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Yu Q, Qu C, Liang J, Chen P, Zhang K, Zhang Y, Zhang Y, Li Z, Liu S, Yang Z, Sun H, Yang A. ESF1 and MIPEP proteins promote estrogen receptor-positive breast cancer proliferation and are associated with patient prognosis. Clin Proteomics 2024; 21:50. [PMID: 39004717 PMCID: PMC11247778 DOI: 10.1186/s12014-024-09502-8] [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: 02/21/2024] [Accepted: 07/01/2024] [Indexed: 07/16/2024] Open
Abstract
BACKGROUND Estrogen receptor-positive (ER+) breast cancer accounts for two-thirds of all breast cancers, and its early and late recurrences still threaten patients' long-term survival and quality of life. Finding candidate tumor antigens and potential therapeutic targets is critical to addressing these unmet needs. METHOD The isobaric tags for relative and absolute quantitation (iTRAQ) proteomic analysis was employed to identify the differentially expressed proteins (DEPs) between ER + breast cancer and corresponding adjacent normal tissue. Candidate DEPs were screened by bioinformatic analyses, and their expression was confirmed by immunohistochemical (IHC) staining and western blot. A series of in vitro experiments, including wound healing assay, colony formation, and cell cycle assay, were performed to reveal the functions of selected DEPs. Additionally, their clinical significances were further analyzed. RESULT A total of 369 DEPs (fold change ≥ 2.0 or ≤ 0.66, P < 0.05) were discovered. Compared with normal tissue, 358 proteins were up-regulated and 11 proteins were down-regulated in ER + breast cancer. GO and KEGG enrichment analysis showed that DEPs were closely associated with RNA regulation and metabolic pathways. STRING analysis found ESF1 and MIPEP were the hub genes in breast cancer, whose increased expressions were verified by the IHC staining and western blot. Knocking down ESF1 and MIPEP inhibited colony formation and increased cell apoptosis. Besides, knocking down ESF1 inhibited wound healing but not MIPEP. In addition, ESF1 and MIPEP expression were negatively associated with patient prognosis. CONCLUSION The upregulation of ESF1 and MIPEP promoted ER + breast cancer proliferation, which might provide novel targets for the development of new therapies.
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Affiliation(s)
- Qing Yu
- Department of Clinical Laboratory, Shenzhen Kangning Hospital, Shenzhen, 518000, P. R. China
- Department of Clinical Laboratory, Maternal & Child Health Hospital of Foshan, Foshan, 528000, P.R. China
| | - Chunhua Qu
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, P. R. China
| | - Jinliang Liang
- Guangdong Key Laboratory of Liver Disease Research, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510630, P. R. China
| | - Peiqi Chen
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, P. R. China
| | - Kaiying Zhang
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, P. R. China
| | - Yanji Zhang
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, P. R. China
| | - Yuening Zhang
- Zhongshan Medical College, Sun Yat-sen University, Guangzhou, 510080, P.R. China
| | - Zherui Li
- The Third Clinical Medical School, Guangzhou Medical University, Guangzhou, 510180, P.R. China
| | - Shaojun Liu
- Guangzhou Institute of Cardiovascular Disease, the Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510260, P.R. China
| | - Zhaoshou Yang
- The First Affiliated Hospital, The First Clinical Medicine School of Guangdong Pharmaceutical University, Guangdong Pharmaceutical University, Guangzhou, 510080, P.R. China.
| | - Hongyan Sun
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, P. R. China.
| | - Anli Yang
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, P. R. China.
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Jansson M, Lindberg J, Rask G, Svensson J, Billing O, Nazemroaya A, Berglund A, Wärnberg F, Sund M. Stromal Type I Collagen in Breast Cancer: Correlation to Prognostic Biomarkers and Prediction of Chemotherapy Response. Clin Breast Cancer 2024; 24:e360-e369.e4. [PMID: 38485557 DOI: 10.1016/j.clbc.2024.02.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 12/17/2023] [Accepted: 02/19/2024] [Indexed: 06/23/2024]
Abstract
INTRODUCTION Fibrillar collagens accumulate in the breast cancer stroma and appear as poorly defined spiculated masses in mammography imaging. The prognostic value of tissue type I collagen remains elusive in treatment-naïve and chemotherapy-treated breast cancer patients. Here, type I collagen mRNA and protein expression were analysed in 2 large independent breast cancer cohorts. Levels were related to clinicopathological parameters, prognostic biomarkers, and outcome. METHOD COL1A1 mRNA expression was analysed in 2509 patients with breast cancer obtained from the cBioPortal database. Type I collagen protein expression was studied by immunohistochemistry in 1395 women diagnosed with early invasive breast cancer. RESULTS Low COL1A1 mRNA and protein levels correlated with poor prognosis features, such as hormone receptor negativity, high histological grade, triple-negative subtype, node positivity, and tumour size. In unadjusted analysis, high stromal type I collagen protein expression was associated with improved overall survival (OS) (HR = 0.78, 95% CI = 0.61-0.99, p = .043) and trended towards improved breast cancer-specific survival (BCSS) (HR = 0.65, 95% CI = 0.42-1.01, P = 0.053), although these findings were lost after adjustment for other clinical variables. In unadjusted analysis, high expression of type I collagen was associated with better OS (HR = 0.70, 95% CI = 0.55-0.90, P = .006) and BCSS (HR = 0.55, 95% CI = 0.34-0.88, P = .014) among patients not receiving chemotherapy. Strikingly, the opposite was observed among patients receiving chemotherapy. There, high expression of type I collagen was instead associated with worse OS (HR = 1.83, 95% CI = 0.65-5.14, P = .25) and BCSS (HR = 1.72, 95% CI = 0.54-5.50, P = .357). CONCLUSION Low stromal type I collagen mRNA and protein expression are associated with unfavourable tumour characteristics in breast cancer. Stromal type I collagen might predict chemotherapy response.
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Affiliation(s)
- Malin Jansson
- Department of Surgery and Perioperative Sciences/Surgery, Umeå University, Umeå, Sweden.
| | - Jessica Lindberg
- Department of Surgery and Perioperative Sciences/Surgery, Umeå University, Umeå, Sweden
| | - Gunilla Rask
- Department of Medical Biosciences/Pathology, Umeå University, Umeå, Sweden
| | - Johan Svensson
- Department of Surgery and Perioperative Sciences/Surgery, Umeå University, Umeå, Sweden; Department of Statistics, Umeå School of Business, Economics and Statistics, Umeå University, Umeå, Sweden
| | - Ola Billing
- Department of Surgery and Perioperative Sciences/Surgery, Umeå University, Umeå, Sweden
| | | | - Anette Berglund
- Department of Surgery and Perioperative Sciences/Surgery, Umeå University, Umeå, Sweden
| | - Fredrik Wärnberg
- Department of Surgery, Institute of Clinical Sciences, Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
| | - Malin Sund
- Department of Surgery and Perioperative Sciences/Surgery, Umeå University, Umeå, Sweden; Department of Surgery, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
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Choi E, Jeon K, Lee H, Mun G, Kim J, Shin J, Kwon Y, Na Y, Lee Y. Radiosensitizing effect of a novel CTSS inhibitor by enhancing BRCA1 protein stability in triple-negative breast cancer cells. Cancer Sci 2024; 115:2036-2048. [PMID: 38613358 PMCID: PMC11145138 DOI: 10.1111/cas.16174] [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: 10/18/2023] [Revised: 03/19/2024] [Accepted: 03/24/2024] [Indexed: 04/14/2024] Open
Abstract
Triple-negative breast cancer (TNBC) patients harboring wild-type breast cancer susceptibility gene 1 (BRCA1) account for most TNBC patients but lack adequate targeted therapeutic options. Although radiotherapy (RT) is the primary treatment modality for TNBC patients, radioresistance is one of the major challenges. RT-induced increase in cathepsin S (CTSS) causes radioresistance through suppressing BRCA1-mediated apoptosis of tumor cells, which was induced by CTSS-mediated degradation of BRCA1. Targeting CTSS may provide a novel therapeutic opportunity for TNBC patients. Publicly available data and human tissue microarray slides were analyzed to investigate the relationship between CTSS and BRCA1 in breast cancer patients. A CTSS enzyme assay and in silico docking analysis were conducted to identify a novel CTSS inhibitor. RO5461111 was used first to confirm the concept of targeting CTSS for radiosensitizing effects. The MDA-MB-231 TNBC cell line was used for in vitro and in vivo assays. Western blotting, promoter assay, cell death assay, clonogenic survival assay, and immunohistochemistry staining were conducted to evaluate novel CTSS inhibitors. CTSS inhibitors were further evaluated for their additional benefit of inhibiting cell migration. A novel CTSS inhibitor, TS-24, increased BRCA1 protein levels and showed radiosensitization in TNBC cells with wild-type BRCA1 and in vivo in a TNBC xenograft mouse model. These effects were attributed by BRCA1-mediated apoptosis facilitated by TS-24. Furthermore, TS-24 demonstrated the additional effect of inhibiting cell migration. Our study suggests that employing CTSS inhibitors for the functional restoration of BRCA1 to enhance RT-induced apoptosis may provide a novel therapeutic opportunity for TNBC patients harboring wild-type BRCA1.
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Affiliation(s)
- Eun Choi
- Graduate School of Pharmaceutical Sciences and College of PharmacyEwha Women's UniversitySeoulKorea
| | - Kyung‐Hwa Jeon
- Graduate School of Pharmaceutical Sciences and College of PharmacyEwha Women's UniversitySeoulKorea
| | - Hanhee Lee
- Graduate School of Pharmaceutical Sciences and College of PharmacyEwha Women's UniversitySeoulKorea
| | - Gil‐Im Mun
- Graduate School of Pharmaceutical Sciences and College of PharmacyEwha Women's UniversitySeoulKorea
| | - Jeong‐Ahn Kim
- Graduate School of Pharmaceutical Sciences and College of PharmacyEwha Women's UniversitySeoulKorea
| | - Jae‐Ho Shin
- College of Pharmacy, CHA UniversityPocheonKorea
| | - Youngjoo Kwon
- Graduate School of Pharmaceutical Sciences and College of PharmacyEwha Women's UniversitySeoulKorea
| | - Younghwa Na
- College of Pharmacy, CHA UniversityPocheonKorea
| | - Yun‐Sil Lee
- Graduate School of Pharmaceutical Sciences and College of PharmacyEwha Women's UniversitySeoulKorea
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Yang M, Jiang H, Ding X, Zhang L, Zhang H, Chen J, Li L, He X, Huang Z, Chen Q. Multi-omics integration highlights the role of ubiquitination in endometriosis fibrosis. J Transl Med 2024; 22:445. [PMID: 38735939 PMCID: PMC11089738 DOI: 10.1186/s12967-024-05245-0] [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: 03/02/2024] [Accepted: 04/28/2024] [Indexed: 05/14/2024] Open
Abstract
BACKGROUND Endometriosis, characterized by the presence of active endometrial-like tissues outside the uterus, causes symptoms like dysmenorrhea and infertility due to the fibrosis of endometrial cells, which involves excessive deposition of extracellular matrix (ECM) proteins. Ubiquitination, an important post-transcriptional modification, regulates various biological processes in human diseases. However, its role in the fibrosis process in endometriosis remains unclear. METHODS We employed multi-omics approaches on two cohorts of endometriosis patients with 39 samples. GO terms and KEGG pathways enrichment analyses were used to investigate the functional changes involved in endometriosis. Pearson's correlation coefficient analysis was conducted to explore the relationship between global proteome and ubiquitylome in endometriosis. The protein expression levels of ubiquitin-, fibrosis-related proteins, and E3 ubiquitin-protein ligase TRIM33 were validated via Western blot. Transfecting human endometrial stroma cells (hESCs) with TRIM33 small interfering RNA (siRNA) in vitro to explore how TRIM33 affects fibrosis-related proteins. RESULTS Integration of proteomics and transcriptomics showed genes with concurrent change of both mRNA and protein level which involved in ECM production in ectopic endometria. Ubiquitylomics distinguished 1647 and 1698 ubiquitinated lysine sites in the ectopic (EC) group compared to the normal (NC) and eutopic (EU) groups, respectively. Further multi-omics integration highlighted the essential role of ubiquitination in key fibrosis regulators in endometriosis. Correlation analysis between proteome and ubiquitylome showed correlation coefficients of 0.32 and 0.36 for ubiquitinated fibrosis proteins in EC/NC and EC/EU groups, respectively, indicating positive regulation of fibrosis-related protein expression by ubiquitination in ectopic lesions. We identified ubiquitination in 41 pivotal proteins within the fibrosis-related pathway of endometriosis. Finally, the elevated expression of TGFBR1/α-SMA/FAP/FN1/Collagen1 proteins in EC tissues were validated across independent samples. More importantly, we demonstrated that both the mRNA and protein levels of TRIM33 were reduced in endometriotic tissues. Knockdown of TRIM33 promoted TGFBR1/p-SMAD2/α-SMA/FN1 protein expressions in hESCs but did not significantly affect Collagen1/FAP levels, suggesting its inhibitory effect on fibrosis in vitro. CONCLUSIONS This study, employing multi-omics approaches, provides novel insights into endometriosis ubiquitination profiles and reveals aberrant expression of the E3 ubiquitin ligase TRIM33 in endometriotic tissues, emphasizing their critical involvement in fibrosis pathogenesis and potential therapeutic targets.
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Affiliation(s)
- Mengjie Yang
- Clinical Medical Research Center for Gynecological Reproductive Health of Fujian Province, Laboratory of Research and Diagnosis of Gynecological Diseases of Xiamen City, Department of Obstetrics and Gynecology, the First Affliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
- National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
| | - Hong Jiang
- Reproductive Medicine Center, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Xinyu Ding
- Clinical Medical Research Center for Gynecological Reproductive Health of Fujian Province, Laboratory of Research and Diagnosis of Gynecological Diseases of Xiamen City, Department of Obstetrics and Gynecology, the First Affliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Lu Zhang
- Clinical Medical Research Center for Gynecological Reproductive Health of Fujian Province, Laboratory of Research and Diagnosis of Gynecological Diseases of Xiamen City, Department of Obstetrics and Gynecology, the First Affliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
- National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
| | - Huaying Zhang
- Clinical Medical Research Center for Gynecological Reproductive Health of Fujian Province, Laboratory of Research and Diagnosis of Gynecological Diseases of Xiamen City, Department of Obstetrics and Gynecology, the First Affliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Jiahao Chen
- Clinical Medical Research Center for Gynecological Reproductive Health of Fujian Province, Laboratory of Research and Diagnosis of Gynecological Diseases of Xiamen City, Department of Obstetrics and Gynecology, the First Affliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Lijun Li
- Clinical Medical Research Center for Gynecological Reproductive Health of Fujian Province, Laboratory of Research and Diagnosis of Gynecological Diseases of Xiamen City, Department of Obstetrics and Gynecology, the First Affliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Xinqin He
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China.
| | - Zhixiong Huang
- Clinical Medical Research Center for Gynecological Reproductive Health of Fujian Province, Laboratory of Research and Diagnosis of Gynecological Diseases of Xiamen City, Department of Obstetrics and Gynecology, the First Affliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China.
| | - Qionghua Chen
- Clinical Medical Research Center for Gynecological Reproductive Health of Fujian Province, Laboratory of Research and Diagnosis of Gynecological Diseases of Xiamen City, Department of Obstetrics and Gynecology, the First Affliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China.
- National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China.
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5
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Rose M, Burgess JT, Cheong CM, Adams MN, Shahrouzi P, O’Byrne KJ, Richard DJ, Bolderson E. The expression and role of the Lem-D proteins Ankle2, Emerin, Lemd2, and TMPO in triple-negative breast cancer cell growth. Front Oncol 2024; 14:1222698. [PMID: 38720803 PMCID: PMC11076778 DOI: 10.3389/fonc.2024.1222698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 02/28/2024] [Indexed: 05/12/2024] Open
Abstract
Background Triple-negative breast cancer (TNBC) is a sub-classification of breast carcinomas, which leads to poor survival outcomes for patients. TNBCs do not possess the hormone receptors that are frequently targeted as a therapeutic in other cancer subtypes and, therefore, chemotherapy remains the standard treatment for TNBC. Nuclear envelope proteins are frequently dysregulated in cancer cells, supporting their potential as novel cancer therapy targets. The Lem-domain (Lem-D) (LAP2, Emerin, MAN1 domain, and Lem-D) proteins are a family of inner nuclear membrane proteins, which share a ~45-residue Lem-D. The Lem-D proteins, including Ankle2, Lemd2, TMPO, and Emerin, have been shown to be associated with many of the hallmarks of cancer. This study aimed to define the association between the Lem-D proteins and TNBC and determine whether these proteins could be promising therapeutic targets. Methods GENT2, TCGA, and KM plotter were utilized to investigate the expression and prognostic implications of several Lem-D proteins: Ankle2, TMPO, Emerin, and Lemd2 in publicly available breast cancer patient data. Immunoblotting and immunofluorescent analysis of immortalized non-cancerous breast cells and a panel of TNBC cells were utilized to establish whether protein expression of the Lem-D proteins was significantly altered in TNBC. SiRNA was used to decrease individual Lem-D protein expression, and functional assays, including proliferation assays and apoptosis assays, were conducted. Results The Lem-D proteins were generally overexpressed in TNBC patient samples at the mRNA level and showed variable expression at the protein level in TNBC cell lysates. Similarly, protein levels were generally negatively correlated with patient survival outcomes. siRNA-mediated depletion of the individual Lem-D proteins in TNBC cells induced aberrant nuclear morphology, decreased proliferation, and induced cell death. However, minimal effects on nuclear morphology or cell viability were observed following Lem-D depletion in non-cancerous MCF10A cells. Conclusion There is evidence to suggest that Ankle2, TMPO, Emerin, and Lemd2 expressions are correlated with breast cancer patient outcomes, but larger patient sample numbers are required to confirm this. siRNA-mediated depletion of these proteins was shown to specifically impair TNBC cell growth, suggesting that the Lem-D proteins may be a specific anti-cancer target.
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Affiliation(s)
- Maddison Rose
- Cancer and Ageing Research Program, Centre for Genomics and Personalised Health, School of Biomedical Sciences, Translational Research Institute, Queensland University of Technology, Brisbane, QLD, Australia
| | - Joshua T. Burgess
- Cancer and Ageing Research Program, Centre for Genomics and Personalised Health, School of Biomedical Sciences, Translational Research Institute, Queensland University of Technology, Brisbane, QLD, Australia
| | - Chee Man Cheong
- Cancer and Ageing Research Program, Centre for Genomics and Personalised Health, School of Biomedical Sciences, Translational Research Institute, Queensland University of Technology, Brisbane, QLD, Australia
| | - Mark N. Adams
- Cancer and Ageing Research Program, Centre for Genomics and Personalised Health, School of Biomedical Sciences, Translational Research Institute, Queensland University of Technology, Brisbane, QLD, Australia
| | - Parastoo Shahrouzi
- Department of Medical Genetics, Faculty of Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Kenneth J. O’Byrne
- Cancer and Ageing Research Program, Centre for Genomics and Personalised Health, School of Biomedical Sciences, Translational Research Institute, Queensland University of Technology, Brisbane, QLD, Australia
- Cancer Services, Princess Alexandra Hospital, Brisbane, QLD, Australia
| | - Derek J. Richard
- Cancer and Ageing Research Program, Centre for Genomics and Personalised Health, School of Biomedical Sciences, Translational Research Institute, Queensland University of Technology, Brisbane, QLD, Australia
| | - Emma Bolderson
- Cancer and Ageing Research Program, Centre for Genomics and Personalised Health, School of Biomedical Sciences, Translational Research Institute, Queensland University of Technology, Brisbane, QLD, Australia
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Cerutti C, Lucotti S, Menendez ST, Reymond N, Garg R, Romero IA, Muschel R, Ridley AJ. IQGAP1 and NWASP promote human cancer cell dissemination and metastasis by regulating β1-integrin via FAK and MRTF/SRF. Cell Rep 2024; 43:113989. [PMID: 38536816 DOI: 10.1016/j.celrep.2024.113989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Revised: 02/01/2024] [Accepted: 03/07/2024] [Indexed: 04/28/2024] Open
Abstract
Attachment of circulating tumor cells to the endothelial cells (ECs) lining blood vessels is a critical step in cancer metastatic colonization, which leads to metastatic outgrowth. Breast and prostate cancers are common malignancies in women and men, respectively. Here, we observe that β1-integrin is required for human prostate and breast cancer cell adhesion to ECs under shear-stress conditions in vitro and to lung blood vessel ECs in vivo. We identify IQGAP1 and neural Wiskott-Aldrich syndrome protein (NWASP) as regulators of β1-integrin transcription and protein expression in prostate and breast cancer cells. IQGAP1 and NWASP depletion in cancer cells decreases adhesion to ECs in vitro and retention in the lung vasculature and metastatic lung nodule formation in vivo. Mechanistically, NWASP and IQGAP1 act downstream of Cdc42 to increase β1-integrin expression both via extracellular signal-regulated kinase (ERK)/focal adhesion kinase signaling at the protein level and by myocardin-related transcription factor/serum response factor (SRF) transcriptionally. Our results identify IQGAP1 and NWASP as potential therapeutic targets to reduce early metastatic dissemination.
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Affiliation(s)
- Camilla Cerutti
- School of Cellular and Molecular Medicine, University of Bristol, Bristol BS8 1TD, UK; Randall Centre for Cell and Molecular Biophysics, King's College London, London SE1 U1L, UK; Department of Life Sciences, Centre for Inflammation Research and Translational Medicine (CIRTM), Brunel University London, Uxbridge UB8 3PH, UK.
| | - Serena Lucotti
- CRUK/MRC Oxford Institute for Radiation Oncology, University of Oxford, Oxford OX3 7DQ, UK
| | - Sofia T Menendez
- Randall Centre for Cell and Molecular Biophysics, King's College London, London SE1 U1L, UK
| | - Nicolas Reymond
- Randall Centre for Cell and Molecular Biophysics, King's College London, London SE1 U1L, UK
| | - Ritu Garg
- Randall Centre for Cell and Molecular Biophysics, King's College London, London SE1 U1L, UK
| | - Ignacio A Romero
- School of Life, Health and Chemical Sciences, The Open University, Milton Keynes MK7 6AA, UK
| | - Ruth Muschel
- CRUK/MRC Oxford Institute for Radiation Oncology, University of Oxford, Oxford OX3 7DQ, UK
| | - Anne J Ridley
- School of Cellular and Molecular Medicine, University of Bristol, Bristol BS8 1TD, UK; Randall Centre for Cell and Molecular Biophysics, King's College London, London SE1 U1L, UK.
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7
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Ke S, Dang F, Wang L, Chen JY, Naik MT, Li W, Thavamani A, Kim N, Naik NM, Sui H, Tang W, Qiu C, Koikawa K, Batalini F, Stern Gatof E, Isaza DA, Patel JM, Wang X, Clohessy JG, Heng YJ, Lahav G, Liu Y, Gray NS, Zhou XZ, Wei W, Wulf GM, Lu KP. Reciprocal antagonism of PIN1-APC/C CDH1 governs mitotic protein stability and cell cycle entry. Nat Commun 2024; 15:3220. [PMID: 38622115 PMCID: PMC11018817 DOI: 10.1038/s41467-024-47427-w] [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: 05/01/2023] [Accepted: 04/02/2024] [Indexed: 04/17/2024] Open
Abstract
Induced oncoproteins degradation provides an attractive anti-cancer modality. Activation of anaphase-promoting complex (APC/CCDH1) prevents cell-cycle entry by targeting crucial mitotic proteins for degradation. Phosphorylation of its co-activator CDH1 modulates the E3 ligase activity, but little is known about its regulation after phosphorylation and how to effectively harness APC/CCDH1 activity to treat cancer. Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 (PIN1)-catalyzed phosphorylation-dependent cis-trans prolyl isomerization drives tumor malignancy. However, the mechanisms controlling its protein turnover remain elusive. Through proteomic screens and structural characterizations, we identify a reciprocal antagonism of PIN1-APC/CCDH1 mediated by domain-oriented phosphorylation-dependent dual interactions as a fundamental mechanism governing mitotic protein stability and cell-cycle entry. Remarkably, combined PIN1 and cyclin-dependent protein kinases (CDKs) inhibition creates a positive feedback loop of PIN1 inhibition and APC/CCDH1 activation to irreversibly degrade PIN1 and other crucial mitotic proteins, which force permanent cell-cycle exit and trigger anti-tumor immunity, translating into synergistic efficacy against triple-negative breast cancer.
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Affiliation(s)
- Shizhong Ke
- Division of Hematology/Oncology, Department of Medicine and Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA
| | - Fabin Dang
- Department of Pathology, Beth Israel Deaconess Medical Center and Cancer Research Institute, Harvard Medical School, Boston, MA, 02215, USA
| | - Lin Wang
- Division of Hematology/Oncology, Department of Medicine and Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA
| | - Jia-Yun Chen
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02215, USA
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, 02215, USA
| | - Mandar T Naik
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI, 02912, USA
| | - Wenxue Li
- Yale Cancer Biology Institute, West Haven, CT, 06516, USA
| | - Abhishek Thavamani
- Division of Hematology/Oncology, Department of Medicine and Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA
| | - Nami Kim
- Division of Hematology/Oncology, Department of Medicine and Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA
| | - Nandita M Naik
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI, 02912, USA
| | - Huaxiu Sui
- Key Laboratory of Functional and Clinical Translational Medicine, Fujian Province University, Xiamen Medical College, Xiamen, 361023, China
| | - Wei Tang
- Data Science & Artificial Intelligence, R&D, AstraZeneca, Gaithersburg, MD, USA
| | - Chenxi Qiu
- Division of Hematology/Oncology, Department of Medicine and Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Kazuhiro Koikawa
- Division of Hematology/Oncology, Department of Medicine and Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA
| | - Felipe Batalini
- Division of Hematology/Oncology, Department of Medicine and Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA
- Department of Medicine, Division of Medical Oncology, Mayo Clinic, Phoenix, AZ, USA
| | - Emily Stern Gatof
- Division of Hematology/Oncology, Department of Medicine and Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA
| | - Daniela Arango Isaza
- Division of Hematology/Oncology, Department of Medicine and Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA
| | - Jaymin M Patel
- Division of Hematology/Oncology, Department of Medicine and Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA
| | - Xiaodong Wang
- Molecular and Integrative Physiological Sciences, Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, 02215, USA
| | - John G Clohessy
- Preclinical Murine Pharmacogenetics Facility, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA
| | - Yujing J Heng
- Department of Pathology, Beth Israel Deaconess Medical Center and Cancer Research Institute, Harvard Medical School, Boston, MA, 02215, USA
| | - Galit Lahav
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02215, USA
| | - Yansheng Liu
- Yale Cancer Biology Institute, West Haven, CT, 06516, USA
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, 06510, USA
| | - Nathanael S Gray
- Department of Chemical and Systems Biology, Chem-H and Stanford Cancer Institute, Stanford University, Stanford, CA, 94305, USA
| | - Xiao Zhen Zhou
- Departments of Pathology and Laboratory Medicine, Biochemistry, and Oncology, and Lawson Health Research Institute, Schulich School of Medicine and Dentistry, Western University, London, ON, N6A 3K7, Canada.
| | - Wenyi Wei
- Department of Pathology, Beth Israel Deaconess Medical Center and Cancer Research Institute, Harvard Medical School, Boston, MA, 02215, USA.
| | - Gerburg M Wulf
- Division of Hematology/Oncology, Department of Medicine and Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA.
| | - Kun Ping Lu
- Departments of Biochemistry and Oncology, and Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, ON, N6A 3K7, Canada.
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8
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Banerjee S, Hatimuria M, Sarkar K, Das J, Pabbathi A, Sil PC. Recent Contributions of Mass Spectrometry-Based "Omics" in the Studies of Breast Cancer. Chem Res Toxicol 2024; 37:137-180. [PMID: 38011513 DOI: 10.1021/acs.chemrestox.3c00223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Breast cancer (BC) is one of the most heterogeneous groups of cancer. As every biotype of BC is unique and presents a particular "omic" signature, they are increasingly characterized nowadays with novel mass spectrometry (MS) strategies. BC therapeutic approaches are primarily based on the two features of human epidermal growth factor receptor 2 (HER2) and estrogen receptor (ER) positivity. Various strategic MS implementations are reported in studies of BC also involving data independent acquisitions (DIAs) of MS which report novel differential proteomic, lipidomic, proteogenomic, phosphoproteomic, and metabolomic characterizations associated with the disease and its therapeutics. Recently many "omic" studies have aimed to identify distinct subsidiary biotypes for diagnosis, prognosis, and targets of treatment. Along with these, drug-induced-resistance phenotypes are characterized by "omic" changes. These identifying aspects of the disease may influence treatment outcomes in the near future. Drug quantifications and characterizations are also done regularly and have implications in therapeutic monitoring and in drug efficacy assessments. We report these studies, mentioning their implications toward the understanding of BC. We briefly provide the MS instrumentation principles that are adopted in such studies as an overview with a brief outlook on DIA-MS strategies. In all of these, we have chosen a model cancer for its revelations through MS-based "omics".
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Affiliation(s)
- Subhrajit Banerjee
- Department of Physiology, Surendranath College, University of Calcutta, Kolkata 700009, India
- Department of Microbiology, St. Xavier's College, Kolkata 700016, India
| | - Madushmita Hatimuria
- Department of Industrial Chemistry, School of Physical Sciences, Mizoram University, Aizawl 796004, Mizoram India
| | - Kasturi Sarkar
- Department of Microbiology, St. Xavier's College, Kolkata 700016, India
| | - Joydeep Das
- Department of Chemistry, School of Physical Sciences, Mizoram University, Aizawl 796004, Mizoram, India
| | - Ashok Pabbathi
- Department of Industrial Chemistry, School of Physical Sciences, Mizoram University, Aizawl 796004, Mizoram India
| | - Parames C Sil
- Department of Molecular Medicine Bose Institute, Kolkata 700054, India
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9
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Van Stiphout CM, Kelly G, Pallegar NK, Elbakry E, Vilchis-Celis AV, Christian SL, Viloria-Petit AM. Identification of lysyl oxidase as an adipocyte-secreted mediator that promotes a partial mesenchymal-to-epithelial transition in MDA-MB-231 cells. EXPLORATION OF TARGETED ANTI-TUMOR THERAPY 2024; 5:1-19. [PMID: 38468823 PMCID: PMC10927314 DOI: 10.37349/etat.2024.00201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 11/16/2023] [Indexed: 03/13/2024] Open
Abstract
Aim Breast cancer (BC) is the most common cancer in women worldwide, where adiposity has been linked to BC morbidity. In general, obese premenopausal women diagnosed with triple-negative BC (TNBC) tend to have larger tumours with more metastases, particularly to the bone marrow, and worse prognosis. Previous work using a 3-dimensional (3D) co-culture system consisting of TNBC cells, adipocytes and the laminin-rich extracellular matrix (ECM) trademarked as Matrigel, demonstrated that adipocytes and adipocyte-derived conditioned media (CM) caused a partial mesenchymal-to-epithelial transition (MET). Given that MET has been associated with secondary tumour formation, this study sought to identify molecular mediators responsible for this phenotypic change. Methods Adipocytes were cultured with and without Matrigel, where semi-quantitative proteomics was used to identify proteins whose presence in the CM was induced or enhanced by Matrigel, which were referred to as adipocyte-secreted ECM-induced proteins (AEPs). The AEPs identified were assessed for association with prognosis in published proteomic datasets and prior literature. Of these, 4 were evaluated by the reverse transcription-quantitative polymerase chain reaction (RT-qPCR) and enzyme-linked immunosorbent assay (ELISA), followed by a functional and MET marker analysis of 1 AEP on MDA-MB-231 cells grown on Matrigel or as monolayers. Results The 4 AEPs showed a positive correlation between protein expression and poor prognosis. RT-qPCR analysis reported no significant change in AEPs mRNA expression. However, lysyl oxidase (LOX) was increased in CM of ECM-exposed adipocytes. Recombinant LOX (rLOX) caused the mesenchymal MDA-MB-231 TNBC cells to form less branched 3D structures and reduced the expression of vimentin. Conclusions The data suggest that adipocyte-secreted LOX changes the mesenchymal phenotype of BC cells in a manner that could promote secondary tumour formation, particularly at sites high in adipocytes such as the bone marrow. Future efforts should focus on determining whether targeting LOX could reduce BC metastasis in obese individuals.
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Affiliation(s)
- Cassidy M. Van Stiphout
- Department of Biomedical Sciences, Ontario Veterinary College, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Grant Kelly
- Department of Biochemistry, Memorial University of Newfoundland, St. John’s, NL A1B 3X9, Canada
- Beatrice Hunter Cancer Research Institute, Halifax, NS B3H 4R2, Canada
| | - Nikitha K. Pallegar
- Department of Biochemistry, Memorial University of Newfoundland, St. John’s, NL A1B 3X9, Canada
| | - Eman Elbakry
- Department of Biochemistry, Memorial University of Newfoundland, St. John’s, NL A1B 3X9, Canada
| | - Ana Valeria Vilchis-Celis
- Department of Biomedical Sciences, Ontario Veterinary College, University of Guelph, Guelph, ON N1G 2W1, Canada
- Department of Morphology, National Polytechnic Institute, Mexico City, CDMX 07738, Mexico
| | - Sherri L. Christian
- Department of Biochemistry, Memorial University of Newfoundland, St. John’s, NL A1B 3X9, Canada
- Beatrice Hunter Cancer Research Institute, Halifax, NS B3H 4R2, Canada
| | - Alicia M. Viloria-Petit
- Department of Biomedical Sciences, Ontario Veterinary College, University of Guelph, Guelph, ON N1G 2W1, Canada
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10
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Liu CH, Lai YL, Shen PC, Liu HC, Tsai MH, Wang YD, Lin WJ, Chen FH, Li CY, Wang SC, Hung MC, Cheng WC. DriverDBv4: a multi-omics integration database for cancer driver gene research. Nucleic Acids Res 2024; 52:D1246-D1252. [PMID: 37956338 PMCID: PMC10767848 DOI: 10.1093/nar/gkad1060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 10/12/2023] [Accepted: 10/25/2023] [Indexed: 11/15/2023] Open
Abstract
Advancements in high-throughput technology offer researchers an extensive range of multi-omics data that provide deep insights into the complex landscape of cancer biology. However, traditional statistical models and databases are inadequate to interpret these high-dimensional data within a multi-omics framework. To address this limitation, we introduce DriverDBv4, an updated iteration of the DriverDB cancer driver gene database (http://driverdb.bioinfomics.org/). This updated version offers several significant enhancements: (i) an increase in the number of cohorts from 33 to 70, encompassing approximately 24 000 samples; (ii) inclusion of proteomics data, augmenting the existing types of omics data and thus expanding the analytical scope; (iii) implementation of multiple multi-omics algorithms for identification of cancer drivers; (iv) new visualization features designed to succinctly summarize high-context data and redesigned existing sections to accommodate the increased volume of datasets and (v) two new functions in Customized Analysis, specifically designed for multi-omics driver identification and subgroup expression analysis. DriverDBv4 facilitates comprehensive interpretation of multi-omics data across diverse cancer types, thereby enriching the understanding of cancer heterogeneity and aiding in the development of personalized clinical approaches. The database is designed to foster a more nuanced understanding of the multi-faceted nature of cancer.
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Affiliation(s)
- Chia-Hsin Liu
- Cancer Biology and Precision Therapeutics Center, China Medical University, Taichung 404328, Taiwan
| | - Yo-Liang Lai
- Department of Radiation Oncology, China Medical University, Taichung 404328, Taiwan
| | - Pei-Chun Shen
- Cancer Biology and Precision Therapeutics Center, China Medical University, Taichung 404328, Taiwan
| | - Hsiu-Cheng Liu
- Cancer Biology and Precision Therapeutics Center, China Medical University, Taichung 404328, Taiwan
| | - Meng-Hsin Tsai
- Cancer Biology and Precision Therapeutics Center, China Medical University, Taichung 404328, Taiwan
| | - Yu-De Wang
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung 404328, Taiwan
- Department of Urology, China Medical University, Taichung 404328, Taiwan
| | - Wen-Jen Lin
- Cancer Biology and Precision Therapeutics Center, China Medical University, Taichung 404328, Taiwan
- School of Medicine, China Medical University, Taichung 404328, Taiwan
| | - Fang-Hsin Chen
- Institute of Nuclear Engineering and Science, National Tsing Hua University, Hsinchu 300044, Taiwan
| | - Chia-Yang Li
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Shu-Chi Wang
- Department of Medical Laboratory Science and Biotechnology, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Mien-Chie Hung
- Cancer Biology and Precision Therapeutics Center, China Medical University, Taichung 404328, Taiwan
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung 404328, Taiwan
- Institute of Biochemistry and Molecular Biology, China Medical University, Taichung 404328, Taiwan
- Molecular Medicine Center, China Medical University Hospital, China Medical University, Taichung 404328, Taiwan
- Department of Biotechnology, Asia University, Taichung 413305, Taiwan
| | - Wei-Chung Cheng
- Cancer Biology and Precision Therapeutics Center, China Medical University, Taichung 404328, Taiwan
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung 404328, Taiwan
- The Ph.D. program for Cancer Biology and Drug Discovery, China Medical University and Academia Sinica, Taichung 404328, Taiwan
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11
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Jiang B, Yang J, He R, Wang D, Huang Y, Zhao G, Ning M, Zeng T, Li G. Integrated multi-omics analysis for lung adenocarcinoma in Xuanwei, China. Aging (Albany NY) 2023; 15:14263-14291. [PMID: 38095636 PMCID: PMC10756121 DOI: 10.18632/aging.205300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 11/02/2023] [Indexed: 12/21/2023]
Abstract
BACKGROUND Xuanwei lung cancer (XWLC) is well-known for its high incidence and mortality. However, the molecular mechanism is still unclear. METHODS We performed a comprehensive transcriptomic, proteomic, and phosphoproteomic characterization of tumors and matched normal adjacent tissues from three XWLC patients with lung adenocarcinoma (LUAD). RESULTS Integrated transcriptome and proteome analysis revealed dysregulated molecules and pathways in tumors and identified enhanced metabolic-disease coupling. Non-coding RNAs were widely involved in post-transcriptional regulatory mechanisms to coordinate the progress of LUAD and partially explained the molecular differences between RNA and protein expression patterns. Phosphoproteome provided evidence support for new phosphate sites, reporting the potential roles of core kinase family members and key kinase pathways involved in metabolism, immunity, and homeostasis. In addition, by comparing with the previous LUAD researches, we emphasized the higher degree of oxidative phosphorylation in Xuanwei LUAD and pointed that VIPR1 deficiency aggravated metabolic dysfunction. CONCLUSION Our integrated multi-omics analysis provided a powerful resource for a systematic understanding of the molecular structure of XWLC and proposed therapeutic opportunities based on redox metabolism.
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Affiliation(s)
- Boyi Jiang
- Department of Thoracic Surgery, The Third Affiliated Hospital of Kunming Medical University, Yunnan Cancer Hospital, Kunming, Yunnan 650032, China
| | - Jiapeng Yang
- Department of Thoracic Surgery, The Third Affiliated Hospital of Kunming Medical University, Yunnan Cancer Hospital, Kunming, Yunnan 650032, China
| | - Rui He
- Department of Thoracic Surgery, The Third Affiliated Hospital of Kunming Medical University, Yunnan Cancer Hospital, Kunming, Yunnan 650032, China
| | - Dong Wang
- Department of Thoracic Surgery, The Third Affiliated Hospital of Kunming Medical University, Yunnan Cancer Hospital, Kunming, Yunnan 650032, China
| | - Yunchao Huang
- Department of Thoracic Surgery, The Third Affiliated Hospital of Kunming Medical University, Yunnan Cancer Hospital, Kunming, Yunnan 650032, China
| | - Guangqiang Zhao
- Department of Thoracic Surgery, The Third Affiliated Hospital of Kunming Medical University, Yunnan Cancer Hospital, Kunming, Yunnan 650032, China
| | - Mingjie Ning
- Department of Thoracic Surgery, The Third Affiliated Hospital of Kunming Medical University, Yunnan Cancer Hospital, Kunming, Yunnan 650032, China
| | - Teng Zeng
- Department of Thoracic Surgery, The Third Affiliated Hospital of Kunming Medical University, Yunnan Cancer Hospital, Kunming, Yunnan 650032, China
| | - Guangjian Li
- Department of Thoracic Surgery, The Third Affiliated Hospital of Kunming Medical University, Yunnan Cancer Hospital, Kunming, Yunnan 650032, China
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12
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Das S, Srivastava DK. ioSearch: An approach for identifying interacting multiomics biomarkers using a novel algorithm with application on breast cancer data sets. Genet Epidemiol 2023; 47:600-616. [PMID: 37795815 DOI: 10.1002/gepi.22536] [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: 01/20/2023] [Revised: 08/04/2023] [Accepted: 09/18/2023] [Indexed: 10/06/2023]
Abstract
Identification of biomarkers by integrating multiple omics together is important because complex diseases occur due to an intricate interplay of various genetic materials. Traditional single-omics association tests neither explore this crucial interomics dependence nor identify moderately weak signals due to the multiple-testing burden. Conversely, multiomics data integration imparts complementary information but suffers from an increased multiple-testing burden, data diversity inherent with different omics features, high-dimensionality, and so forth. Most of the available methods address subtype classification using dimension-reduction techniques to circumvent the sample size issue but interacting multiomics biomarker identification methods are unavailable. We propose a two-step model that first investigates phenotype-omics association using logistic regression. Then, selects disease-associated omics using sparse principal components which explores the interrelationship of multiple variables from two omics in a multivariate multiple regression framework. On the basis of this model, we developed a multiomics biomarker identification algorithm, interacting omics search (ioSearch), that jointly tests the effect of multiple omics with disease and between-omics associations by using pathway information that subsequently reduces the multiple-testing burden. Further, inference in terms of p values potentially makes it an easily interpretable biomarker identification tool. Extensive simulation demonstrates ioSearch as statistically powerful with a controlled Type-I error rate. Its application to publicly available breast cancer data sets identified relevant omics features in important pathways.
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Affiliation(s)
- Sarmistha Das
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Deo Kumar Srivastava
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
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13
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Lei JT, Jaehnig EJ, Smith H, Holt MV, Li X, Anurag M, Ellis MJ, Mills GB, Zhang B, Labrie M. The Breast Cancer Proteome and Precision Oncology. Cold Spring Harb Perspect Med 2023; 13:a041323. [PMID: 37137501 PMCID: PMC10547392 DOI: 10.1101/cshperspect.a041323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The goal of precision oncology is to translate the molecular features of cancer into predictive and prognostic tests that can be used to individualize treatment leading to improved outcomes and decreased toxicity. Success for this strategy in breast cancer is exemplified by efficacy of trastuzumab in tumors overexpressing ERBB2 and endocrine therapy for tumors that are estrogen receptor positive. However, other effective treatments, including chemotherapy, immune checkpoint inhibitors, and CDK4/6 inhibitors are not associated with strong predictive biomarkers. Proteomics promises another tier of information that, when added to genomic and transcriptomic features (proteogenomics), may create new opportunities to improve both treatment precision and therapeutic hypotheses. Here, we review both mass spectrometry-based and antibody-dependent proteomics as complementary approaches. We highlight how these methods have contributed toward a more complete understanding of breast cancer and describe the potential to guide diagnosis and treatment more accurately.
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Affiliation(s)
- Jonathan T Lei
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Eric J Jaehnig
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Hannah Smith
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon 97239, USA
| | - Matthew V Holt
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Xi Li
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon 97239, USA
| | - Meenakshi Anurag
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Matthew J Ellis
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Gordon B Mills
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon 97239, USA
| | - Bing Zhang
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Marilyne Labrie
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon 97239, USA
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14
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Kao HY, Pai CP, Wang H, Agarwal N, Adams J, Liu Z, Seachrist D, Keri R, Schiemann W. The PML1-WDR5 axis regulates H3K4me3 marks and promotes stemness of estrogen receptor-positive breast cancer. RESEARCH SQUARE 2023:rs.3.rs-3266720. [PMID: 37720048 PMCID: PMC10503857 DOI: 10.21203/rs.3.rs-3266720/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/19/2023]
Abstract
The alternative splicing of PML precursor mRNA gives rise to various PML isoforms, yet their expression profile in breast cancer cells remains uncharted. We discovered that PML1 is the most abundant isoform in all breast cancer subtypes, and its expression is associated with unfavorable prognosis in estrogen receptor-positive (ER+) breast cancers. PML depletion reduces cell proliferation, invasion, and stemness, while heterologous PML1 expression augments these processes and fuels tumor growth and resistance to fulvestrant, an FDA-approved drug for ER + breast cancer, in a mouse model. Moreover, PML1, rather than the well-known tumor suppressor isoform PML4, rescues the proliferation of PML knockdown cells. ChIP-seq analysis reveals significant overlap between PML-, ER-, and Myc-bound promoters, suggesting their coordinated regulation of target gene expression, including genes involved in breast cancer stem cells (BCSCs), such as JAG1, KLF4, YAP1, SNAI1, and MYC. Loss of PML reduces BCSC-related gene expression, and exogenous PML1 expression elevates their expression. Consistently, PML1 restores the association of PML with these promoters in PML-depleted cells. We identified a novel association between PML1 and WDR5, a key component of H3K4 methyltransferase (HMTs) complexes that catalyze H3K4me1 and H3K4me3. ChIP-seq analyses showed that the loss of PML1 reduces H3K4me3 in numerous loci, including BCSC-associated gene promoters. Additionally, PML1, not PML4, re-establishes the H3K4me3 mark on these promoters in PML-depleted cells. Significantly, PML1 is essential for recruiting WDR5, MLL1, and MLL2 to these gene promoters. Inactivating WDR5 by knockdown or inhibitors phenocopies the effects of PML1 loss, reducing BCSC-related gene expression and tumorsphere formation and enhancing fulvestrant's anticancer activity. Our findings challenge the conventional understanding of PML as a tumor suppressor, redefine its role as a promoter of tumor growth in breast cancer and offer new insights into the unique roles of PML isoforms in breast cancer.
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Affiliation(s)
| | | | | | | | - Joshua Adams
- Washington University School of Medicine in St. Louis
| | | | | | - Ruth Keri
- Cleveland Clinic Lerner Research Institute
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15
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Li Y, Dou Y, Da Veiga Leprevost F, Geffen Y, Calinawan AP, Aguet F, Akiyama Y, Anand S, Birger C, Cao S, Chaudhary R, Chilappagari P, Cieslik M, Colaprico A, Zhou DC, Day C, Domagalski MJ, Esai Selvan M, Fenyö D, Foltz SM, Francis A, Gonzalez-Robles T, Gümüş ZH, Heiman D, Holck M, Hong R, Hu Y, Jaehnig EJ, Ji J, Jiang W, Katsnelson L, Ketchum KA, Klein RJ, Lei JT, Liang WW, Liao Y, Lindgren CM, Ma W, Ma L, MacCoss MJ, Martins Rodrigues F, McKerrow W, Nguyen N, Oldroyd R, Pilozzi A, Pugliese P, Reva B, Rudnick P, Ruggles KV, Rykunov D, Savage SR, Schnaubelt M, Schraink T, Shi Z, Singhal D, Song X, Storrs E, Terekhanova NV, Thangudu RR, Thiagarajan M, Wang LB, Wang JM, Wang Y, Wen B, Wu Y, Wyczalkowski MA, Xin Y, Yao L, Yi X, Zhang H, Zhang Q, Zuhl M, Getz G, Ding L, Nesvizhskii AI, Wang P, Robles AI, Zhang B, Payne SH. Proteogenomic data and resources for pan-cancer analysis. Cancer Cell 2023; 41:1397-1406. [PMID: 37582339 PMCID: PMC10506762 DOI: 10.1016/j.ccell.2023.06.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 11/15/2022] [Accepted: 06/27/2023] [Indexed: 08/17/2023]
Abstract
The National Cancer Institute's Clinical Proteomic Tumor Analysis Consortium (CPTAC) investigates tumors from a proteogenomic perspective, creating rich multi-omics datasets connecting genomic aberrations to cancer phenotypes. To facilitate pan-cancer investigations, we have generated harmonized genomic, transcriptomic, proteomic, and clinical data for >1000 tumors in 10 cohorts to create a cohesive and powerful dataset for scientific discovery. We outline efforts by the CPTAC pan-cancer working group in data harmonization, data dissemination, and computational resources for aiding biological discoveries. We also discuss challenges for multi-omics data integration and analysis, specifically the unique challenges of working with both nucleotide sequencing and mass spectrometry proteomics data.
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Affiliation(s)
- Yize Li
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63130, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Yongchao Dou
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Yifat Geffen
- Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA
| | - Anna P Calinawan
- Department of Genetic and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - François Aguet
- Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA
| | - Yo Akiyama
- Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA
| | - Shankara Anand
- Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA
| | - Chet Birger
- Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA
| | - Song Cao
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63130, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63130, USA
| | | | | | - Marcin Cieslik
- Department of Computational Medicine & Bioinformatics, Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Antonio Colaprico
- Department of Public Health Sciences, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Daniel Cui Zhou
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63130, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Corbin Day
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
| | | | - Myvizhi Esai Selvan
- Department of Genetic and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - David Fenyö
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Steven M Foltz
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63130, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63130, USA
| | | | - Tania Gonzalez-Robles
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA; Department of Medicine, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Zeynep H Gümüş
- Department of Genetic and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - David Heiman
- Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA
| | | | - Runyu Hong
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Yingwei Hu
- Department of Pathology, Johns Hopkins University, Baltimore, MD 21231, USA
| | - Eric J Jaehnig
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jiayi Ji
- Tisch Cancer Institute and Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Wen Jiang
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Lizabeth Katsnelson
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | | | - Robert J Klein
- Department of Genetic and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jonathan T Lei
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Wen-Wei Liang
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63130, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Yuxing Liao
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Caleb M Lindgren
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
| | - Weiping Ma
- Department of Genetic and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Lei Ma
- ICF, Rockville, MD 20850, USA
| | - Michael J MacCoss
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Fernanda Martins Rodrigues
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63130, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Wilson McKerrow
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | | | - Robert Oldroyd
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
| | | | - Pietro Pugliese
- Department of Sciences and Technologies, University of Sannio, Benevento 82100, Italy
| | - Boris Reva
- Department of Genetic and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Paul Rudnick
- Spectragen Informatics, Bainbridge Island, WA 98110, USA
| | - Kelly V Ruggles
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY 10016, USA; Department of Medicine, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Dmitry Rykunov
- Department of Genetic and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sara R Savage
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Michael Schnaubelt
- Department of Pathology, Johns Hopkins University, Baltimore, MD 21231, USA
| | - Tobias Schraink
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA; Department of Medicine, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Zhiao Shi
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Xiaoyu Song
- Tisch Cancer Institute and Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Erik Storrs
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63130, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Nadezhda V Terekhanova
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63130, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63130, USA
| | | | | | - Liang-Bo Wang
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63130, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Joshua M Wang
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Ying Wang
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Bo Wen
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yige Wu
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63130, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Matthew A Wyczalkowski
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63130, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Yi Xin
- ICF, Rockville, MD 20850, USA
| | - Lijun Yao
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63130, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Xinpei Yi
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Hui Zhang
- Department of Pathology, Johns Hopkins University, Baltimore, MD 21231, USA
| | - Qing Zhang
- Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA
| | | | - Gad Getz
- Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA; Cancer Center and Department of Pathology, Mass. General Hospital, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Li Ding
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63130, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63130, USA; Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63130, USA; Department of Genetics, Washington University in St. Louis, St. Louis, MO 63130, USA
| | | | - Pei Wang
- Department of Genetic and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ana I Robles
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Rockville, MD 20850, USA.
| | - Bing Zhang
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Samuel H Payne
- Department of Biology, Brigham Young University, Provo, UT 84602, USA.
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Li X, Poire A, Jeong KJ, Zhang D, Chen G, Sun C, Mills GB. Single-cell trajectory analysis reveals a CD9 positive state to contribute to exit from stem cell-like and embryonic diapause states and transit to drug-resistant states. Cell Death Discov 2023; 9:285. [PMID: 37542044 PMCID: PMC10403509 DOI: 10.1038/s41420-023-01586-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 07/12/2023] [Accepted: 07/27/2023] [Indexed: 08/06/2023] Open
Abstract
Bromo- and extra-terminal domain (BET) inhibitors (BETi) have been shown to decrease tumor growth in preclinical models and clinical trials. However, toxicity and rapid emergence of resistance have limited their clinical implementation. To identify state changes underlying acquisition of resistance to the JQ1 BETi, we reanalyzed single-cell RNAseq data from JQ1 sensitive and resistant SUM149 and SUM159 triple-negative breast cancer cell lines. Parental and JQ1-resistant SUM149 and SUM159 exhibited a stem cell-like and embryonic diapause (SCLED) cell state as well as a transitional cell state between the SCLED state that is present in both treatment naïve and JQ1 treated cells, and a number of JQ1 resistant cell states. A transitional cell state transcriptional signature but not a SCLED state transcriptional signature predicted worsened outcomes in basal-like breast cancer patients suggesting that transit from the SCLED state to drug-resistant states contributes to patient outcomes. Entry of SUM149 and SUM159 into the transitional cell state was characterized by elevated expression of the CD9 tetraspanin. Knockdown or inhibition of CD9-sensitized cells to multiple targeted and cytotoxic drugs in vitro. Importantly, CD9 knockdown or blockade sensitized SUM149 to JQ1 in vivo by trapping cells in the SCLED state and limiting transit to resistant cell states. Thus, CD9 appears to be critical for the transition from a SCLED state into treatment-resistant cell states and warrants exploration as a therapeutic target in basal-like breast cancer.
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Affiliation(s)
- Xi Li
- Division of Oncological Sciences Knight Cancer Institute, Oregon Health and Science University, Portland, OR, 97201, USA.
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430030, Wuhan, China.
| | - Alfonso Poire
- Division of Oncological Sciences Knight Cancer Institute, Oregon Health and Science University, Portland, OR, 97201, USA
| | - Kang Jin Jeong
- Division of Oncological Sciences Knight Cancer Institute, Oregon Health and Science University, Portland, OR, 97201, USA
| | - Dong Zhang
- Division of Oncological Sciences Knight Cancer Institute, Oregon Health and Science University, Portland, OR, 97201, USA
| | - Gang Chen
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430030, Wuhan, China
| | - Chaoyang Sun
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430030, Wuhan, China
| | - Gordon B Mills
- Division of Oncological Sciences Knight Cancer Institute, Oregon Health and Science University, Portland, OR, 97201, USA
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17
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Zhu H, Lin Y, Lu D, Wang S, Liu Y, Dong L, Meng Q, Gao J, Wang Y, Song N, Suo Y, Ding L, Wang P, Zhang B, Gao D, Fan J, Gao Q, Zhou H. Proteomics of adjacent-to-tumor samples uncovers clinically relevant biological events in hepatocellular carcinoma. Natl Sci Rev 2023; 10:nwad167. [PMID: 37575948 PMCID: PMC10416816 DOI: 10.1093/nsr/nwad167] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 05/10/2023] [Accepted: 06/01/2023] [Indexed: 08/15/2023] Open
Abstract
Normal adjacent tissues (NATs) of hepatocellular carcinoma (HCC) differ from healthy liver tissues and their heterogeneity may contain biological information associated with disease occurrence and clinical outcome that has yet to be fully evaluated at the proteomic level. This study provides a detailed description of the heterogeneity of NATs and the differences between NATs and healthy livers and revealed that molecular features of tumor subgroups in HCC were partially reflected in their respective NATs. Proteomic data classified HCC NATs into two subtypes (Subtypes 1 and 2), and Subtype 2 was associated with poor prognosis and high-risk recurrence. The pathway and immune features of these two subtypes were characterized. Proteomic differences between the two NAT subtypes and healthy liver tissues were further investigated using data-independent acquisition mass spectrometry, revealing the early molecular alterations associated with the progression from healthy livers to NATs. This study provides a high-quality resource for HCC researchers and clinicians and may significantly expand the knowledge of tumor NATs to eventually benefit clinical practice.
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Affiliation(s)
- Hongwen Zhu
- Department of Analytical Chemistry, State Key Laboratory of Drug Research and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Youpei Lin
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, and Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, Fudan University, Shanghai 200032, China
| | - Dayun Lu
- Department of Analytical Chemistry, State Key Laboratory of Drug Research and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Shisheng Wang
- Institutes for Systems Genetics and NHC Key Lab of Transplant Engineering and Immunology, Sichuan Provincial Engineering Laboratory of Pathology in Clinical Application, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Yuejia Liu
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Liangqing Dong
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, and Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, Fudan University, Shanghai 200032, China
| | - Qian Meng
- Department of Analytical Chemistry, State Key Laboratory of Drug Research and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Jing Gao
- Department of Analytical Chemistry, State Key Laboratory of Drug Research and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Yuqiu Wang
- Department of Analytical Chemistry, State Key Laboratory of Drug Research and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Nixue Song
- Department of Analytical Chemistry, State Key Laboratory of Drug Research and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Yuying Suo
- Department of Analytical Chemistry, State Key Laboratory of Drug Research and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Li Ding
- Department of Medicine, McDonnell Genome Institute, Siteman Cancer Center, Washington University, St. Louis, MI 63108, USA
| | - Pei Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, NewYork, NY 10029, USA
| | - Bing Zhang
- Lester and Sue Smith Breast Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Daming Gao
- University of Chinese Academy of Sciences, Beijing 100049, China
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Jia Fan
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, and Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, Fudan University, Shanghai 200032, China
| | - Qiang Gao
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, and Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, Fudan University, Shanghai 200032, China
| | - Hu Zhou
- Department of Analytical Chemistry, State Key Laboratory of Drug Research and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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18
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Begolli R, Chatziangelou M, Samiotaki M, Goutas A, Barda S, Goutzourelas N, Kevrekidis DP, Malea P, Trachana V, Liu M, Lin X, Kollatos N, Stagos D, Giakountis A. Transcriptome and proteome analysis reveals the anti-cancer properties of Hypnea musciformis marine macroalga extract in liver and intestinal cancer cells. Hum Genomics 2023; 17:71. [PMID: 37525271 PMCID: PMC10388463 DOI: 10.1186/s40246-023-00517-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 07/18/2023] [Indexed: 08/02/2023] Open
Abstract
BACKGROUND Marine seaweeds are considered as a rich source of health-promoting compounds by the food and pharmaceutical industry. Hypnea musciformis is a marine red macroalga (seaweed) that is widely distributed throughout the world, including the Mediterranean Sea. It is known to contain various bioactive compounds, including sulfated polysaccharides, flavonoids, and phlorotannins. Recent studies have investigated the potential anticancer effects of extracts from H. musciformis demonstrating their cytotoxic effects on various cancer cell lines. The anticancer effects of these extracts are thought to be due to the presence of bioactive compounds, particularly sulfated polysaccharides, which have been shown to have anticancer and immunomodulatory effects. However, further studies are needed to fully understand the molecular mechanisms that underlie their anticancer effects and to determine their potential as therapeutic agents for cancer treatment. METHODS H. musciformis was collected from the Aegean Sea (Greece) and used for extract preparation. Transcriptome and proteome analysis was performed in liver and colon cancer human cell lines following treatment with H. musciformis seaweed extracts to characterize its anticancer effect in detail at the molecular level and to link transcriptome and proteome responses to the observed phenotypes in cancer cells. RESULTS We have identified that treatment with the seaweed extract triggers a p53-mediated response at the transcriptional and protein level in liver cancer cells, in contrast to colon cancer cells in which the effects are more associated with metabolic changes. Furthermore, we show that in treated HepG2 liver cancer cells, p53 interacts with the chromatin of several target genes and facilitates their upregulation possibly through the recruitment of the p300 co-activator. CONCLUSIONS Overall, the available evidence suggests that extracts from H. musciformis have the potential to serve as a source of anticancer agents in liver cancer cells mainly through activation of a p53-mediated anti-tumor response that is linked to inhibition of cellular proliferation and induction of cell death.
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Affiliation(s)
- Rodiola Begolli
- Department of Biochemistry and Biotechnology, School of Health Sciences, University of Thessaly, 41500, Biopolis, Larissa, Greece
| | - Myrto Chatziangelou
- Department of Biochemistry and Biotechnology, School of Health Sciences, University of Thessaly, 41500, Biopolis, Larissa, Greece
| | | | - Andreas Goutas
- Department of Biochemistry and Biotechnology, School of Health Sciences, University of Thessaly, 41500, Biopolis, Larissa, Greece
- Department of Biology, Faculty of Medicine, University of Thessaly, 41500, Biopolis, Larissa, Greece
| | - Sofia Barda
- Department of Biochemistry and Biotechnology, School of Health Sciences, University of Thessaly, 41500, Biopolis, Larissa, Greece
| | - Nikolaos Goutzourelas
- Department of Biochemistry and Biotechnology, School of Health Sciences, University of Thessaly, 41500, Biopolis, Larissa, Greece
| | - Dimitrios Phaedon Kevrekidis
- Laboratory of Forensic Medicine and Toxicology, Department of Medicine, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - Paraskevi Malea
- Department of Botany, School of Biology, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - Varvara Trachana
- Department of Biology, Faculty of Medicine, University of Thessaly, 41500, Biopolis, Larissa, Greece
| | - Ming Liu
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
- Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| | - Xiukun Lin
- College of Marine Sciences, Beibu Gulf University, 12 Binhai Rd, Qinzhou, 535011, Guangxi, China
| | - Nikolaos Kollatos
- Department of Biochemistry and Biotechnology, School of Health Sciences, University of Thessaly, 41500, Biopolis, Larissa, Greece
| | - Dimitrios Stagos
- Department of Biochemistry and Biotechnology, School of Health Sciences, University of Thessaly, 41500, Biopolis, Larissa, Greece.
| | - Antonis Giakountis
- Department of Biochemistry and Biotechnology, School of Health Sciences, University of Thessaly, 41500, Biopolis, Larissa, Greece.
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19
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Neagu AN, Whitham D, Bruno P, Morrissiey H, Darie CA, Darie CC. Omics-Based Investigations of Breast Cancer. Molecules 2023; 28:4768. [PMID: 37375323 DOI: 10.3390/molecules28124768] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 06/08/2023] [Accepted: 06/12/2023] [Indexed: 06/29/2023] Open
Abstract
Breast cancer (BC) is characterized by an extensive genotypic and phenotypic heterogeneity. In-depth investigations into the molecular bases of BC phenotypes, carcinogenesis, progression, and metastasis are necessary for accurate diagnoses, prognoses, and therapy assessments in predictive, precision, and personalized oncology. This review discusses both classic as well as several novel omics fields that are involved or should be used in modern BC investigations, which may be integrated as a holistic term, onco-breastomics. Rapid and recent advances in molecular profiling strategies and analytical techniques based on high-throughput sequencing and mass spectrometry (MS) development have generated large-scale multi-omics datasets, mainly emerging from the three "big omics", based on the central dogma of molecular biology: genomics, transcriptomics, and proteomics. Metabolomics-based approaches also reflect the dynamic response of BC cells to genetic modifications. Interactomics promotes a holistic view in BC research by constructing and characterizing protein-protein interaction (PPI) networks that provide a novel hypothesis for the pathophysiological processes involved in BC progression and subtyping. The emergence of new omics- and epiomics-based multidimensional approaches provide opportunities to gain insights into BC heterogeneity and its underlying mechanisms. The three main epiomics fields (epigenomics, epitranscriptomics, and epiproteomics) are focused on the epigenetic DNA changes, RNAs modifications, and posttranslational modifications (PTMs) affecting protein functions for an in-depth understanding of cancer cell proliferation, migration, and invasion. Novel omics fields, such as epichaperomics or epimetabolomics, could investigate the modifications in the interactome induced by stressors and provide PPI changes, as well as in metabolites, as drivers of BC-causing phenotypes. Over the last years, several proteomics-derived omics, such as matrisomics, exosomics, secretomics, kinomics, phosphoproteomics, or immunomics, provided valuable data for a deep understanding of dysregulated pathways in BC cells and their tumor microenvironment (TME) or tumor immune microenvironment (TIMW). Most of these omics datasets are still assessed individually using distinct approches and do not generate the desired and expected global-integrative knowledge with applications in clinical diagnostics. However, several hyphenated omics approaches, such as proteo-genomics, proteo-transcriptomics, and phosphoproteomics-exosomics are useful for the identification of putative BC biomarkers and therapeutic targets. To develop non-invasive diagnostic tests and to discover new biomarkers for BC, classic and novel omics-based strategies allow for significant advances in blood/plasma-based omics. Salivaomics, urinomics, and milkomics appear as integrative omics that may develop a high potential for early and non-invasive diagnoses in BC. Thus, the analysis of the tumor circulome is considered a novel frontier in liquid biopsy. Omics-based investigations have applications in BC modeling, as well as accurate BC classification and subtype characterization. The future in omics-based investigations of BC may be also focused on multi-omics single-cell analyses.
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Affiliation(s)
- Anca-Narcisa Neagu
- Laboratory of Animal Histology, Faculty of Biology, "Alexandru Ioan Cuza" University of Iasi, Carol I Bvd, No. 20A, 700505 Iasi, Romania
| | - Danielle Whitham
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699, USA
| | - Pathea Bruno
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699, USA
| | - Hailey Morrissiey
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699, USA
| | - Celeste A Darie
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699, USA
| | - Costel C Darie
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699, USA
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20
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Hung YW, Ouyang C, Ping X, Qi Y, Wang YC, Kung HJ, Ann DK. Extracellular arginine availability modulates eIF2α O-GlcNAcylation and heme oxygenase 1 translation for cellular homeostasis. J Biomed Sci 2023; 30:32. [PMID: 37217939 PMCID: PMC10201738 DOI: 10.1186/s12929-023-00924-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 05/04/2023] [Indexed: 05/24/2023] Open
Abstract
BACKGROUND Nutrient limitations often lead to metabolic stress during cancer initiation and progression. To combat this stress, the enzyme heme oxygenase 1 (HMOX1, commonly known as HO-1) is thought to play a key role as an antioxidant. However, there is a discrepancy between the level of HO-1 mRNA and its protein, particularly in cells under stress. O-linked β-N-acetylglucosamine (O-GlcNAc) modification of proteins (O-GlcNAcylation) is a recently discovered cellular signaling mechanism that rivals phosphorylation in many proteins, including eukaryote translation initiation factors (eIFs). The mechanism by which eIF2α O-GlcNAcylation regulates translation of HO-1 during extracellular arginine shortage (ArgS) remains unclear. METHODS We used mass spectrometry to study the relationship between O-GlcNAcylation and Arg availability in breast cancer BT-549 cells. We validated eIF2α O-GlcNAcylation through site-specific mutagenesis and azido sugar N-azidoacetylglucosamine-tetraacylated labeling. We then evaluated the effect of eIF2α O-GlcNAcylation on cell recovery, migration, accumulation of reactive oxygen species (ROS), and metabolic labeling during protein synthesis under different Arg conditions. RESULTS Our research identified eIF2α, eIF2β, and eIF2γ, as key O-GlcNAcylation targets in the absence of Arg. We found that O-GlcNAcylation of eIF2α plays a crucial role in regulating antioxidant defense by suppressing the translation of the enzyme HO-1 during Arg limitation. Our study showed that O-GlcNAcylation of eIF2α at specific sites suppresses HO-1 translation despite high levels of HMOX1 transcription. We also found that eliminating eIF2α O-GlcNAcylation through site-specific mutagenesis improves cell recovery, migration, and reduces ROS accumulation by restoring HO-1 translation. However, the level of the metabolic stress effector ATF4 is not affected by eIF2α O-GlcNAcylation under these conditions. CONCLUSIONS Overall, this study provides new insights into how ArgS fine-tunes the control of translation initiation and antioxidant defense through eIF2α O-GlcNAcylation, which has potential biological and clinical implications.
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Affiliation(s)
- Yu-Wen Hung
- Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes & Metabolism Research Institute, Beckman Research Institute of City of Hope, City of Hope Comprehensive Cancer Center, Duarte, CA, 91010-3000, USA
- Irell & Manella Graduate School of Biological Sciences, Beckman Research Institute of City of Hope, Duarte, CA, 91010, USA
| | - Ching Ouyang
- Department of Computational and Quantitative Medicine, Beckman Research Institute of City of Hope, Duarte, CA, 91010, USA
| | - Xiaoli Ping
- Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes & Metabolism Research Institute, Beckman Research Institute of City of Hope, City of Hope Comprehensive Cancer Center, Duarte, CA, 91010-3000, USA
| | - Yue Qi
- Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes & Metabolism Research Institute, Beckman Research Institute of City of Hope, City of Hope Comprehensive Cancer Center, Duarte, CA, 91010-3000, USA
| | - Yi-Chang Wang
- Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes & Metabolism Research Institute, Beckman Research Institute of City of Hope, City of Hope Comprehensive Cancer Center, Duarte, CA, 91010-3000, USA
| | - Hsing-Jien Kung
- Cancer Center, School of Medicine, University of California, Davis, CA, 95817, USA
| | - David K Ann
- Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes & Metabolism Research Institute, Beckman Research Institute of City of Hope, City of Hope Comprehensive Cancer Center, Duarte, CA, 91010-3000, USA.
- Irell & Manella Graduate School of Biological Sciences, Beckman Research Institute of City of Hope, Duarte, CA, 91010, USA.
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21
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Bartish M, Abraham MJ, Gonçalves C, Larsson O, Rolny C, Del Rincón SV. The role of eIF4F-driven mRNA translation in regulating the tumour microenvironment. Nat Rev Cancer 2023; 23:408-425. [PMID: 37142795 DOI: 10.1038/s41568-023-00567-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/27/2023] [Indexed: 05/06/2023]
Abstract
Cells can rapidly adjust their proteomes in dynamic environments by regulating mRNA translation. There is mounting evidence that dysregulation of mRNA translation supports the survival and adaptation of cancer cells, which has stimulated clinical interest in targeting elements of the translation machinery and, in particular, components of the eukaryotic initiation factor 4F (eIF4F) complex such as eIF4E. However, the effect of targeting mRNA translation on infiltrating immune cells and stromal cells in the tumour microenvironment (TME) has, until recently, remained unexplored. In this Perspective article, we discuss how eIF4F-sensitive mRNA translation controls the phenotypes of key non-transformed cells in the TME, with an emphasis on the underlying therapeutic implications of targeting eIF4F in cancer. As eIF4F-targeting agents are in clinical trials, we propose that a broader understanding of their effect on gene expression in the TME will reveal unappreciated therapeutic vulnerabilities that could be used to improve the efficacy of existing cancer therapies.
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Affiliation(s)
- Margarita Bartish
- Department of Oncology, Faculty of Medicine, McGill University, Montreal, QC, Canada
- Segal Cancer Center, Lady Davis Institute and Jewish General Hospital, Montreal, QC, Canada
- Science for Life Laboratory, Stockholm, Sweden
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Madelyn J Abraham
- Department of Oncology, Faculty of Medicine, McGill University, Montreal, QC, Canada
- Segal Cancer Center, Lady Davis Institute and Jewish General Hospital, Montreal, QC, Canada
| | - Christophe Gonçalves
- Department of Oncology, Faculty of Medicine, McGill University, Montreal, QC, Canada
- Segal Cancer Center, Lady Davis Institute and Jewish General Hospital, Montreal, QC, Canada
| | - Ola Larsson
- Science for Life Laboratory, Stockholm, Sweden
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Charlotte Rolny
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden.
| | - Sonia V Del Rincón
- Department of Oncology, Faculty of Medicine, McGill University, Montreal, QC, Canada.
- Segal Cancer Center, Lady Davis Institute and Jewish General Hospital, Montreal, QC, Canada.
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22
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Ding Z, Xiong L, Wang X, Guo S, Cao M, Kang Y, La Y, Bao P, Pei J, Guo X. Comparative Analysis of Epididymis Cauda of Yak before and after Sexual Maturity. Animals (Basel) 2023; 13:ani13081355. [PMID: 37106918 PMCID: PMC10135020 DOI: 10.3390/ani13081355] [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: 03/09/2023] [Revised: 04/08/2023] [Accepted: 04/13/2023] [Indexed: 04/29/2023] Open
Abstract
Epididymis development is the basis of male reproduction and is a crucial site where sperm maturation occurs. In order to further understand the epididymal development of yak and how to regulate sperm maturation, we conducted a multi-omics analysis. We detected 2274 differential genes, 222 differential proteins and 117 co-expression genes in the cauda epididymis of yak before and after sexual maturity by RNA-seq and proteomics techniques, which included TGFBI, COL1A1, COL1A2, COL3A1, COL12A1, SULT2B1, KRT19, and NPC2. These high abundance genes are mainly related to cell growth, differentiation, adhesion and sperm maturation, and are mainly enriched via extracellular matrix receptor interaction, protein differentiation and absorption, and lysosome and estrogen signaling pathways. The abnormal expression of these genes may lead to the retardation of epididymal cauda development and abnormal sperm function in yak. In conclusion, through single and combined analysis, we provided a theoretical basis for the development of the yak epididymal cauda, sperm maturation, and screening of key genes involved in the regulation of male yak reproduction.
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Affiliation(s)
- Ziqiang Ding
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Lin Xiong
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Xingdong Wang
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Shaoke Guo
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Mengli Cao
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Yandong Kang
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Yongfu La
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Pengjia Bao
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Jie Pei
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Xian Guo
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
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23
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Higgins L, Gerdes H, Cutillas PR. Principles of phosphoproteomics and applications in cancer research. Biochem J 2023; 480:403-420. [PMID: 36961757 PMCID: PMC10212522 DOI: 10.1042/bcj20220220] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 02/24/2023] [Accepted: 02/28/2023] [Indexed: 03/25/2023]
Abstract
Phosphorylation constitutes the most common and best-studied regulatory post-translational modification in biological systems and archetypal signalling pathways driven by protein and lipid kinases are disrupted in essentially all cancer types. Thus, the study of the phosphoproteome stands to provide unique biological information on signalling pathway activity and on kinase network circuitry that is not captured by genetic or transcriptomic technologies. Here, we discuss the methods and tools used in phosphoproteomics and highlight how this technique has been used, and can be used in the future, for cancer research. Challenges still exist in mass spectrometry phosphoproteomics and in the software required to provide biological information from these datasets. Nevertheless, improvements in mass spectrometers with enhanced scan rates, separation capabilities and sensitivity, in biochemical methods for sample preparation and in computational pipelines are enabling an increasingly deep analysis of the phosphoproteome, where previous bottlenecks in data acquisition, processing and interpretation are being relieved. These powerful hardware and algorithmic innovations are not only providing exciting new mechanistic insights into tumour biology, from where new drug targets may be derived, but are also leading to the discovery of phosphoproteins as mediators of drug sensitivity and resistance and as classifiers of disease subtypes. These studies are, therefore, uncovering phosphoproteins as a new generation of disruptive biomarkers to improve personalised anti-cancer therapies.
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Affiliation(s)
- Luke Higgins
- Cell Signaling and Proteomics Group, Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, U.K
| | - Henry Gerdes
- Cell Signaling and Proteomics Group, Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, U.K
| | - Pedro R. Cutillas
- Cell Signaling and Proteomics Group, Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, U.K
- Alan Turing Institute, The British Library, London, U.K
- Digital Environment Research Institute, Queen Mary University of London, London, U.K
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24
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Pateras IS, Williams C, Gianniou DD, Margetis AT, Avgeris M, Rousakis P, Legaki AI, Mirtschink P, Zhang W, Panoutsopoulou K, Delis AD, Pagakis SN, Tang W, Ambs S, Warpman Berglund U, Helleday T, Varvarigou A, Chatzigeorgiou A, Nordström A, Tsitsilonis OE, Trougakos IP, Gilthorpe JD, Frisan T. Short term starvation potentiates the efficacy of chemotherapy in triple negative breast cancer via metabolic reprogramming. J Transl Med 2023; 21:169. [PMID: 36869333 PMCID: PMC9983166 DOI: 10.1186/s12967-023-03935-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 01/27/2023] [Indexed: 03/05/2023] Open
Abstract
BACKGROUND Chemotherapy (CT) is central to the treatment of triple negative breast cancer (TNBC), but drug toxicity and resistance place strong restrictions on treatment regimes. Fasting sensitizes cancer cells to a range of chemotherapeutic agents and also ameliorates CT-associated adverse effects. However, the molecular mechanism(s) by which fasting, or short-term starvation (STS), improves the efficacy of CT is poorly characterized. METHODS The differential responses of breast cancer or near normal cell lines to combined STS and CT were assessed by cellular viability and integrity assays (Hoechst and PI staining, MTT or H2DCFDA staining, immunofluorescence), metabolic profiling (Seahorse analysis, metabolomics), gene expression (quantitative real-time PCR) and iRNA-mediated silencing. The clinical significance of the in vitro data was evaluated by bioinformatical integration of transcriptomic data from patient data bases: The Cancer Genome Atlas (TCGA), European Genome-phenome Archive (EGA), Gene Expression Omnibus (GEO) and a TNBC cohort. We further examined the translatability of our findings in vivo by establishing a murine syngeneic orthotopic mammary tumor-bearing model. RESULTS We provide mechanistic insights into how preconditioning with STS enhances the susceptibility of breast cancer cells to CT. We showed that combined STS and CT enhanced cell death and increased reactive oxygen species (ROS) levels, in association with higher levels of DNA damage and decreased mRNA levels for the NRF2 targets genes NQO1 and TXNRD1 in TNBC cells compared to near normal cells. ROS enhancement was associated with compromised mitochondrial respiration and changes in the metabolic profile, which have a significant clinical prognostic and predictive value. Furthermore, we validate the safety and efficacy of combined periodic hypocaloric diet and CT in a TNBC mouse model. CONCLUSIONS Our in vitro, in vivo and clinical findings provide a robust rationale for clinical trials on the therapeutic benefit of short-term caloric restriction as an adjuvant to CT in triple breast cancer treatment.
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Affiliation(s)
- Ioannis S Pateras
- 2nd Department of Pathology, "Attikon" University Hospital, Medical School, National and Kapodistrian University of Athens, 124 62, Athens, Greece.
| | - Chloe Williams
- Department of Integrative Medical Biology, Umeå University, 901 87, Umeå, Sweden
| | - Despoina D Gianniou
- Department of Cell Biology and Biophysics, Faculty of Biology, National and Kapodistrian University of Athens, 157 84, Athens, Greece
| | - Aggelos T Margetis
- 2nd Department of Internal Medicine, Athens Naval and Veterans Hospital, 115 21, Athens, Greece
| | - Margaritis Avgeris
- Laboratory of Clinical Biochemistry-Molecular Diagnostics, Second Department of Pediatrics, School of Medicine, National and Kapodistrian University of Athens, "P. & A. Kyriakou" Children's Hospital, 115 27, Athens, Greece.,Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, 157 71, Athens, Greece
| | - Pantelis Rousakis
- Department of Biology, School of Science, National and Kapodistrian University of Athens, 157 84, Athens, Greece
| | - Aigli-Ioanna Legaki
- Department of Physiology, Medical School, National and Kapodistrian University of Athens, 115 27, Athens, Greece
| | - Peter Mirtschink
- Institute for Clinical Chemistry and Laboratory Medicine, University Hospital and Faculty of Medicine, Technische Universität Dresden, 013 07, Dresden, Germany
| | - Wei Zhang
- Swedish Metabolomics Centre, Department of Plant Physiology, Umeå University, 901 87, Umeå, Sweden
| | - Konstantina Panoutsopoulou
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, 157 71, Athens, Greece
| | - Anastasios D Delis
- Centre for Basic Research, Bioimaging Unit, Biomedical Research Foundation, Academy of Athens, 115 27, Athens, Greece
| | - Stamatis N Pagakis
- Centre for Basic Research, Bioimaging Unit, Biomedical Research Foundation, Academy of Athens, 115 27, Athens, Greece
| | - Wei Tang
- Molecular Epidemiology Section, Laboratory of Human Carcinogenesis, Center for Cancer Research (CCR), NCI, NIH, Bethesda, MD, 20892-4258, USA.,Data Science & Artificial Intelligence, R&D, AstraZeneca, Gaithersburg, MD, USA
| | - Stefan Ambs
- Molecular Epidemiology Section, Laboratory of Human Carcinogenesis, Center for Cancer Research (CCR), NCI, NIH, Bethesda, MD, 20892-4258, USA
| | - Ulrika Warpman Berglund
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, 171 76, Stockholm, Sweden
| | - Thomas Helleday
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, 171 76, Stockholm, Sweden.,Weston Park Cancer Centre, Department of Oncology and Metabolism, University of Sheffield, Sheffield, S10 2RX, UK
| | - Anastasia Varvarigou
- Department of Paediatrics, University of Patras Medical School, General University Hospital, 265 04, Patras, Greece
| | - Antonios Chatzigeorgiou
- Department of Physiology, Medical School, National and Kapodistrian University of Athens, 115 27, Athens, Greece.,Institute for Clinical Chemistry and Laboratory Medicine, University Hospital and Faculty of Medicine, Technische Universität Dresden, 013 07, Dresden, Germany
| | - Anders Nordström
- Swedish Metabolomics Centre, Department of Plant Physiology, Umeå University, 901 87, Umeå, Sweden
| | - Ourania E Tsitsilonis
- Department of Biology, School of Science, National and Kapodistrian University of Athens, 157 84, Athens, Greece
| | - Ioannis P Trougakos
- Department of Cell Biology and Biophysics, Faculty of Biology, National and Kapodistrian University of Athens, 157 84, Athens, Greece
| | - Jonathan D Gilthorpe
- Department of Integrative Medical Biology, Umeå University, 901 87, Umeå, Sweden
| | - Teresa Frisan
- Department of Molecular Biology and Umeå Centre for Microbial Research (UCMR), Umeå University, 901 87, Umeå, Sweden.
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25
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Gibson SV, Tomas Bort E, Rodríguez-Fernández L, Allen MD, Gomm JJ, Goulding I, Auf dem Keller U, Agnoletto A, Brisken C, Peck B, Cameron AJ, Marshall JF, Jones JL, Carter EP, Grose RP. TGFβ-mediated MMP13 secretion drives myoepithelial cell dependent breast cancer progression. NPJ Breast Cancer 2023; 9:9. [PMID: 36864079 PMCID: PMC9981685 DOI: 10.1038/s41523-023-00513-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 02/15/2023] [Indexed: 03/04/2023] Open
Abstract
Ductal carcinoma in situ (DCIS) is a non-obligate precursor of invasive breast cancer. Virtually all women with DCIS are treated, despite evidence suggesting up to half would remain with stable, non-threatening, disease. Overtreatment thus presents a pressing issue in DCIS management. To understand the role of the normally tumour suppressive myoepithelial cell in disease progression we present a 3D in vitro model incorporating both luminal and myoepithelial cells in physiomimetic conditions. We demonstrate that DCIS-associated myoepithelial cells promote striking myoepithelial-led invasion of luminal cells, mediated by the collagenase MMP13 through a non-canonical TGFβ - EP300 pathway. In vivo, MMP13 expression is associated with stromal invasion in a murine model of DCIS progression and is elevated in myoepithelial cells of clinical high-grade DCIS cases. Our data identify a key role for myoepithelial-derived MMP13 in facilitating DCIS progression and point the way towards a robust marker for risk stratification in DCIS patients.
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Affiliation(s)
- Shayin V Gibson
- Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Elena Tomas Bort
- Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Lucía Rodríguez-Fernández
- Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Michael D Allen
- Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Jennifer J Gomm
- Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Iain Goulding
- Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Ulrich Auf dem Keller
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Andrea Agnoletto
- ISREC - Swiss Institute for Experimental Cancer Research, School of Life Sciences, Ecole polytechnique fédérale de Lausanne (EPFL), SV2.832 Station 19, 1015, Lausanne, Switzerland
| | - Cathrin Brisken
- ISREC - Swiss Institute for Experimental Cancer Research, School of Life Sciences, Ecole polytechnique fédérale de Lausanne (EPFL), SV2.832 Station 19, 1015, Lausanne, Switzerland
| | - Barrie Peck
- Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Angus J Cameron
- Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ, UK
| | - John F Marshall
- Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ, UK
| | - J Louise Jones
- Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Edward P Carter
- Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ, UK.
| | - Richard P Grose
- Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ, UK.
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26
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Cellular Transcriptomics of Carboplatin Resistance in a Metastatic Canine Osteosarcoma Cell Line. Genes (Basel) 2023; 14:genes14030558. [PMID: 36980828 PMCID: PMC10048144 DOI: 10.3390/genes14030558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 02/18/2023] [Accepted: 02/20/2023] [Indexed: 02/25/2023] Open
Abstract
Osteosarcoma prognosis has remained unchanged for the past three decades. In both humans and canines, treatment is limited to excision, radiation, and chemotherapy. Chemoresistance is the primary cause of treatment failure, and the trajectory of tumor evolution while under selective pressure from treatment is thought to be the major contributing factor in both species. We sought to understand the nature of platinum-based chemotherapy resistance by investigating cells that were subjected to repeated treatment and recovery cycles with increased carboplatin concentrations. Three HMPOS-derived cell lines, two resistant and one naïve, underwent single-cell RNA sequencing to examine transcriptomic perturbation and identify pathways leading to resistance and phenotypic changes. We identified the mechanisms of acquired chemoresistance and inferred the induced cellular trajectory that evolved with repeated exposure. The gene expression patterns indicated that acquired chemoresistance was strongly associated with a process similar to epithelial–mesenchymal transition (EMT), a phenomenon associated with the acquisition of migratory and invasive properties associated with metastatic disease. We conclude that the observed trajectory of tumor adaptability is directly correlated with chemoresistance and the phase of the EMT-like phenotype is directly affected by the level of chemoresistance. We infer that the EMT-like phenotype is a critical component of tumor evolution under treatment pressure and is vital to understanding the mechanisms of chemoresistance and to improving osteosarcoma prognosis.
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27
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Ke S, Dang F, Wang L, Chen JY, Naik MT, Thavamani A, Liu Y, Li W, Kim N, Naik NM, Sui H, Tang W, Qiu C, Koikawa K, Batalini F, Wang X, Clohessy JG, Heng YJ, Lahav G, Gray NS, Zho XZ, Wei W, Wulf GM, Lu KP. Reciprocal inhibition of PIN1 and APC/C CDH1 controls timely G1/S transition and creates therapeutic vulnerability. RESEARCH SQUARE 2023:rs.3.rs-2447544. [PMID: 36711754 PMCID: PMC9882653 DOI: 10.21203/rs.3.rs-2447544/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Cyclin-dependent kinases (CDKs) mediated phosphorylation inactivates the anaphase-promoting complex (APC/CCDH1), an E3 ubiquitin ligase that contains the co-activator CDH1, to promote G1/S transition. PIN1 is a phosphorylation-directed proline isomerase and a master cancer signaling regulator. However, little are known about APC/CCDH1 regulation after phosphorylation and about PIN1 ubiquitin ligases. Here we uncover a domain-oriented reciprocal inhibition that controls the timely G1/S transition: The non-phosphorylated APC/CCDH1 E3 ligase targets PIN1 for degradation in G1 phase, restraining G1/S transition; APC/CCDH1 itself, after phosphorylation by CDKs, is inactivated by PIN1-catalyzed isomerization, promoting G1/S transition. In cancer, PIN1 overexpression and APC/CCDH1 inactivation reinforce each other to promote uncontrolled proliferation and tumorigenesis. Importantly, combined PIN1- and CDK4/6-inhibition reactivates APC/CCDH1 resulting in PIN1 degradation and an insurmountable G1 arrest that translates into synergistic anti-tumor activity against triple-negative breast cancer in vivo. Reciprocal inhibition of PIN1 and APC/CCDH1 is a novel mechanism to control timely G1/S transition that can be harnessed for synergistic anti-cancer therapy.
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Affiliation(s)
- Shizhong Ke
- Division of Hematology/Oncology, Department of Medicine and Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
- These authors contributed equally to this work
| | - Fabin Dang
- Department of Pathology, Beth Israel Deaconess Medical Center and Cancer Research Institute, Harvard Medical School, Boston, MA 02215, USA
- These authors contributed equally to this work
| | - Lin Wang
- Division of Hematology/Oncology, Department of Medicine and Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
- These authors contributed equally to this work
| | - Jia-Yun Chen
- Department of Systems Biology, Harvard Medical School, Boston, MA 02215, USA
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA 02215, USA
- These authors contributed equally to this work
| | - Mandar T Naik
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI 02912, USA
| | - Abhishek Thavamani
- Division of Hematology/Oncology, Department of Medicine and Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Yansheng Liu
- Yale Cancer Biology Institute, West Haven, CT 06516, USA
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06510
| | - Wenxue Li
- Yale Cancer Biology Institute, West Haven, CT 06516, USA
| | - Nami Kim
- Division of Hematology/Oncology, Department of Medicine and Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Nandita M Naik
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI 02912, USA
| | - Huaxiu Sui
- Key Laboratory of Functional and Clinical Translational Medicine, Fujian Province University, Xiamen Medical College, Xiamen 361023, China
| | - Wei Tang
- Data Science & Artificial Intelligence, R&D, AstraZeneca, Gaithersburg, USA
| | - Chenxi Qiu
- Division of Hematology/Oncology, Department of Medicine and Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Kazuhiro Koikawa
- Division of Hematology/Oncology, Department of Medicine and Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Felipe Batalini
- Division of Hematology/Oncology, Department of Medicine and Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
- Department of Medicine, Division of Medical Oncology, Mayo Clinic, Arizona, USA
| | - Xiaodong Wang
- Molecular and Integrative Physiological Sciences, Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA 02215, USA
| | - John G Clohessy
- Preclinical Murine Pharmacogenetics Facility, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Yujing Jan Heng
- Department of Pathology, Beth Israel Deaconess Medical Center and Cancer Research Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Galit Lahav
- Department of Systems Biology, Harvard Medical School, Boston, MA 02215, USA
| | - Nathanael S Gray
- Department of Chemical and Systems Biology, Chem-H and Stanford Cancer Institute, Stanford University, Stanford, CA 94305, USA
| | - Xiao Zhen Zho
- Division of Hematology/Oncology, Department of Medicine and Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
- Departments of Biochemistry & Oncology, Schulich School of Medicine and Dentistry, and Robarts Research Institute, Western University, London, ON N6A 3K7, Canada
| | - Wenyi Wei
- Department of Pathology, Beth Israel Deaconess Medical Center and Cancer Research Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Gerburg M Wulf
- Division of Hematology/Oncology, Department of Medicine and Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Kun Ping Lu
- Division of Hematology/Oncology, Department of Medicine and Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
- Departments of Biochemistry & Oncology, Schulich School of Medicine and Dentistry, and Robarts Research Institute, Western University, London, ON N6A 3K7, Canada
- Lead Contact
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28
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Pérez-Benavente B, Fathinajafabadi A, de la Fuente L, Gandía C, Martínez-Férriz A, Pardo-Sánchez JM, Milián L, Conesa A, Romero OA, Carretero J, Matthiesen R, Jariel-Encontre I, Piechaczyk M, Farràs R. New roles for AP-1/JUNB in cell cycle control and tumorigenic cell invasion via regulation of cyclin E1 and TGF-β2. Genome Biol 2022; 23:252. [PMID: 36494864 PMCID: PMC9733061 DOI: 10.1186/s13059-022-02800-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 10/20/2022] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND JUNB transcription factor contributes to the formation of the ubiquitous transcriptional complex AP-1 involved in the control of many physiological and disease-associated functions. The roles of JUNB in the control of cell division and tumorigenic processes are acknowledged but still unclear. RESULTS Here, we report the results of combined transcriptomic, genomic, and functional studies showing that JUNB promotes cell cycle progression via induction of cyclin E1 and repression of transforming growth factor (TGF)-β2 genes. We also show that high levels of JUNB switch the response of TGF-β2 stimulation from an antiproliferative to a pro-invasive one, induce endogenous TGF-β2 production by promoting TGF-β2 mRNA translation, and enhance tumor growth and metastasis in mice. Moreover, tumor genomic data indicate that JUNB amplification associates with poor prognosis in breast and ovarian cancer patients. CONCLUSIONS Our results reveal novel functions for JUNB in cell proliferation and tumor aggressiveness through regulation of cyclin E1 and TGF-β2 expression, which might be exploited for cancer prognosis and therapy.
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Affiliation(s)
| | | | - Lorena de la Fuente
- grid.418274.c0000 0004 0399 600XCentro de Investigación Príncipe Felipe, Valencia, Spain ,Present Address: PerkinElmer Informatics, Tres Cantos, Madrid, Spain
| | - Carolina Gandía
- grid.418274.c0000 0004 0399 600XCentro de Investigación Príncipe Felipe, Valencia, Spain
| | | | | | - Lara Milián
- grid.5338.d0000 0001 2173 938XDepartment of Pathology, Faculty of Medicine and Dentistry, Universitat de València, Valencia, Spain ,grid.429003.c0000 0004 7413 8491INCLIVA Biomedical Research Institute, 46010 Valencia, Spain
| | - Ana Conesa
- grid.507638.fSpanish National Research Council, Institute for Integrative Systems Biology, Paterna, Valencia, Spain ,grid.15276.370000 0004 1936 8091Microbiology and Cell Science, University of Florida, Gainesville, FL USA
| | - Octavio A. Romero
- grid.429289.cCancer Genetics Group, Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Spain
| | - Julián Carretero
- grid.5338.d0000 0001 2173 938XDepartament de Fisiologia, Facultat de Farmacia, Universitat de València, Burjassot, Valencia, Spain
| | - Rune Matthiesen
- grid.10772.330000000121511713Computational and Experimental Biology Group, NOVA Medical School-Research, Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, Lisbon, Portugal
| | - Isabelle Jariel-Encontre
- grid.121334.60000 0001 2097 0141Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, Montpellier, France ,grid.488845.d0000 0004 0624 6108Present address: IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, Montpellier, France
| | - Marc Piechaczyk
- grid.121334.60000 0001 2097 0141Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, Montpellier, France
| | - Rosa Farràs
- grid.418274.c0000 0004 0399 600XCentro de Investigación Príncipe Felipe, Valencia, Spain
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Monteiro FL, Stepanauskaite L, Williams C, Helguero LA. SETD7 Expression Is Associated with Breast Cancer Survival Outcomes for Specific Molecular Subtypes: A Systematic Analysis of Publicly Available Datasets. Cancers (Basel) 2022; 14:cancers14246029. [PMID: 36551516 PMCID: PMC9775934 DOI: 10.3390/cancers14246029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 12/02/2022] [Indexed: 12/13/2022] Open
Abstract
SETD7 is a lysine N-methyltransferase that targets many proteins important in breast cancer (BC). However, its role and clinical significance remain unclear. Here, we used online tools and multiple public datasets to explore the predictive potential of SETD7 expression (high or low quartile) considering BC subtype, grade, stage, and therapy. We also investigated overrepresented biological processes associated with its expression using TCGA-BRCA data. SETD7 expression was highest in the Her2 (ERBB2)-enriched molecular subtype and lowest in the basal-like subtype. For the basal-like subtype specifically, higher SETD7 was consistently correlated with worse recurrence-free survival (p < 0.009). High SETD7-expressing tumours further exhibited a higher rate of ERBB2 mutation (20% vs. 5%) along with a poorer response to anti-Her2 therapy. Overall, high SETD7-expressing tumours showed higher stromal and lower immune scores. This was specifically related to higher counts of cancer-associated fibroblasts and endothelial cells, but lower B and T cell signatures, especially in the luminal A subtype. Genes significantly associated with SETD7 expression were accordingly overrepresented in immune response processes, with distinct subtype characteristics. We conclude that the prognostic value of SETD7 depends on the BC subtype and that SETD7 may be further explored as a potential treatment-predictive marker for immune checkpoint inhibitors.
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Affiliation(s)
- Fátima Liliana Monteiro
- Department of Medical Sciences, Institute of Biomedicine—iBiMED, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Lina Stepanauskaite
- SciLifeLab, Department of Protein Science, KTH Royal Institute of Technology, 114 28 Stockholm, Sweden
- Department of Biosciences and Nutrition, Karolinska Institute, 141 83 Stockholm, Sweden
| | - Cecilia Williams
- SciLifeLab, Department of Protein Science, KTH Royal Institute of Technology, 114 28 Stockholm, Sweden
- Department of Biosciences and Nutrition, Karolinska Institute, 141 83 Stockholm, Sweden
| | - Luisa A. Helguero
- SciLifeLab, Department of Protein Science, KTH Royal Institute of Technology, 114 28 Stockholm, Sweden
- Correspondence:
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Shi J, Zhu T, Lin H, Liu Z, Zhou M, Yu Z, Zhou X, Song X, Wang Y, Jia R, Fan X, Zhou Y. Proteotranscriptomics of ocular adnexal B-cell lymphoma reveals an oncogenic role of alternative splicing and identifies a diagnostic marker. J Exp Clin Cancer Res 2022; 41:234. [PMID: 35906682 PMCID: PMC9338531 DOI: 10.1186/s13046-022-02445-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 07/20/2022] [Indexed: 11/10/2022] Open
Abstract
Background Ocular adnexal B-cell lymphoma (OABL) is a rare subtype of non-Hodgkin lymphoma. The molecular characteristics of OABL remain poorly understood. We performed an integrated study to investigate the proteotranscriptome landscape and identify novel molecular characteristics and biomarkers of OABL. Methods Integrated quantitative proteome and transcriptome were performed on 40 OABL 12 idiopathic orbital inflammation, 6 reactive lymphoid hyperplasia, and 13 aesthetic orbital plastic surgery specimens. Complete clinicopathologic and prognostic data of the patients were recorded. Results We identified high global protein-mRNA concordance as a novel characteristic of OABL. High concordance was related to OABL recurrence. By integrated expression profile, motif enrichment and trend analysis, we found that alternative splicing is inflammation-independently dysregulated in OABL. After portraying the aberrant alternative splicing event landscape, we demonstrated the oncogenic role of ADAR, a core splicing regulator that regulates the splicing of Rho GTPase and cell cycle members. We found that ADAR regulates cell proliferation and Rho GTPase inhibitor sensitivity of lymphoma. We identified DNAJC9 as a potential biomarker for OABL in proteomic analyses. Immunohistochemistry and immunofluorescent staining showed the nuclear staining of DNAJC9 was significantly higher in extranodal marginal zone lymphomas compared with inflammation specimens. Conclusions These results provide an integrated gene expression profiling and demonstrate that high global protein-mRNA concordance is a prognosis-related molecular characteristic of OABL. We portray the alternative splicing events landscape of OABL, and reveal the oncogenic role of ADAR. We identified strong nuclear staining of DNAJC9 as a promising pathology diagnostic biomarker for extranodal marginal zone lymphomas. Supplementary Information The online version contains supplementary material available at 10.1186/s13046-022-02445-8.
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Integrative Proteomics and Transcriptomics Profiles of the Oviduct Reveal the Prolificacy-Related Candidate Biomarkers of Goats ( Capra hircus) in Estrous Periods. Int J Mol Sci 2022; 23:ijms232314888. [PMID: 36499219 PMCID: PMC9737051 DOI: 10.3390/ijms232314888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 11/16/2022] [Accepted: 11/24/2022] [Indexed: 11/29/2022] Open
Abstract
The oviduct is a dynamic reproductive organ for mammalian reproduction and is required for gamete storage, maturation, fertilization, and early embryonic development, and it directly affects fecundity. However, the molecular regulation of prolificacy occurring in estrous periods remain poorly understood. This study aims to gain a better understanding of the genes involved in regulating goat fecundity in the proteome and transcriptome levels of the oviducts. Twenty female Yunshang black goats (between 2 and 3 years old, weight 52.22 ± 0.43 kg) were divided into high- and low-fecundity groups in the follicular (FH and FL, five individuals per group) and luteal (LH and LL, five individuals per group) phases, respectively. The DIA-based high-resolution mass spectrometry (MS) method was used to quantify proteins in twenty oviducts. A total of 5409 proteins were quantified, and Weighted gene co-expression network analysis (WGCNA) determined that the tan module was highly associated with the high-fecundity trait in the luteal phase, and identified NUP107, ANXA11, COX2, AKP13, and ITF140 as hub proteins. Subsequently, 98 and 167 differentially abundant proteins (DAPs) were identified in the FH vs. FL and LH vs. LL comparison groups, respectively. Parallel reaction monitoring (PRM) was used to validate the results of the proteomics data, and the hub proteins were analyzed with Western blot (WB). In addition, biological adhesion and transporter activity processes were associated with oviductal function, and several proteins that play roles in oviductal communication with gametes or embryos were identified, including CAMSAP3, ITGAM, SYVN1, EMG1, ND5, RING1, CBS, PES1, ELP3, SEC24C, SPP1, and HSPA8. Correlation analysis of proteomics and transcriptomic revealed that the DAPs and differentially expressed genes (DEGs) are commonly involved in the metabolic processes at the follicular phase; they may prepare the oviductal microenvironment for gamete reception; and the MAP kinase activity, estrogen receptor binding, and angiotensin receptor binding terms were enriched in the luteal phase, which may be actively involved in reproductive processes. By generating the proteome data of the oviduct at two critical phases and integrating transcriptome analysis, we uncovered novel aspects of oviductal gene regulation of fecundity and provided a reference for other mammals.
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Integrative analysis of differentially expressed mRNAs and proteins induced by PGC-1β in breast cancer cells. Biochem Biophys Res Commun 2022; 637:73-82. [DOI: 10.1016/j.bbrc.2022.11.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 10/24/2022] [Accepted: 11/03/2022] [Indexed: 11/09/2022]
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Hamel KM, Liimatta KQ, Belgodere JA, Bunnell BA, Gimble JM, Martin EC. Adipose-Derived Stromal/Stem Cell Response to Tumors and Wounds: Evaluation of Patient Age. Stem Cells Dev 2022; 31:579-592. [PMID: 35262397 PMCID: PMC9836707 DOI: 10.1089/scd.2021.0280] [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: 10/20/2021] [Accepted: 03/05/2022] [Indexed: 01/22/2023] Open
Abstract
Tumors were characterized as nonhealing wounds by Virchow in 1858 and Dvorak in 1986. Since then, researchers have analyzed tumors from a new perspective. The parallels between tumorigenesis and physiological wound healing can provide a new framework for developing antitumor therapeutics. One commonality between tumors and wounds is the involvement of the stromal environment, particularly adipose stromal/stem cells (ASCs). ASCs exhibit dual functions, in which they stimulate tumor progression and assist in tissue repair and regeneration. Numerous studies have focused on the role of ASCs in cancer and wound healing, but none to date has linked age, cancer, and wound healing. Furthermore, very few studies have focused on the role of donor-specific characteristics of ASCs, such as age and their role in facilitating ASC behavior in cancer and wound healing. This review article is designed to provide important insights into the impact of donor age on ASC tumor and wound response and their role in facilitating ASC behavior in cancer and wound healing.
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Affiliation(s)
- Katie M. Hamel
- Department of Biological Engineering, Louisiana State University, Baton Rouge, Louisiana, USA
| | - Kara Q. Liimatta
- Department of Biological Engineering, Louisiana State University, Baton Rouge, Louisiana, USA
| | - Jorge A. Belgodere
- Department of Biological Engineering, Louisiana State University, Baton Rouge, Louisiana, USA
| | - Bruce A. Bunnell
- University of North Texas Health Sciences Center, Fort Worth, Texas, USA
| | | | - Elizabeth C. Martin
- Department of Biological Engineering, Louisiana State University, Baton Rouge, Louisiana, USA
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Targeted proteomics using parallel reaction monitoring confirms salivary proteins indicative of metastatic triple-negative breast cancer. J Proteomics 2022; 267:104701. [PMID: 35995384 DOI: 10.1016/j.jprot.2022.104701] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 06/28/2022] [Accepted: 08/04/2022] [Indexed: 12/11/2022]
Abstract
Triple-negative breast cancer (TNBC) is the most aggressive subtype due to the absence of hormonal receptors. Our study aimed to identify and determine the effectiveness of salivary proteins as candidate markers for metastatic TNBC subtype using parallel reaction monitoring mass spectrometry (PRM-MS). Three salivary proteins (lipocalin-1, SMR3B, and plastin-2) that showed significant differential expression in label-free quantitation (LFQ) between TNBC (N = 6) and health subjects (HS; N = 6) were selected for further validation. The developed PRM assay was used to quantify peptides GLST and NNLE (lipocalin-1), VYAL and MINL (Plastin-2) and GPYP, and IPPP (SMR3B) on a different cohort of TNBC patients (N = 20) and HS (N = 20) for evaluating their discriminating performances. Quantitative validation using PRM correlated well with the LFQ results, and 5 peptides from three proteins showed a similar up-or down-regulation. Subsequently, these proteins were validated by Western blot analysis. Compared to one protein's performance as an individual marker, the five-signature panel with salivary GLST, VYAL, MINL, GPYP, and IPPP achieved better performance in differentiating aggressive TNBC and HS with sensitivity (80%) and specificity (95%). Targeted proteomic analysis of the prioritized proteins highlights a peptide-based signature in saliva as the potential predictor to distinguish between TNBC and HS. SIGNIFICANCE OF THE STUDY: This study was designed to identify and quantify potential markers in saliva from the triple-negative breast cancer (TNBC) patients using parallel reaction monitoring assay. Three salivary proteins, Lipocalin-1 (LCN-1), Submaxillary androgen-regulated protein 3B (SMR3B), and Plastin-2 (LCP-1) selected in the discovery-phase were further quantified by targeted proteomics and Western blots. The salivary proteins successfully differentiated TNBC patients from healthy subjects with a sensitivity (80%) and specificity (95%).
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Uddin MH, Zhou JY, Pimentel J, Patrick SM, Kim S, Shekhar MP, Wu GS. Proteomic Analysis Identifies p62/SQSTM1 as a Critical Player in PARP Inhibitor Resistance. Front Oncol 2022; 12:908603. [PMID: 35847859 PMCID: PMC9277186 DOI: 10.3389/fonc.2022.908603] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 05/27/2022] [Indexed: 02/04/2023] Open
Abstract
Poly (ADP-ribose) polymerase (PARP) inhibitors (PARPis) are currently being used for treating breast cancer patients with deleterious or suspected deleterious germline BRCA-mutated, HER2-negative locally advanced or metastatic diseases. Despite durable responses, almost all patients receiving PARPis ultimately develop resistance and succumb to their illness, but the mechanism of PARPi resistance is not fully understood. To better understand the mechanism of PARPi resistance, we established two olaparib-resistant SUM159 and MDA468 cells by chronically exposing olaparib-sensitive SUM159 and MDA468 cells to olaparib. Olaparib-resistant SUM159 and MDA468 cells displayed 5-fold and 7-fold more resistance over their corresponding counterparts. Despite defects in PARPi-induced DNA damage, these olaparib-resistant cells are sensitive to cisplatin-induced cell death. Using an unbiased proteomic approach, we identified 6 447 proteins, of which 107 proteins were differentially expressed between olaparib-sensitive and -resistant cells. Ingenuity pathway analysis (IPA) revealed a number of pathways that are significantly altered, including mTOR and ubiquitin pathways. Among these differentially expressed proteins, p62/SQSTM1 (thereafter p62), a scaffold protein, plays a critical role in binding to and delivering the ubiquitinated proteins to the autophagosome membrane for autophagic degradation, was significantly downregulated in olaparib-resistant cells. We found that autophagy inducers rapamycin and everolimus synergistically sensitize olaparib-resistant cells to olaparib. Moreover, p62 protein expression was correlated with better overall survival in estrogen receptor-negative breast cancer. Thus, these findings suggest that PARPi-sensitive TNBC cells hyperactivate autophagy as they develop acquired resistance and that pharmacological stimulation of excessive autophagy could lead to cell death and thus overcome PARPi resistance.
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Affiliation(s)
- Mohammed Hafiz Uddin
- Molecular Therapeutics Program, Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI, United States
| | - Jun-Ying Zhou
- Molecular Therapeutics Program, Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI, United States
| | - Julio Pimentel
- Cancer Biology Program, Wayne State University School of Medicine, Detroit, MI, United States
| | - Steve M. Patrick
- Molecular Therapeutics Program, Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI, United States,Cancer Biology Program, Wayne State University School of Medicine, Detroit, MI, United States,Department of Oncology, Wayne State University School of Medicine, Detroit, MI, United States
| | - Seongho Kim
- Cancer Biology Program, Wayne State University School of Medicine, Detroit, MI, United States,Department of Oncology, Wayne State University School of Medicine, Detroit, MI, United States
| | - Malathy P. Shekhar
- Molecular Therapeutics Program, Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI, United States,Cancer Biology Program, Wayne State University School of Medicine, Detroit, MI, United States,Department of Oncology, Wayne State University School of Medicine, Detroit, MI, United States
| | - Gen Sheng Wu
- Molecular Therapeutics Program, Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI, United States,Cancer Biology Program, Wayne State University School of Medicine, Detroit, MI, United States,Department of Oncology, Wayne State University School of Medicine, Detroit, MI, United States,*Correspondence: Gen Sheng Wu,
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Xu X, Zhang M, Zhang X, Liu Y, Cai L, Zhang Q, Chen Q, Lin L, Lin S, Song Y, Zhu Z, Yang C. Decoding Expression Dynamics of Protein and Transcriptome at the Single-Cell Level in Paired Picoliter Chambers. Anal Chem 2022; 94:8164-8173. [PMID: 35650660 DOI: 10.1021/acs.analchem.1c05312] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Simultaneous analysis of mRNAs and proteins at the single-cell level provides information about the dynamics and correlations of gene and protein expressions in individual cells, enabling a comprehensive study of cellular heterogeneity and expression patterns. Here, we present a platform for about 1000 cellular indexing of mRNAs and membrane proteins, named multi-Paired-seq, with high cell utilization, accurate molecular measurement, and low cost. Based on hydrodynamic differential flow resistance, multi-Paired-seq largely improves cell utilization in the percentage of cells measured in population (>95%). Combined with the pump/valve structure, cell-free antibodies and mRNAs can be removed completely for highly accurate detection (R = 0.96) of protein copies. The picoliter reaction chambers allow high detection sensitivity for both mRNA transcripts and protein copies and low sequencing cost. Using multi-Paired-seq, three clusters of known breast cancer cell types are identified according to multimodal measurements, and the expression correlations between mRNAs and proteins under altered conditions are quantified. Multi-Paired-seq provides multimodal measurements at the single-cell level, which offers a new tool for cell biology, developmental biology, drug discovery, and precision medicine.
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Affiliation(s)
- Xing Xu
- Collaborative Innovation Center of Chemistry for Energy Materials, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
| | - Mingxia Zhang
- Collaborative Innovation Center of Chemistry for Energy Materials, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China.,Suzhou Dynamic Biosystems Co., Ltd., Suzhou, Jiangsu 215000, China
| | - Xuebing Zhang
- Suzhou Dynamic Biosystems Co., Ltd., Suzhou, Jiangsu 215000, China
| | - Yilong Liu
- Collaborative Innovation Center of Chemistry for Energy Materials, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
| | - Linfeng Cai
- Collaborative Innovation Center of Chemistry for Energy Materials, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
| | - Qianqian Zhang
- Collaborative Innovation Center of Chemistry for Energy Materials, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
| | - Qin Chen
- Suzhou Dynamic Biosystems Co., Ltd., Suzhou, Jiangsu 215000, China
| | - Li Lin
- Collaborative Innovation Center of Chemistry for Energy Materials, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
| | - Shichao Lin
- Collaborative Innovation Center of Chemistry for Energy Materials, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
| | - Yanling Song
- Collaborative Innovation Center of Chemistry for Energy Materials, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
| | - Zhi Zhu
- Collaborative Innovation Center of Chemistry for Energy Materials, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
| | - Chaoyong Yang
- Collaborative Innovation Center of Chemistry for Energy Materials, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China.,Institute of Molecular Medicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
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Sibilano M, Tullio V, Adorno G, Savini I, Gasperi V, Catani MV. Platelet-Derived miR-126-3p Directly Targets AKT2 and Exerts Anti-Tumor Effects in Breast Cancer Cells: Further Insights in Platelet-Cancer Interplay. Int J Mol Sci 2022; 23:ijms23105484. [PMID: 35628294 PMCID: PMC9141257 DOI: 10.3390/ijms23105484] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 05/09/2022] [Accepted: 05/12/2022] [Indexed: 02/07/2023] Open
Abstract
Among the surrounding cells influencing tumor biology, platelets are recognized as novel players as they release microvesicles (MVs) that, once delivered to cancer cells, modulate signaling pathways related to cell growth and dissemination. We have previously shown that physiological delivery of platelet MVs enriched in miR-126 exerted anti-tumor effects in different breast cancer (BC) cell lines. Here, we seek further insight by identifying AKT2 kinase as a novel miR-126-3p direct target, as assessed by bioinformatic analysis and validated by luciferase assay. Both ectopic expression and platelet MV-mediated delivery of miR-126-3p downregulated AKT2 expression, thus suppressing proliferating and invading properties, in either triple negative (BT549 cells) or less aggressive Luminal A (MCF-7 cells) BC subtypes. Accordingly, as shown by bioinformatic analysis, both high miR-126 and low AKT2 levels were associated with favorable long-term prognosis in BC patients. Our results, together with the literature data, indicate that miR-126-3p exerts suppressor activity by specifically targeting components of the PIK3/AKT signaling cascade. Therefore, management of platelet-derived MV production and selective delivery of miR-126-3p to tumor cells may represent a useful tool in multimodal therapeutic approaches in BC patients.
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Affiliation(s)
- Matteo Sibilano
- Department of Experimental Medicine, University of Rome Tor Vergata, 00133 Rome, Italy; (M.S.); (V.T.); (I.S.)
| | - Valentina Tullio
- Department of Experimental Medicine, University of Rome Tor Vergata, 00133 Rome, Italy; (M.S.); (V.T.); (I.S.)
| | - Gaspare Adorno
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, 00133 Rome, Italy;
| | - Isabella Savini
- Department of Experimental Medicine, University of Rome Tor Vergata, 00133 Rome, Italy; (M.S.); (V.T.); (I.S.)
| | - Valeria Gasperi
- Department of Experimental Medicine, University of Rome Tor Vergata, 00133 Rome, Italy; (M.S.); (V.T.); (I.S.)
- Correspondence: (V.G.); (M.V.C.); Tel.: +39-06-7259-6465 (V.G.); +39-06-7259-6465 (M.V.C.)
| | - Maria Valeria Catani
- Department of Experimental Medicine, University of Rome Tor Vergata, 00133 Rome, Italy; (M.S.); (V.T.); (I.S.)
- Correspondence: (V.G.); (M.V.C.); Tel.: +39-06-7259-6465 (V.G.); +39-06-7259-6465 (M.V.C.)
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Liu X, Zhou T, Wang Y, Pei M, Wang G, Chu W, Wang Q, Du S, Wang H, Wang C. TROP2 as Patient-Tailoring but Not Prognostic Biomarker for Breast Cancer. Onco Targets Ther 2022; 15:509-520. [PMID: 35535168 PMCID: PMC9078428 DOI: 10.2147/ott.s354048] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 03/04/2022] [Indexed: 12/11/2022] Open
Abstract
Purpose Methods Results Conclusion
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Affiliation(s)
- Xiaoyue Liu
- Biotherapeutics Discovery Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Tianhao Zhou
- State Key Laboratory of Oncogenes and Related Genes, Department of Oncology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People’s Republic of China
| | - Yongmei Wang
- Biotherapeutics Discovery Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Min Pei
- Biotherapeutics Discovery Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Guifeng Wang
- Biotherapeutics Discovery Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Wendi Chu
- Biotherapeutics Discovery Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Qi Wang
- Biotherapeutics Discovery Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Shaoqian Du
- State Key Laboratory of Oncogenes and Related Genes, Department of Oncology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People’s Republic of China
| | - Hongxia Wang
- State Key Laboratory of Oncogenes and Related Genes, Department of Oncology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People’s Republic of China
- Hongxia Wang, Shanghai General Hospital, 650 Xinsongjiang Road, Shanghai, People’s Republic of China, Email
| | - Chunhe Wang
- Biotherapeutics Discovery Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing, People’s Republic of China
- Research and Development Center, Dartsbio Pharmaceuticals, Zhongshan, People’s Republic of China
- Correspondence: Chunhe Wang, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Lane 720 Cai Lun Road, Bldg 1, Room 342, Shanghai, People’s Republic of China, Email
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Huang A, Huang SY, Shah P, Ku WC, Huang KT, Liu YF, Su CL, Huang RFS. Suboptimal folic acid exposure rewires oncogenic metabolism and proteomics signatures to mediate human breast cancer malignancy. J Nutr Biochem 2022; 106:109000. [PMID: 35460832 DOI: 10.1016/j.jnutbio.2022.109000] [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: 06/05/2021] [Revised: 11/25/2021] [Accepted: 02/22/2022] [Indexed: 11/27/2022]
Abstract
Whether treatment with folic acid (FA) affects human breast cancer positively or negatively remains unclear. We subjected human MCF-7 cells, a human breast cancer cell line, to suboptimal FA at low levels (10 nM; LF) and high levels (50 μM; HF) and investigated the molecular mechanisms underlying their effects through metabolic flux and systematic proteomics analyses. The data indicated that LF induced and HF aggravated 2-fold higher mitochondrial toxicity in terms of suppressed oxidative respiration, increased fermented glycolysis, and enhanced anchorage-independent oncospheroid formation. Quantitative proteomics and Gene Ontology enrichment analysis were used to profile LF- and HF-altered proteins involved in metabolism, apoptosis, and malignancy pathways. Through STRING analysis, we identified a connection network between LF- and HF-altered proteins with mTOR. Rapamycin-induced blockage of mTOR complex 1 (mTORC1) signaling, which regulates metabolism, differentially inhibited LF- and HF-modulated protein signatures of mitochondrial NADH dehydrogenase ubiquinone flavoprotein 2, mitochondrial glutathione peroxidase 4, kynureninase, and alpha-crystallin B chain as well as programmed cell death 5 in transcript levels; it subsequently diminished apoptosis and oncospheroid formation in LF/HF-exposed cells. Taken together, our data indicate that suboptimal FA treatment rewired oncogenic metabolism and mTORC1-mediated proteomics signatures to promote breast cancer development.
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Affiliation(s)
- Angel Huang
- Department of Nutritional Science, Fu Jen Catholic University, New Taipei City, Taiwan.
| | - Su-Yu Huang
- Department of Nutritional Science, Fu Jen Catholic University, New Taipei City, Taiwan.
| | - Pramod Shah
- Department of Nutritional Science, Fu Jen Catholic University, New Taipei City, Taiwan.
| | - Wei-Chi Ku
- School of Medicine, College of Medicine, Fu Jen Catholic University, New Taipei City, Taiwan.
| | - Kuang-Ta Huang
- Ph.D. Program in Nutrition and Food Science, Fu Jen Catholic University, New Taipei City, Taiwan.
| | - Yi-Fang Liu
- Department of Nutritional Science, Fu Jen Catholic University, New Taipei City, Taiwan.
| | - Chun-Li Su
- Graduate Program of Nutrition Science, School of Life Science, National Taiwan Normal University, Taiwan.
| | - Rwei-Fen S Huang
- Department of Nutritional Science, Fu Jen Catholic University, New Taipei City, Taiwan; Ph.D. Program in Nutrition and Food Science, Fu Jen Catholic University, New Taipei City, Taiwan.
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Alcaraz AJG, Baraniuk S, Mikulášek K, Park B, Lane T, Burbridge C, Ewald J, Potěšil D, Xia J, Zdráhal Z, Schneider D, Crump D, Basu N, Hogan N, Brinkmann M, Hecker M. Comparative analysis of transcriptomic points-of-departure (tPODs) and apical responses in embryo-larval fathead minnows exposed to fluoxetine. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 295:118667. [PMID: 34896397 DOI: 10.1016/j.envpol.2021.118667] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 11/17/2021] [Accepted: 12/08/2021] [Indexed: 06/14/2023]
Abstract
Current approaches in chemical hazard assessment face significant challenges because they rely on live animal testing, which is time-consuming, expensive, and ethically questionable. These concerns serve as an impetus to develop new approach methodologies (NAMs) that do not rely on live animal tests. This study explored a molecular benchmark dose (BMD) approach using a 7-day embryo-larval fathead minnow (FHM) assay to derive transcriptomic points-of-departure (tPODs) to predict apical BMDs of fluoxetine (FLX), a highly prescribed and potent selective serotonin reuptake inhibitor frequently detected in surface waters. Fertilized FHM embryos were exposed to graded concentrations of FLX (confirmed at < LOD, 0.19, 0.74, 3.38, 10.2, 47.5 μg/L) for 32 days. Subsets of fish were subjected to omics and locomotor analyses at 7 days post-fertilization (dpf) and to histological and biometric measurements at 32 dpf. Enrichment analyses of transcriptomics and proteomics data revealed significant perturbations in gene sets associated with serotonergic and axonal functions. BMD analysis resulted in tPOD values of 0.56 μg/L (median of the 20 most sensitive gene-level BMDs), 5.0 μg/L (tenth percentile of all gene-level BMDs), 7.51 μg/L (mode of the first peak of all gene-level BMDs), and 5.66 μg/L (pathway-level BMD). These tPODs were protective of locomotor and reduced body weight effects (LOEC of 10.2 μg/L) observed in this study and were reflective of chronic apical BMDs of FLX reported in the literature. Furthermore, the distribution of gene-level BMDs followed a bimodal pattern, revealing disruption of sensitive neurotoxic pathways at low concentrations and metabolic pathway perturbations at higher concentrations. This is one of the first studies to derive protective tPODs for FLX using a short-term embryo assay at a life stage not considered to be a live animal under current legislations.
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Affiliation(s)
| | - Shaina Baraniuk
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, S7N 5B3, Canada
| | - Kamil Mikulášek
- Central European Institute of Technology, Masaryk University, Brno, CZ-625 00, Czech Republic
| | - Bradley Park
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, S7N 5B3, Canada
| | - Taylor Lane
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, S7N 5B3, Canada; Department of Environment and Geography, University of York, Heslington, YO10 5NG, United Kingdom
| | - Connor Burbridge
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK, S7N 0W9, Canada
| | - Jessica Ewald
- Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, QC, H9X 3V9, Canada
| | - David Potěšil
- Central European Institute of Technology, Masaryk University, Brno, CZ-625 00, Czech Republic
| | - Jianguo Xia
- Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, QC, H9X 3V9, Canada
| | - Zbyněk Zdráhal
- Central European Institute of Technology, Masaryk University, Brno, CZ-625 00, Czech Republic
| | - David Schneider
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK, S7N 0W9, Canada; School of the Environment and Sustainability, University of Saskatchewan, Saskatoon, SK, S7N 5C8, Canada
| | - Doug Crump
- Environment and Climate Change Canada, National Wildlife Research Centre, Ottawa, ON, K1A 0H3, Canada
| | - Niladri Basu
- Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, QC, H9X 3V9, Canada
| | - Natacha Hogan
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, S7N 5B3, Canada; Department of Animal and Poultry Science, College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, SK, S7N 5A8, Canada
| | - Markus Brinkmann
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, S7N 5B3, Canada; School of the Environment and Sustainability, University of Saskatchewan, Saskatoon, SK, S7N 5C8, Canada; Global Institute for Water Security, University of Saskatchewan, Saskatoon, SK, S7N 3H5, Canada
| | - Markus Hecker
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, S7N 5B3, Canada; School of the Environment and Sustainability, University of Saskatchewan, Saskatoon, SK, S7N 5C8, Canada; Global Institute for Water Security, University of Saskatchewan, Saskatoon, SK, S7N 3H5, Canada.
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Erdem M, Ozgul İ, Dioken DN, Gurcuoglu I, Guntekin Ergun S, Cetin-Atalay R, Can T, Erson-Bensan AE. Identification of an mRNA isoform switch for HNRNPA1 in breast cancers. Sci Rep 2021; 11:24444. [PMID: 34961772 PMCID: PMC8712528 DOI: 10.1038/s41598-021-04007-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 12/06/2021] [Indexed: 12/02/2022] Open
Abstract
Roles of HNRNPA1 are beginning to emerge in cancers; however, mechanisms causing deregulation of HNRNPA1 function remain elusive. Here, we describe an isoform switch between the 3'-UTR isoforms of HNRNPA1 in breast cancers. We show that the dominantly expressed isoform in mammary tissue has a short half-life. In breast cancers, this isoform is downregulated in favor of a stable isoform. The stable isoform is expressed more in breast cancers, and more HNRNPA1 protein is synthesized from this isoform. High HNRNPA1 protein levels correlate with poor survival in patients. In support of this, silencing of HNRNPA1 causes a reversal in neoplastic phenotypes, including proliferation, clonogenic potential, migration, and invasion. In addition, silencing of HNRNPA1 results in the downregulation of microRNAs that map to intragenic regions. Among these miRNAs, miR-21 is known for its transcriptional upregulation in breast and numerous other cancers. Altogether, the cancer-specific isoform switch we describe here for HNRNPA1 emphasizes the need to study gene expression at the isoform level in cancers to identify novel cases of oncogene activation.
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Affiliation(s)
- Murat Erdem
- Department of Biological Sciences, Middle East Technical University (METU), Dumlupinar Blv No: 1 Universiteler Mah., Cankaya, Ankara, 06800, Turkey
| | - İbrahim Ozgul
- Department of Biological Sciences, Middle East Technical University (METU), Dumlupinar Blv No: 1 Universiteler Mah., Cankaya, Ankara, 06800, Turkey
| | - Didem Naz Dioken
- Department of Biological Sciences, Middle East Technical University (METU), Dumlupinar Blv No: 1 Universiteler Mah., Cankaya, Ankara, 06800, Turkey
| | - Irmak Gurcuoglu
- Department of Biological Sciences, Middle East Technical University (METU), Dumlupinar Blv No: 1 Universiteler Mah., Cankaya, Ankara, 06800, Turkey
| | - Sezen Guntekin Ergun
- Cancer Systems Biology Laboratory, CanSyL, Graduate School of Informatics, Middle East Technical University, 06800, Ankara, Turkey
- Department of Medical Biology, Hacettepe University, Ankara, Turkey
| | - Rengul Cetin-Atalay
- Cancer Systems Biology Laboratory, CanSyL, Graduate School of Informatics, Middle East Technical University, 06800, Ankara, Turkey
| | - Tolga Can
- Cancer Systems Biology Laboratory, CanSyL, Graduate School of Informatics, Middle East Technical University, 06800, Ankara, Turkey
- Department of Computer Engineering, Middle East Technical University (METU), Dumlupinar Blv No: 1 Universiteler Mah, Ankara, 06800, Turkey
| | - Ayse Elif Erson-Bensan
- Department of Biological Sciences, Middle East Technical University (METU), Dumlupinar Blv No: 1 Universiteler Mah., Cankaya, Ankara, 06800, Turkey.
- Cancer Systems Biology Laboratory, CanSyL, Graduate School of Informatics, Middle East Technical University, 06800, Ankara, Turkey.
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Maarouf A, Boissard A, Henry C, Leman G, Coqueret O, Guette C, Lelièvre E. Anterior gradient protein 2 is a marker of tumor aggressiveness in breast cancer and favors chemotherapy‑induced senescence escape. Int J Oncol 2021; 60:5. [PMID: 34913074 PMCID: PMC8727137 DOI: 10.3892/ijo.2021.5295] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 11/09/2021] [Indexed: 11/05/2022] Open
Abstract
Among the different chemotherapies available, genotoxic drugs are widely used. In response to these drugs, particularly doxorubicin, tumor cells can enter into senescence. Chemotherapy‑induced senescence (CIS) is a complex response. Long described as a definitive arrest of cell proliferation, the present authors and various groups have shown that this state may not be complete and could allow certain cells to reproliferate. The mechanism could be due to the activation of new signaling pathways. In the laboratory, the proteins involved in these pathways and triggering cell proliferation were studied. The present study determined a new role for anterior gradient protein 2 (AGR2) in vivo in patients and in vitro in a senescence escape model. AGR2's implication in breast cancer patients and proliferation of senescent cells was assessed based on a SWATH‑MS proteomic study of patients' samples and RNA interference technology on cell lines. First, AGR2 was identified and it was found that its concentration is higher in the serum of patients with breast cancer and that this high concentration is associated with metastasis occurrence. An inverse correlation between intratumoral AGR2 expression and the senescence marker p16 was also observed. This observation led to the study of the role of AGR2 in the CIS escape model. In this model, it was found that AGR2 is overexpressed in cells during senescence escape and that its loss considerably reduces this phenomenon. Furthermore, it was shown that the extracellular form of AGR2 stimulated the reproliferation of senescent cells. The power of proteomic analysis based on the SWATH‑MS approach allowed the present study to highlight the mammalian target of rapamycin (mTOR)/AKT signaling pathway in the senescence escape mechanism mediated by AGR2. Analysis of the two signaling pathways revealed that AGR2 modulated RICTOR and AKT phosphorylation. All these results showed that AGR2 expression in sera and tumors of breast cancer patients is a marker of tumor progression and metastasis occurrence. They also showed that its overexpression regulates CIS escape via activation of the mTOR/AKT signaling pathway.
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Affiliation(s)
- Amine Maarouf
- Paul Papin ICO Cancer Center, CRCINA, INSERM U1232, Université de Nantes, Université d'Angers, 49055 Angers, France
| | - Alice Boissard
- Paul Papin ICO Cancer Center, CRCINA, INSERM U1232, Université de Nantes, Université d'Angers, 49055 Angers, France
| | - Cécile Henry
- Paul Papin ICO Cancer Center, CRCINA, INSERM U1232, Université de Nantes, Université d'Angers, 49055 Angers, France
| | - Géraldine Leman
- Paul Papin ICO Cancer Center, CRCINA, INSERM U1232, Université de Nantes, Université d'Angers, 49055 Angers, France
| | - Olivier Coqueret
- Paul Papin ICO Cancer Center, CRCINA, INSERM U1232, Université de Nantes, Université d'Angers, 49055 Angers, France
| | - Catherine Guette
- Paul Papin ICO Cancer Center, CRCINA, INSERM U1232, Université de Nantes, Université d'Angers, 49055 Angers, France
| | - Eric Lelièvre
- Paul Papin ICO Cancer Center, CRCINA, INSERM U1232, Université de Nantes, Université d'Angers, 49055 Angers, France
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Park MK, Zhang L, Min KW, Cho JH, Yeh CC, Moon H, Hormaechea-Agulla D, Mun H, Ko S, Lee JW, Jathar S, Smith AS, Yao Y, Giang NT, Vu HH, Yan VC, Bridges MC, Kourtidis A, Muller F, Chang JH, Song SJ, Nakagawa S, Hirose T, Yoon JH, Song MS. NEAT1 is essential for metabolic changes that promote breast cancer growth and metastasis. Cell Metab 2021; 33:2380-2397.e9. [PMID: 34879239 PMCID: PMC8813003 DOI: 10.1016/j.cmet.2021.11.011] [Citation(s) in RCA: 76] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 08/27/2021] [Accepted: 11/16/2021] [Indexed: 01/08/2023]
Abstract
Accelerated glycolysis is the main metabolic change observed in cancer, but the underlying molecular mechanisms and their role in cancer progression remain poorly understood. Here, we show that the deletion of the long noncoding RNA (lncRNA) Neat1 in MMTV-PyVT mice profoundly impairs tumor initiation, growth, and metastasis, specifically switching off the penultimate step of glycolysis. Mechanistically, NEAT1 directly binds and forms a scaffold bridge for the assembly of PGK1/PGAM1/ENO1 complexes and thereby promotes substrate channeling for high and efficient glycolysis. Notably, NEAT1 is upregulated in cancer patients and correlates with high levels of these complexes, and genetic and pharmacological blockade of penultimate glycolysis ablates NEAT1-dependent tumorigenesis. Finally, we demonstrate that Pinin mediates glucose-stimulated nuclear export of NEAT1, through which it exerts isoform-specific and paraspeckle-independent functions. These findings establish a direct role for NEAT1 in regulating tumor metabolism, provide new insights into the Warburg effect, and identify potential targets for therapy.
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Affiliation(s)
- Mi Kyung Park
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Li Zhang
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Kyung-Won Min
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA; Department of Biology, College of Natural Sciences, Gangneung-Wonju National University, Gangneung-si, Gangwon-do 25457, Republic of Korea
| | - Jung-Hyun Cho
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Chih-Chen Yeh
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Hyesu Moon
- Soonchunhyang Institute of Medi-bio Science, Soonchunhyang University, Cheonan-si, Chungcheongnam-do 31151, Republic of Korea
| | - Daniel Hormaechea-Agulla
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Hyejin Mun
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Seungbeom Ko
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Ji Won Lee
- Department of Biology, College of Natural Sciences, Gangneung-Wonju National University, Gangneung-si, Gangwon-do 25457, Republic of Korea
| | - Sonali Jathar
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA; Laboratory of lncRNA Biology, National Center for Cell Science, Pune, Maharashtra 411007, India
| | - Aubrey S Smith
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Yixin Yao
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Nguyen Thu Giang
- Department of Biology Education, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Hong Ha Vu
- Department of Biology Education, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Victoria C Yan
- Department of Cancer Systems Imaging, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Mary C Bridges
- Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Antonis Kourtidis
- Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Florian Muller
- Department of Cancer Systems Imaging, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jeong Ho Chang
- Department of Biology Education, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Su Jung Song
- Soonchunhyang Institute of Medi-bio Science, Soonchunhyang University, Cheonan-si, Chungcheongnam-do 31151, Republic of Korea
| | - Shinichi Nakagawa
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Hokkaido 060-0812, Japan
| | - Tetsuro Hirose
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 565-0871, Japan
| | - Je-Hyun Yoon
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA.
| | - Min Sup Song
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
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Wu Q, Tang X, Zhu W, Li Q, Zhang X, Li H. The Potential Prognostic Role of Oligosaccharide-Binding Fold-Containing Protein 2A (OBFC2A) in Triple-Negative Breast Cancer. Front Oncol 2021; 11:751430. [PMID: 34868954 PMCID: PMC8634334 DOI: 10.3389/fonc.2021.751430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Accepted: 10/28/2021] [Indexed: 11/13/2022] Open
Abstract
Background Patients with triple-negative breast cancer (TNBC) have poor overall survival. The present study aimed to investigate the potential prognostics of TNBC by analyzing breast cancer proteomic and transcriptomic datasets. Methods Candidate proteins selected from CPTAC (the National Cancer Institute's Clinical Proteomic Tumor Analysis Consortium) were validated using datasets from METABRIC (Molecular Taxonomy of Breast Cancer International Consortium). Kaplan-Meier analysis and ROC (receiver operating characteristic) curve analysis were performed to explore the prognosis of candidate genes. GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) enrichment analysis were performed on the suspected candidate genes. Single-cell RNA-seq (scRNA-seq) data from GSE118389 were used to analyze the cell clusters in which OBFC2A (Oligosaccharide-Binding Fold-Containing Protein 2A) was mainly distributed. TIMER (Tumor Immune Estimation Resource) was used to verify the correlation between OBFC2A expression and immune infiltration. Clone formation assays and wound healing assays were used to detect the role of OBFC2A expression on the proliferation, invasion, and migration of breast cancer cells. Flow cytometry was used to analyze the effects of silencing OBFC2A on breast cancer cell cycle and apoptosis. Results Six candidate proteins were found to be differentially expressed in non-TNBC and TNBC groups from CPTAC. However, only OBFC2A was identified as an independently poor prognostic gene marker in METABRIC (HR=3.658, 1.881-7.114). And OBFC2A was associated with immune functions in breast cancer. Biological functional experiments showed that OBFC2A might promote the proliferation and migration of breast cancer cells. The inhibition of OBFC2A expression blocked the cell cycle in G1 phase and inhibited the transformation from G1 phase to S phase. Finally, downregulation of OBFC2A also increased the total apoptosis rate of cells. Conclusion On this basis, OBFC2A may be a potential prognostic biomarker for TNBC.
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Affiliation(s)
- Qianxue Wu
- Department of the Endocrine and Breast Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing Medical University, Chongqing, China
| | - Xin Tang
- Department of Oncology, Chongqing University Cancer Hospital, Chongqing, China
| | - Wenming Zhu
- Department of the Endocrine and Breast Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing Medical University, Chongqing, China
| | - Qing Li
- Department of the Endocrine and Breast Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing Medical University, Chongqing, China
| | - Xiang Zhang
- Department of the Endocrine and Breast Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing Medical University, Chongqing, China
| | - Hongyuan Li
- Department of the Endocrine and Breast Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing Medical University, Chongqing, China
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Bai X, Ni J, Beretov J, Wang S, Dong X, Graham P, Li Y. THOC2 and THOC5 Regulate Stemness and Radioresistance in Triple-Negative Breast Cancer. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:e2102658. [PMID: 34708581 PMCID: PMC8693071 DOI: 10.1002/advs.202102658] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 08/07/2021] [Indexed: 05/04/2023]
Abstract
Triple-negative breast cancer (TNBC) is the most aggressive subtype of breast cancer. Radioresistance and stemness are substantial obstacles to TNBC treatment. The THO complex (THOC) is a subunit of the TRanscription-EXport complex that functions in the coupling of transcription to nascent RNA splicing, elongation, and export. However, its role in regulating TNBC therapeutic resistance is not reported yet. In this study, the authors demonstrate that cancer stem cells are enriched in radioresistant TNBC cells and describe the role of the THOC in regulating TNBC radioresistance and stemness. The authors find that THOC2 and THOC5 are upregulated in radioresistant TNBC cells and associated with a poor prognosis in TNBC patients. Further investigation reveals that THOC2 promotes the stem-like properties and radioresistance of TNBC cells in a THOC5-dependent manner by facilitating the release of sex-determining region Y (SRY)-box transcription factor 2 (SOX2) and homeobox transcription factor (NANOG) transcripts from the nucleus. Silencing THOC2 or THOC5 expression decreases the protein expression of SOX2 and NANOG, depletes the stem-like properties, and causes radiosensitization in these TNBC cells. Moreover, THOC2 or THOC5 depletion blocks the xenograft tumorigenesis and growth of radioresistant TNBC in vivo. These findings uncover the novel correlations of THOC with TNBC stemness and therapeutic resistance, proposing alternative therapeutic strategies against relapsed TNBC.
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Affiliation(s)
- Xupeng Bai
- St George and Sutherland Clinical SchoolFaculty of MedicineUNSW SydneyKensingtonNSW2052Australia
- Cancer Care CentreSt George HospitalKogarahNSW2217Australia
| | - Jie Ni
- St George and Sutherland Clinical SchoolFaculty of MedicineUNSW SydneyKensingtonNSW2052Australia
- Cancer Care CentreSt George HospitalKogarahNSW2217Australia
| | - Julia Beretov
- St George and Sutherland Clinical SchoolFaculty of MedicineUNSW SydneyKensingtonNSW2052Australia
- Cancer Care CentreSt George HospitalKogarahNSW2217Australia
- Anatomical PathologyNSW Health PathologySt George HospitalKogarahNSW2217Australia
| | - Shanping Wang
- Institute of Biomedical and Pharmaceutical SciencesGuangdong University of TechnologyGuangzhou510006China
| | - Xingli Dong
- Department of Biopharmaceutical SciencesCollege of PharmacyHarbin Medical UniversityHarbin150081China
| | - Peter Graham
- St George and Sutherland Clinical SchoolFaculty of MedicineUNSW SydneyKensingtonNSW2052Australia
- Cancer Care CentreSt George HospitalKogarahNSW2217Australia
| | - Yong Li
- St George and Sutherland Clinical SchoolFaculty of MedicineUNSW SydneyKensingtonNSW2052Australia
- Cancer Care CentreSt George HospitalKogarahNSW2217Australia
- School of Basic MedicineZhengzhou UniversityZhengzhou450001China
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Dynamic Landscape of Extracellular Vesicle-Associated Proteins Is Related to Treatment Response of Patients with Metastatic Breast Cancer. MEMBRANES 2021; 11:membranes11110880. [PMID: 34832109 PMCID: PMC8619728 DOI: 10.3390/membranes11110880] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 11/09/2021] [Accepted: 11/11/2021] [Indexed: 12/13/2022]
Abstract
Breast cancer is the leading cause of cancer death in women. The majority of these deaths are due to disease metastasis, in which cancer cells disseminate to multiple organs and disrupt vital physiological functions. It is widely accepted that breast cancer cells secrete extracellular vesicles (EVs), which contain dynamic molecular cargo that act as versatile mediators of intercellular communication. Therefore, Evs. secreted by breast cancer cells could be involved in the development of metastatic disease and resistance to treatment. Moreover, changes in EV cargo could reflect the effects of therapy on their parent tumor cells. The aim of this feasibility study was to quantitatively profile the proteomes of Evs. isolated from blood samples taken from treatment sensitive and resistant metastatic breast cancer patients to identify proteins associated with responses. Three serial blood samples were collected from three patients with metastatic breast cancer receiving systemic therapy including a responder, a non-responder, and a mixed-responder. Evs. were isolated from plasma using size exclusion chromatography and their protein cargo was prepared for tandem mass tag (TMT)-labelling and quantitative analyses using two-dimensional high-performance liquid chromatography followed by tandem mass spectrometry. After filtering, we quantitatively identified 286 proteins with high confidence using a q value of 0.05. Of these, 149 were classified as EV associated candidate proteins and 137 as classical, high abundant plasma proteins. After comparing EV protein abundance between the responder and non-responder, we identified 35 proteins with unique de-regulated abundance patterns that was conserved at multiple time points. We propose that this proof-of-concept approach can be used to identify proteins which have potential as predictors of metastatic breast cancer response to treatment.
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Reinspection of a Clinical Proteomics Tumor Analysis Consortium (CPTAC) Dataset with Cloud Computing Reveals Abundant Post-Translational Modifications and Protein Sequence Variants. Cancers (Basel) 2021; 13:cancers13205034. [PMID: 34680183 PMCID: PMC8534219 DOI: 10.3390/cancers13205034] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 09/14/2021] [Accepted: 10/01/2021] [Indexed: 12/14/2022] Open
Abstract
The Clinical Proteomic Tumor Analysis Consortium (CPTAC) has provided some of the most in-depth analyses of the phenotypes of human tumors ever constructed. Today, the majority of proteomic data analysis is still performed using software housed on desktop computers which limits the number of sequence variants and post-translational modifications that can be considered. The original CPTAC studies limited the search for PTMs to only samples that were chemically enriched for those modified peptides. Similarly, the only sequence variants considered were those with strong evidence at the exon or transcript level. In this multi-institutional collaborative reanalysis, we utilized unbiased protein databases containing millions of human sequence variants in conjunction with hundreds of common post-translational modifications. Using these tools, we identified tens of thousands of high-confidence PTMs and sequence variants. We identified 4132 phosphorylated peptides in nonenriched samples, 93% of which were confirmed in the samples which were chemically enriched for phosphopeptides. In addition, our results also cover 90% of the high-confidence variants reported by the original proteogenomics study, without the need for sample specific next-generation sequencing. Finally, we report fivefold more somatic and germline variants that have an independent evidence at the peptide level, including mutations in ERRB2 and BCAS1. In this reanalysis of CPTAC proteomic data with cloud computing, we present an openly available and searchable web resource of the highest-coverage proteomic profiling of human tumors described to date.
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Wei Z, Sijia F, Rui T, Yang L, Jianjun H, Bin W, Jing X. Analysis of differentially expressed proteins between HER2 positive and triple negative breast cancer and their prognostic significance. Ann Diagn Pathol 2021; 55:151834. [PMID: 34610510 DOI: 10.1016/j.anndiagpath.2021.151834] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Accepted: 09/19/2021] [Indexed: 01/08/2023]
Abstract
Both triple negative breast cancer (TNBA) and HER2-positive breast cancer lack expression of estrogen receptor alpha (ER) and progesterone receptor (PR), while human epidermal growth factor receptor 2 (HER2) in TNBC is also negative. This study aimed to identify the differentially expressed proteins (DEPs) between TNBC and HER2-positive breast cancer and to improve understanding of their role in the prognosis of breast cancer. By analyzing the breast cancer data set in The Cancer Proteome Atlas (TCPA) database, 15 DEPs between TNBC and HER2-positive breast cancer were identified. GO and pathway enrichment analysis were performed on DEPs, and the protein-protein interaction (PPI) network was constructed. The overall survival (OS) analysis of the breast cancer protein dataset in the Kaplan-Meier plotter showed that low expression of ACC1 suggested a higher OS of HER2-positive breast cancer (HR = 5.34, P < 0.05) and TNBC (HR = 2.88, P < 0.05). And TNBC patients with high TBA1B (HR = 0.16, P < 0.01) or low INPP4B (HR = 3.47, P < 0.05) expression have a better prognosis. Our research provides new insights into the prognostic indicators of TNBC and HER2-positive breast cancer, which could be further studied.
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Affiliation(s)
- Zhang Wei
- Department of Breast Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China.
| | - Fei Sijia
- Department of Geriatric Endocrinology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
| | - Tong Rui
- Department of Geriatric Endocrinology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
| | - Liu Yang
- Department of Breast Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
| | - He Jianjun
- Department of Breast Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
| | - Wan Bin
- Department of Breast Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
| | - Xu Jing
- Department of Geriatric Endocrinology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China.
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49
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Zingone A, Sinha S, Ante M, Nguyen C, Daujotyte D, Bowman ED, Sinha N, Mitchell KA, Chen Q, Yan C, Loher P, Meerzaman D, Ruppin E, Ryan BM. A comprehensive map of alternative polyadenylation in African American and European American lung cancer patients. Nat Commun 2021; 12:5605. [PMID: 34556645 PMCID: PMC8460807 DOI: 10.1038/s41467-021-25763-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 07/22/2021] [Indexed: 11/09/2022] Open
Abstract
Deciphering the post-transcriptional mechanisms (PTM) regulating gene expression is critical to understand the dynamics underlying transcriptomic regulation in cancer. Alternative polyadenylation (APA)-regulation of mRNA 3'UTR length by alternating poly(A) site usage-is a key PTM mechanism whose comprehensive analysis in cancer remains an important open challenge. Here we use a method and analysis pipeline that sequences 3'end-enriched RNA directly to overcome the saturation limitation of traditional 5'-3' based sequencing. We comprehensively map the APA landscape in lung cancer in a cohort of 98 tumor/non-involved tissues derived from European American and African American patients. We identify a global shortening of 3'UTR transcripts in lung cancer, with notable functional implications on the expression of both coding and noncoding genes. We find that APA of non-coding RNA transcripts (long non-coding RNAs and microRNAs) is a recurrent event in lung cancer and discover that the selection of alternative polyA sites is a form of non-coding RNA expression control. Our results indicate that mRNA transcripts from EAs are two times more likely than AAs to undergo APA in lung cancer. Taken together, our findings comprehensively map and identify the important functional role of alternative polyadenylation in determining transcriptomic heterogeneity in lung cancer.
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Affiliation(s)
- Adriana Zingone
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892, US
| | - Sanju Sinha
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892, US
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, Bethesda, MD, US
| | - Michael Ante
- Lexogen GmbH, Campus Vienna Biocenter 5, 1030, Vienna, Austria
- Ares Genetics GmbH, Karl-Farkas-Gasse 18, 1030, Vienna, Austria
| | - Cu Nguyen
- Computational Genomics Research, Center for Biomedical Informatics and Information Technology (CBIIT), National Cancer Institute, 9609 Medical Center Drive, Rockville, MD, 20850, US
| | - Dalia Daujotyte
- Lexogen GmbH, Campus Vienna Biocenter 5, 1030, Vienna, Austria
| | - Elise D Bowman
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892, US
| | - Neelam Sinha
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, Bethesda, MD, US
| | - Khadijah A Mitchell
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892, US
| | - Qingrong Chen
- Computational Genomics Research, Center for Biomedical Informatics and Information Technology (CBIIT), National Cancer Institute, 9609 Medical Center Drive, Rockville, MD, 20850, US
| | - Chunhua Yan
- Computational Genomics Research, Center for Biomedical Informatics and Information Technology (CBIIT), National Cancer Institute, 9609 Medical Center Drive, Rockville, MD, 20850, US
| | - Phillipe Loher
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, 19017, US
| | - Daoud Meerzaman
- Computational Genomics Research, Center for Biomedical Informatics and Information Technology (CBIIT), National Cancer Institute, 9609 Medical Center Drive, Rockville, MD, 20850, US
| | - Eytan Ruppin
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, Bethesda, MD, US
| | - Bríd M Ryan
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892, US.
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50
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Argininosuccinate lyase is a metabolic vulnerability in breast development and cancer. NPJ Syst Biol Appl 2021; 7:36. [PMID: 34535676 PMCID: PMC8448827 DOI: 10.1038/s41540-021-00195-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 08/09/2021] [Indexed: 02/07/2023] Open
Abstract
Epithelial-to-mesenchymal transition (EMT) is fundamental to both normal tissue development and cancer progression. We hypothesized that EMT plasticity defines a range of metabolic phenotypes and that individual breast epithelial metabolic phenotypes are likely to fall within this phenotypic landscape. To determine EMT metabolic phenotypes, the metabolism of EMT was described within genome-scale metabolic models (GSMMs) using either transcriptomic or proteomic data from the breast epithelial EMT cell culture model D492. The ability of the different data types to describe breast epithelial metabolism was assessed using constraint-based modeling which was subsequently verified using 13C isotope tracer analysis. The application of proteomic data to GSMMs provided relatively higher accuracy in flux predictions compared to the transcriptomic data. Furthermore, the proteomic GSMMs predicted altered cholesterol metabolism and increased dependency on argininosuccinate lyase (ASL) following EMT which were confirmed in vitro using drug assays and siRNA knockdown experiments. The successful verification of the proteomic GSMMs afforded iBreast2886, a breast GSMM that encompasses the metabolic plasticity of EMT as defined by the D492 EMT cell culture model. Analysis of breast tumor proteomic data using iBreast2886 identified vulnerabilities within arginine metabolism that allowed prognostic discrimination of breast cancer patients on a subtype-specific level. Taken together, we demonstrate that the metabolic reconstruction iBreast2886 formalizes the metabolism of breast epithelial cell development and can be utilized as a tool for the functional interpretation of high throughput clinical data.
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