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Jiang Y, Hu X, Wang Z, Zhang Q, Chen D, Zhao P. RPTOR mutation: a novel predictor of efficacious immunotherapy in melanoma. Invest New Drugs 2024; 42:60-69. [PMID: 38071684 DOI: 10.1007/s10637-023-01413-z] [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: 10/25/2023] [Accepted: 11/14/2023] [Indexed: 02/24/2024]
Abstract
Identifying biomarkers to evaluate the therapeutic effect of immune checkpoint inhibitors (ICIs) is crucial. Regulatory Associated Protein of MTOR Complex 1 (RPTOR), one of the genes in the mTOR pathway, plays a role in regulating tumor progression. However, the connection between RPTOR mutation and the efficacy of ICIs in melanoma remains unclear. The data of ICIs-treated melanoma patients in discovery (n = 384) and validation (n = 320) cohorts were obtained from cBioPortal databases. The genomic data in the two cohorts was used to investigate the connection between RPTOR mutation and immunotherapy efficacy. The underlying mechanisms were explored based on data from the The Cancer Genome Atlas (TCGA)-skin cutaneous melanoma (SKCM) cohort. Compared to melanoma patients with RPTOR wildtype (RPTOR-WT), RPTOR-mutation (RPTOR-Mut) patients achieved prolonged overall survival (OS) in both discovery cohort (median OS of 49.3 months vs. 21.7 months; HR = 0.41, 95% CI: 0.18-0.92; P = 0.026) and validation cohorts (not reached vs. 42.0 months; HR = 0.34, 95% CI: 0.11-1.06; P = 0.049). RPTOR-Mut melanoma patients exhibited a higher objective response rate (ORR) than RPTOR-WT patients in the discovery cohort (55.0% vs. 29.0%, P = 0.022). RPTOR-Mut patients exhibited higher TMB than RPTOR-WT patients in both discovery and validation cohorts (P < 0.001). RPTOR-Mut melanoma patients had an increased number of DNA damage response (DDR) mutations in TCGA-SKCM cohort. Immune cell infiltration analysis suggested that activated CD4 memory T cells were more enriched in RPTOR-Mut tumors. RPTOR-Mut melanoma patients had higher expression levels of immune-related genes than the RPTOR-WT patients. Our results suggest that RPTOR mutation could serve as a predictor of effective immunotherapy for melanoma.
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Affiliation(s)
- Yanfang Jiang
- Genetic Diagnosis Center, The First Hospital of Jilin University, Changchun, 130021, China
| | - Xintong Hu
- Genetic Diagnosis Center, The First Hospital of Jilin University, Changchun, 130021, China
| | - Zhouyu Wang
- Jiangsu Simcere Diagnostics Co.,Ltd, The State Key Laboratory of Neurology and Oncology Drug Development, Nanjing, 210002, China
| | - Qin Zhang
- Jiangsu Simcere Diagnostics Co.,Ltd, The State Key Laboratory of Neurology and Oncology Drug Development, Nanjing, 210002, China
| | - Dongsheng Chen
- Jiangsu Simcere Diagnostics Co.,Ltd, The State Key Laboratory of Neurology and Oncology Drug Development, Nanjing, 210002, China.
| | - Pingwei Zhao
- General Surgery Center, The First Hospital of Jilin University, Changchun, 130021, China.
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Pan D, Hao J, Wu T, Shen T, Yu K, Li Q, Hu R, Yang Z, Li Y. Sodium Butyrate Inhibits the Malignant Proliferation of Colon Cancer Cells via the miR-183/DNAJB4 Axis. Biochem Genet 2024:10.1007/s10528-023-10599-z. [PMID: 38244156 DOI: 10.1007/s10528-023-10599-z] [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: 08/24/2023] [Accepted: 11/11/2023] [Indexed: 01/22/2024]
Abstract
Colorectal carcinoma (CRC) is one of the most common malignant tumors in the digestive tract. It was found that butyric acid could inhibit the expression of miR-183 to slow down malignant progression of CRC in the early stage. However, its regulatory mechanism remains unclear. This study screened the IC50 value of butyrate on inhibition of CRC cells malignant progression. Its inhibitory effects were detected by MTT assay, colony formation experiment, Transwell migration experiment, and apoptosis evaluation by flow cytometry. Next, the expressions of miR-183 and DNAJB4 were, respectively, determined in butyrate treated and miR-183 analog or si-DNAJB4-transfected CRC cells to further detect the role of upregulated miR-183 or silencing DNAJB4 in CRC cells malignant progression. Subsequently, the targeted regulatory relationship between miR-183 and si-DNAJB4 was confirmed by bioinformatic prediction tools and double luciferase report genes analysis method. The regulatory mechanism of butyrate on miR-183/DNAJB4 axis signal pathway was evaluated in molecular level, and verified in nude mouse xerograft tumor model and immunohistochemical analysis tests of Ki67 positive rates. The results displayed that butyrate with increased concentration can hinder the proliferation and improve apoptosis of CRC cells by decreasing the expression of miR-183. Thus, butyrate reduces miR-183 expression and increases DNAJB4 expression via the miR-183/DNAJB4 axis, ultimately inhibiting the malignant progression and increasing apoptosis of CRC. While over expression of miR-183 downregulate the expression of DNAJB4, which can reverse the inhibitory effect of butyrate.
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Affiliation(s)
- Dingguo Pan
- Department of Colorectal Surgery, Third Affiliated Hospital of Kunming Medical University, Kunming, 650118, China
- Kunming Medical University, Kunming, 650500, Yunnan, China
| | - Jingchao Hao
- School of Pharmaceutical Science & Key Laboratory of Natural Pharmacology of Yunnan Province, Kunming Medical University, Kunming, 650500, Yunnan, China
- Kunming Medical University, Kunming, 650500, Yunnan, China
| | - Tao Wu
- Department of Colorectal Surgery, Third Affiliated Hospital of Kunming Medical University, Kunming, 650118, China
| | - Tao Shen
- Department of Colorectal Surgery, Third Affiliated Hospital of Kunming Medical University, Kunming, 650118, China
| | - Kun Yu
- Department of Colorectal Surgery, Third Affiliated Hospital of Kunming Medical University, Kunming, 650118, China
| | - Qiang Li
- Department of Colorectal Surgery, Third Affiliated Hospital of Kunming Medical University, Kunming, 650118, China
| | - Ruixi Hu
- Department of Colorectal Surgery, Third Affiliated Hospital of Kunming Medical University, Kunming, 650118, China
| | - Zhaoyu Yang
- Department of Colorectal Surgery, Third Affiliated Hospital of Kunming Medical University, Kunming, 650118, China
- Kunming Medical University, Kunming, 650500, Yunnan, China
| | - Yunfeng Li
- Department of Colorectal Surgery, Third Affiliated Hospital of Kunming Medical University, Kunming, 650118, China.
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Chen XF, Chen XQ, Luo HL, Xia LN, Huang SH, Chen Q. PRM-based quantitative proteomics analysis of altered HSP abundance in villi and decidua of patients with early missed abortion. Proteome Sci 2023; 21:12. [PMID: 37587463 PMCID: PMC10429090 DOI: 10.1186/s12953-023-00213-w] [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: 09/12/2022] [Accepted: 08/07/2023] [Indexed: 08/18/2023] Open
Abstract
OBJECTIVE In this study, we aimed to identify differentially expressed heat shock protein (HSP) profiles in the villi and decidua from patients with early missed abortion (EMA). METHODS By using high-throughput and high-precision parallel reaction monitoring (PRM)-based targeted proteomics techniques, this study examined the abundance of HSPs in the villi and decidua of 10 patients with EMA and 10 controls. Moreover, the abundance of 3 HSPs in the villi of another 22 patients with EMA and 22 controls was verified with Western blotting and immunohistochemistry (IHC). RESULTS There were potential differences in the abundance of 16 HSPs and 42 polypeptides in human villi and decidua compared with those of the control group. Among them, HSP90AB1, HSPD1 and HSPA13 were downregulated in abundance in villi of patients with EMA, with a statistically significant difference, which was consistent with the verification results of Western blots and IHC. CONCLUSION Using a PRM-based targeted proteomics technique, this study is the first to screen and quantitatively analyze the expression profile of HSPs in the villi and decidua of patients with EMA. The significant downregulation of HSP90AB1, HSPD1 and HSPA13 was found to have a potentially intimate association with the occurrence of EMA. The findings in our study may provide novel potential research targets related to HSPs for the pathogenesis, prevention and treatment of EMA.
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Affiliation(s)
- Xiao-Fang Chen
- Department of Obstetrics and Gynecology, the Second Affiliated Hospital of Nanchang University, Nanchang, 330000, Jiangxi, China
- Department of Obstetrics and Gynecology, Jiangxi Maternal and Child Health Hospital, Nanchang, 330000, Jiangxi, China
| | - Xiao-Qing Chen
- Department of Obstetrics and Gynecology, Jiangxi Maternal and Child Health Hospital, Nanchang, 330000, Jiangxi, China
| | - Hai-Lian Luo
- Department of Pathology, Jiangxi Maternal and Child Health Hospital, Nanchang, 330000, Jiangxi, China
| | - Li-Na Xia
- Department of Pathology, Jiangxi Maternal and Child Health Hospital, Nanchang, 330000, Jiangxi, China
| | - Shu-Hui Huang
- Key Laboratory of Birth Defect for Prevention and Control of Jiangxi Province, Jiangxi Maternal and Child Health Hospital, Nanchang, 330000, Jiangxi, China.
| | - Qi Chen
- Department of Obstetrics and Gynecology, the Second Affiliated Hospital of Nanchang University, Nanchang, 330000, Jiangxi, China.
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Chen Y, Li J, Pu L, Hu J, Fang L, Zhou F, Zhang H, Yang Y, Rong X, Deng S, Hou L. DNAJB4 suppresses breast cancer progression and promotes tumor immunity by regulating the Hippo signaling pathway. Discov Oncol 2023; 14:144. [PMID: 37548821 PMCID: PMC10406735 DOI: 10.1007/s12672-023-00762-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 07/31/2023] [Indexed: 08/08/2023] Open
Abstract
PURPOSE Breast cancer is the most common cancer worldwide. Low DNAJB4 expression levels are strongly correlated with poor prognosis in breast cancer patients. However, the molecular mechanism by which DNAJB4 regulates breast cancer progression is unclear. METHODS The expression of DNAJB4 was validated in human breast cancer tissues, normal human breast tissues, and breast cancer cell lines. CCK-8, colony-forming, and wound healing assays were used to assess the biological effect of DNAJB4 overexpression on cell proliferation and migration in MCF-7 cell lines. Bioinformatic analysis was used to identify the DNAJB4 related pathways in breast cancer. Epithelial-mesenchymal transition (EMT)-related biomarkers and Hippo pathway components were quantified by Western blots. Luciferase and Western blot assays were used to validate which miRNA regulates DNAJB4. In addition, the effects of DNAJB4 on in vivo tumor growth were assessed in xenograft models. RESULTS DNAJB4 was expressed at low levels in human breast cancer tissues and breast cancer cell lines and correlated with poor prognosis. DNAJB4 overexpression significantly inhibited cell proliferation and migration in vitro by activating the Hippo pathway. The dual-luciferase assay showed that hsa-miR-183-5p targeted DNAJB4. Moreover, the effects of DNAJB4 could be reversed by miR-183-5p. In addition, the expression of DNAJB4 was strongly correlated with immune infiltration levels. Notably, DNAJB4 overexpression markedly enhanced CD4 + and CD8 + T cells and reduced PD-L1 levels in 4T1 tumors via the Hippo pathway, which retarded tumor growth in a subcutaneous xenograft tumor mouse model of 4T1 cells. CONCLUSIONS The present study demonstrated that DNAJB4 overexpression inhibited the malignant biological behavior of breast cancer by regulating the Hippo pathway and tumor immunosuppressive environment.
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Affiliation(s)
- Yanru Chen
- Academician (Expert) Workstation, Medical Imaging Key Laboratory of Sichuan Province, Biological Targeting Laboratory of Breast Cancer, Department of Breast and Thyroid Surgery, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan, China
- Medical Imaging Key Laboratory of Sichuan Province, Institute of Basic Medicine and Forensic Medicine, North Sichuan Medical College, Nanchong, Sichuan, China
| | - Jingjia Li
- Academician (Expert) Workstation, Medical Imaging Key Laboratory of Sichuan Province, Biological Targeting Laboratory of Breast Cancer, Department of Breast and Thyroid Surgery, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan, China
- Medical Imaging Key Laboratory of Sichuan Province, Institute of Basic Medicine and Forensic Medicine, North Sichuan Medical College, Nanchong, Sichuan, China
| | - Lulan Pu
- Academician (Expert) Workstation, Medical Imaging Key Laboratory of Sichuan Province, Biological Targeting Laboratory of Breast Cancer, Department of Breast and Thyroid Surgery, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan, China
- Medical Imaging Key Laboratory of Sichuan Province, Institute of Basic Medicine and Forensic Medicine, North Sichuan Medical College, Nanchong, Sichuan, China
| | - Jinghua Hu
- Academician (Expert) Workstation, Medical Imaging Key Laboratory of Sichuan Province, Biological Targeting Laboratory of Breast Cancer, Department of Breast and Thyroid Surgery, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan, China
- Medical Imaging Key Laboratory of Sichuan Province, Institute of Basic Medicine and Forensic Medicine, North Sichuan Medical College, Nanchong, Sichuan, China
| | - Lingyu Fang
- Academician (Expert) Workstation, Medical Imaging Key Laboratory of Sichuan Province, Biological Targeting Laboratory of Breast Cancer, Department of Breast and Thyroid Surgery, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan, China
- Medical Imaging Key Laboratory of Sichuan Province, Institute of Basic Medicine and Forensic Medicine, North Sichuan Medical College, Nanchong, Sichuan, China
| | - Fangfang Zhou
- Academician (Expert) Workstation, Medical Imaging Key Laboratory of Sichuan Province, Biological Targeting Laboratory of Breast Cancer, Department of Breast and Thyroid Surgery, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan, China
- Medical Imaging Key Laboratory of Sichuan Province, Institute of Basic Medicine and Forensic Medicine, North Sichuan Medical College, Nanchong, Sichuan, China
| | - Hongying Zhang
- The Fifth People's Hospital of Nanchong City, Nanchong, Sichuan, China
| | - Yi Yang
- Academician (Expert) Workstation, Medical Imaging Key Laboratory of Sichuan Province, Biological Targeting Laboratory of Breast Cancer, Department of Breast and Thyroid Surgery, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan, China
- Medical Imaging Key Laboratory of Sichuan Province, Institute of Basic Medicine and Forensic Medicine, North Sichuan Medical College, Nanchong, Sichuan, China
| | - Xinxin Rong
- Academician (Expert) Workstation, Medical Imaging Key Laboratory of Sichuan Province, Biological Targeting Laboratory of Breast Cancer, Department of Breast and Thyroid Surgery, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan, China
- Medical Imaging Key Laboratory of Sichuan Province, Institute of Basic Medicine and Forensic Medicine, North Sichuan Medical College, Nanchong, Sichuan, China
| | - Shishan Deng
- Academician (Expert) Workstation, Medical Imaging Key Laboratory of Sichuan Province, Biological Targeting Laboratory of Breast Cancer, Department of Breast and Thyroid Surgery, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan, China.
- Medical Imaging Key Laboratory of Sichuan Province, Institute of Basic Medicine and Forensic Medicine, North Sichuan Medical College, Nanchong, Sichuan, China.
| | - Lingmi Hou
- Academician (Expert) Workstation, Medical Imaging Key Laboratory of Sichuan Province, Biological Targeting Laboratory of Breast Cancer, Department of Breast and Thyroid Surgery, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan, China.
- Medical Imaging Key Laboratory of Sichuan Province, Institute of Basic Medicine and Forensic Medicine, North Sichuan Medical College, Nanchong, Sichuan, China.
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Qi TF, Tang F, Yin J, Miao W, Wang Y. Parallel-reaction monitoring revealed altered expression of a number of epitranscriptomic reader, writer, and eraser proteins accompanied with colorectal cancer metastasis. Proteomics 2023; 23:e2200059. [PMID: 35443089 PMCID: PMC9582037 DOI: 10.1002/pmic.202200059] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Revised: 03/25/2022] [Accepted: 04/12/2022] [Indexed: 11/09/2022]
Abstract
RNA contains more than 170 types of chemical modifications, and these modified nucleosides are recognized, installed and removed by their reader, writer, and eraser (RWE) proteins, respectively. Here, we employed a parallel-reaction monitoring (PRM)-based targeted proteomic method, in conjunction with stable isotope labeling by amino acids in cell culture (SILAC), to examine comprehensively the differential expression of epitranscriptomic RWE proteins in a matched pair of primary/metastatic colorectal cancer (CRC) cells, namely SW480/SW620. We were able to quantify 113 nonredundant epitranscriptomic RWE proteins; among them, 48 and 5 were up- and down-regulated by >1.5-fold in SW620 over SW480 cells, respectively. Some of those proteins with marked up-regulation in metastatic CRC cells, including NAT10, hnRNPC, and DKC1, were documented to assume important roles in the metastasis of CRC and other types of cancer. Interrogation of the Clinical Proteomic Tumor Analysis Consortium data revealed the involvement of DUS1L in the initiation and metastatic transformation of CRC. It can be envisaged that the PRM method can be utilized, in the future, to identify epitranscriptomic RWE proteins involved in the metastatic transformations of other types of cancer.
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Affiliation(s)
- Tianyu F Qi
- Environmental Toxicology Graduate Program, Riverside, California, USA
| | - Feng Tang
- Department of Chemistry, University of California, Riverside, California, USA
| | - Jiekai Yin
- Environmental Toxicology Graduate Program, Riverside, California, USA
| | - Weili Miao
- Department of Chemistry, University of California, Riverside, California, USA
| | - Yinsheng Wang
- Environmental Toxicology Graduate Program, Riverside, California, USA
- Department of Chemistry, University of California, Riverside, California, USA
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6
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Dicanio M, Giaccherini M, Clay‐Gilmour A, Macauda A, Sainz J, Machiela MJ, Rybicka‐Ramos M, Norman AD, Tyczyńska A, Chanock SJ, Barington T, Kumar SK, Bhatti P, Cozen W, Brown EE, Suska A, Haastrup EK, Orlowski RZ, Dudziński M, Garcia‐Sanz R, Kruszewski M, Martinez‐Lopez J, Beider K, Iskierka‐Jazdzewska E, Pelosini M, Berndt SI, Raźny M, Jamroziak K, Rajkumar SV, Jurczyszyn A, Vangsted AJ, Collado PG, Vogel U, Hofmann JN, Petrini M, Butrym A, Slager SL, Ziv E, Subocz E, Giles GG, Andersen NF, Mazur G, Watek M, Lesueur F, Hildebrandt MAT, Zawirska D, Ebbesen LH, Marques H, Gemignani F, Dumontet C, Várkonyi J, Buda G, Nagler A, Druzd‐Sitek A, Wu X, Kadar K, Camp NJ, Grzasko N, Waller RG, Vachon C, Canzian F, Campa D. A pleiotropic variant in DNAJB4 is associated with multiple myeloma risk. Int J Cancer 2023; 152:239-248. [PMID: 36082445 PMCID: PMC9828677 DOI: 10.1002/ijc.34278] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 06/01/2022] [Accepted: 06/07/2022] [Indexed: 01/12/2023]
Abstract
Pleiotropy, which consists of a single gene or allelic variant affecting multiple unrelated traits, is common across cancers, with evidence for genome-wide significant loci shared across cancer and noncancer traits. This feature is particularly relevant in multiple myeloma (MM) because several susceptibility loci that have been identified to date are pleiotropic. Therefore, the aim of this study was to identify novel pleiotropic variants involved in MM risk using 28 684 independent single nucleotide polymorphisms (SNPs) from GWAS Catalog that reached a significant association (P < 5 × 10-8 ) with their respective trait. The selected SNPs were analyzed in 2434 MM cases and 3446 controls from the International Lymphoma Epidemiology Consortium (InterLymph). The 10 SNPs showing the strongest associations with MM risk in InterLymph were selected for replication in an independent set of 1955 MM cases and 1549 controls from the International Multiple Myeloma rESEarch (IMMEnSE) consortium and 418 MM cases and 147 282 controls from the FinnGen project. The combined analysis of the three studies identified an association between DNAJB4-rs34517439-A and an increased risk of developing MM (OR = 1.22, 95%CI 1.13-1.32, P = 4.81 × 10-7 ). rs34517439-A is associated with a modified expression of the FUBP1 gene, which encodes a multifunctional DNA and RNA-binding protein that it was observed to influence the regulation of various genes involved in cell cycle regulation, among which various oncogenes and oncosuppressors. In conclusion, with a pleiotropic scan approach we identified DNAJB4-rs34517439 as a potentially novel MM risk locus.
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Affiliation(s)
| | | | - Alyssa Clay‐Gilmour
- Department of Epidemiology and Biostatistics, Arnold School of Public HealthUniversity of South CarolinaGreenvilleSouth CarolinaUSA
| | - Angelica Macauda
- Genomic Epidemiology Group, German Cancer Research Center (DKFZ)HeidelbergGermany
| | - Juan Sainz
- Genomic Oncology Area, GENYO. Center for Genomics and Oncological Research: PfizerUniversity of Granada/Andalusian Regional GovernmentGranadaSpain,Department of HematologyVirgen de las Nieves University HospitalGranadaSpain,Department of MedicineUniversity of GranadaGranadaSpain
| | - Mitchell J. Machiela
- Division of Cancer Epidemiology and Genetics, National Cancer InstituteNational Institues of HealthBethesdaMarylandUSA
| | | | - Aaron D. Norman
- Division of Epidemiology, Department of Health Sciences ResearchMayo ClinicRochesterOntarioUSA,Division of Biomedical Statistics and Informatics, Department of Health Sciences ResearchMayo ClinicRochesterOntarioUSA
| | - Agata Tyczyńska
- Department of Hematology and TransplantologyMedical University of GdańskGdańskPoland
| | - Stephen J. Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer InstituteNational Institues of HealthBethesdaMarylandUSA
| | | | - Shaji K. Kumar
- Division of Hematology, Department of Internal MedicineMayo ClinicRochesterOntarioUSA
| | - Parveen Bhatti
- Cancer Control ResearchBC CancerVancouverCanada,Program in Epidemiology, Public Health Sciences DivisionFred Hutchinson Cancer Research CenterSeattleWashingtonUSA
| | - Wendy Cozen
- Division of Hematology/Oncology, Department of Medicine, School of Medicine, Susan and Henry Samueli College of Health SciencesChao Family Comprehensive Cancer Center, University of CaliforniaIrvineCaliforniaUSA,Department of Pathology, School of Medicine, Susan and Henry Samueli College of Health SciencesChao Family Comprehensive Cancer Center, University of CaliforniaIrvineCaliforniaUSA
| | - Elizabeth E. Brown
- Department of Pathology, School of MedicineUniversity of Alabama at BirminghamBirminghamAlabamaUSA
| | - Anna Suska
- Plasma Cell Dyscrasia Center Department of Hematology Jagiellonian University Faculty of MedicineKrakówPoland
| | | | - Robert Z. Orlowski
- Department of Lymphoma ‐ Myeloma, Division of Cancer MedicineUniversity of Texas MD Anderson Cancer CenterHoustonTexasUSA
| | - Marek Dudziński
- Department of Hematology, Institute of Medical Sciences, College of Medical SciencesUniversity of RzeszowRzeszowPoland
| | - Ramon Garcia‐Sanz
- Medina A. Department of Hematology, University Hospital of Salamanca (HUS/IBSAL)CIBERONC and Cancer Research Institute of Salamanca‐IBMCC (USAL‐CSIC)SalamancaSpain
| | - Marcin Kruszewski
- Department of HematologyUniversity Hospital No. 2 in BydgoszczBydgoszczPoland
| | | | - Katia Beider
- Hematology Division Chaim Sheba Medical CenterTel HashomerIsrael
| | | | - Matteo Pelosini
- U.O. Dipartimento di EmatologiaAzienda USL Toscana Nord OvestLivornoItaly,Present address:
Ospedale Santa ChiaraPisaItaly
| | - Sonja I. Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer InstituteNational Institues of HealthBethesdaMarylandUSA
| | | | - Krzysztof Jamroziak
- Department of HematologyInstitute of Hematology and Transfusion MedicineWarsawPoland
| | - S. Vincent Rajkumar
- Division of Hematology, Department of Internal MedicineMayo ClinicRochesterOntarioUSA
| | - Artur Jurczyszyn
- Plasma Cell Dyscrasia Center Department of Hematology Jagiellonian University Faculty of MedicineKrakówPoland
| | | | | | - Ulla Vogel
- National Research Center for the Working EnvironmentCopenhagenDenmark
| | - Jonathan N. Hofmann
- Division of Cancer Epidemiology and Genetics, National Cancer InstituteNational Institues of HealthBethesdaMarylandUSA
| | - Mario Petrini
- Hematology Unit, Department of Clinical and Experimental MedicineUniversity of PisaPisaItaly
| | - Aleksandra Butrym
- Department of Cancer Prevention and TherapyWroclaw Medical UniversityWroclawPoland
| | - Susan L. Slager
- Division of Epidemiology, Department of Health Sciences ResearchMayo ClinicRochesterOntarioUSA
| | - Elad Ziv
- Department of MedicineUniversity of California San Francisco Helen Diller Family Comprehensive Cancer CenterSan FranciscoCaliforniaUSA
| | - Edyta Subocz
- Department of HematologyMilitary Institute of MedicineWarsawPoland
| | - Graham G. Giles
- Cancer Epidemiology DivisionCancer Council VictoriaMelbourneVictoriaAustralia,Center for Epidemiology and Biostatistics, School of Population and Global HealthThe University of MelbourneMelbourneVictoriaAustralia,Precision Medicine, School of Clinical Sciences at Monash HealthMonash UniversityClaytonVictoriaAustralia
| | | | - Grzegorz Mazur
- Department of Internal Diseases, Occupational Medicine, Hypertension and Clinical OncologyWroclaw Medical UniversityWroclawPoland
| | - Marzena Watek
- Department of HematologyInstitute of Hematology and Transfusion MedicineWarsawPoland,Department of HematologyHolycross Cancer CenterKielcePoland
| | - Fabienne Lesueur
- Inserm, U900, Institut Curie, PSL Research University, Mines ParisTechParisFrance
| | - Michelle A. T. Hildebrandt
- Department of Lymphoma ‐ Myeloma, Division of Cancer MedicineUniversity of Texas MD Anderson Cancer CenterHoustonTexasUSA
| | - Daria Zawirska
- Department of HematologyUniversity Hospital in CracowCracowPoland
| | | | - Herlander Marques
- Life and Health Sciences Research Institute (ICVS), School of Health SciencesUniversity of Minho, Braga, Portugal and ICVS/3B's – PT Government Associate LaboratoryBraga/GuimarãesPortugal
| | | | | | - Judit Várkonyi
- Department of Hematology and Internal MedicineSemmelweis UniversityBudapestHungary
| | - Gabriele Buda
- Hematology Unit, Department of Clinical and Experimental MedicineUniversity of PisaPisaItaly
| | - Arnon Nagler
- Hematology Division Chaim Sheba Medical CenterTel HashomerIsrael
| | - Agnieszka Druzd‐Sitek
- Department of Lymphoproliferative DiseasesMaria Skłodowska‐Curie National Research Institute of OncologyWarsawPoland
| | - Xifeng Wu
- Department of Epidemiology, Division of Cancer Prevention and Population SciencesUniversity of Texas MD Anderson Cancer CenterHoustonTexasUSA
| | - Katalin Kadar
- Department of Hematology and Internal MedicineSemmelweis UniversityBudapestHungary
| | - Nicola J. Camp
- Division of Hematology and Huntsman Cancer InstituteUniversity of UtahSalt Lake CityUtahUSA
| | - Norbert Grzasko
- Department of Experimental HematooncologyMedical University of LublinLublinPoland
| | - Rosalie G. Waller
- Division of Biomedical Statistics and Informatics, Department of Health Sciences ResearchMayo ClinicRochesterOntarioUSA
| | - Celine Vachon
- Division of Epidemiology, Department of Health Sciences ResearchMayo ClinicRochesterOntarioUSA
| | - Federico Canzian
- Genomic Epidemiology Group, German Cancer Research Center (DKFZ)HeidelbergGermany
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7
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Qi TF, Miao W, Wang Y. Targeted Profiling of Epitranscriptomic Reader, Writer, and Eraser Proteins Accompanied with Radioresistance in Breast Cancer Cells. Anal Chem 2022; 94:1525-1530. [PMID: 35021009 PMCID: PMC8792366 DOI: 10.1021/acs.analchem.1c05441] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Epitranscriptomic reader, writer, and eraser (RWE) proteins recognize, install, and remove modified nucleosides in RNA, which are known to play crucial roles in RNA processing, splicing, and stability. Here, we established a liquid chromatography-parallel-reaction monitoring (LC-PRM) method for high-throughput profiling of a total of 152 epitranscriptomic RWE proteins. We also applied the LC-PRM method, in conjunction with stable isotope labeling by amino acids in cell culture (SILAC), to quantify these proteins in two pairs of matched parental/radioresistant breast cancer cells (i.e., MDA-MB-231 and MCF-7 cells and their corresponding radioresistant C5 and C6 clones), with the goal of assessing the roles of these proteins in radioresistance. We found that eight epitranscriptomic RWE proteins were commonly altered by over 1.5-fold in the two pairs of breast cancer cells. Among them, TRMT1 (an m2,2G writer) may play a role in promoting breast cancer radioresistance due to its clinical relevance and its correlation with DNA repair gene sets. To our knowledge, this is the first report of a targeted proteomic method for comprehensive quantifications of epitranscriptomic RWE proteins. We envision that the LC-PRM method is applicable for studying the roles of these proteins in the metastatic transformation of cancer and therapeutic resistance of other types of cancer in the future.
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8
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Yu K, Qi TF, Miao W, Liu X, Wang Y. Quantitative proteomics revealed new functions of ALKBH4. Proteomics 2021; 22:e2100231. [PMID: 34951099 DOI: 10.1002/pmic.202100231] [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: 09/19/2021] [Revised: 12/15/2021] [Accepted: 12/16/2021] [Indexed: 11/11/2022]
Abstract
ALKBH4 is a versatile demethylase capable of catalyzing the demethylation of monomethylated lysine-84 on actin and N6 -methyladenine in DNA. In this study, we conducted a quantitative proteomic experiment to reveal the altered expression of proteins in HEK293T cells upon genetic ablation of ALKBH4. Our results showed markedly diminished levels of GSTP1 and HSPB1 proteins in ALKBH4-depleted cells, which emanate from an augmented expression level of DNA (cytosine-5)-methyltransferase 1 (DNMT1) and the ensuing elevated cytosine methylation in the promoter regions of GSTP1 and HSPB1 genes. Together, our results revealed a role of ALKBH4 in modulating DNA cytosine methylation through regulating the expression level of DNMT1 protein. This article is protected by copyright. All rights reserved.
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Affiliation(s)
| | - Tianyu F Qi
- Environmental Toxicology Graduate Program, University of California, Riverside, California, 92521, USA
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9
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Zhu K, Xiaoqiang L, Deng W, Wang G, Fu B. Identification of a novel signature based on unfolded protein response-related gene for predicting prognosis in bladder cancer. Hum Genomics 2021; 15:73. [PMID: 34930465 PMCID: PMC8686253 DOI: 10.1186/s40246-021-00372-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 12/03/2021] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND The unfolded protein response (UPR) served as a vital role in the progression of tumors, but the molecule mechanisms of UPR in bladder cancer (BLCA) have been not fully investigated. METHODS We identified differentially expressed unfolded protein response-related genes (UPRRGs) between BLCA samples and normal bladder samples in the Cancer Genome Atlas (TCGA) database. Univariate Cox analysis and the least absolute shrinkage and selection operator penalized Cox regression analysis were used to construct a prognostic signature in the TCGA set. We implemented the validation of the prognostic signature in GSE13507 from the Gene Expression Omnibus database. The ESTIMATE, CIBERSORT, and ssGSEA algorithms were used to explore the correlation between the prognostic signature and immune cells infiltration as well as key immune checkpoints (PD-1, PD-L1, CTLA-4, and HAVCR2). GDSC database analyses were conducted to investigate the chemotherapy sensitivity among different groups. GSEA analysis was used to explore the potential mechanisms of UPR-based signature. RESULTS A prognostic signature comprising of seven genes (CALR, CRYAB, DNAJB4, KDELR3, CREB3L3, HSPB6, and FBXO6) was constructed to predict the outcome of BLCA. Based on the UPRRGs signature, the patients with BLCA could be classified into low-risk groups and high-risk groups. Patients with BLCA in the low-risk groups showed the more favorable outcomes than those in the high-risk groups, which was verified in GSE13507 set. This signature could serve as an autocephalous prognostic factor in BLCA. A nomogram based on risk score and clinical characteristics was established to predict the over survival of BLCA patients. Furthermore, the signature was closely related to immune checkpoints (PD-L1, CTLA-4, and HAVCR2) and immune cells infiltration including CD8+ T cells, follicular helper T cells, activated dendritic cells, and M2 macrophages. GSEA analysis indicated that immune and carcinogenic pathways were enriched in high-risk group. CONCLUSIONS We identified a novel unfolded protein response-related gene signature which could predict the over survival, immune microenvironment, and chemotherapy response of patients with bladder cancer.
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Affiliation(s)
- Ke Zhu
- Department of Urology, The First Affiliated Hospital of Nanchang University, 17 Yongwaizheng Street, Nanchang, 330006, Jiangxi, People's Republic of China
| | - Liu Xiaoqiang
- Department of Urology, The First Affiliated Hospital of Nanchang University, 17 Yongwaizheng Street, Nanchang, 330006, Jiangxi, People's Republic of China
| | - Wen Deng
- Department of Urology, The First Affiliated Hospital of Nanchang University, 17 Yongwaizheng Street, Nanchang, 330006, Jiangxi, People's Republic of China
| | - Gongxian Wang
- Department of Urology, The First Affiliated Hospital of Nanchang University, 17 Yongwaizheng Street, Nanchang, 330006, Jiangxi, People's Republic of China. .,Jiangxi Institute of Urology, Nanchang, 330006, Jiangxi, People's Republic of China.
| | - Bin Fu
- Department of Urology, The First Affiliated Hospital of Nanchang University, 17 Yongwaizheng Street, Nanchang, 330006, Jiangxi, People's Republic of China. .,Jiangxi Institute of Urology, Nanchang, 330006, Jiangxi, People's Republic of China.
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10
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Kaida A, Iwakuma T. Regulation of p53 and Cancer Signaling by Heat Shock Protein 40/J-Domain Protein Family Members. Int J Mol Sci 2021; 22:13527. [PMID: 34948322 PMCID: PMC8706882 DOI: 10.3390/ijms222413527] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 12/13/2021] [Accepted: 12/14/2021] [Indexed: 12/27/2022] Open
Abstract
Heat shock proteins (HSPs) are molecular chaperones that assist diverse cellular activities including protein folding, intracellular transportation, assembly or disassembly of protein complexes, and stabilization or degradation of misfolded or aggregated proteins. HSP40, also known as J-domain proteins (JDPs), is the largest family with over fifty members and contains highly conserved J domains responsible for binding to HSP70 and stimulation of the ATPase activity as a co-chaperone. Tumor suppressor p53 (p53), the most frequently mutated gene in human cancers, is one of the proteins that functionally interact with HSP40/JDPs. The majority of p53 mutations are missense mutations, resulting in acquirement of unexpected oncogenic activities, referred to as gain of function (GOF), in addition to loss of the tumor suppressive function. Moreover, stability and levels of wild-type p53 (wtp53) and mutant p53 (mutp53) are crucial for their tumor suppressive and oncogenic activities, respectively. However, the regulatory mechanisms of wtp53 and mutp53 are not fully understood. Accumulating reports demonstrate regulation of wtp53 and mutp53 levels and/or activities by HSP40/JDPs. Here, we summarize updated knowledge related to the link of HSP40/JDPs with p53 and cancer signaling to improve our understanding of the regulation of tumor suppressive wtp53 and oncogenic mutp53 GOF activities.
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Affiliation(s)
- Atsushi Kaida
- Department of Oral Radiation Oncology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo 113-8510, Japan;
- Department of Cancer Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Tomoo Iwakuma
- Department of Cancer Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA
- Department of Pediatrics, Children’s Mercy Research Institute, Kansas City, MO 64108, USA
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11
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Du H, Tang J, Li X, Wang X, Wu L, Zhang R, Hu P, Yang Y. Siglec-15 Is an Immune Suppressor and Potential Target for Immunotherapy in the Pre-Metastatic Lymph Node of Colorectal Cancer. Front Cell Dev Biol 2021; 9:691937. [PMID: 34722496 PMCID: PMC8548766 DOI: 10.3389/fcell.2021.691937] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 09/06/2021] [Indexed: 01/25/2023] Open
Abstract
Lymph node metastasis indicates a poor prognosis in colorectal cancer. To better understand the underlying mechanisms of lymph node metastasis, we analyzed transcriptome characteristics of the pre-metastatic lymph node, a putative microenvironment favorable for the seeding and proliferation of cancer cells. Thus, we tried to compare and elucidate the transcriptional and immune characteristics of sentinel lymph nodes (SNs) with matched non-sentinel lymph nodes (NSNs) in colorectal cancer patients. In this study, a total of 38 pairs of SNs and NSNs were collected, in which 26 pairs of non-metastatic lymph nodes were subjected to RNA-seq and bioinformatics analysis for the gene expression profiles. There were 16 differentially expressed genes between SNs and NSNs being identified, including 9 upregulated and 7 downregulated genes in SN. Gene Ontology (GO) classification analysis revealed that the differentially expressed genes were mainly involved in leukocyte differentiation, chemokine secretion, and immune system regulation. In the meantime, gene set enrichment analysis (GSEA) showed that immune-related signaling pathways, such as transforming growth factor beta (TGF-β) signaling and tumor necrosis factor alpha (TNF-α)/nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) signaling, were enriched in NSN, while cell proliferation–related signaling pathways were enriched in SN, including MYC signaling and G2M checkpoint signaling. We further identified SIGLEC15 as a top upregulated gene in SN. However, RNAscope assay showed that SIGLEC15 was not largely co-expressed with M2 macrophage marker CD163. We then selected eight pairs of lymph nodes for further cytological studies. Flow cytometry analysis revealed that Siglec-15 was expressed on all myeloid cell subsets. The relative expression of SEGLEC15 (SN/NSN) was correlated with the microsatellite instability (MSI) status in colorectal cancer patients. Further studies found that small interfering ribonucleic acid (siRNA)-mediated silencing of SLGLEC15 can enhance the anti-tumor function of T cells, as indicated by cytokine release analysis. In conclusion, we presented here a first report on the gene expression profiling of the pre-metastatic lymph node in colorectal cancer. The findings in this study suggest that SIGLEC15 plays an important role in SN immunosuppression. SEGLEC15 silencing could be a therapeutic strategy for restoring T cell function in tumor SNs.
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Affiliation(s)
- Hang Du
- Clinical Medical Research Center, The Affiliated Hospital of Guizhou Medical University, Guizhou, China
| | - Jingling Tang
- Clinical Medical Research Center, The Affiliated Hospital of Guizhou Medical University, Guizhou, China
| | - Xiaoyun Li
- Department of Anorectal Surgery, The Affiliated Hospital of Guizhou Medical University, Guizhou, China
| | - Xinjun Wang
- Clinical Medical Research Center, The Affiliated Hospital of Guizhou Medical University, Guizhou, China
| | - Liyun Wu
- Department of Research and Development, Sinorda Biotechnology Co., Ltd, Guizhou, China
| | - Ruyi Zhang
- Department of Anorectal Surgery, The Affiliated Hospital of Guizhou Medical University, Guizhou, China
| | - Pingsheng Hu
- Department of Research and Development, Sinorda Biotechnology Co., Ltd, Guizhou, China
| | - Yuan Yang
- Clinical Medical Research Center, The Affiliated Hospital of Guizhou Medical University, Guizhou, China
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12
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Zhang Q, Dong X, Lu J, Song J, Wang Y. Chemoproteomic Approach toward Probing the Interactomes of Perfluoroalkyl Substances. Anal Chem 2021; 93:9634-9639. [PMID: 34185510 PMCID: PMC8760635 DOI: 10.1021/acs.analchem.1c01948] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Poly- and perfluoroalkyl substances (PFASs) are widely used in industrial products and consumer goods. Due to their extremely recalcitrant nature and potential bioaccumulation and toxicity, exposure to PFASs may result in adverse health outcomes in humans and wildlife. In this study, we developed a chemoproteomic strategy, based on the use of isotope-coded desthiobiotin-perfluorooctanephosphonic acid (PFOPA) probe and liquid chromatography with tandem mass spectrometry (LC-MS/MS) analysis, to profile PFAS-binding proteins. Targeted proteins were labeled with the desthiobiotin-PFOPA probe, digested with trypsin, and the ensuing desthiobiotin-conjugated peptides were enriched with streptavidin beads for LC-MS/MS analysis. We were able to identify 469 putative PFOPA-binding proteins. By conducting competitive binding experiments using low (10 μM) and high (100 μM) concentrations of stable isotope-labeled PFOPA probes, we further identified 128 nonredundant peptides derived from 75 unique proteins that exhibit selective binding toward PFOPA. Additionally, we demonstrated that one of these proteins, fatty acid-binding protein 5 (FABP5), could interact directly with PFASs, including perfluorooctanoic acid (PFOA), perfluorooctanesulfonic acid (PFOS), perfluorohexanesulfonic acid (PFHxS), and perfluorobutanesulfonic acid (PFBS). Furthermore, desthiobiotin-labeled lysine residues are located close to the fatty acid-binding pocket of FABP5, and the binding affinity varies with the structures of PFASs. Taken together, we developed a novel chemoproteomic method for interrogating the PFAS-interacting proteome. The identification of these proteins sets the stage for understanding the mechanisms through which exposure to PFASs confers adverse human health effects.
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13
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Miao W, Yang YY, Wang Y. Quantitative Proteomic Analysis Revealed Broad Roles of N6-Methyladenosine in Heat Shock Response. J Proteome Res 2021; 20:3611-3620. [PMID: 34043365 DOI: 10.1021/acs.jproteome.1c00191] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
As optimum temperature is essential for all living organisms, heat shock represents a challenging problem for their survival. Therefore, cellular response to heat shock is among the most extensively investigated stress response pathways; however, how the human proteome responds to heat shock has not been comprehensively investigated. In this study, we employed stable isotope labeling by amino acids in cell culture (SILAC), together with liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis, to fulfill an in-depth analysis of the alterations in the human proteome in M14 human melanoma cells in response to heat shock stress. We found that, after heat shock, 284 and 278 out of the 4319 quantified proteins were with substantially diminished and elevated expressions, respectively. We also examined the alterations in human kinome after heat shock by using our recently developed targeted proteomic method relying on parallel-reaction monitoring. Our results showed that the expression levels of 11 and 22 kinase proteins were increased and decreased, respectively, by at least 1.5-fold upon heat shock. By interrogating publicly available RNA-seq and m6A sequencing data, we observed that the elevated expression of more than 30 proteins, including CHEK1 and CCND3 kinases, could occur via an m6A-mediated mechanism. Furthermore, our results from single-base elongation and ligation-based quantitative polymerase chain reaction (qPCR) amplification (SELECT) and luciferase reporter assays revealed that heat shock gave rise to elevated m6A levels at A280 and A286 sites in the 5'-untranslated region of HSPH1 mRNA, thereby leading to increased translation of HSPH1 protein. Together, our discovery and targeted proteomic methods revealed the reprogramming of human proteome and kinome upon heat shock stress and provided insights into cellular responses toward heat shock stress.
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Affiliation(s)
- Weili Miao
- Department of Chemistry, University of California, Riverside, California 92521-0403, United States
| | - Yen-Yu Yang
- Department of Chemistry, University of California, Riverside, California 92521-0403, United States
| | - Yinsheng Wang
- Department of Chemistry, University of California, Riverside, California 92521-0403, United States
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14
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Han Y, Li X, Yan J, Ma C, Wang X, Pan H, Zheng X, Zhang Z, Gao B, Ji XY. Bioinformatic Analysis Identifies Potential Key Genes in the Pathogenesis of Melanoma. Front Oncol 2020; 10:581985. [PMID: 33178610 PMCID: PMC7596746 DOI: 10.3389/fonc.2020.581985] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 09/24/2020] [Indexed: 01/19/2023] Open
Abstract
Melanoma is the deadliest skin tumor and is prone to distant metastases. The incidence of melanoma has increased rapidly in the past few decades, and current trends indicate that this growth is continuing. This study was aimed to explore the molecular mechanisms of melanoma pathogenesis and discover underlying pathways and genes associated with melanoma. We used high-throughput expression data to study differential expression profiles of related genes in melanoma. The differentially expressed genes (DEGs) of melanoma in GSE15605, GSE46517, GSE7553, and the Cancer Genome Atlas (TCGA) datasets were analyzed. Differentially expressed genes (DEGs) were identified by paired t-test. Then the DEGs were performed cluster and principal component analyses and protein–protein interaction (PPI) network construction. After that, we analyzed the differential genes through bioinformatics and got hub genes. Finally, the expression of hub genes was confirmed in the TCGA databases and collected patient tissue samples. Total 144 up-regulated DEGs and 16 down-regulated DEGs were identified. A total of 17 gene ontology analysis (GO) terms and 11 pathways were closely related to melanoma. Pathway of pathways in cancer was enriched in 8 DEGs, such as junction plakoglobin (JUP) and epidermal growth factor receptor (EGFR). In the PPI networks, 9 hub genes were obtained, such as loricrin (LOR), filaggrin (FLG), keratin 5 (KRT5), corneodesmosin (CDSN), desmoglein 1 (DSG1), desmoglein 3 (DSG3), keratin 1 (KRT1), involucrin (IVL), and EGFR. The pathway of pathways in cancer and its enriched DEGs may play important roles in the process of melanoma. The hub genes of DEGs may become promising melanoma candidate genes. Five key genes FLG, DSG1, DSG3, IVL, and EGFR were identified in the TCGA database and melanoma tissues. The results suggested that FLG, DSG1, DSG3, IVL, and EGFR might play important roles and potentially be valuable in the prognosis and treatment of melanoma. These hub genes might well have clinical significance as diagnostic markers.
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Affiliation(s)
- Yanjie Han
- Clinical Laboratory, Functional Laboratory and Department of Stomatology, Kaifeng Central Hospital, Kaifeng, China
| | - Xinxin Li
- Clinical Laboratory, Functional Laboratory and Department of Stomatology, Kaifeng Central Hospital, Kaifeng, China
| | - Jiliang Yan
- Clinical Laboratory, Functional Laboratory and Department of Stomatology, Kaifeng Central Hospital, Kaifeng, China
| | - Chunyan Ma
- Clinical Laboratory, Functional Laboratory and Department of Stomatology, Kaifeng Central Hospital, Kaifeng, China
| | - Xin Wang
- Clinical Laboratory, Functional Laboratory and Department of Stomatology, Kaifeng Central Hospital, Kaifeng, China
| | - Hong Pan
- Clinical Laboratory, Functional Laboratory and Department of Stomatology, Kaifeng Central Hospital, Kaifeng, China
| | - Xiaoli Zheng
- Hospital Infection Control Office, First Affiliated Hospital of Henan University, Kaifeng, China
| | - Zhen Zhang
- Clinical Laboratory, Functional Laboratory and Department of Stomatology, Kaifeng Central Hospital, Kaifeng, China
| | - Biao Gao
- Clinical Laboratory, Functional Laboratory and Department of Stomatology, Kaifeng Central Hospital, Kaifeng, China
| | - Xin-Ying Ji
- Kaifeng Key Laboratory for Infectious Diseases and Biosafety, Henan International Joint Laboratory of Nuclear Protein Regulation, Henan School of Basic Medical Sciences, Henan University College of Medicine, Kaifeng, China
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15
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A Targeted Quantitative Proteomic Method Revealed a Substantial Reprogramming of Kinome during Melanoma Metastasis. Sci Rep 2020; 10:2485. [PMID: 32051510 PMCID: PMC7015909 DOI: 10.1038/s41598-020-59572-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 01/31/2020] [Indexed: 12/15/2022] Open
Abstract
Kinases are involved in numerous critical cell signaling processes, and dysregulation in kinase signaling is implicated in many types of human cancers. In this study, we applied a parallel-reaction monitoring (PRM)-based targeted proteomic method to assess kinome reprogramming during melanoma metastasis in three pairs of matched primary/metastatic human melanoma cell lines. Around 300 kinases were detected in each pair of cell lines, and the results showed that Janus kinase 3 (JAK3) was with reduced expression in the metastatic lines of all three pairs of melanoma cells. Interrogation of The Cancer Genome Atlas (TCGA) data showed that reduced expression of JAK3 is correlated with poorer prognosis in melanoma patients. Additionally, metastatic human melanoma cells/tissues exhibited diminished levels of JAK3 mRNA relative to primary melanoma cells/tissues. Moreover, JAK3 suppresses the migration and invasion of cultured melanoma cells by modulating the activities of matrix metalloproteinases 2 and 9 (MMP-2 and MMP-9). In summary, our targeted kinome profiling method provided by far the most comprehensive dataset for kinome reprogramming associated with melanoma progression, which builds a solid foundation for examining the functions of other kinases in melanoma metastasis. Moreover, our results reveal a role of JAK3 as a potential suppressor for melanoma metastasis.
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16
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Miao W, Li L, Wang Y. High-Throughput Targeted Quantitative Analysis of the Interaction between HSP90 and Kinases. Anal Chem 2019; 91:11507-11509. [PMID: 31476117 DOI: 10.1021/acs.analchem.9b03320] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Kinases, which function in numerous cell signaling processes, are among the best characterized groups of client proteins for the 90-kDa heat shock protein (HSP90), a molecular chaperone that suppresses the aggregation and maintains the proper folding of its substrate proteins (i.e., clients). No high-throughput proteomic method, however, has been developed for the characterizations of the interactions between HSP90 and the human kinome. Herein, by employing a parallel-reaction monitoring (PRM)-based targeted proteomic method, we found that 99 out of the 249 detected kinase proteins display diminished expression in cultured human cells upon treatment with ganetespib, a small-molecule HSP90 inhibitor. PRM analysis of kinase proteins in the affinity pull-down samples showed that 86 out of the 120 detected kinases are enriched from the CRISPR-engineered cells where a tandem affinity tag was conjugated with the C-terminus of endogenous HSP90β protein over the parental cells. Together, our results from the two complementary quantitative proteomic experiments offer systematic characterizations about the HSP90-kinase interactions at the entire proteome scale and reveal extensive interactions between HSP90 and kinase proteins in human cells.
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Affiliation(s)
- Weili Miao
- Department of Chemistry , University of California Riverside , Riverside , California 92521-0403 , United States
| | - Lin Li
- Department of Chemistry , University of California Riverside , Riverside , California 92521-0403 , United States
| | - Yinsheng Wang
- Department of Chemistry , University of California Riverside , Riverside , California 92521-0403 , United States
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17
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HSP90 inhibitors stimulate DNAJB4 protein expression through a mechanism involving N 6-methyladenosine. Nat Commun 2019; 10:3613. [PMID: 31399576 PMCID: PMC6688989 DOI: 10.1038/s41467-019-11552-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 07/22/2019] [Indexed: 12/26/2022] Open
Abstract
Small-molecule inhibitors for the 90-kDa heat shock protein (HSP90) have been extensively exploited in preclinical studies for the therapeutic interventions of human diseases accompanied with proteotoxic stress. By using an unbiased quantitative proteomic method, we uncover that treatment with three HSP90 inhibitors results in elevated expression of a large number of heat shock proteins. We also demonstrate that the HSP90 inhibitor-mediated increase in expression of DNAJB4 protein occurs partly through an epitranscriptomic mechanism, and is substantially modulated by the writer, eraser, and reader proteins of N6-methyladenosine (m6A). Furthermore, exposure to ganetespib leads to elevated modification levels at m6A motif sites in the 5′-UTR of DNAJB4 mRNA, and the methylation at adenosine 114 site in the 5′-UTR promotes the translation of the reporter gene mRNA. This m6A-mediated mechanism is also at play upon heat shock treatment. Cumulatively, we unveil that HSP90 inhibitors stimulate the translation of DNAJB4 through an epitranscriptomic mechanism. Cells respond to heat shock with transcriptional and translational adaptations but how HSP90 inhibition alters the heat shock proteome is largely unclear. Here, the authors analyze proteome changes upon HSP90 inhibition and show that an m6A-mediated mechanism contributes to the heat shock-induced upregulation of DNAJB4.
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18
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Miao W, Yuan J, Li L, Wang Y. Parallel-Reaction-Monitoring-Based Proteome-Wide Profiling of Differential Kinase Protein Expression during Prostate Cancer Metastasis in Vitro. Anal Chem 2019; 91:9893-9900. [PMID: 31241916 DOI: 10.1021/acs.analchem.9b01561] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Prostate cancer is the most common type of cancer in men, and kinases are heavily pursued as drug targets for anticancer therapy. In this study, we applied our recently reported parallel-reaction-monitoring (PRM)-based targeted proteomic method to examine the reprogramming of the human kinome associated with bone metastasis of prostate cancer in vitro. The method displayed superior sensitivity over the shotgun-proteomic approach, and it facilitated the quantification of the relative expression of 276 kinase proteins in a pair of bone metastatic prostate cancer cells. Among the differentially expressed kinases, mitogen-activated protein kinase kinase kinase kinase 4 (MAP4K4) stimulates the migration and invasion of cultured prostate cancer cells, partially by modulating the activity of secreted matrix metalloproteinases 9 (MMP-9). We also found that the upregulation of MAP4K4 in metastatic prostate cancer cells is driven by the MYC proto-oncogene. Cumulatively, we identify MAP4K4 as a potential promoter for prostate cancer metastasis in vitro.
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Miao W, Wang Y. Quantitative Interrogation of the Human Kinome Perturbed by Two BRAF Inhibitors. J Proteome Res 2019; 18:2624-2631. [PMID: 30994353 DOI: 10.1021/acs.jproteome.9b00134] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Oncogenic BRAF mutations contribute to the development of a number of cancers, and small-molecule BRAF inhibitors have been approved by the Food and Drug Administration (FDA) for anticancer therapy. In this study, we employed two targeted quantitative proteomics approaches for monitoring separately the alterations in protein expression and ATP binding affinities of kinases in cultured human melanoma cells elicited by two FDA-approved small-molecule BRAF inhibitors, dabrafenib and vemurafenib. Our results showed that treatment with the two inhibitors led to markedly different reprograming of the human kinome. Furthermore, we confirmed that vemurafenib could compromise the ATP binding capacity of MAP2K5 in vitro and inhibit its kinase activity in cells. Together, our targeted quantitative proteomic methods revealed profound changes in expression levels of kinase proteins in cultured melanoma cells upon treatment with clinically used BRAF inhibitors and led to the discovery of novel putative target kinases for these inhibitors.
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Affiliation(s)
- Weili Miao
- Department of Chemistry , University of California , Riverside , California 92521-0403 , United States
| | - Yinsheng Wang
- Department of Chemistry , University of California , Riverside , California 92521-0403 , United States
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Miao W, Wang Y. Targeted Quantitative Kinome Analysis Identifies PRPS2 as a Promoter for Colorectal Cancer Metastasis. J Proteome Res 2019; 18:2279-2286. [PMID: 30908912 DOI: 10.1021/acs.jproteome.9b00119] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Kinases are among the most important families of enzymes involved in cell signaling. In this study, we employed a recently developed parallel-reaction monitoring (PRM)-based targeted proteomic method to examine the reprogramming of the human kinome during colorectal cancer (CRC) metastasis. We were able to quantify the relative expression of 299 kinase proteins in a pair of matched primary/metastatic CRC cell lines. We also found that, among the differentially expressed kinases, phosphoribosyl pyrophosphate synthetase 2 (PRPS2) promotes the migration and invasion of cultured CRC cells through regulating the activity of matrix metalloproteinase 9 (MMP-9) and the expression of E-cadherin. Moreover, we found that the up-regulation of PRPS2 in metastatic CRC cells could be induced by the MYC proto-oncogene. Together, our unbiased kinome profiling approach led to the identification, for the first time, of PRPS2 as a promoter for CRC metastasis.
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Affiliation(s)
- Weili Miao
- Department of Chemistry , University of California , Riverside , California 92521-0403 , United States
| | - Yinsheng Wang
- Department of Chemistry , University of California , Riverside , California 92521-0403 , United States
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Miao W, Guo L, Wang Y. Imatinib-Induced Changes in Protein Expression and ATP-Binding Affinities of Kinases in Chronic Myelocytic Leukemia Cells. Anal Chem 2019; 91:3209-3214. [PMID: 30773012 DOI: 10.1021/acs.analchem.9b00289] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Kinases are crucial components in numerous cell signaling pathways. Aberrant expression and activation of protein kinases are known to be accompanied by many types of cancer, and more than 30 small-molecule kinase inhibitors have been approved by the Food and Drug Administration (FDA) for cancer chemotherapy. Biological and clinical applications of small-molecule kinase inhibitors require comprehensive characterizations about how these inhibitors modulate the protein expression and activities of kinases at the entire proteome scale. In this study, we developed a parallel-reaction monitoring (PRM)-based targeted proteomic method to monitor the alterations in protein expression of kinases in K-562 chronic myelocytic leukemia (CML) cells elicited by treatment with imatinib, an ABL kinase inhibitor approved by the FDA for CML treatment. By employing isotope-coded ATP affinity probes together with liquid chromatography-multiple-reaction monitoring (LC-MRM) analysis, we also examined the modulation of the ATP-binding affinities of kinases induced by imatinib treatment. The results revealed profound increases in protein expression levels of a large number of kinases in K-562 cells upon treatment with imatinib, which is accompanied by substantial decreases in ATP-binding capacities of many kinases. Apart from ABL kinases, we identified a number of other kinases whose ATP-binding affinities are markedly diminished upon imatinib treatment, including CHK1, a checkpoint kinase involved in DNA damage response signaling. Together, our targeted quantitative proteomic methods enabled, for the first time, dual assessments of small-molecule kinase inhibitor-induced changes in protein expression and ATP-binding affinities of kinases in live cells.
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Miao W, Fan M, Huang M, Li JJ, Wang Y. Targeted Profiling of Heat Shock Proteome in Radioresistant Breast Cancer Cells. Chem Res Toxicol 2019; 32:326-332. [PMID: 30596229 DOI: 10.1021/acs.chemrestox.8b00330] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Breast cancer is the most commonly diagnosed cancer and the second leading cause of cancer death in women. Radioresistance remains one of the most critical barriers in radiation therapy for breast cancer. In this study, we employed a parallel-reaction monitoring (PRM)-based targeted proteomic method to examine the reprogramming of the heat shock proteome during the development of radioresistance in breast cancer. In particular, we investigated the differential expression of heat shock proteins (HSPs) in two pairs of matched parental/radioresistant breast cancer cell lines. We were able to quantify 43 and 42 HSPs in the MCF-7 and MDA-MB-231 pairs of cell lines, respectively. By analyzing the commonly altered proteins, we found that several members of the HSP70 and HSP40 subfamilies of HSPs exhibited substantially altered expression upon development of radioresistance. Moreover, the expression of HSPB8 is markedly elevated in the radioresistant lines relative to the parental MCF-7 and MDA-MB-231 cells. Together, our PRM-based targeted proteomics method revealed the reprogramming of the heat shock proteome during the development of radioresistance in breast cancer cells and offered potential targets for sensitizing breast cancer cells toward radiation therapy.
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Abstract
The 90-kDa heat shock protein (HSP90) is a molecular chaperone that maintains the proper folding of its client proteins including protein kinases and steroid hormone receptors. Helicases are a group of nucleic acid-binding ATPases that can unwind DNA and/or RNA and function in almost every aspect of nucleic acid metabolism. Not much, however, is known about the interactions between HSP90 and helicase proteins. Herein, we developed a parallel-reaction monitoring (PRM)-based targeted proteomic method that allows for quantifying >80% of the human helicase proteome. By employing this method, we demonstrated that a large number of helicase proteins exhibited diminished expression in cultured human cells upon treatment with two small-molecule inhibitors of HSP90. We further introduced a tandem affinity tag to the C-terminus of endogenous HSP90β protein by using the CRISPR-Cas9 genome editing method. Affinity purification followed by LC-PRM analysis revealed an enrichment of 40 out of the 66 quantified helicases from the lysate of cells expressing tagged HSP90β. Together, we developed a high-throughput targeted proteomic method for assessing quantitatively the human helicase proteome, and our results support that helicases may constitute an important group of client proteins for HSP90.
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Affiliation(s)
- Weili Miao
- Department of Chemistry , University of California Riverside , Riverside , California 92521-0403 , United States
| | - Lin Li
- Department of Chemistry , University of California Riverside , Riverside , California 92521-0403 , United States
| | - Yinsheng Wang
- Department of Chemistry , University of California Riverside , Riverside , California 92521-0403 , United States
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