervical cancer through the suppression of C16orf74 expression by recruiting transcription factor E2F4. This study highlights the potential of lncRNA HAND2-AS1 as a target in the treatment of cervical cancer.
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Affiliation(s)
- Junling Gong
- Department of Obstetrics and Gynecology, Linyi People's Hospital, Linyi, China
| | - Haiying Fan
- Hemodialysis Room, Linyi People's Hospital, Linyi, China
| | - Jing Deng
- Department of Internal Medicine, Miaoshan Health Center, Linyi, China
| | - Qiumei Zhang
- Department of Obstetrics and Gynecology, Linyi People's Hospital, Linyi, China
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