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Yu R, Yang S, Liu Y, Zhu Z. Identification and validation of serum autoantibodies in children with B-cell acute lymphoblastic leukemia by serological proteome analysis. Proteome Sci 2022; 20:3. [PMID: 35109855 PMCID: PMC8808998 DOI: 10.1186/s12953-021-00184-w] [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: 09/01/2021] [Accepted: 12/16/2021] [Indexed: 01/20/2023] Open
Abstract
Background B-cell acute lymphoblastic leukemia (B-ALL) is the most common malignancy of childhood. Even though significant progresses have been made in the treatment of B-ALL, some pediatric B-ALL have still poor prognosis. The identification of tumor autoantibodies may have utility in early cancer diagnosis and immunotherapy. In this study, we used serological proteome analysis (SERPA) to screen serum autoantibodies of pediatric B-ALL, aiming to contribute to the early detection of B-ALL in children. Methods The total proteins from three pooled B-ALL cell lines (NALM-6, REH and BALL-1 cells) were separated using two-dimensional gel electrophoresis (2-DE), which was followed by Western blot by mixed serum samples from children with B-ALL (n=20) or healthy controls (n=20). We analyzed the images of 2-D gel and Western blot by PDQuest software, and then identified the spots of immune responses in B-ALL samples compared with those in control samples. The proteins from spots were identified using mass spectrometry (MS). The autoantibodies against alpha-enolase (α-enolase) and voltage-dependent anion-selective channel protein 1 (VDAC1) were further validated in sera from another 30 children with B-ALL and 25 normal individuals by the use of enzyme-linked immunosorbent assay (ELISA). The protein expression levels of the candidate antigens α-enolase and VDAC1 in B-ALL were thoroughly studied by immunohistochemical analysis. Results Utilizing the SERPA approach, α-enolase and VDAC1 were identified as candidate autoantigens in children with B-ALL. The frequencies of autoantibodies against α-enolase and VDAC1 in children with B-ALL were 27% and 23% by using ELISA analysis, respectively, which were significantly higher than those in normal controls (4% and 0, p<0.05). Immunohistochemical analysis showed the expression of α-enolase and VDAC1 was positive in 95% and 85% of B-ALL patients, respectively, but negative expression levels were showed in the control group. Conclusions This study incidated that α-enolase and VDAC1 may be the autoantigens associated with B-ALL. Therefore, α-enolase and VDAC1 autoantibodies may be the potential serological markers for children with B-ALL. Supplementary Information The online version contains supplementary material available at 10.1186/s12953-021-00184-w.
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Affiliation(s)
- Runhong Yu
- Institute of Hematology, Henan Provincial People's Hospital, 7 Weiwu Road, Jinshui District, Zhengzhou, Henan, 450003, China.,Henan Key laboratory of Stem Cell Differentiation and Modification, Henan Provincial People's Hospital, Zhengzhou, Henan, China
| | - Shiwei Yang
- Institute of Hematology, Henan Provincial People's Hospital, 7 Weiwu Road, Jinshui District, Zhengzhou, Henan, 450003, China.,Henan Key laboratory of Stem Cell Differentiation and Modification, Henan Provincial People's Hospital, Zhengzhou, Henan, China
| | - Yufeng Liu
- Department of Pediatrics, The First Affiliated Hospital of Zhengzhou University, 1 Jianshe Road, Erqi District, Zhengzhou, Henan, 450052, China
| | - Zunmin Zhu
- Institute of Hematology, Henan Provincial People's Hospital, 7 Weiwu Road, Jinshui District, Zhengzhou, Henan, 450003, China. .,Henan Key laboratory of Stem Cell Differentiation and Modification, Henan Provincial People's Hospital, Zhengzhou, Henan, China. .,Department of Hematology, People's Hospital of Zhengzhou University, Henan, Zhengzhou, China.
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Ma Y, Wang X, Qiu C, Qin J, Wang K, Sun G, Jiang D, Li J, Wang L, Shi J, Wang P, Ye H, Dai L, Jiang BH, Zhang J. Using protein microarray to identify and evaluate autoantibodies to tumor-associated antigens in ovarian cancer. Cancer Sci 2020; 112:537-549. [PMID: 33185955 PMCID: PMC7894002 DOI: 10.1111/cas.14732] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 11/06/2020] [Accepted: 11/08/2020] [Indexed: 12/16/2022] Open
Abstract
The aim of this study was to develop a noninvasive serological diagnostic approach in identifying and evaluating a panel of candidate autoantibodies to tumor‐associated antigens (TAAs) based on protein microarray technology for early detection of ovarian cancer (OC). Protein microarray based on 154 proteins encoded by 138 cancer driver genes was used to screen candidate anti‐TAA autoantibodies in a discovery cohort containing 17 OC and 27 normal controls (NC). Indirect enzyme‐linked immunosorbent assay (ELISA) was used to detect the content of candidate anti‐TAA autoantibodies in sera from 140 subjects in the training cohort. Differential anti‐TAA autoantibodies were further validated in the validation cohort with 328 subjects. Subsequently, 112 sera from the patients with ovarian benign diseases with 104 OC sera and 104 NC sera together were recruited to identify the specificity of representative autoantibodies to OC among ovarian diseases. Five TAAs (GNAS, NPM1, FUBP1, p53, and KRAS) were screened out in the discovery phase, in which four of them presented higher levels in OC than controls (P < .05) in the training cohort, which was consistent with the result in the subsequent validation cohort. An optimized panel of three anti‐TAA (GNAS, p53, and NPM1) autoantibodies was identified to have relatively high sensitivity (51.2%), specificity (86.0%), and accuracy (68.6%), respectively. This panel can identify 51% of OC patients with CA125 negative. This study supports our assumption that anti‐TAA autoantibodies can be considered as potential diagnostic biomarkers for detection of OC; especially a panel of three anti‐TAA autoantibodies could be a good tool in immunodiagnosis of OC.
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Affiliation(s)
- Yan Ma
- Department of Epidemiology and Health Statistics & Henan Key Laboratory of Tumor Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, China.,Laboratory of Molecular Biology, Henan Luoyang Orthopedic Hospital & Henan Provincial Orthopedic Institute, Zhengzhou, China
| | - Xiao Wang
- Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China.,Department of Pathology, The University of Iowa, Iowa City, IA, USA
| | - Cuipeng Qiu
- Department of Epidemiology and Health Statistics & Henan Key Laboratory of Tumor Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Jiejie Qin
- Department of Epidemiology and Health Statistics & Henan Key Laboratory of Tumor Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Keyan Wang
- Department of Epidemiology and Health Statistics & Henan Key Laboratory of Tumor Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Guiying Sun
- Department of Epidemiology and Health Statistics & Henan Key Laboratory of Tumor Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Di Jiang
- Department of Epidemiology and Health Statistics & Henan Key Laboratory of Tumor Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Jitian Li
- Laboratory of Molecular Biology, Henan Luoyang Orthopedic Hospital & Henan Provincial Orthopedic Institute, Zhengzhou, China
| | - Lin Wang
- Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China.,Department of Pathology, The University of Iowa, Iowa City, IA, USA
| | - Jianxiang Shi
- Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | - Peng Wang
- Department of Epidemiology and Health Statistics & Henan Key Laboratory of Tumor Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Hua Ye
- Department of Epidemiology and Health Statistics & Henan Key Laboratory of Tumor Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Liping Dai
- Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | - Bing-Hua Jiang
- Department of Pathology, The University of Iowa, Iowa City, IA, USA
| | - Jianying Zhang
- Department of Epidemiology and Health Statistics & Henan Key Laboratory of Tumor Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, China.,Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
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3
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Akhtar J, Priya R, Jain V, Sakhuja P, Agarwal AK, Goyal S, Polisetty RV, Sirdeshmukh R, Kar S, Gautam P. Immunoproteomics approach revealed elevated autoantibody levels against ANXA1 in early stage gallbladder carcinoma. BMC Cancer 2020; 20:1175. [PMID: 33261560 PMCID: PMC7709428 DOI: 10.1186/s12885-020-07676-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 11/22/2020] [Indexed: 11/22/2022] Open
Abstract
Background Early diagnosis is important for the timely treatment of gallbladder carcinoma (GBC) patients and may lead to increased survival outcomes. Here, we have applied serological proteome analysis (SERPA), an immunoproteomics approach, for the detection of ‘tumor-associated antigens (TAAs) that elicit humoral response’ in early stage GBC patients. Methods Total protein from pooled tumor tissue of GBC patients (n = 7) was resolved by two-dimensional gel electrophoresis (2-DE) followed by immunoblotting using pooled blood plasma from healthy volunteers (n = 11) or gallstone disease (GSD) cases (n = 11) or early stage GBC (Stage I and II) (n = 5) or GBC stage IIIA (n = 9). 2-D gel and immunoblot images were acquired and analyzed using PDQuest software to identify immunoreactive spots in GBC cases in comparison to controls. Proteins from immunoreactive spots were identified by liquid chromatography- tandem mass spectrometric analysis (LC-MS/MS). Autoantibody levels for two of the functionally relevant proteins were investigated in individual plasma samples (52 cases and 89 controls) by dot blot assay using recombinant proteins. Results Image analysis using PDQuest software identified 25 protein spots with significantly high or specific immunoreactivity in GBC cases. Mass spectrometric analysis of 8 corresponding protein spots showing intense immunoreactivity (based on densitometric analysis) in early stage GBC or GBC stage IIIA cases led to the identification of 27 proteins. Some of the identified proteins include ANXA1, HSPD1, CA1, CA2, ALDOA and CTSD. Among the two proteins, namely ANXA1 and HSPD1 verified using a cohort of samples, significantly elevated autoantibody levels against ANXA1 were observed in early stage GBC cases in comparison to healthy volunteers or GSD cases (unpaired t-test, p < 0.05). Receiver operating characteristic (ROC) curve analysis for ANXA1 showed an Area under the Curve (AUC) of 0.69, with 41.7% sensitivity against a specificity of 89.9% for early stage GBC. IHC analysis for ANXA1 protein showed ‘high’ expression levels in 72% of GBC cases whereas all the controls showed ‘low’ expression levels. Conclusions The study suggests that the ANXA1 autoantibody levels against ANXA1 may be potentially employed for early stage detection of GBC patients. Other proteins could also be explored and verified in a large cohort of clinical samples. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-020-07676-6.
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Affiliation(s)
- Javed Akhtar
- Laboratory of Molecular Oncology, ICMR- National Institute of Pathology, Safdarjung Hospital Campus, New Delhi, 110029, India.,Jamia Hamdard- Institute of Molecular Medicine, Jamia Hamdard, New Delhi, 110062, India
| | - Ratna Priya
- Laboratory of Molecular Oncology, ICMR- National Institute of Pathology, Safdarjung Hospital Campus, New Delhi, 110029, India.,Jamia Hamdard- Institute of Molecular Medicine, Jamia Hamdard, New Delhi, 110062, India
| | - Vaishali Jain
- Laboratory of Molecular Oncology, ICMR- National Institute of Pathology, Safdarjung Hospital Campus, New Delhi, 110029, India.,Manipal Academy of Higher Education (MAHE) , 576104, Manipal, India
| | - Puja Sakhuja
- Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, 110002, India
| | - Anil Kumar Agarwal
- Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, 110002, India
| | - Surbhi Goyal
- Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, 110002, India
| | - Ravindra Varma Polisetty
- Department of Biochemistry, Sri Venkateswara College, University of Delhi, New Delhi, 110021, India
| | - Ravi Sirdeshmukh
- Manipal Academy of Higher Education (MAHE) , 576104, Manipal, India.,Institute of Bioinformatics, International Tech Park, Bangalore, 560066, India
| | - Sudeshna Kar
- Jamia Hamdard- Institute of Molecular Medicine, Jamia Hamdard, New Delhi, 110062, India
| | - Poonam Gautam
- Laboratory of Molecular Oncology, ICMR- National Institute of Pathology, Safdarjung Hospital Campus, New Delhi, 110029, India.
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Cai X, Ge W, Yi X, Sun R, Zhu J, Lu C, Sun P, Zhu T, Ruan G, Yuan C, Liang S, Lyu M, Huang S, Zhu Y, Guo T. PulseDIA: Data-Independent Acquisition Mass Spectrometry Using Multi-Injection Pulsed Gas-Phase Fractionation. J Proteome Res 2020; 20:279-288. [PMID: 32975123 DOI: 10.1021/acs.jproteome.0c00381] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The performance of data-independent acquisition (DIA) mass spectrometry (MS) depends on the separation efficiency of peptide precursors. In Orbitrap-based mass spectrometers, separation efficiency of peptide precursors is limited by the relatively slow scanning rate compared to time of flight (TOF)-based MS. Here, we present PulseDIA, a multi-injection gas-phase fractionation (GPF) strategy for enhanced DIA-MS. This is achieved by equally dividing the conventional DIA analysis covering the entire mass range into multiple injections for DIA analyses with complementary windows. Using mouse liver digests, the PulseDIA method identified up to 50% more peptides and 29% more protein groups than that by conventional DIA with the same length of effective gradient time. Compared to conventional multi-injection GPF, PusleDIA exhibited higher flexibility and identified up to 18% more peptides and 8% more protein groups using two injections. The gain of peptides per effective time unit was the highest in PulseDIA compared to conventional DIA and GPF. We further applied the PulseDIA method to profile the proteome of 18 human tissue samples (benign and malignant) from nine cholangiocarcinoma (CCA) patients. PulseDIA identified 7796 protein groups in these CCA samples, with a 14% increase of protein group identification compared to the conventional DIA method. The missing value for protein matrix dropped by 7% using PulseDIA compared to DIA. A total of 681 significantly altered proteins were detected in CCA samples using PulseDIA, including several dysregulated proteins, which were absent in the conventional DIA analysis. Taken together, we present PulseDIA as an enhanced DIA-MS method with improved sensitivity and reproducibility.
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Affiliation(s)
- Xue Cai
- Zhejiang Provincial Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou 310024, Zhejiang, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, Zhejiang, China
| | - Weigang Ge
- Zhejiang Provincial Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou 310024, Zhejiang, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, Zhejiang, China
| | - Xiao Yi
- Zhejiang Provincial Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou 310024, Zhejiang, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, Zhejiang, China
| | - Rui Sun
- Zhejiang Provincial Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou 310024, Zhejiang, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, Zhejiang, China
| | - Jiang Zhu
- Center for Stem Cell Research and Application, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei, China
| | - Cong Lu
- Center for Stem Cell Research and Application, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei, China
| | - Ping Sun
- Department of Hepatobiliary Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei, China
| | - Tiansheng Zhu
- Zhejiang Provincial Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou 310024, Zhejiang, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, Zhejiang, China
| | - Guan Ruan
- Zhejiang Provincial Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou 310024, Zhejiang, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, Zhejiang, China
| | - Chunhui Yuan
- Zhejiang Provincial Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou 310024, Zhejiang, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, Zhejiang, China
| | - Shuang Liang
- Zhejiang Provincial Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou 310024, Zhejiang, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, Zhejiang, China
| | - Mengge Lyu
- Zhejiang Provincial Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou 310024, Zhejiang, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, Zhejiang, China
| | - Shiang Huang
- Center for Stem Cell Research and Application, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei, China
| | - Yi Zhu
- Zhejiang Provincial Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou 310024, Zhejiang, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, Zhejiang, China
| | - Tiannan Guo
- Zhejiang Provincial Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou 310024, Zhejiang, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, Zhejiang, China
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Beutgen VM, Schmelter C, Pfeiffer N, Grus FH. Autoantigens in the trabecular meshwork and glaucoma-specific alterations in the natural autoantibody repertoire. Clin Transl Immunology 2020; 9:e01101. [PMID: 32140226 PMCID: PMC7049230 DOI: 10.1002/cti2.1101] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 11/18/2019] [Accepted: 12/07/2019] [Indexed: 12/18/2022] Open
Abstract
OBJECTIVES Primary open-angle glaucoma (POAG) is a neurodegenerative disorder leading to a gradual vision loss caused by progressive damage to the optic nerve. Immunological processes are proposed to be involved in POAG pathogenesis. Altered serological autoantibody levels have been frequently reported, but complete analyses of the natural autoantibodies with respect to disease-related alterations are scarce. Here, we provide an explorative analysis of pathways and biological processes that may involve naturally immunogenic proteins and highlight POAG-specific alterations. METHODS Mass spectrometry-based antibody-mediated identification of autoantigens (MS-AMIDA) was carried out in healthy and glaucomatous trabecular meshwork (TM) cell lines, using antibody pools purified from serum samples of 30 POAG patients and 30 non-glaucomatous subjects. Selected antigens were validated by protein microarray (n = 120). Bioinformatic assessment of identified autoantigens, including Gene Ontology (GO) enrichment analysis and protein-protein interaction networks, was applied. RESULTS Overall, we identified 106 potential autoantigens [false discovery rate (FDR) < 0.01], from which we considered 66 as physiological targets of natural autoantibodies. Twenty-one autoantigens appeared to be related to POAG. Bioinformatic analysis revealed that the platelet-derived growth factor receptor beta (PDGFRB) pathway involved in TM fibrosis was particularly rich in POAG-related antigens. Antibodies to threonine-tRNA ligase (TARS), component 1 Q subcomponent-binding protein (C1QBP) and paraneoplastic antigen Ma2 (PNMA2) showed significantly (P < 0.05) higher levels in POAG patients as validated by protein microarray. CONCLUSION This study provides new insights into autoimmunity in health and glaucoma. Bioinformatic analysis of POAG-related autoantigens showed a strong association with the PDGFRB pathway and also increased levels of PNMA2, TARS, and C1QBP autoantibodies in the serum of POAG patients as potential glaucoma biomarkers.
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Affiliation(s)
- Vanessa M Beutgen
- Experimental and Translational OphthalmologyDepartment of OphthalmologyUniversity Medical Center of the Johannes Gutenberg ‐ UniversityMainzGermany
| | - Carsten Schmelter
- Experimental and Translational OphthalmologyDepartment of OphthalmologyUniversity Medical Center of the Johannes Gutenberg ‐ UniversityMainzGermany
| | - Norbert Pfeiffer
- Experimental and Translational OphthalmologyDepartment of OphthalmologyUniversity Medical Center of the Johannes Gutenberg ‐ UniversityMainzGermany
| | - Franz H Grus
- Experimental and Translational OphthalmologyDepartment of OphthalmologyUniversity Medical Center of the Johannes Gutenberg ‐ UniversityMainzGermany
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Kobayashi M, Katayama H, Fahrmann JF, Hanash SM. Development of autoantibody signatures for common cancers. Semin Immunol 2020; 47:101388. [DOI: 10.1016/j.smim.2020.101388] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 01/01/2020] [Indexed: 12/14/2022]
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7
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Wu HY, Xia S, Liu AG, Wei MD, Chen ZB, Li YX, He Y, Liao MJ, Hu QP, Pan SL. Upregulation of miR‑132‑3p in cholangiocarcinoma tissues: A study based on RT‑qPCR, The Cancer Genome Atlas miRNA sequencing, Gene Expression Omnibus microarray data and bioinformatics analyses. Mol Med Rep 2019; 20:5002-5020. [PMID: 31638221 PMCID: PMC6854587 DOI: 10.3892/mmr.2019.10730] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 04/05/2019] [Indexed: 02/06/2023] Open
Abstract
MicroRNAs (miRNAs/miRs) have been reported to be closely associated with numerous human diseases, including cholangiocarcinoma (CCA). However, the number of miRNAs known to be involved in CCA is limited, and the association between miR-132-3p and CCA remains unknown. In the present study, the clinical role of miR-132-3p and its potential signaling pathways were investigated by multiple approaches. Reverse transcription-quantitative PCR (RT-qPCR), CCA-associated Gene Expression Omnibus (GEO), ArrayExpress and Sequence Read Archive (SRA) miRNA-microarray or miRNA-sequencing data were screened, and meta-analyses were conducted, in order to calculate the receiver operating characteristic (ROC) curve and standardized mean difference (SMD). The predicted target genes of miR-132-3p were obtained from 12 online databases and were combined with the downregulated differentially expressed genes identified in the RNA-sequencing data of CCA. Gene Ontology annotation and pathway analysis were performed in WebGestalt. Protein-protein interaction analyses were conducted in STRING. The Cancer Genome Atlas (TCGA) mRNA expression profiles were used to validate the expression levels of hub genes at the mRNA level. The Human Protein Atlas was used to identify the protein expression levels of hub genes in CCA tissues and non-tumor biliary epithelium. The meta-analyses comprised 10 groups of RT-qPCR data, eight GEO microarray datasets and one TCGA miRNA-sequencing dataset. The SMD of miR-132-3p in CCA was 0.75 (95% CI: 0.25, 1.24), which indicated that miR-132-3p was overexpressed in CCA tissues. This finding was supported by a summary ROC value of 0.80 (95% CI: 0.76, 0.83). The pooled sensitivity and specificity were 0.81 (95% CI: 0.59, 0.93) and 0.71 (95% CI: 0.58, 0.81), respectively. The relative expression level of miR-132-3p in the early stage of CCA (stages I–II) was 6.8754±0.5279, which was markedly lower than that in the advanced stage (stages III–IVB), 7.3034±0.3267 (P=0.003). Consistently, the miR-132-3p level in low-grade CCA (grades G1-G2) was 6.7581±0.5297, whereas it was 7.1191±0.4651 in patients with high-grade CCA (grades G3-G4) (P=0.037). Furthermore, 555 potential target genes of miR-132-3p in CCA were mainly enriched in the ‘Focal Adhesion-PI3K-Akt-mTOR-signaling pathway’. In conclusion, upregulation of miR-132-3p may serve a pivotal role in the tumorigenesis and progression of CCA by targeting different pathways. Further in vitro and in vivo studies are required to support the current findings.
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Affiliation(s)
- Hua-Yu Wu
- Department of Pathophysiology, School of Pre‑clinical Medicine, Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Shuang Xia
- Department of Human Anatomy, School of Pre‑clinical Medicine, Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - An-Gui Liu
- Department of Pathophysiology, School of Pre‑clinical Medicine, Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Min-Da Wei
- Department of Pathophysiology, School of Pre‑clinical Medicine, Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Zhong-Biao Chen
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Yu-Xin Li
- Department of Pathophysiology, School of Pre‑clinical Medicine, Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Yu He
- Department of Pathophysiology, School of Pre‑clinical Medicine, Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Min-Jun Liao
- Department of Pathophysiology, School of Pre‑clinical Medicine, Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Qi-Ping Hu
- Department of Cell Biology and Genetics, School of Pre‑clinical Medicine, Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Shang-Ling Pan
- Department of Pathophysiology, School of Pre‑clinical Medicine, Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
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Beutgen VM, Perumal N, Pfeiffer N, Grus FH. Autoantibody Biomarker Discovery in Primary Open Angle Glaucoma Using Serological Proteome Analysis (SERPA). Front Immunol 2019; 10:381. [PMID: 30899261 PMCID: PMC6417464 DOI: 10.3389/fimmu.2019.00381] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 02/14/2019] [Indexed: 12/18/2022] Open
Abstract
Glaucoma is an optic neurological disorder and the leading cause of irreversible blindness worldwide, with primary open angle glaucoma (POAG) as its most prevalent form. An early diagnosis of the disease is crucial to prevent loss of vision. Mechanisms behind glaucoma pathogenesis are not completely understood, but disease related alterations in the serological autoantibody profile indicate an immunologic component. These changes in immunoreactivity may serve as potential biomarkers for glaucoma diagnostics. We aimed to identify novel disease related autoantibodies targeting antigens in the trabecular meshwork as biomarkers to support early detection of POAG. We used serological proteome analysis (SERPA) for initial autoantibody profiling in a discovery sample set. The identified autoantibodies were validated by protein microarray analysis in a larger cohort with 60 POAG patients and 45 control subjects. In this study, we discovered CALD1, PGAM1, and VDAC2 as new biomarker candidates. With the use of artificial neural networks, the panel of these candidates and the already known markers HSPD1 and VIM was able to classify subjects into POAG patients and non-glaucomatous controls with a sensitivity of 81% and a specificity of 93%. These results suggest the benefit of these potential autoantibody biomarkers for utilization in glaucoma diagnostics.
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Affiliation(s)
- Vanessa M Beutgen
- Experimental and Translational Ophthalmology, Department of Ophthalmology, University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Natarajan Perumal
- Experimental and Translational Ophthalmology, Department of Ophthalmology, University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Norbert Pfeiffer
- Experimental and Translational Ophthalmology, Department of Ophthalmology, University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Franz H Grus
- Experimental and Translational Ophthalmology, Department of Ophthalmology, University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany
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Fulton KM, Ananchenko A, Wolfraim L, Martin S, Twine SM. Classical Immunoproteomics: Serological Proteome Analysis (SERPA) for Antigen Identification. Methods Mol Biol 2019; 2024:59-78. [PMID: 31364042 DOI: 10.1007/978-1-4939-9597-4_3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The study of the humoral immune response to infectious and chronic diseases is important for understanding the disease progression, identification of protective antigens, vaccine development, and discovery of biomarkers for early diagnosis. Proteomic approaches, including serological proteome analysis (SERPA), have been used to identify the repertoire of immunoreactive proteins in various diseases. In this chapter, we provide an outline of the SERPA approach, using the analysis of sera from mice vaccinated with a live attenuated tularemia vaccine as an example.
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Affiliation(s)
- Kelly M Fulton
- Human Health Therapeutics Research Centre, National Research Council of Canada, Ottawa, ON, Canada.
| | - Anna Ananchenko
- Human Health Therapeutics Research Centre, National Research Council of Canada, Ottawa, ON, Canada
| | | | | | - Susan M Twine
- Human Health Therapeutics Research Centre, National Research Council of Canada, Ottawa, ON, Canada
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10
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Qian F, Guo J, Jiang Z, Shen B. Translational Bioinformatics for Cholangiocarcinoma: Opportunities and Challenges. Int J Biol Sci 2018; 14:920-929. [PMID: 29989102 PMCID: PMC6036745 DOI: 10.7150/ijbs.24622] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Accepted: 02/02/2018] [Indexed: 02/07/2023] Open
Abstract
Translational bioinformatics is becoming a driven force and a new scientific paradigm for cancer research in the era of big data. To promote the cross-disciplinary communication and research, we take cholangiocarcinoma as an example to review the present status and the future perspectives of the bioinformatics models applied in cancer study. We first summarize the present application of computational methods to the study of cholangiocarcinoma ranged from pattern recognition of biological data, knowledge based data annotation to systems biological level modeling and clinical translation. Then the future opportunities and challenges about database or knowledge base building, novel model developing and molecular mechanism exploring as well as the intelligent decision supporting system construction for the precision diagnosis, prognosis and treatment of cholangiocarcinoma are discussed.
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Affiliation(s)
- Fuliang Qian
- Center for Systems Biology, Soochow University, Suzhou 215006, China
| | - Junping Guo
- The Affiliated Yixing Hospital of Jiangsu University, Yixing, 214200, China
| | - Zhi Jiang
- Center for Systems Biology, Soochow University, Suzhou 215006, China
| | - Bairong Shen
- Center for Systems Biology, Soochow University, Suzhou 215006, China.,Guizhou University School of Medicine, Guiyang, 550025, China.,Institute for Systems Genetics, West China Hospital, Sichuan University, Chengdu, 610041, China
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11
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Antigenicity of Bovine Pericardium Determined by a Novel Immunoproteomic Approach. Sci Rep 2017; 7:2446. [PMID: 28550302 PMCID: PMC5446425 DOI: 10.1038/s41598-017-02719-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 04/13/2017] [Indexed: 12/16/2022] Open
Abstract
Despite bovine pericardium (BP) being the primary biomaterial used in heart valve bioprostheses, recipient graft-specific immune responses remain a significant cause of graft failure. Consequently, tissue antigenicity remains the principal barrier for expanding use of such biomaterials in clinical practice. We hypothesize that our understanding of BP antigenicity can be improved by application of a combined affinity chromatography shotgun immunoproteomic approach to identify antigens that have previously been overlooked. Liquid Chromatography Tandem Mass Spectrometry (LC-MS/MS) analysis of affinity chromatography purified antigens resulted in identification of 133 antigens. Most importantly, antigens were identified from all subcellular locations, including 18 integral membrane protein antigens. Critically, isoforms of several protein families were found to be antigenic suggesting the possibility that shared epitope domains may exist. Furthermore, proteins associated with immune, coagulation, and inflammatory pathways were over-represented, suggesting that these biological processes play a key role in antigenicity. This study brings to light important determinants of antigenicity in a clinically relevant xenogeneic biomaterial (i.e. BP) and further validates a rapid, high-throughput method for immunoproteomic antigen identification.
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12
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Duval F, Cruz-Vega DE, González-Gamboa I, González-Garza MT, Ponz F, Sánchez F, Alarcón-Galván G, Moreno-Cuevas JE. Detection of Autoantibodies to Vascular Endothelial Growth Factor Receptor-3 in Bile Duct Ligated Rats and Correlations with a Panel of Traditional Markers of Liver Diseases. DISEASE MARKERS 2016; 2016:6597970. [PMID: 27212785 PMCID: PMC4860220 DOI: 10.1155/2016/6597970] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 04/05/2016] [Indexed: 12/14/2022]
Abstract
There is a need for new noninvasive biomarkers (NIBMs) able to assess cholestasis and fibrosis in chronic cholestatic liver diseases (CCLDs). Tumorigenesis can arise from CCLDs. Therefore, autoantibodies to tumor-associated antigens (TAA) may be early produced in response to abnormal self-antigen expression caused by cholestatic injury. Vascular endothelial growth factor receptor-3 (VEGFR-3) has TAA potential since it is involved in cholangiocytes and lymphatic vessels proliferations during CCLDs. This study aims to detect autoantibodies directed at VEGFR-3 during bile duct ligation- (BDL-) induced cholestatic injury in rat sera and investigate whether they could be associated with traditional markers of liver damage, cholestasis, and fibrosis. An ELISA was performed to detect anti-VEGFR-3 autoantibodies in sera of rats with different degree of liver injury and results were correlated with aminotransferases, total bilirubin, and the relative fibrotic area. Mean absorbances of anti-VEGFR-3 autoantibodies were significantly increased from week one to week five after BDL. The highest correlation was observed with total bilirubin (R (2) = 0.8450, P = 3.04e - 12). In conclusion, anti-VEGFR-3 autoantibodies are early produced during BDL-induced cholestatic injury, and they are closely related to cholestasis, suggesting the potential of anti-VEGFR-3 autoantibodies as NIBMs of cholestasis in CCLDs and justifying the need for further investigations in patients with CCLD.
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Affiliation(s)
- Florent Duval
- Catedra de Terapia Celular, Escuela de Medicina, Tecnológico de Monterrey, Avenida Morones Prieto 3000 Pte., 64710 Monterrey, NL, Mexico
| | - Delia Elva Cruz-Vega
- Catedra de Terapia Celular, Escuela de Medicina, Tecnológico de Monterrey, Avenida Morones Prieto 3000 Pte., 64710 Monterrey, NL, Mexico
| | - Ivonne González-Gamboa
- Centro de Biotecnología y Genómica de Plantas (CBGP), UPM-INIA, Campus de Montegancedo, Autovía M40, Km 38, Pozuelo de Alarcón, 28223 Madrid, Spain
| | - María Teresa González-Garza
- Catedra de Terapia Celular, Escuela de Medicina, Tecnológico de Monterrey, Avenida Morones Prieto 3000 Pte., 64710 Monterrey, NL, Mexico
| | - Fernando Ponz
- Centro de Biotecnología y Genómica de Plantas (CBGP), UPM-INIA, Campus de Montegancedo, Autovía M40, Km 38, Pozuelo de Alarcón, 28223 Madrid, Spain
| | - Flora Sánchez
- Centro de Biotecnología y Genómica de Plantas (CBGP), UPM-INIA, Campus de Montegancedo, Autovía M40, Km 38, Pozuelo de Alarcón, 28223 Madrid, Spain
| | - Gabriela Alarcón-Galván
- Servicio de Anatomía Patológica y Citopatología, Hospital Universitario “Dr. José Eleuterio González”, Universidad Autónoma de Nuevo León, Madero y Dr. Aguirre Pequeño, 64460 Monterrey, NL, Mexico
| | - Jorge E. Moreno-Cuevas
- Catedra de Terapia Celular, Escuela de Medicina, Tecnológico de Monterrey, Avenida Morones Prieto 3000 Pte., 64710 Monterrey, NL, Mexico
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