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Zhang X, Dai Y, Ma F, Ma Y, Wang J, Li X, Qin W. Effect of electroacupuncture on global cerebral ischemia-reperfusion injury in rats: A urine proteome analysis. Brain Behav 2024; 14:e3382. [PMID: 38376040 PMCID: PMC10772847 DOI: 10.1002/brb3.3382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Accepted: 12/20/2023] [Indexed: 02/21/2024] Open
Abstract
BACKGROUND This study aimed to investigate dynamic urinary proteome changes of electroacupuncture (EP) on cerebral ischemia-reperfusion (CI/R) injured rats and to explore the therapeutic biological mechanisms of EP. METHODS First, changed urinary proteins were found in EP stimulation in healthy rats. Then, we used a CI/R injury rat model induced by Pulsinelli's four-vessel occlusion (4-VO) method to explore the function of EP on urinary proteome in CI/R injury. Urine samples were collected for proteome analysis by liquid chromatography-tandem mass spectrometry (LC-MS/MS) and bioinformatics analysis. RESULTS In total, 384 proteins were identified, among which 47 proteins (23 upregulated, 24 downregulated) were differentially expressed with 0.6-log FC and p < .05. Gene ontology analysis revealed that the cell redox homeostasis, acute-phase response, response to lipopolysaccharide, and cellular response to glucocorticoid stimulus were significantly enriched. The partially biologically connected differential proteins were found by the Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis in the EP group. With the CI/R rat model, 80 proteins (27 upregulated, 53 downregulated) were significantly changed in the CI/R rats compared to the controls. Among these differentially expressed proteins (DEPs), 23 proteins (17 upregulated, six downregulated) showed significant changes after EP treatment (0.6-log FC change, p < .05). The main related biological processes were aging, immune response, acute-phase response, liver regeneration, protein catabolic process, and response to oxidative stress. Many metabolic pathways were enriched by KEGG analysis. CONCLUSION Our results indicate that the EP could alleviate cerebral damage induced by ischemia-reperfusion through an anti-inflammatory and metabolism regulation mechanism. The urinary proteome might reflect the pathophysiological changes in EP pretreatment in the treatment and prevention of CI/R injury.
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Affiliation(s)
- Xiao Zhang
- Department of AnesthesiologyQingdao HospitalUniversity of Health and Rehabilitation Sciences (Qingdao Municipal Hospital)QingdaoChina
| | - Yuting Dai
- Department of AnesthesiologyQingdao HospitalUniversity of Health and Rehabilitation Sciences (Qingdao Municipal Hospital)QingdaoChina
| | - Fuguo Ma
- Department of AnesthesiologyQingdao HospitalUniversity of Health and Rehabilitation Sciences (Qingdao Municipal Hospital)QingdaoChina
| | - Yuan Ma
- Department of AnesthesiologyQingdao HospitalUniversity of Health and Rehabilitation Sciences (Qingdao Municipal Hospital)QingdaoChina
| | - Jiajia Wang
- Department of AnesthesiologyQingdao HospitalUniversity of Health and Rehabilitation Sciences (Qingdao Municipal Hospital)QingdaoChina
| | - Xiaoxia Li
- Department of Genetics and Cell Biology, Basic Medical CollegeQingdao UniversityQingdaoChina
| | - Weiwei Qin
- Department of AnesthesiologyQingdao HospitalUniversity of Health and Rehabilitation Sciences (Qingdao Municipal Hospital)QingdaoChina
- Department of Genetics and Cell Biology, Basic Medical CollegeQingdao UniversityQingdaoChina
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2
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Zhang S, Yao HF, Li H, Su T, Jiang SH, Wang H, Zhang ZG, Dong FY, Yang Q, Yang XM. Transglutaminases are oncogenic biomarkers in human cancers and therapeutic targeting of TGM2 blocks chemoresistance and macrophage infiltration in pancreatic cancer. Cell Oncol (Dordr) 2023; 46:1473-1492. [PMID: 37246171 DOI: 10.1007/s13402-023-00824-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/02/2023] [Indexed: 05/30/2023] Open
Abstract
PURPOSE Transglutaminases (TGs) are multifunctional enzymes exhibiting transglutaminase crosslinking, as well as atypical GTPase/ATPase and kinase activities. Here, we used an integrated comprehensive analysis to assess the genomic, transcriptomic and immunological landscapes of TGs across cancers. METHODS Gene expression and immune cell infiltration patterns across cancers were obtained from The Cancer Genome Atlas (TCGA) database and Gene Set Enrichment Analysis (GSEA) datasets. Western blotting, immunofluorescence staining, enzyme-linked immunosorbent assays, and orthotopic xenograft models were used to validate our database-derived results. RESULTS We found that the overall expression of TGs (designated as the TG score) is significantly upregulated in multiple cancers and related to a worse patient survival. The expression of TG family members can be regulated through multiple mechanisms at the genetic, epigenetic and transcriptional levels. The expression of transcription factors crucial for epithelial-to-mesenchymal transition (EMT) is commonly correlated with the TG score in many cancer types. Importantly, TGM2 expression displays a close connection with chemoresistance to a wide range of chemotherapeutic drugs. We found that TGM2 expression, F13A1 expression and the overall TG score were positively correlated with the infiltration of immune cells in all cancer types tested. Functional and clinical verification revealed that a higher TGM2 expression is linked with a worse patient survival, an increased IC50 value of gemcitabine, and a higher abundance of tumor-infiltrating macrophages in pancreatic cancer. Mechanistically, we found that increased C-C motif chemokine ligand 2 (CCL2) release mediated by TGM2 contributes to macrophage infiltration into the tumor microenvironment. CONCLUSIONS Our results reveal the relevance and molecular networks of TG genes in human cancers and highlight the importance of TGM2 in pancreatic cancer, which may provide promising directions for immunotherapy and for addressing chemoresistance.
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Affiliation(s)
- Shan Zhang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
| | - Hong-Fei Yao
- Department of Biliary-Pancreatic Surgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200217, People's Republic of China
| | - Hui Li
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
| | - Tong Su
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, 200011, China
| | - Shu-Heng Jiang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
| | - Hao Wang
- Department of Oncology, Shanghai East Hospital, School of Medicine, Tongji University, 1800 Yuntai Road, Pudong District, Shanghai, 200123, China
| | - Zhi-Gang Zhang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China.
| | - Fang-Yuan Dong
- Department of Gastroenterology, Huadong Hospital, Shanghai Medical College, Fudan University, Shanghai, 200040, People's Republic of China.
| | - Qin Yang
- Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Xiao-Mei Yang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China.
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3
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Atobatele AG, Tonoli E, Vadakekolathu J, Savoca MP, Barr M, Kataria Y, Rossanese M, Burhan I, McArdle S, Caccamo D, Verderio EAM. Canonical and truncated transglutaminase-2 regulate mucin-1 expression and androgen independency in prostate cancer cell lines. Cell Death Dis 2023; 14:317. [PMID: 37160910 PMCID: PMC10170068 DOI: 10.1038/s41419-023-05818-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 04/13/2023] [Accepted: 04/19/2023] [Indexed: 05/11/2023]
Abstract
Androgen independency is associated with poor prostate cancer (PCa) survival. Here we report that silencing of transglutaminase-2 (TG2) expression by CRISPR-Cas9 is associated with upregulation of androgen receptor (AR) transcription in PCa cell lines. Knockout of TG2 reversed the migratory potential and anchorage independency of PC3 and DU145 cells and revealed a reduced level of mucin-1 (MUC1) RNA transcript through unbiased multi-omics profiling, which was restored by selective add-back of the truncated TG2 isoform (TGM2_v2). Silencing of AR resulted into increased MUC1 in TG2KO PC3 cells showing that TG2 affects transcriptional regulation of MUC1 via repressing AR expression. Treatment of PC3 WT cell line with TG2 inhibitor ZDON led to a significant increase in AR expression and decrease in MUC1. ZDON also blocked the formation of MUC1-multimers labelled with TG amine-donor substrates in reducing conditions, revealing for the first time a role for TG2, which we show to be externalised via extracellular vesicles, in MUC1 stabilisation via calcium-dependent transamidation. A specific antibody towards TGM2_v2 revealed its restricted nuclear location compared to the canonical long form of TG2 (TGM2_v1), which is predominantly cytosolic, suggesting that this form contributes to the previously suggested TG2-mediated NF-κB activation and AR transcriptional repression. As TGM2_v2 transcription was increased in biopsies of early-stage prostate adenocarcinoma (PRAD) patients compared to subjects presenting inflammatory prostatitis, and total TG2 protein expression significantly increased in PRAD versus normal tissue, the role of TG2 and its truncated form as a prostate malignancy marker is suggested. In conclusion, this investigation has provided the first unbiased discovery of a novel pathway mediated by TG2 via MUC1, which is shown to contribute to androgen insensitivity and malignancy of PCa cells and be upregulated in PCa biopsies, with potential relevance to cancer immune evasion.
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Affiliation(s)
- Adeola Grace Atobatele
- School of Science and Technology, Centre for Health, Ageing and Understanding of Disease, Nottingham Trent University, Nottingham, NG11 8NS, UK
- Department of Biological and Biomedical Sciences, Science Centre, School of Health, Science and Wellbeing, Staffordshire University, Leek Road, Stoke-on-Trent, ST4 2DF, UK
| | - Elisa Tonoli
- School of Science and Technology, Centre for Health, Ageing and Understanding of Disease, Nottingham Trent University, Nottingham, NG11 8NS, UK
| | - Jayakumar Vadakekolathu
- John van Geest Cancer Research Centre, Nottingham Trent University, Clifton Lane, Nottingham, NG11 8NS, UK
| | - Maria Pia Savoca
- School of Science and Technology, Centre for Health, Ageing and Understanding of Disease, Nottingham Trent University, Nottingham, NG11 8NS, UK
| | - Melissa Barr
- School of Science and Technology, Centre for Health, Ageing and Understanding of Disease, Nottingham Trent University, Nottingham, NG11 8NS, UK
| | - Yukti Kataria
- School of Science and Technology, Centre for Health, Ageing and Understanding of Disease, Nottingham Trent University, Nottingham, NG11 8NS, UK
| | - Marta Rossanese
- Department of Human and Paediatric Pathology, Polyclinic Hospital University, Via C. Valeria 1, 98125, Messina, Italy
| | - Izhar Burhan
- School of Science and Technology, Centre for Health, Ageing and Understanding of Disease, Nottingham Trent University, Nottingham, NG11 8NS, UK
| | - Stephanie McArdle
- John van Geest Cancer Research Centre, Nottingham Trent University, Clifton Lane, Nottingham, NG11 8NS, UK
| | - Daniela Caccamo
- Department of Biomedical Sciences, Dental Sciences & Morpho-Functional Imaging, Polyclinic Hospital University, Via C. Valeria 1, 98125, Messina, Italy
| | - Elisabetta A M Verderio
- School of Science and Technology, Centre for Health, Ageing and Understanding of Disease, Nottingham Trent University, Nottingham, NG11 8NS, UK.
- Biological Sciences Department (BiGeA), University of Bologna, Bologna, 40126, Italy.
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4
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Bajo-Santos C, Brokāne A, Zayakin P, Endzeliņš E, Soboļevska K, Belovs A, Jansons J, Sperga M, Llorente A, Radoviča-Spalviņa I, Lietuvietis V, Linē A. Plasma and urinary extracellular vesicles as a source of RNA biomarkers for prostate cancer in liquid biopsies. Front Mol Biosci 2023; 10:980433. [PMID: 36818049 PMCID: PMC9935579 DOI: 10.3389/fmolb.2023.980433] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 01/20/2023] [Indexed: 02/05/2023] Open
Abstract
Introduction: Extracellular vesicles (EVs) have emerged as a very attractive source of cancer- derived RNA biomarkers for the early detection, prognosis and monitoring of various cancers, including prostate cancer (PC). However, biofluids contain a mixture of EVs released from a variety of tissues and the fraction of total EVs that are derived from PC tissue is not known. Moreover, the optimal biofluid-plasma or urine-that is more suitable for the detection of EV- enclosed RNA biomarkers is not yet clear. Methodology: In the current study, we performed RNA sequencing analysis of plasma and urinary EVs collected before and after radical prostatectomy, and matched tumor and normal prostate tissues of 10 patients with prostate cancer. Results and Discussion: The most abundant RNA biotypes in EVs were miRNA, piRNA, tRNA, lncRNA, rRNA and mRNA. To identify putative cancer-derived RNA biomarkers, we searched for RNAs that were overexpressed in tumor as compared to normal tissues, present in the pre-operation EVs and decreased in the post-operation EVs in each RNA biotype. The levels of 63 mRNAs, 3 lncRNAs, 2 miRNAs and 1 piRNA were significantly increased in the tumors and decreased in the post-operation urinary EVs, thus suggesting that these RNAs mainly originate from PC tissue. No such RNA biomarkers were identified in plasma EVs. This suggests that the fraction of PC-derived EVs in urine is larger than in plasma and allows the detection and tracking of PC-derived RNAs.
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Affiliation(s)
| | - Agnese Brokāne
- Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Pawel Zayakin
- Latvian Biomedical Research and Study Centre, Riga, Latvia
| | | | | | | | | | | | - Alicia Llorente
- Department Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway,Department for Mechanical, Electronics and Chemical Engineering, Oslo Metropolitan University, Oslo, Norway
| | | | | | - Aija Linē
- Latvian Biomedical Research and Study Centre, Riga, Latvia,*Correspondence: Aija Linē,
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5
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Lopez-Bujanda ZA, Obradovic A, Nirschl TR, Crowley L, Macedo R, Papachristodoulou A, O'Donnell T, Laserson U, Zarif JC, Reshef R, Yuan T, Soni MK, Antonarakis ES, Haffner MC, Larman HB, Shen MM, Muranski P, Drake CG. TGM4: an immunogenic prostate-restricted antigen. J Immunother Cancer 2021; 9:e001649. [PMID: 34193566 PMCID: PMC8246381 DOI: 10.1136/jitc-2020-001649] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/08/2021] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Prostate cancer is the second leading cause of cancer-related death in men in the USA; death occurs when patients progress to metastatic castration-resistant prostate cancer (CRPC). Although immunotherapy with the Food and Drug Administration-approved vaccine sipuleucel-T, which targets prostatic acid phosphatase (PAP), extends survival for 2-4 months, the identification of new immunogenic tumor-associated antigens (TAAs) continues to be an unmet need. METHODS We evaluated the differential expression profile of castration-resistant prostate epithelial cells that give rise to CRPC from mice following an androgen deprivation/repletion cycle. The expression levels of a set of androgen-responsive genes were further evaluated in prostate, brain, colon, liver, lung, skin, kidney, and salivary gland from murine and human databases. The expression of a novel prostate-restricted TAA was then validated by immunostaining of mouse tissues and analyzed in primary tumors across all human cancer types in The Cancer Genome Atlas. Finally, the immunogenicity of this TAA was evaluated in vitro and in vivo using autologous coculture assays with cells from healthy donors as well as by measuring antigen-specific antibodies in sera from patients with prostate cancer (PCa) from a neoadjuvant clinical trial. RESULTS We identified a set of androgen-responsive genes that could serve as potential TAAs for PCa. In particular, we found transglutaminase 4 (Tgm4) to be highly expressed in prostate tumors that originate from luminal epithelial cells and only expressed at low levels in most extraprostatic tissues evaluated. Furthermore, elevated levels of TGM4 expression in primary PCa tumors correlated with unfavorable prognosis in patients. In vitro and in vivo assays confirmed the immunogenicity of TGM4. We found that activated proinflammatory effector memory CD8 and CD4 T cells were expanded by monocyte-derived dendritic cell (moDCs) pulsed with TGM4 to a greater extent than moDCs pulsed with either PAP or prostate-specific antigen (PSA), and T cells primed with TGM4-pulsed moDCs produce functional cytokines following a prime/boost regiment or in vitro stimulation. An IgG antibody response to TGM4 was detected in 30% of vaccinated patients, while fewer than 8% of vaccinated patients developed antibody responses to PSA or prostate-specific membrane antigen (PSMA). CONCLUSIONS These results suggest that TGM4 is an immunogenic, prostate-restricted antigen with the potential for further development as an immunotherapy target.
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Affiliation(s)
- Zoila A Lopez-Bujanda
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, New York, USA
- Bloomberg~Kimmel Institute for Cancer Immunotherapy, Johns Hopkins Medicine Sidney Kimmel Comprehensive Cancer Center, Baltimore, Maryland, USA
- Current: Molecular Pathogenesis Program, The Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, NY, USA
| | - Aleksandar Obradovic
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, New York, USA
| | - Thomas R Nirschl
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Bloomberg~Kimmel Institute for Cancer Immunotherapy, Johns Hopkins Medicine Sidney Kimmel Comprehensive Cancer Center, Baltimore, Maryland, USA
| | - Laura Crowley
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, New York, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, New York, USA
- Department of Medicine, Columbia University Irving Medical Center, New York, New York, USA
- Department of Systems Biology, Columbia University Irving Medical Center, New York, New York, USA
- Department of Urology, Columbia University Irving Medical Center, New York, New York, USA
| | - Rodney Macedo
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, New York, USA
| | - Alexandros Papachristodoulou
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, New York, USA
- Department of Molecular Pharmacology and Therapeutics, Columbia University Irving Medical Center, New York, New York, USA
| | - Timothy O'Donnell
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Uri Laserson
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Jelani C Zarif
- Bloomberg~Kimmel Institute for Cancer Immunotherapy, Johns Hopkins Medicine Sidney Kimmel Comprehensive Cancer Center, Baltimore, Maryland, USA
- Department of Oncology, Johns Hopkins Medicine Sidney Kimmel Comprehensive Cancer Center, Baltimore, Maryland, USA
| | - Ran Reshef
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, New York, USA
- Division of Hematology Oncology, Columbia University Irving Medical Center, New York, New York, USA
| | - Tiezheng Yuan
- Division of Immunology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Institute of Cell Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | - Mithil K Soni
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, New York, USA
| | - Emmanuel S Antonarakis
- Department of Oncology, Johns Hopkins Medicine Sidney Kimmel Comprehensive Cancer Center, Baltimore, Maryland, USA
| | - Michael C Haffner
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - H Benjamin Larman
- Division of Immunology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Institute of Cell Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | - Michael M Shen
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, New York, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, New York, USA
- Department of Medicine, Columbia University Irving Medical Center, New York, New York, USA
- Department of Systems Biology, Columbia University Irving Medical Center, New York, New York, USA
- Department of Urology, Columbia University Irving Medical Center, New York, New York, USA
| | - Pawel Muranski
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, New York, USA
- Department of Medicine, Columbia University Irving Medical Center, New York, New York, USA
| | - Charles G Drake
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, New York, USA
- Department of Urology, Columbia University Irving Medical Center, New York, New York, USA
- Division of Hematology Oncology, Columbia University Irving Medical Center, New York, New York, USA
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6
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Xie J, Wang M, Xu S, Huang Z, Grant PW. The Unsupervised Feature Selection Algorithms Based on Standard Deviation and Cosine Similarity for Genomic Data Analysis. Front Genet 2021; 12:684100. [PMID: 34054930 PMCID: PMC8155687 DOI: 10.3389/fgene.2021.684100] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 04/16/2021] [Indexed: 01/04/2023] Open
Abstract
To tackle the challenges in genomic data analysis caused by their tens of thousands of dimensions while having a small number of examples and unbalanced examples between classes, the technique of unsupervised feature selection based on standard deviation and cosine similarity is proposed in this paper. We refer to this idea as SCFS (Standard deviation and Cosine similarity based Feature Selection). It defines the discernibility and independence of a feature to value its distinguishable capability between classes and its redundancy to other features, respectively. A 2-dimensional space is constructed using discernibility as x-axis and independence as y-axis to represent all features where the upper right corner features have both comparatively high discernibility and independence. The importance of a feature is defined as the product of its discernibility and its independence (i.e., the area of the rectangular enclosed by the feature’s coordinate lines and axes). The upper right corner features are by far the most important, comprising the optimal feature subset. Based on different definitions of independence using cosine similarity, there are three feature selection algorithms derived from SCFS. These are SCEFS (Standard deviation and Exponent Cosine similarity based Feature Selection), SCRFS (Standard deviation and Reciprocal Cosine similarity based Feature Selection) and SCAFS (Standard deviation and Anti-Cosine similarity based Feature Selection), respectively. The KNN and SVM classifiers are built based on the optimal feature subsets detected by these feature selection algorithms, respectively. The experimental results on 18 genomic datasets of cancers demonstrate that the proposed unsupervised feature selection algorithms SCEFS, SCRFS and SCAFS can detect the stable biomarkers with strong classification capability. This shows that the idea proposed in this paper is powerful. The functional analysis of these biomarkers show that the occurrence of the cancer is closely related to the biomarker gene regulation level. This fact will benefit cancer pathology research, drug development, early diagnosis, treatment and prevention.
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Affiliation(s)
- Juanying Xie
- School of Computer Science, Shaanxi Normal University, Xi'an, China
| | - Mingzhao Wang
- School of Computer Science, Shaanxi Normal University, Xi'an, China.,College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Shengquan Xu
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Zhao Huang
- School of Computer Science, Shaanxi Normal University, Xi'an, China
| | - Philip W Grant
- Department of Computer Science, Swansea University, Swansea, United Kingdom
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7
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Abstract
While studying the human public IgM igome as represented by a library of 224,087 linear mimotopes, three exact matches to peptides in the proteins of SARS-CoV-2 were found: two in the open reading frame 1ab and one in the spike protein. Joining the efforts to fast track SARS-CoV-2 vaccine development, here we describe briefly these potential epitopes in comparison to mimotopes representing peptides of SARS-CoV, HCoV 229E and OC43.
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Affiliation(s)
- Velizar Shivarov
- Laboratory of Clinical Immunology and Department of Clinical Hematology, Sofiamed University Hospital, Sofia, Bulgaria
- Faculty of Biology, Sofia University, Sofia, Bulgaria
| | - Peter K. Petrov
- Department of Analysis, Geometry and Topology, Institute of Mathematics and Informatics, Bulgarian Academy of Sciences (BAS), Sofia, Bulgaria
| | - Anastas D. Pashov
- Department of Immunology, Stephan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences (BAS), Sofia, Bulgaria
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8
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Drabovich AP, Saraon P, Drabovich M, Karakosta TD, Dimitromanolakis A, Hyndman ME, Jarvi K, Diamandis EP. Multi-omics Biomarker Pipeline Reveals Elevated Levels of Protein-glutamine Gamma-glutamyltransferase 4 in Seminal Plasma of Prostate Cancer Patients. Mol Cell Proteomics 2019; 18:1807-1823. [PMID: 31249104 PMCID: PMC6731075 DOI: 10.1074/mcp.ra119.001612] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Indexed: 11/06/2022] Open
Abstract
Seminal plasma, because of its proximity to prostate, is a promising fluid for biomarker discovery and noninvasive diagnostics. In this study, we investigated if seminal plasma proteins could increase diagnostic specificity of detecting primary prostate cancer and discriminate between high- and low-grade cancers. To select 147 most promising biomarker candidates, we combined proteins identified through five independent experimental or data mining approaches: tissue transcriptomics, seminal plasma proteomics, cell line secretomics, tissue specificity, and androgen regulation. A rigorous biomarker development pipeline based on selected reaction monitoring assays was designed to evaluate the most promising candidates. As a result, we qualified 76, and verified 19 proteins in seminal plasma of 67 negative biopsy and 152 prostate cancer patients. Verification revealed a prostate-specific, secreted and androgen-regulated protein-glutamine gamma-glutamyltransferase 4 (TGM4), which predicted prostate cancer on biopsy and outperformed age and serum Prostate-Specific Antigen (PSA). A machine-learning approach for data analysis provided improved multi-marker combinations for diagnosis and prognosis. In the independent verification set measured by an in-house immunoassay, TGM4 protein was upregulated 3.7-fold (p = 0.006) and revealed AUC = 0.66 for detecting prostate cancer on biopsy for patients with serum PSA ≥4 ng/ml and age ≥50. Very low levels of TGM4 (120 pg/ml) were detected in blood serum. Collectively, our study demonstrated rigorous evaluation of one of the remaining and not well-explored prostate-specific proteins within the medium-abundance proteome of seminal plasma. Performance of TGM4 warrants its further investigation within the distinct genomic subtypes and evaluation for the inclusion into emerging multi-biomarker panels.
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Affiliation(s)
- Andrei P Drabovich
- ‡Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, M5T 3L9 Canada; §Department of Clinical Biochemistry, University Health Network, Toronto, Ontario, M5T 3L9 Canada; ¶Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario, M5T 3L9 Canada.
| | - Punit Saraon
- ‡Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, M5T 3L9 Canada
| | | | - Theano D Karakosta
- §Department of Clinical Biochemistry, University Health Network, Toronto, Ontario, M5T 3L9 Canada
| | | | - M Eric Hyndman
- **Department of Surgery, Division of Urology, Southern Alberta Institute of Urology, University of Calgary, Calgary, AB T2V 1P9, Canada
| | - Keith Jarvi
- ‡‡Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, M5T 3L9 Canada; §§Department of Surgery, Division of Urology, Mount Sinai Hospital, University of Toronto, Toronto, Ontario, M5T 3L9 Canada.
| | - Eleftherios P Diamandis
- ‡Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, M5T 3L9 Canada; §Department of Clinical Biochemistry, University Health Network, Toronto, Ontario, M5T 3L9 Canada; ¶Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario, M5T 3L9 Canada; ‡‡Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, M5T 3L9 Canada.
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9
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Eckert RL. Transglutaminase 2 takes center stage as a cancer cell survival factor and therapy target. Mol Carcinog 2019; 58:837-853. [PMID: 30693974 DOI: 10.1002/mc.22986] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 01/22/2019] [Accepted: 01/25/2019] [Indexed: 12/14/2022]
Abstract
Transglutaminase 2 (TG2) has emerged as a key cancer cell survival factor that drives epithelial to mesenchymal transition, angiogenesis, metastasis, inflammation, drug resistance, cancer stem cell survival and stemness, and invasion and migration. TG2 can exist in a GTP-bound signaling-active conformation or in a transamidase-active conformation. The GTP bound conformation of TG2 contributes to cell survival and the transamidase conformation can contribute to cell survival or death. We present evidence suggesting that TG2 has a role in human cancer, summarize what is known about the TG2 mechanism of action in a range of cancer types, and discuss TG2 as a cancer therapy target.
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Affiliation(s)
- Richard L Eckert
- Department of Biochemistry and Molecular Biology, Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, Maryland
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Kim H, Choi SM, Park S. GSEH: A Novel Approach to Select Prostate Cancer-Associated Genes Using Gene Expression Heterogeneity. IEEE/ACM Trans Comput Biol Bioinform 2018; 15:129-146. [PMID: 27775535 DOI: 10.1109/tcbb.2016.2618927] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
When a gene shows varying levels of expression among normal people but similar levels in disease patients or shows similar levels of expression among normal people but different levels in disease patients, we can assume that the gene is associated with the disease. By utilizing this gene expression heterogeneity, we can obtain additional information that abets discovery of disease-associated genes. In this study, we used collaborative filtering to calculate the degree of gene expression heterogeneity between classes and then scored the genes on the basis of the degree of gene expression heterogeneity to find "differentially predicted" genes. Through the proposed method, we discovered more prostate cancer-associated genes than 10 comparable methods. The genes prioritized by the proposed method are potentially significant to biological processes of a disease and can provide insight into them.
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Abstract
Although serotonin was discovered over 65 years ago, it has been only within the past decade that serotonin was found to be involved in a covalent post-translational modification to proteins. The enzyme transglutaminase catalyzes the transamidation of serotonin to a protein-bound glutamine residue; the amino group of serotonin is covalently bound to the gamma carboxamide of glutamine. The term serotonylation is used to describe this transamidation reaction to serotonin. Not only can serotonin be a substrate for transamidation to proteins but also other monoamine neurotransmitters are substrates including histamine, dopamine, and noradrenaline. The term monoaminylation has been coined to describe the transamidation of monoamines to protein substrates. Small G proteins have emerged as the most common substrate for monoaminylation and are activated by this post-translational modification. Fibronectin and cytoskeletal proteins are also substrates for monoaminylation. Serotonylation and monoaminylation are involved in a number of physiological functions, including platelet activation, insulin release, smooth muscle contraction, and regulation of membrane localization of the serotonin transporter. Stimulation of 5-HT2A receptors increases serotonylation and activates the small G protein Rac1, which plays a role in dendritic spine regulation. Monoaminylation is implicated in pathophysiological processes as well such as diabetes and hypertension. The availability of monoamines for monoaminylation is altered by antidepressants that target serotonin transporters, noradrenaline transporters, or the enzymatic degradation of monoamines as well as drugs of abuse such as cocaine and amphetamines. Further research on monoaminylation is needed to elucidate its physiological and pathophysiological roles and to explore monoaminylation as a novel target for drug therapy.
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Affiliation(s)
- Nancy A. Muma
- Department
of Pharmacology
and Toxicology, University of Kansas School of Pharmacy, Lawrence, Kansas 66045, United States
| | - Zhen Mi
- Department
of Pharmacology
and Toxicology, University of Kansas School of Pharmacy, Lawrence, Kansas 66045, United States
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Han AL, Kumar S, Fok JY, Tyagi AK, Mehta K. Tissue transglutaminase expression promotes castration-resistant phenotype and transcriptional repression of androgen receptor. Eur J Cancer 2014; 50:1685-96. [PMID: 24656569 DOI: 10.1016/j.ejca.2014.02.014] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Revised: 01/28/2014] [Accepted: 02/15/2014] [Indexed: 01/08/2023]
Abstract
Many studies have supported a role for inflammation in prostate tumour growth. However, the contribution of inflammation to the development of castration-resistant prostate cancer remains largely unknown. Based on observations that aberrant expression of the proinflammatory protein tissue transglutaminase (TG2) is associated with development of drug resistance and metastatic phenotype in multiple cancer types, we determined TG2 expression in prostate cancer cells. Herein we report that human prostate cancer cell lines with low expression of androgen receptor (AR) had high basal levels of TG2 expression. Also, overexpression of TG2 negatively regulated AR mRNA and protein expression and attenuated androgen sensitivity of prostate cancer cells. TG2 expression in prostate cancer cells was associated with increased invasion and resistance to chemotherapy. Mechanistically, TG2 activated nuclear factor (NF)-κB and induced epithelial-mesenchymal transition. TG2/NF-κB-mediated decrease in AR expression resulted from transcriptional repression involving cis-interaction of NF-κB in a complex with TG2 with the 5'-untranslated region of AR. Negative regulation of AR could be partially abrogated by repression of TG2 or NF-κB (p65/RelA) by gene-specific small interfering RNA. These results suggested that a novel pathway links androgen dependence with TG2-regulated inflammatory signalling and hence may make TG2 a novel therapeutic target for the prevention and treatment of castration-resistant prostate cancer.
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Affiliation(s)
- Amy Lee Han
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, United States
| | - Santosh Kumar
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, United States
| | - Jansina Y Fok
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, United States
| | - Amit K Tyagi
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, United States
| | - Kapil Mehta
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, United States.
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