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Kathrikolly T, Nair SN, Mathew A, Saxena PPU, Nair S. Can serum autoantibodies be a potential early detection biomarker for breast cancer in women? A diagnostic test accuracy review and meta-analysis. Syst Rev 2022; 11:215. [PMID: 36210467 PMCID: PMC9549667 DOI: 10.1186/s13643-022-02088-y] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 09/28/2022] [Indexed: 12/01/2022] Open
Abstract
BACKGROUND The increasing incidence of breast cancer necessitates the need to explore alternate screening strategies that circumvent the setbacks of conventional techniques especially among population that report earlier age at diagnosis. Serum autoantibodies is one such potential area of interest. However, their ubiquitous presence across cancer types limits its applicability to any one specific type of cancer. This review was therefore carried out to explore and consolidate available evidence on autoantibodies for early detection of breast cancer and to identify those that demonstrated a higher sensitivity. METHODS A diagnostic test accuracy (DTA) review was carried out to ascertain serum autoantibodies that could be used for early detection of breast cancer among women. All relevant articles that investigated the role of autoantibodies in early detection of breast cancer were included for the review. MEDLINE, Scopus, ProQuest, Ovid SP, and Cochrane Library were searched extensively for eligible studies. Quality of the included studies was assessed using Quality Assessment of Diagnostic Accuracy Studies (QUADAS)-2 tool. RevMan 5.3 was used for exploratory and MetaDTA 2019 for hierarchical analyses. The review helped identify the most frequently investigated autoantibodies and a meta-analysis further consolidated the findings. RESULTS A total of 53 articles were included for the final analysis that reported over a 100 autoantibodies that were studied for early detection of breast cancer in women. P53, MUC1, HER2, HSP60, P16, Cyclin B1, and c-Myc were the most frequently investigated autoantibodies. Of these P53, MUC1, HER2, and HSP60 exhibited higher summary sensitivity measures. While the individual pooled sensitivity estimates ranged between 10 and 56%, the panel sensitivity values reported across studies were higher with an estimated range of 60-87%. CONCLUSION Findings from the review indicate a higher sensitivity for an autoantibody panel in comparison to individual assays. A panel comprising of P53, MUC1, HER2, and HSP60 autoantibodies has the potential to be investigated as an early detection biomarker for breast cancer.
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Affiliation(s)
- Thejas Kathrikolly
- Department of Community Oncology, Sri Shankara Cancer Hospital and Research Centre, Bengaluru, India.,Department of Community Medicine, Kasturba Medical College, Manipal Academy of Higher Education (MAHE), Manipal, India
| | - Sreekumaran N Nair
- Department of Biostatistics, Jawaharlal Institute of Postgraduate Medical Education & Research (JIPMER), Puducherry, India
| | - Aju Mathew
- Department of Oncology, MOSC Medical College Kolenchery, Kerala, India.,Department of Internal Medicine, University of Kentucky Markey Cancer Center, Lexington, USA
| | - Prakash P U Saxena
- Department of Radiation Oncology, Kasturba Medical College, Mangalore, India
| | - Suma Nair
- Department of Community Medicine, Kasturba Medical College, Manipal Academy of Higher Education (MAHE), Manipal, India. .,School of Public Health, DY Patil Deemed to be University, Navi Mumbai, India.
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2
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Cheng J, Sun R, Nie D, Li B, Gui SB, Li CZ, Zhang YZ, Zhao P. Identification and Verification of SLC27A1, PTBP1 and EIF5A With Significantly Altered Expression in Aggressive Pituitary Adenomas. Front Surg 2022; 9:923143. [PMID: 35836612 PMCID: PMC9275011 DOI: 10.3389/fsurg.2022.923143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 06/06/2022] [Indexed: 11/24/2022] Open
Abstract
Background Aggressive pituitary adenoma encircling the internal carotid artery has a poor clinical prognosis because of a high surgical risk and a high recurrence rate. This seriously affects patients’ quality of life and yet there is no effective medical treatment. The European Diagnostic Guidelines have recommended the use of temozolomide (TMZ) for these aggressive pituitary adenomas, but the treatment remission rate has been less than 50%. Methods In this study, transcriptome sequencing of pituitary tumour tissues and TMZ-treated pituitary tumour cell lines were employed to explore the significance gene expressions affecting the efficacy of TMZ treatment for pituitary tumours. To clarify the roles of these gene expressions, six adult patients with pituitary adenomas treated in Tiantan Hospital from 2015 to 2020 and a pituitary adenoma cell line (Att20 sensitive to TMZ treatment) were analyzed by mRNA transcriptome sequencing. The differentially expressed genes were assayed by analyzing the sequencing results, and the expression level of these genes was further verified by immunohistochemistry. In addition, Ki67, VEGF, and p53 of the tumour tissues were also verified by immunohistochemistry. Results In tumour tissues, mRNA sequencing showed that PTBP1 and EIF5A were significantly overexpressed in primary pituitary adenomas and SLC27A1 was significantly overexpressed in aggressive pituitary adenomas. Also in the pituitary adenoma cell line (AtT20), SLC27A1 expression levels were suppressed by TMZ treatment. Subsequent immunohistochemistry confirmed the sequencing results. Conclusion High expression of SLC27A1 and low expression of EIF5A and PTBP1 may be potential indicators to predict the progression of aggressive pituitary adenomas, and patients with high SLC27A1 subtype may be sensitive to TMZ in clinical treatments.
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Affiliation(s)
- Jianhua Cheng
- Department of Cell and Biology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Ruya Sun
- Department of Biomedical Informatics, Department of Physiology and Pathophysiology, Center for Noncoding RNA Medicine, MOE Key Lab of Cardiovascular Sciences, School of Basic Medical Sciences, Peking University, Beijing, China
| | - Ding Nie
- Department of Cell and Biology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Bin Li
- Department of Cell and Biology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Song Bai Gui
- Neurosurgical Department, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Chu Zhong Li
- Department of Cell and Biology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Ya Zhuo Zhang
- Department of Cell and Biology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Peng Zhao
- Neurosurgical Department, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- Correspondence: Peng Zhao
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Wang JY, Roehrl MW, Roehrl VB, Roehrl MH. A Master Autoantigen-ome Links Alternative Splicing, Female Predilection, and COVID-19 to Autoimmune Diseases. bioRxiv 2021:2021.07.30.454526. [PMID: 34373855 PMCID: PMC8351778 DOI: 10.1101/2021.07.30.454526] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Chronic and debilitating autoimmune sequelae pose a grave concern for the post-COVID-19 pandemic era. Based on our discovery that the glycosaminoglycan dermatan sulfate (DS) displays peculiar affinity to apoptotic cells and autoantigens (autoAgs) and that DS-autoAg complexes cooperatively stimulate autoreactive B1 cell responses, we compiled a database of 751 candidate autoAgs from six human cell types. At least 657 of these have been found to be affected by SARS-CoV-2 infection based on currently available multi-omic COVID data, and at least 400 are confirmed targets of autoantibodies in a wide array of autoimmune diseases and cancer. The autoantigen-ome is significantly associated with various processes in viral infections, such as translation, protein processing, and vesicle transport. Interestingly, the coding genes of autoAgs predominantly contain multiple exons with many possible alternative splicing variants, short transcripts, and short UTR lengths. These observations and the finding that numerous autoAgs involved in RNA-splicing showed altered expression in viral infections suggest that viruses exploit alternative splicing to reprogram host cell machinery to ensure viral replication and survival. While each cell type gives rise to a unique pool of autoAgs, 39 common autoAgs associated with cell stress and apoptosis were identified from all six cell types, with several being known markers of systemic autoimmune diseases. In particular, the common autoAg UBA1 that catalyzes the first step in ubiquitination is encoded by an X-chromosome escape gene. Given its essential function in apoptotic cell clearance and that X-inactivation escape tends to increase with aging, UBA1 dysfunction can therefore predispose aging women to autoimmune disorders. In summary, we propose a model of how viral infections lead to extensive molecular alterations and host cell death, autoimmune responses facilitated by autoAg-DS complexes, and ultimately autoimmune diseases. Overall, this master autoantigen-ome provides a molecular guide for investigating the myriad of autoimmune sequalae to COVID-19 and clues to the rare but reported adverse effects of the currently available COVID vaccines.
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Affiliation(s)
| | | | | | - Michael H. Roehrl
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA
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4
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Bareke H, Juanes-Velasco P, Landeira-Viñuela A, Hernandez AP, Cruz JJ, Bellido L, Fonseca E, Niebla-Cárdenas A, Montalvillo E, Góngora R, Fuentes M. Autoimmune Responses in Oncology: Causes and Significance. Int J Mol Sci 2021; 22:ijms22158030. [PMID: 34360795 PMCID: PMC8347170 DOI: 10.3390/ijms22158030] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 07/19/2021] [Accepted: 07/23/2021] [Indexed: 12/20/2022] Open
Abstract
Specific anti-tumor immune responses have proven to be pivotal in shaping tumorigenesis and tumor progression in solid cancers. These responses can also be of an autoimmune nature, and autoantibodies can sometimes be present even before the onset of clinically overt disease. Autoantibodies can be generated due to mutated gene products, aberrant expression and post-transcriptional modification of proteins, a pro-immunogenic milieu, anti-cancer treatments, cross-reactivity of tumor-specific lymphocytes, epitope spreading, and microbiota-related and genetic factors. Understanding these responses has implications for both basic and clinical immunology. Autoantibodies in solid cancers can be used for early detection of cancer as well as for biomarkers of prognosis and treatment response. High-throughput techniques such as protein microarrays make parallel detection of multiple autoantibodies for increased specificity and sensitivity feasible, affordable, and quick. Cancer immunotherapy has revolutionized cancer treatments and has made a considerable impact on reducing cancer-associated morbidity and mortality. However, immunotherapeutic interventions such as immune checkpoint inhibition can induce immune-related toxicities, which can even be life-threatening. Uncovering the reasons for treatment-induced autoimmunity can lead to fine-tuning of cancer immunotherapy approaches to evade toxic events while inducing an effective anti-tumor immune response.
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Affiliation(s)
- Halin Bareke
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Institute of Health Sciences, Marmara University, Istanbul 34722, Turkey;
- Department of Medicine and General Cytometry Service-Nucleus, CIBERONC CB16/12/00400, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain; (P.J.-V.); (A.L.-V.); (A.-P.H.); (E.M.); (R.G.)
| | - Pablo Juanes-Velasco
- Department of Medicine and General Cytometry Service-Nucleus, CIBERONC CB16/12/00400, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain; (P.J.-V.); (A.L.-V.); (A.-P.H.); (E.M.); (R.G.)
| | - Alicia Landeira-Viñuela
- Department of Medicine and General Cytometry Service-Nucleus, CIBERONC CB16/12/00400, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain; (P.J.-V.); (A.L.-V.); (A.-P.H.); (E.M.); (R.G.)
| | - Angela-Patricia Hernandez
- Department of Medicine and General Cytometry Service-Nucleus, CIBERONC CB16/12/00400, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain; (P.J.-V.); (A.L.-V.); (A.-P.H.); (E.M.); (R.G.)
| | - Juan Jesús Cruz
- Medical Oncology Service, Hospital Universitario de Salamanca-IBSAL, 37007 Salamanca, Spain; (J.J.C.); (L.B.); (E.F.)
| | - Lorena Bellido
- Medical Oncology Service, Hospital Universitario de Salamanca-IBSAL, 37007 Salamanca, Spain; (J.J.C.); (L.B.); (E.F.)
| | - Emilio Fonseca
- Medical Oncology Service, Hospital Universitario de Salamanca-IBSAL, 37007 Salamanca, Spain; (J.J.C.); (L.B.); (E.F.)
| | - Alfonssina Niebla-Cárdenas
- Department of Nursing and Physiotherapy, Faculty of Nursing and Physiotherapy, University of Salamanca, 37007 Salamanca, Spain;
| | - Enrique Montalvillo
- Department of Medicine and General Cytometry Service-Nucleus, CIBERONC CB16/12/00400, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain; (P.J.-V.); (A.L.-V.); (A.-P.H.); (E.M.); (R.G.)
| | - Rafael Góngora
- Department of Medicine and General Cytometry Service-Nucleus, CIBERONC CB16/12/00400, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain; (P.J.-V.); (A.L.-V.); (A.-P.H.); (E.M.); (R.G.)
| | - Manuel Fuentes
- Department of Medicine and General Cytometry Service-Nucleus, CIBERONC CB16/12/00400, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain; (P.J.-V.); (A.L.-V.); (A.-P.H.); (E.M.); (R.G.)
- Proteomics Unit, Cancer Research Center (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain
- Correspondence: ; Tel.: +34-923-294-811
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Wang JY, Zhang W, Roehrl MW, Roehrl VB, Roehrl MH. An Autoantigen Profile from Jurkat T-Lymphoblasts Provides a Molecular Guide for Investigating Autoimmune Sequelae of COVID-19. bioRxiv 2021:2021.07.05.451199. [PMID: 34729561 PMCID: PMC8562547 DOI: 10.1101/2021.07.05.451199] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
In order to understand autoimmune phenomena contributing to the pathophysiology of COVID-19 and post-COVID syndrome, we have been profiling autoantigens (autoAgs) from various cell types. Although cells share numerous autoAgs, each cell type gives rise to unique COVID-altered autoAg candidates, which may explain the wide range of symptoms experienced by patients with autoimmune sequelae of SARS-CoV-2 infection. Based on the unifying property of affinity between autoantigens (autoAgs) and the glycosaminoglycan dermatan sulfate (DS), this paper reports 140 candidate autoAgs identified from proteome extracts of human Jurkat T-cells, of which at least 105 (75%) are known targets of autoantibodies. Comparison with currently available multi-omic COVID-19 data shows that 125 (89%) of DS-affinity proteins are altered at protein and/or RNA levels in SARS-CoV-2-infected cells or patients, with at least 94 being known autoAgs in a wide spectrum of autoimmune diseases and cancer. Protein alterations by ubiquitination and phosphorylation in the viral infection are major contributors of autoAgs. The autoAg protein network is significantly associated with cellular response to stress, apoptosis, RNA metabolism, mRNA processing and translation, protein folding and processing, chromosome organization, cell cycle, and muscle contraction. The autoAgs include clusters of histones, CCT/TriC chaperonin, DNA replication licensing factors, proteasome and ribosome proteins, heat shock proteins, serine/arginine-rich splicing factors, 14-3-3 proteins, and cytoskeletal proteins. AutoAgs such as LCP1 and NACA that are altered in the T cells of COVID patients may provide insight into T-cell responses in the viral infection and merit further study. The autoantigen-ome from this study contributes to a comprehensive molecular map for investigating acute, subacute, and chronic autoimmune disorders caused by SARS-CoV-2.
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Affiliation(s)
| | - Wei Zhang
- Department of Gastroenterology, Affiliated Hospital of Guizhou Medical University, Guizhou, China
| | | | | | - Michael H. Roehrl
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, USA
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6
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Qiu C, Wang B, Wang P, Wang X, Ma Y, Dai L, Shi J, Wang K, Sun G, Ye H, Zhang J. Identification of novel autoantibody signatures and evaluation of a panel of autoantibodies in breast cancer. Cancer Sci 2021; 112:3388-3400. [PMID: 34115421 PMCID: PMC8353906 DOI: 10.1111/cas.15021] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 06/06/2021] [Accepted: 06/08/2021] [Indexed: 12/24/2022] Open
Abstract
Tumor-associated autoantibodies (TAAb) could be serological tumor markers. This study aims to discover novel TAAb signatures for breast cancer (BC) detection. The protein microarray was used to identify candidate TAAb, which were further validated in 1197 sera from BC, benign breast diseases (BD), and healthy controls (HC) by enzyme-linked immunosorbent assay. In addition, 319 preoperative and postoperative sera were evaluated. A panel was determined using four different classifiers. Twelve TAAb were identified with frequencies of 15.8%-59.2%; their levels were significantly decreased in postoperative sera compared to those in preoperative sera (P < .05). A panel with six TAAb was developed and evaluated. The area under the curve (AUC) was 0.879 (74.3% sensitivity, 91.9% specificity) and 0.865 (69.7% sensitivity, 91.7% specificity) for distinguishing BC from HC in the training set and test set, respectively. The panel had an AUC of .884 (71.2% sensitivity, 90.5% specificity) for discriminating BC from BD. For identifying BC from all controls (HC+BD), the AUC was .916 (78.9% sensitivity, 90.2% specificity). The AUC of the panel was .920 and .934 for distinguishing stage I-II and age < 50 BC from HC, respectively. These identified TAAb have the potential to provide a non-invasive approach to detect BC.
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Affiliation(s)
- Cuipeng Qiu
- BGI College & Henan Academy of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China.,State Key Laboratory of Esophageal Cancer Prevention and Treatment and Henan Key Laboratory of Tumor Epidemiology, Zhengzhou, China.,Department of Epidemiology and Health Statistics, College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Bofei Wang
- State Key Laboratory of Esophageal Cancer Prevention and Treatment and Henan Key Laboratory of Tumor Epidemiology, Zhengzhou, China
| | - Peng Wang
- State Key Laboratory of Esophageal Cancer Prevention and Treatment and Henan Key Laboratory of Tumor Epidemiology, Zhengzhou, China.,Department of Epidemiology and Health Statistics, College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Xiao Wang
- BGI College & Henan Academy of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China.,State Key Laboratory of Esophageal Cancer Prevention and Treatment and Henan Key Laboratory of Tumor Epidemiology, Zhengzhou, China
| | - Yan Ma
- State Key Laboratory of Esophageal Cancer Prevention and Treatment and Henan Key Laboratory of Tumor Epidemiology, Zhengzhou, China.,Department of Epidemiology and Health Statistics, College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Liping Dai
- BGI College & Henan Academy of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China.,State Key Laboratory of Esophageal Cancer Prevention and Treatment and Henan Key Laboratory of Tumor Epidemiology, Zhengzhou, China
| | - Jianxiang Shi
- BGI College & Henan Academy of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China.,State Key Laboratory of Esophageal Cancer Prevention and Treatment and Henan Key Laboratory of Tumor Epidemiology, Zhengzhou, China
| | - Keyan Wang
- BGI College & Henan Academy of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China.,State Key Laboratory of Esophageal Cancer Prevention and Treatment and Henan Key Laboratory of Tumor Epidemiology, Zhengzhou, China
| | - Guiying Sun
- State Key Laboratory of Esophageal Cancer Prevention and Treatment and Henan Key Laboratory of Tumor Epidemiology, Zhengzhou, China.,Department of Epidemiology and Health Statistics, College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Hua Ye
- State Key Laboratory of Esophageal Cancer Prevention and Treatment and Henan Key Laboratory of Tumor Epidemiology, Zhengzhou, China.,Department of Epidemiology and Health Statistics, College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Jianying Zhang
- BGI College & Henan Academy of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China.,State Key Laboratory of Esophageal Cancer Prevention and Treatment and Henan Key Laboratory of Tumor Epidemiology, Zhengzhou, China.,Department of Epidemiology and Health Statistics, College of Public Health, Zhengzhou University, Zhengzhou, China
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7
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Stanton SE, Gad E, Ramos E, Corulli L, Annis J, Childs J, Katayama H, Hanash S, Marks J, Disis ML. Tumor-associated autoantibodies from mouse breast cancer models are found in serum of breast cancer patients. NPJ Breast Cancer 2021; 7:50. [PMID: 33976232 PMCID: PMC8113561 DOI: 10.1038/s41523-021-00257-1] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 04/08/2021] [Indexed: 12/11/2022] Open
Abstract
B cell responses to tumor antigens occur early in breast tumors and may identify immunogenic drivers of tumorigenesis. Sixty-two candidate antigens were identified prior to palpable tumor development in TgMMTV-neu and C3(1)Tag transgenic mouse mammary tumor models. Five antigens (VPS35, ARPC2, SERBP1, KRT8, and PDIA6) were selected because their decreased expression decreased survival in human HER2 positive and triple negative cell lines in a siRNA screen. Vaccination with antigen-specific epitopes, conserved between mouse and human, inhibited tumor growth in both transgenic mouse models. Increased IgG autoantibodies to the antigens were elevated in serum from women with ductal carcinoma in situ (DCIS) and invasive breast cancer (IBC). The autoantibodies differentiated women with DCIS from control with AUC 0.93 (95% CI 0.88-0.98, p < 0.0001). The tumor antigens identified early in the development of breast cancer in mouse mammary tumor models were conserved in human disease, and potentially identify early diagnostic markers in human breast tumors.
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Affiliation(s)
- Sasha E Stanton
- Cancer Vaccine Institute, University of Washington, Seattle, WA, USA.
| | - Ekram Gad
- Cancer Vaccine Institute, University of Washington, Seattle, WA, USA
| | - Erik Ramos
- Cancer Vaccine Institute, University of Washington, Seattle, WA, USA
| | - Lauren Corulli
- Cancer Vaccine Institute, University of Washington, Seattle, WA, USA
| | - James Annis
- Quellos High Throughput Facility, Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
| | - Jennifer Childs
- Cancer Vaccine Institute, University of Washington, Seattle, WA, USA
| | - Hiroyuki Katayama
- Department of Clinical Cancer Prevention, MD Anderson Cancer Center, Houston, TX, USA
| | - Samir Hanash
- Department of Clinical Cancer Prevention, MD Anderson Cancer Center, Houston, TX, USA
| | - Jeffrey Marks
- Division of Surgical Sciences, Duke University, Durham, NC, USA
| | - Mary L Disis
- Cancer Vaccine Institute, University of Washington, Seattle, WA, USA
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8
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Wang JY, Zhang W, Roehrl MW, Roehrl VB, Roehrl MH. An autoantigen profile of human A549 lung cells reveals viral and host etiologic molecular attributes of autoimmunity in COVID-19. J Autoimmun 2021; 120:102644. [PMID: 33971585 PMCID: PMC8075847 DOI: 10.1016/j.jaut.2021.102644] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Accepted: 04/08/2021] [Indexed: 12/13/2022]
Abstract
We aim to establish a comprehensive COVID-19 autoantigen atlas in order to understand autoimmune diseases caused by SARS-CoV-2 infection. Based on the unique affinity between dermatan sulfate and autoantigens, we identified 348 proteins from human lung A549 cells, of which 198 are known targets of autoantibodies. Comparison with current COVID data identified 291 proteins that are altered at protein or transcript level in SARS-CoV-2 infection, with 191 being known autoantigens. These known and putative autoantigens are significantly associated with viral replication and trafficking processes, including gene expression, ribonucleoprotein biogenesis, mRNA metabolism, translation, vesicle and vesicle-mediated transport, and apoptosis. They are also associated with cytoskeleton, platelet degranulation, IL-12 signaling, and smooth muscle contraction. Host proteins that interact with and that are perturbed by viral proteins are a major source of autoantigens. Orf3 induces the largest number of protein alterations, Orf9 affects the mitochondrial ribosome, and they and E, M, N, and Nsp proteins affect protein localization to membrane, immune responses, and apoptosis. Phosphorylation and ubiquitination alterations by viral infection define major molecular changes in autoantigen origination. This study provides a large list of autoantigens as well as new targets for future investigation, e.g., UBA1, UCHL1, USP7, CDK11A, PRKDC, PLD3, PSAT1, RAB1A, SLC2A1, platelet activating factor acetylhydrolase, and mitochondrial ribosomal proteins. This study illustrates how viral infection can modify host cellular proteins extensively, yield diverse autoantigens, and trigger a myriad of autoimmune sequelae. Our work provides a rich resource for studies into “long COVID” and related autoimmune sequelae.
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Affiliation(s)
| | - Wei Zhang
- Department of Gastroenterology, Affiliated Hospital of Guizhou Medical University, Guizhou, China
| | | | | | - Michael H Roehrl
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, USA.
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9
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Wang JY, Zhang W, Roehrl VB, Roehrl MW, Roehrl MH. An Autoantigen-ome from HS-Sultan B-Lymphoblasts Offers a Molecular Map for Investigating Autoimmune Sequelae of COVID-19. bioRxiv 2021:2021.04.05.438500. [PMID: 33851168 PMCID: PMC8043459 DOI: 10.1101/2021.04.05.438500] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
To understand how COVID-19 may induce autoimmune diseases, we have been compiling an atlas of COVID-autoantigens (autoAgs). Using dermatan sulfate (DS) affinity enrichment of autoantigenic proteins extracted from HS-Sultan lymphoblasts, we identified 362 DS-affinity proteins, of which at least 201 (56%) are confirmed autoAgs. Comparison with available multi-omic COVID data shows that 315 (87%) of the 362 proteins are affected in SARS-CoV-2 infection via altered expression, interaction with viral components, or modification by phosphorylation or ubiquitination, at least 186 (59%) of which are known autoAgs. These proteins are associated with gene expression, mRNA processing, mRNA splicing, translation, protein folding, vesicles, and chromosome organization. Numerous nuclear autoAgs were identified, including both classical ANAs and ENAs of systemic autoimmune diseases and unique autoAgs involved in the DNA replication fork, mitotic cell cycle, or telomerase maintenance. We also identified many uncommon autoAgs involved in nucleic acid and peptide biosynthesis and nucleocytoplasmic transport, such as aminoacyl-tRNA synthetases. In addition, this study found autoAgs that potentially interact with multiple SARS-CoV-2 Nsp and Orf components, including CCT/TriC chaperonin, insulin degrading enzyme, platelet-activating factor acetylhydrolase, and the ezrin-moesin-radixin family. Furthermore, B-cell-specific IgM-associated ER complex (including MBZ1, BiP, heat shock proteins, and protein disulfide-isomerases) is enriched by DS-affinity and up-regulated in B-cells of COVID-19 patients, and a similar IgH-associated ER complex was also identified in autoreactive pre-B1 cells in our previous study, which suggests a role of autoreactive B1 cells in COVID-19 that merits further investigation. In summary, this study demonstrates that virally infected cells are characterized by alterations of proteins with propensity to become autoAgs, thereby providing a possible explanation for infection-induced autoimmunity. The COVID autoantigen-ome provides a valuable molecular resource and map for investigation of COVID-related autoimmune sequelae and considerations for vaccine design.
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Affiliation(s)
| | - Wei Zhang
- Department of Gastroenterology, Affiliated Hospital of Guizhou Medical University, Guizhou, China
| | | | | | - Michael H. Roehrl
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, USA
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Wang JY, Zhang W, Roehrl MW, Roehrl VB, Roehrl MH. An Autoantigen Profile of Human A549 Lung Cells Reveals Viral and Host Etiologic Molecular Attributes of Autoimmunity in COVID-19. bioRxiv 2021:2021.02.21.432171. [PMID: 33655248 PMCID: PMC7924268 DOI: 10.1101/2021.02.21.432171] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
We aim to establish a comprehensive COVID-19 autoantigen atlas in order to understand autoimmune diseases caused by SARS-CoV-2 infection. Based on the unique affinity between dermatan sulfate and autoantigens, we identified 348 proteins from human lung A549 cells, of which 198 are known targets of autoantibodies. Comparison with current COVID data identified 291 proteins that are altered at protein or transcript level in SARS-CoV-2 infection, with 191 being known autoantigens. These known and putative autoantigens are significantly associated with viral replication and trafficking processes, including gene expression, ribonucleoprotein biogenesis, mRNA metabolism, translation, vesicle and vesicle-mediated transport, and apoptosis. They are also associated with cytoskeleton, platelet degranulation, IL-12 signaling, and smooth muscle contraction. Host proteins that interact with and that are perturbed by viral proteins are a major source of autoantigens. Orf3 induces the largest number of protein alterations, Orf9 affects the mitochondrial ribosome, and they and E, M, N, and Nsp proteins affect protein localization to membrane, immune responses, and apoptosis. Phosphorylation and ubiquitination alterations by viral infection define major molecular changes in autoantigen origination. This study provides a large list of autoantigens as well as new targets for future investigation, e.g., UBA1, UCHL1, USP7, CDK11A, PRKDC, PLD3, PSAT1, RAB1A, SLC2A1, platelet activating factor acetylhydrolase, and mitochondrial ribosomal proteins. This study illustrates how viral infection can modify host cellular proteins extensively, yield diverse autoantigens, and trigger a myriad of autoimmune sequelae.
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Affiliation(s)
| | - Wei Zhang
- Department of Gastroenterology, Affiliated Hospital of Guizhou Medical University, Guizhou, China
| | | | | | - Michael H. Roehrl
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, USA
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