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Sharifi S, Pakdel A, Pakdel MH, Tabashiri R, Bakhtiarizadeh MR, Tahmasebi A. Integrated co-expression analysis of regulatory elements (miRNA, lncRNA, and TFs) in bovine monocytes induced by Str. uberis. Sci Rep 2023; 13:15076. [PMID: 37699972 PMCID: PMC10497586 DOI: 10.1038/s41598-023-42067-4] [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: 04/18/2023] [Accepted: 09/05/2023] [Indexed: 09/14/2023] Open
Abstract
Non-coding RNAs, including long non-coding RNAs (lncRNAs) and microRNAs (miRNAs), together with transcription factors, are critical pre-, co-, and post-transcriptional regulators. In addition to their criteria as ideal biomarkers, they have great potential in disease prognosis, diagnosis, and treatment of complex diseases. Investigation of regulatory mechanisms in the context of bovine mastitis, as most common and economic disease in the dairy industry, to identify elements influencing the expression of candidate genes as key regulators of the mammary immune response is not yet fully understood. Transcriptome profiles (50 RNA-Seq and 50 miRNA-Seq samples) of bovine monocytes induced by Str. uberis were used for co-expression module detection and preservation analysis using the weighted gene co-expression network analysis (WGCNA) approach. Assigned mi-, lnc-, and m-modules used to construct the integrated regulatory networks and miRNA-lncRNA-mRNA regulatory sub-networks. Remarkably, we have identified 18 miRNAs, five lncRNAs, and seven TFs as key regulators of str. uberis-induced mastitis. Most of the genes introduced here, mainly involved in immune response, inflammation, and apoptosis, were new to mastitis. These findings may help to further elucidate the underlying mechanisms of bovine mastitis, and the discovered genes may serve as signatures for early diagnosis and treatment of the disease.
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Affiliation(s)
- Somayeh Sharifi
- Department of Animal Science, College of Agriculture, Isfahan University of Technology, Isfahan, 84156-83111, Islamic Republic of Iran.
| | - Abbas Pakdel
- Department of Animal Science, College of Agriculture, Isfahan University of Technology, Isfahan, 84156-83111, Islamic Republic of Iran.
| | - Mohammad Hossein Pakdel
- Department of Plant Molecular Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Islamic Republic of Iran
| | - Raana Tabashiri
- Agricultural Biotechnology Department, Faculty of Agriculture, Tarbiat Modares University, Tehran, Islamic Republic of Iran
| | - Mohammad Reza Bakhtiarizadeh
- Department of Animal and Poultry Science, College of Aburaihan, University of Tehran, Tehran, 3391653755, Islamic Republic of Iran
| | - Ahmad Tahmasebi
- Institute of Biotechnology, Shiraz University, Shiraz, 71946-84334, Islamic Republic of Iran
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Massó-Vallés D, Beaulieu ME, Soucek L. MYC, MYCL, and MYCN as therapeutic targets in lung cancer. Expert Opin Ther Targets 2020; 24:101-114. [PMID: 32003251 DOI: 10.1080/14728222.2020.1723548] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Introduction: Lung cancer is the leading cause of cancer-related mortality globally. Despite recent advances with personalized therapies and immunotherapy, the prognosis remains dire and recurrence is frequent. Myc is an oncogene deregulated in human cancers, including lung cancer, where it supports tumorigenic processes and progression. Elevated Myc levels have also been associated with resistance to therapy.Areas covered: This article summarizes the genomic and transcriptomic studies that compile evidence for (i) MYC, MYCN, and MYCL amplification and overexpression in lung cancer patients, and (ii) their prognostic significance. We collected the most recent literature regarding the development of Myc inhibitors where the emphasis is on those inhibitors tested in lung cancer experimental models and their potential for future clinical application.Expert opinion: The targeting of Myc in lung cancer is potentially an unprecedented opportunity for inhibiting a key player in tumor progression and maintenance and therapeutic resistance. Myc inhibitory strategies are on the path to their clinical application but further work is necessary for the assessment of their use in combination with standard treatment approaches. Given the role of Myc in immune suppression, a significant opportunity may exist in the combination of Myc inhibitors with immunotherapies.
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Affiliation(s)
| | | | - Laura Soucek
- Peptomyc S.L., Edifici Cellex, Hospital Vall d'Hebron, Barcelona, Spain.,Edifici Cellex, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain.,Institució Catalana De Recerca I Estudis Avançats (ICREA), Barcelona, Spain.,Department of Biochemistry and Molecular Biology, Universitat Autònoma De Barcelona, Bellaterra, Spain
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Cho JY, Sung HJ. Proteomic approaches in lung cancer biomarker development. Expert Rev Proteomics 2014; 6:27-42. [DOI: 10.1586/14789450.6.1.27] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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Mun J, Kim YH, Yu J, Bae J, Noh DY, Yu MH, Lee C. A proteomic approach based on multiple parallel separation for the unambiguous identification of an antibody cognate antigen. Electrophoresis 2011; 31:3428-36. [PMID: 20872419 DOI: 10.1002/elps.201000136] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Autoantibodies obtained from cancer patients have been identified as useful tools for cancer diagnostics, prognostics, and as potential targets for immunotherapy. Serological proteome analysis in combination with 2-DE is a classic strategy for identification of tumor-associated antigens in the serum of cancer patients. However, serological proteome analysis cannot always indicate the true antigen out of a complex proteome identified from a single protein spot because the most abundant protein is not always the most antigenic. To address this problem, we utilized multiple parallel separation (MPS) for proteome separation. The common identities present in the fractions obtained using different separation methods were regarded as the true antigens. The merit of our MPS technique was validated using anti-ARPC2 and anti-PTEN antibodies. Next, we applied the MPS technique for the identification of glycyl-tRNA synthetase as the cognate antigen for an autoantibody that was overexpressed in the plasma of breast cancer patients. These results reveal that MPS can unambiguously identify an antibody cognate antigen by reducing false-positives. Therefore, MPS could be used for the characterization of diagnostic antibodies raised in laboratory animals as well as autoantibodies isolated from diseased patients.
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Affiliation(s)
- Joohee Mun
- Functional Proteomics Center, Korea Institute of Science and Technology, Seongbuk, Seoul, Republic of Korea
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Caron M, Choquet-Kastylevsky G, Joubert-Caron R. Cancer immunomics using autoantibody signatures for biomarker discovery. Mol Cell Proteomics 2007; 6:1115-22. [PMID: 17376768 DOI: 10.1074/mcp.r600016-mcp200] [Citation(s) in RCA: 119] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The increased incidence of autoantibodies in malignancies has been described since the 1970s. Thus the ability to determine molecular fingerprinting of autoantibodies (antibody signatures) may provide useful clinical diagnostic and prognostic information. This review describes the use of several proteomics approaches for the identification of antigens recognized by these autoantibodies. Serological proteome analysis combines separation of tumor cell proteins on two-dimensional gel electrophoresis gels, Western blotting with sera of patients and healthy subjects, and identification of the detected antigens by MS. Alternatively multiple affinity protein profiling combines isolation of the antigens recognized by patient antibodies by two-dimensional immunoaffinity chromatography and identification by MS/MS. The use and limitations of reverse phase protein microarrays for testing patient serum containing autoantibodies are also considered. Lastly the most important difficulty of any proteomically identified autoantibody signature is validation in patient cohorts or clinical samples.
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Affiliation(s)
- Michel Caron
- Protein Biochemistry and Proteomics Laboratory, UMR CNRS 7033 (BioMoCeTi), Unité de Formation et de Recherche Santé-Médecine-Biologie Humaine, Paris 13 University, 93017 Bobigny cedex, France.
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Chang GC, Liu KJ, Hsieh CL, Hu TS, Charoenfuprasert S, Liu HK, Luh KT, Hsu LH, Wu CW, Ting CC, Chen CY, Chen KC, Yang TY, Chou TY, Wang WH, Whang-Peng J, Shih NY. Identification of alpha-enolase as an autoantigen in lung cancer: its overexpression is associated with clinical outcomes. Clin Cancer Res 2006; 12:5746-54. [PMID: 17020980 DOI: 10.1158/1078-0432.ccr-06-0324] [Citation(s) in RCA: 122] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE Although existence of humoral immunity has been previously shown in malignant pleural effusions, only a limited number of immunogenic tumor-associated antigens (TAA) have been identified and associated with lung cancer. In this study, we intended to identify more TAAs in pleural effusion-derived tumor cells. EXPERIMENTAL DESIGN Using morphologically normal lung tissues as a control lysate in Western blotting analyses, 54 tumor samples were screened with autologous effusion antibodies. Biochemical purification and mass spectrometric identification of TAAs were done using established effusion tumor cell lines as antigen sources. We identified a p48 antigen as alpha-enolase (ENO1). Semiquantitative immunohistochemistry was used to evaluate expression status of ENO1 in the tissue samples of 80 patients with non-small cell lung cancer (NSCLC) and then correlated with clinical variables. RESULTS Using ENO1-specifc antiserum, up-regulation of ENO1 expression in effusion tumor cells from 11 of 17 patients was clearly observed compared with human normal lung primary epithelial and non-cancer-associated effusion cells. Immunohistochemical studies consistently showed high level of ENO1 expression in all the tumors we have examined thus far. Log-rank and Cox's analyses of ENO1 expression status revealed that its expression level in primary tumors was a key factor contributing to overall- and progression-free survivals of patients (P < 0.05). The same result was also obtained in the early stage of NSCLC patients, showing that tumors expressing relatively higher ENO1 level were tightly correlated with poorer survival outcomes. CONCLUSIONS Our data strongly support a prognostic role of ENO1 in determining tumor malignancy of patients with NSCLC.
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Affiliation(s)
- Gee-Chen Chang
- Division of Chest Medicine, Department of Internal Medicine, Taichung Veterans General Hospital, Taipei, Taiwan, Republic of China
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Yan Y, Phan L, Yang F, Talpaz M, Yang Y, Xiong Z, Ng B, Timchenko NA, Wu CJ, Ritz J, Wang H, Yang XF. A novel mechanism of alternative promoter and splicing regulates the epitope generation of tumor antigen CML66-L. THE JOURNAL OF IMMUNOLOGY 2004; 172:651-60. [PMID: 14688378 PMCID: PMC3901998 DOI: 10.4049/jimmunol.172.1.651] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
This report describes the difference in the epitope generation of two isoforms of self-tumor Ag CML66 and the regulation mechanism. We identified a new CML66 short isoform, termed CML66-S. The previously identified long CML66 is referred to as CML66-L. CML66-S shares the C terminus with CML66-L but has its unique N terminus. CML66-S is predominantly expressed in testis, but is also expressed in very low levels in tumor cells, whereas CML66-L is expressed in tumor cells and testis. Differential expression of CML66-L and CML66-S in tumor cells resulted from regulation at transcription, although alternative splicing also participated in the generation of the isoforms. In addition, Ab titers to a CML66-L peptide were significantly higher than that to CML66-S peptide in the sera from patients with tumors. Finally, the Abs to full-length CML66-L in the sera from patients with tumors were correlated with the Abs in the sera from these patients to CML66-L-38, which is a fusion protein with a CML66-L-specific N terminus. This suggests that the CML66-L isoform is mainly responsible for the epitope generation. Our studies have identified the alternative promoter in combination with alternative splicing as a novel mechanism for regulation of the epitope generation of a self-tumor Ag.
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MESH Headings
- Alternative Splicing/immunology
- Amino Acid Sequence
- Animals
- Antigens, Neoplasm/biosynthesis
- Antigens, Neoplasm/genetics
- Antigens, Neoplasm/isolation & purification
- Epitopes/biosynthesis
- Epitopes/genetics
- Epitopes/isolation & purification
- Humans
- Interferon-alpha/therapeutic use
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/genetics
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/immunology
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/therapy
- Male
- Mice
- Molecular Sequence Data
- Promoter Regions, Genetic/immunology
- Protein Isoforms/biosynthesis
- Protein Isoforms/genetics
- Testis/immunology
- Testis/metabolism
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Affiliation(s)
- Yan Yan
- Department of Medicine, University of Texas M. D. Anderson Cancer Center, Houston, TX 77030
| | - Leuyen Phan
- Department of Medicine, University of Texas M. D. Anderson Cancer Center, Houston, TX 77030
| | - Fan Yang
- Department of Medicine, University of Texas M. D. Anderson Cancer Center, Houston, TX 77030
| | - Moshe Talpaz
- Department of Bioimmunotherapy, University of Texas M. D. Anderson Cancer Center, Houston, TX 77030
| | - Yu Yang
- Department of Medicine, University of Texas M. D. Anderson Cancer Center, Houston, TX 77030
| | - Zeyu Xiong
- Department of Medicine, University of Texas M. D. Anderson Cancer Center, Houston, TX 77030
| | - Bernard Ng
- Department of Medicine, University of Texas M. D. Anderson Cancer Center, Houston, TX 77030
| | - Nikolai A. Timchenko
- Department of Pathology, Baylor College of Medicine, University of Texas M. D. Anderson Cancer Center, Houston, TX 77030
| | - Catherine J. Wu
- Center for Hematologic Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115
| | - Jerome Ritz
- Center for Hematologic Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115
| | - Hong Wang
- Department of Medicine, University of Texas M. D. Anderson Cancer Center, Houston, TX 77030
| | - Xiao-Feng Yang
- Department of Medicine, University of Texas M. D. Anderson Cancer Center, Houston, TX 77030
- Department of Immunology, University of Texas M. D. Anderson Cancer Center, Houston, TX 77030
- Department of Bioimmunotherapy, University of Texas M. D. Anderson Cancer Center, Houston, TX 77030
- Address correspondence and reprint requests to Dr. Xiao-Feng Yang, Section of Immunology, Allergy, and Rheumatology, Department of Medicine, Biology of Inflammation Center, Baylor College of Medicine, One Baylor Plaza, BCM 285, Suite 672E, Houston, TX 77030-3411.
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Diesinger I, Bauer C, Brass N, Schaefers HJ, Comtesse N, Sybrecht G, Meese E. Toward a more complete recognition of immunoreactive antigens in squamous cell lung carcinoma. Int J Cancer 2002; 102:372-8. [PMID: 12402307 DOI: 10.1002/ijc.10714] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
There is very limited knowledge about the antibody response against tumor-expressed antigens in lung cancer. To arrive at a more complete picture of lung cancer antigens, we generated 2 cDNA libraries from squamous cell lung carcinoma and isolated 15 immunogenic antigens using autologous sera. Among the antigens most frequently identified were the lymphoid blast crisis oncogene (LBC), an unknown hypothetical protein and the p53-binding protein (TP53 BP), which have already been associated with tumor development. Of the immunogenic antigens, 6 map to chromosomes that are frequently altered in squamous cell lung carcinoma. SEREX database analysis showed that 7 of the identified immunogenic antigens have been associated with the humoral immune response in other human tumors. Screening with heterologous sera of patients with lung carcinoma identified 4 antigens, including human protein kinase C and TP53 BP, which have also been found by autologous screening. Only 1 of the 15 identified antigens reacted with any of the 36 control sera, which were taken from individuals without known disease. Sera from adenocarcinoma and large cell carcinoma of the lung were not reactive for the antigens. In summary, using 2 newly established cDNA libraries, we isolated 15 novel antigens, which were subsequently evaluated for the frequency of their corresponding antibodies in autologous, normal and heterologous sera; their chromosomal localization; and their correlation with survival after surgery.
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Affiliation(s)
- Isabel Diesinger
- Department of Human Genetics, Medical School, University of Saarland, Homburg/Saar, Germany
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Meese E, Comtesse N. Cancer genetics and tumor antigens: time for a combined view? Genes Chromosomes Cancer 2002; 33:107-13. [PMID: 11793436 DOI: 10.1002/gcc.1224] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Affiliation(s)
- Eckart Meese
- Institut für Humangenetik, Universitätskliniken des Saarlandes, Homburg/Saar, Germany.
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de la Guardia C, Casiano CA, Trinidad-Pinedo J, Báez A. CENP-F gene amplification and overexpression in head and neck squamous cell carcinomas. Head Neck 2001; 23:104-12. [PMID: 11303627 DOI: 10.1002/1097-0347(200102)23:2<104::aid-hed1005>3.0.co;2-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
BACKGROUND Antibodies against cancer-related genes have been detected in human cancers including head and neck cancers. High titers of c-Myc autoantibodies have been linked to gene amplification and tumor progression. Centromere protein-F (CENP-F) autoantibodies have been detected in patients with various cancers, suggesting similar gene alteration. METHODS CENP-F and c-MYC amplification was assessed in 72 head and neck squamous cell carcinoma (HNSCC) patients. Tumor and matched mucosa from 22 patients were analyzed for CENP-F mRNA levels by RT-PCR. RESULTS The larynx was the site most altered by amplification of either gene. CENP-F and c-MYC were amplified in 11% and 17% of the tumors, respectively. Coamplification was found in 7% of the tumors, most of which showed regional node involvement. CENP-F mRNA was overexpressed in 36% of tumors, and 23% of paired mucosa. CONCLUSION Our results provide the first evidence that CENP-F gene is amplified and overexpressed in HNSCC. No correlation was noted between CENP-F amplification and clinicopathologic parameters. However, CENP-F overexpression correlated with nodal metastasis.
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Affiliation(s)
- C de la Guardia
- Department of Pharmacology, University of Puerto Rico, San Juan, USA
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