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Liu X, Qiu Z, Zhang X, Su Z, Yi R, Zou D, Xie C, Jin N, Long W, Liu X. Generalized machine learning based on multi-omics data to profile the effect of ferroptosis pathway on prognosis and immunotherapy response in patients with bladder cancer. Environ Toxicol 2024; 39:680-694. [PMID: 37647346 DOI: 10.1002/tox.23949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 07/26/2023] [Accepted: 08/13/2023] [Indexed: 09/01/2023]
Abstract
INTRODUCTION Bladder cancer (BLCA) affects millions of people worldwide, with high rates of incidence and mortality. Ferroptosis proves to be a novel form of cell death process that is triggered by oxidative stress. METHODS We procured a total of 25 single nuclear RNA-seq (snRNA-seq) samples from GSE169379 in GEO database. We obtained different cohorts of BLCA patients from the TCGA and GEO databases for model training and validation. A total of 369 ferroptosis-related genes (FRGs) were selected from the FerrDb database. AUCell analysis was performed to assign ferroptosis scores to all the cell types. Weighted Gene Co-Expression Network Analysis (WGCNA), COX, and LASSO regression analysis were conducted to retain and finalize the genes of prognostic values. Various bioinformatic approaches were utilized to depict immune infiltration profile. We conducted a series of colony formation analysis, flow cytometry and western blot (WB) analysis to determine the role of SKAP1 in BLCA. RESULTS We divided the cells into high ferroptosis group and low ferroptosis group according to ferroptosis activity score, and then screened 2150 genes most associated with ferroptosis by differential expression analysis, which are related to UV-induced DNA damage, male hormone response, fatty acid metabolism and hypoxia. Subsequently, WGCNA algorithm further screened 741 ferroptosis related genes from the 2150 genes for the construction of prognostic model. Lasso-Cox regression analysis was used to construct the prognostic model, and the prognostic model consisting of 6 genes was obtained, namely JUN, SYT1, MAP3K8, GALNT14, TCIRG1, and SKAP1. Next, we constructed a nomogram model that integrated clinical factors to improving the accuracy. In addition, we performed drug sensitivity analyses in different subgroups and found that Staurosporine, Rapamycin, Gemcitabine, and BI-2536 may be candidates for the drugs treatment in high-risk populations. The ESTIMATE results showed higher stromal scores, immune scores, and ESTIMATE scores in the low-risk group, indicating a higher overall immunity level and immunogenicity of tumor microenvironment (TME) in this group, and tumor immune dysfunction and exclusion (TIDE) analysis confirmed a better response to immunotherapy in the low-risk group. Finally, we selected the oncogene SKAP1 in the prognostic gene for in vitro validation, and found that SKAP1 directly regulated BLCA cell proliferation and apoptosis. CONCLUSION We identified a set of six genes, JUN, SYT1, MAP3K8, GALNT14, TCIRG1, and SKAP1, that exhibited significant potential in stratification of BLCA patients with varying prognosis. In addition, we uncovered the direct regulatory effect of SKAP1 on BLCA cell proliferation and apoptosis, shedding some light on the role of FRGs in pathogenesis of BLCA.
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Affiliation(s)
- Xinyu Liu
- Department of Urology, Loudi City Central Hospital, Loudi, China
| | - Ziran Qiu
- Department of Surgical Oncology, Loudi City Central Hospital, Loudi, China
| | - Xiongfeng Zhang
- Department of Urology, Loudi City Central Hospital, Loudi, China
| | - Zhouhua Su
- Department of Urology, Loudi City Central Hospital, Loudi, China
| | - Renzheng Yi
- Department of Urology, Loudi City Central Hospital, Loudi, China
| | - Debo Zou
- Department of Urology, Loudi City Central Hospital, Loudi, China
| | - Chaoqun Xie
- Department of Urology, Loudi City Central Hospital, Loudi, China
| | - Na Jin
- Department of Surgical Oncology, Loudi City Central Hospital, Loudi, China
| | - Weibing Long
- Department of Urology, Loudi City Central Hospital, Loudi, China
| | - Xiaobing Liu
- Department of Urology, Loudi City Central Hospital, Loudi, China
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Zhu L, Yu Q, Li Y, Zhang M, Peng Z, Wang S, Quan Z, Gao D. SKAP1 Is a Novel Biomarker and Therapeutic Target for Gastric Cancer: Evidence from Expression, Functional, and Bioinformatic Analyses. Int J Mol Sci 2023; 24:11870. [PMID: 37511629 PMCID: PMC10380396 DOI: 10.3390/ijms241411870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 07/21/2023] [Accepted: 07/22/2023] [Indexed: 07/30/2023] Open
Abstract
Gastric cancer (GC) is the third leading cause of cancer-related death worldwide. Due to the lack of early symptoms, GC is often diagnosed at an advanced stage when treatment options are limited. There is an urgent need to identify biomarkers for early detection, prognosis evaluation, and targeted treatment of GC. Studies have shown that Src kinase-associated phosphoprotein 1 (SKAP1) promotes cell proliferation and invasion and is associated with poor prognosis in colorectal cancer, malignant fibrous histiocytoma, and breast cancer. However, the role and mechanism of SKAP1 in GC are unclear. Here, analyses of multiple databases and experiments revealed that SKAP1 expression was higher in GC than in adjacent normal tissues. The Cancer Genome Atlas data showed that high SKAP1 expression was associated with poor GC prognosis. SKAP1 expression was higher in GC than in normal gastric epithelial cells. SKAP1 silencing reduced the proliferation, migration and invasion of the GC cell lines MKN45 and HGC27. Rescue experiments suggest that SKAP1 may promote GC progression by activating JAK1/PI3K/AKT signaling and regulating GC cell proliferation, invasion, migration, and other functions. Bioinformatics analysis revealed that SKAP1 was associated with immune cell infiltration and checkpoint expression in GC. High SKAP1 expression was associated with poorer immunotherapy outcomes, suggesting its potential as a predictive biomarker of GC immunotherapy efficacy. In summary, SKAP1 is overexpressed in GC, where it promotes cell proliferation, invasion and migration and is associated with poor prognosis and poor immunotherapy outcomes. SKAP1 may represent a biomarker and therapeutic target in GC and regulates cellular functions through JAK1/PI3K/AKT signaling.
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Affiliation(s)
- Lingqin Zhu
- Department of Gastroenterology and Hepatology, Second Affiliated Hospital of Nanchang University, Nanchang 330006, China
| | - Qiongfang Yu
- Department of Gastroenterology and Hepatology, Second Affiliated Hospital of Nanchang University, Nanchang 330006, China
| | - Yuanheng Li
- Queen Mary School, Nanchang University, Nanchang 330031, China
| | - Meng Zhang
- Department of Pathogen Biology and Immunology, Medical College of Nanchang University, Nanchang 330006, China
| | - Zhiwei Peng
- Department of Pathogen Biology and Immunology, Medical College of Nanchang University, Nanchang 330006, China
| | - Song Wang
- Department of Gastroenterology and Hepatology, Second Affiliated Hospital of Nanchang University, Nanchang 330006, China
| | - Ziyi Quan
- Department of Pathogen Biology and Immunology, Medical College of Nanchang University, Nanchang 330006, China
| | - Dian Gao
- Department of Pathogen Biology and Immunology, Medical College of Nanchang University, Nanchang 330006, China
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Liu C, Raab M, Gui Y, Rudd CE. Multi-functional adaptor SKAP1: regulator of integrin activation, the stop-signal, and the proliferation of T cells. Front Immunol 2023; 14:1192838. [PMID: 37325633 PMCID: PMC10264576 DOI: 10.3389/fimmu.2023.1192838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 05/17/2023] [Indexed: 06/17/2023] Open
Abstract
T-cell activation is a complex process involving a network of kinases and downstream molecular scaffolds or adaptors that integrate surface signals with effector functions. One key immune-specific adaptor is Src kinase-associated phosphoprotein 1 (SKAP1), which is also known as src kinase-associated protein of 55 kDa (SKAP55). This mini-review explains how SKAP1 plays multiple roles in regulating integrin activation, the "stop-signal", and the optimization of the cell cycling of proliferating T cells through interactions with various mediators, including the Polo-like kinase 1 (PLK1). Ongoing research on SKAP1 and its binding partners will likely provide important insights into the regulation of immune function and have implications for the development of new treatments for disease states such as cancer and autoimmunity.
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Affiliation(s)
- Chen Liu
- Faculté de Medicine, Université de Montréal, Montréal, QC, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, QC, Canada
- Division of Immunology-Oncology, Centre de Recherche de l’Hôpital Maisonneuve-Rosemont, Montréal, QC, Canada
| | - Monika Raab
- Department of Obstetrics and Gynaecology, School of Medicine, J.W. Goethe-University, Frankfurt, Germany
| | - Yirui Gui
- Faculté de Medicine, Université de Montréal, Montréal, QC, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, QC, Canada
- Division of Immunology-Oncology, Centre de Recherche de l’Hôpital Maisonneuve-Rosemont, Montréal, QC, Canada
| | - Christopher E. Rudd
- Faculté de Medicine, Université de Montréal, Montréal, QC, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, QC, Canada
- Division of Immunology-Oncology, Centre de Recherche de l’Hôpital Maisonneuve-Rosemont, Montréal, QC, Canada
- Division of Experimental Medicine, McGill University, Montreal, QC, Canada
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Canson DM, O’Mara TA, Spurdle AB, Glubb DM. Splicing annotation of endometrial cancer GWAS risk loci reveals potentially causal variants and supports a role for NF1 and SKAP1 as susceptibility genes. HGG Adv 2023; 4:100185. [PMID: 36908940 PMCID: PMC9996439 DOI: 10.1016/j.xhgg.2023.100185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 02/10/2023] [Indexed: 02/17/2023] Open
Abstract
Alternative splicing contributes to cancer development. Indeed, splicing analysis of cancer genome-wide association study (GWAS) risk variants has revealed likely causal variants. To systematically assess GWAS variants for splicing effects, we developed a prioritization workflow using a combination of splicing prediction tools, alternative transcript isoforms, and splicing quantitative trait locus (sQTL) annotations. Application of this workflow to candidate causal variants from 16 endometrial cancer GWAS risk loci highlighted single-nucleotide polymorphisms (SNPs) that were predicted to upregulate alternative transcripts. For two variants, sQTL data supported the predicted impact on splicing. At the 17q11.2 locus, the protective allele for rs7502834 was associated with increased splicing of an exon in a NF1 alternative transcript encoding a truncated protein in adipose tissue and is consistent with an endometrial cancer transcriptome-wide association study (TWAS) finding in adipose tissue. Notably, NF1 haploinsufficiency is protective for obesity, a well-established risk factor for endometrial cancer. At the 17q21.32 locus, the rs2278868 risk allele was predicted to upregulate a SKAP1 transcript that is subject to nonsense-mediated decay, concordant with a corresponding sQTL in lymphocytes. This is consistent with a TWAS finding that indicates decreased SKAP1 expression in blood increases endometrial cancer risk. As SKAP1 is involved in T cell immune responses, decreased SKAP1 expression may impact endometrial tumor immunosurveillance. In summary, our analysis has identified potentially causal endometrial cancer GWAS risk variants with plausible biological mechanisms and provides a splicing annotation workflow to aid interpretation of other GWAS datasets.
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Affiliation(s)
- Daffodil M. Canson
- Population Health Program, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
- Faculty of Medicine, The University of Queensland, Brisbane, QLD 4006, Australia
| | - Tracy A. O’Mara
- Faculty of Medicine, The University of Queensland, Brisbane, QLD 4006, Australia
- Cancer Research Program, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Amanda B. Spurdle
- Population Health Program, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
- Faculty of Medicine, The University of Queensland, Brisbane, QLD 4006, Australia
| | - Dylan M. Glubb
- Faculty of Medicine, The University of Queensland, Brisbane, QLD 4006, Australia
- Cancer Research Program, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
- Corresponding author
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Pu Y, Wei J, Wu Y, Zhao K, Wu Y, Wu S, Yang X, Xing C. THUMPD3-AS1 facilitates cell growth and aggressiveness by the miR-218-5p/ SKAP1 axis in colorectal cancer. Cell Biochem Biophys 2022; 80:483-494. [PMID: 35538197 DOI: 10.1007/s12013-022-01074-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 04/22/2022] [Indexed: 12/11/2022]
Abstract
BACKGROUND Colorectal cancer (CRC) is a malignant cancer with a high mortality. Accumulating studies have revealed that mRNAs involved in ceRNA (competing endogenous RNA) network are implicated in the tumorigenesis and development of CRC. Here, we aimed to elucidate the ceRNA network involving Src kinase associated phosphoprotein 1 (SKAP1) in the biological characteristics of CRC. METHODS Expression levels of genes in colon adenocarcinoma (COAD) samples and prognosis of COAD patients were predicted using publicly available online tool. 3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT), clony formation and Transwell assays were conducted to test the biological functions of SKAP1 and THUMPD3 antisense RNA 1 (THUMPD3-AS1) in CRC cells. Western blot was used to measure the protein levels of SKAP1. Gene expression in CRC cells was detected by reverse transcription quantitative polymerase chain reaction (RT-qPCR). The interaction between miR-218-5p and THUMPD3-AS1 (or SKAP1) was verified by RNA pulldown and luciferase reporter assays. RESULTS SKAP1 was upregulated in COAD tissues and CRC cells and it reflected a poor prognosis in patients with COAD. SKAP1 knockdown inhibited CRC (HT-29 and HCT-116) cell proliferation, migration and invasion. Mechanistically, THUMPD3-AS1 acted as a ceRNA to sponge miR-218-5p and subsequently upregulated SKAP1 expression in CRC cells. SKAP1 overexpression reversed the suppressive effect of THUMPD3-AS1 knockdown on proliferation, migration and invision of CRC cells. CONCLUSIONS THUMPD3-AS1 promotes CRC cell growth and aggressiveness by regulating the miR-218-5p/SKAP1 axis.
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Affiliation(s)
- Yuwei Pu
- Department of General Surgery, The Second Affiliated Hospital of Soochow University, Suzhou, 215004, Jiangsu, China
| | - Jinrong Wei
- Department of General Surgery, The Second Affiliated Hospital of Soochow University, Suzhou, 215004, Jiangsu, China
| | - Yong Wu
- Department of General Surgery, The Second Affiliated Hospital of Soochow University, Suzhou, 215004, Jiangsu, China
| | - Kui Zhao
- Department of General Surgery, The Second Affiliated Hospital of Soochow University, Suzhou, 215004, Jiangsu, China
| | - Yongyou Wu
- Department of General Surgery, The Second Affiliated Hospital of Soochow University, Suzhou, 215004, Jiangsu, China
| | - Shu Wu
- Department of General Surgery, The Second Affiliated Hospital of Soochow University, Suzhou, 215004, Jiangsu, China
| | - Xiaodong Yang
- Department of General Surgery, The Second Affiliated Hospital of Soochow University, Suzhou, 215004, Jiangsu, China.
| | - Chungen Xing
- Department of General Surgery, The Second Affiliated Hospital of Soochow University, Suzhou, 215004, Jiangsu, China.
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Raab M, Strebhardt K, Rudd CE. Immune adaptor protein SKAP1 (SKAP-55) forms homodimers as mediated by the N-terminal region. BMC Res Notes 2018; 11:869. [PMID: 30522503 PMCID: PMC6282339 DOI: 10.1186/s13104-018-3976-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2018] [Accepted: 12/04/2018] [Indexed: 11/10/2022] Open
Abstract
OBJECTIVE Immune cell adaptor protein SKAP1 couples the antigen-receptor (TCR/CD3) with the activation of LFA-1 adhesion in T-cells. Previous work by ourselves and others have shown that SKAP1 can directly bind to other adaptors such as ADAP and RapL. However, it has been unclear whether SKAP1 can form homodimers with itself and the regions within SKAP1 that mediated homodimer formation. RESULTS Here, we show that SKAP1 and SKAP2 form homodimers in cells. Homodimer formation of immune adaptor protein SKAP1 (SKAP-55) are mediated by residues A17 to L21 in the SKAP1 N-terminal region. SKAP1 dimer formation was not needed for its binding to RapL. These data indicate that the pathway linking SKAP1 to RapL is not dependent on the homo-dimerization of SKAP1.
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Affiliation(s)
- Monika Raab
- Department of Obstetrics and Gynaecology, School of Medicine, J.W. Goethe-University, Theodor-Stern-Kai 7, 60590, Frankfurt, Germany
| | - Klaus Strebhardt
- Department of Obstetrics and Gynaecology, School of Medicine, J.W. Goethe-University, Theodor-Stern-Kai 7, 60590, Frankfurt, Germany.,German Cancer Consortium (DKTK)/German Cancer Research Center, Heidelberg, Germany
| | - Christopher E Rudd
- Department of Obstetrics and Gynaecology, School of Medicine, J.W. Goethe-University, Theodor-Stern-Kai 7, 60590, Frankfurt, Germany. .,Research Center-Maisonneuve-Rosemont Hospital (CRHMR), Montreal, QC, H1T 2M4, Canada. .,Cell Signalling Section, Department of Pathology, Cambridge University, Cambridge, CB2 1QP, UK.
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Smith X, Taylor A, Rudd CE. T-cell immune adaptor SKAP1 regulates the induction of collagen-induced arthritis in mice. Immunol Lett 2016; 176:122-7. [PMID: 27181093 PMCID: PMC4965781 DOI: 10.1016/j.imlet.2016.04.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Revised: 04/02/2016] [Accepted: 04/12/2016] [Indexed: 11/30/2022]
Abstract
Skap1-deficient (skap1-/-) mice are resistant to the induction of collagen induced arthritis (CIA). Skap1-/- mice show a reduction in presence of IL-17+ (Th17) T-cells in response to CII peptide. No effect was seen on the production of other cytokines such as IL-10. Our findings implicate SKAP1 as a novel upstream regulator murine autoimmune arthritis.
SKAP1 is an immune cell adaptor that couples the T-cell receptor with the ‘inside-out’ signalling pathway for LFA-1 mediated adhesion in T-cells. A connection of SKAP1 to the regulation of an autoimmune disorder has not previously been reported. In this study, we show that Skap1-deficient (skap1-/-) mice are highly resistant to the induction of collagen-induced arthritis (CIA), both in terms of incidence or severity. Skap1-/- T-cells were characterised by a selective reduction in the presence IL-17+ (Th17) in response to CII peptide and a marked reduction of joint infiltrating T-cells in Skap1-/- mice. SKAP1 therefore represents a novel connection to Th17 producing T-cells and is new potential target in the therapeutic intervention in autoimmune and inflammatory diseases.
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Affiliation(s)
- Xin Smith
- Cell Signalling Section, Department of Pathology, Tennis Court Road, University of Cambridge, Cambridge CB2 1Q, UK
| | - Alison Taylor
- Cell Signalling Section, Department of Pathology, Tennis Court Road, University of Cambridge, Cambridge CB2 1Q, UK
| | - Christopher E Rudd
- Cell Signalling Section, Department of Pathology, Tennis Court Road, University of Cambridge, Cambridge CB2 1Q, UK.
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