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Krainer J, Hendling M, Siebenhandl S, Fuehner S, Kessel C, Verweyen E, Vierlinger K, Foell D, Schönthaler S, Weinhäusel A. Patients with Systemic Juvenile Idiopathic Arthritis (SJIA) Show Differences in Autoantibody Signatures Based on Disease Activity. Biomolecules 2023; 13:1392. [PMID: 37759792 PMCID: PMC10527260 DOI: 10.3390/biom13091392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 09/07/2023] [Accepted: 09/12/2023] [Indexed: 09/29/2023] Open
Abstract
Systemic juvenile idiopathic arthritis (SJIA) is a severe rheumatic disease in children. It is a subgroup of juvenile idiopathic arthritis (JIA; MIM #604302), which is the most common rheumatic disease in children. The diagnosis of SJIA often comes with a significant delay, and the classification between autoinflammatory and autoimmune disease is still discussed. In this study, we analyzed the immunological responses of patients with SJIA, using human proteome arrays presenting immobilized recombinantly expressed human proteins, to analyze the involvement of autoantibodies in SJIA. Results from group comparisons show several differentially reactive antigens involved in inflammatory processes. Intriguingly, many of the identified antigens had a high reactivity against proteins involved in the NF-κB pathway, and it is also notable that many of the detected DIRAGs are described as dysregulated in rheumatoid arthritis. Our data highlight novel proteins and pathways potentially dysregulated in SJIA and offer a unique approach to unraveling the underlying disease pathogenesis in this chronic arthropathy.
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Affiliation(s)
- Julie Krainer
- Center for Health and Bioresources, Molecular Diagnostics, AIT Austrian Institute of Technology GmbH, Giefinggasse 4, 1210 Vienna, Austria; (M.H.); (K.V.); (S.S.)
| | - Michaela Hendling
- Center for Health and Bioresources, Molecular Diagnostics, AIT Austrian Institute of Technology GmbH, Giefinggasse 4, 1210 Vienna, Austria; (M.H.); (K.V.); (S.S.)
| | - Sandra Siebenhandl
- Center for Health and Bioresources, Molecular Diagnostics, AIT Austrian Institute of Technology GmbH, Giefinggasse 4, 1210 Vienna, Austria; (M.H.); (K.V.); (S.S.)
| | - Sabrina Fuehner
- Pediatric Rheumatology & Immunology, University Children’s Hospital, 48149 Münster, Germany; (S.F.); (C.K.); (E.V.); (D.F.)
| | - Christoph Kessel
- Pediatric Rheumatology & Immunology, University Children’s Hospital, 48149 Münster, Germany; (S.F.); (C.K.); (E.V.); (D.F.)
| | - Emely Verweyen
- Pediatric Rheumatology & Immunology, University Children’s Hospital, 48149 Münster, Germany; (S.F.); (C.K.); (E.V.); (D.F.)
| | - Klemens Vierlinger
- Center for Health and Bioresources, Molecular Diagnostics, AIT Austrian Institute of Technology GmbH, Giefinggasse 4, 1210 Vienna, Austria; (M.H.); (K.V.); (S.S.)
| | - Dirk Foell
- Pediatric Rheumatology & Immunology, University Children’s Hospital, 48149 Münster, Germany; (S.F.); (C.K.); (E.V.); (D.F.)
| | - Silvia Schönthaler
- Center for Health and Bioresources, Molecular Diagnostics, AIT Austrian Institute of Technology GmbH, Giefinggasse 4, 1210 Vienna, Austria; (M.H.); (K.V.); (S.S.)
| | - Andreas Weinhäusel
- Center for Health and Bioresources, Molecular Diagnostics, AIT Austrian Institute of Technology GmbH, Giefinggasse 4, 1210 Vienna, Austria; (M.H.); (K.V.); (S.S.)
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Xing H, Jiang X, Yang C, Tan B, Hu J, Zhang M. High expression of RPL27A predicts poor prognosis in patients with hepatocellular carcinoma. World J Surg Oncol 2023; 21:209. [PMID: 37474947 PMCID: PMC10360225 DOI: 10.1186/s12957-023-03102-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 07/12/2023] [Indexed: 07/22/2023] Open
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) is one of the most common cancers in the digestive system with rapid progression and poor prognosis. Recent studies have shown that RPL27A could be used as a biomarker for a variety of cancers, but its role in HCC is not clear. METHOD We analyzed the expression of RPL27A in the pan-cancer analysis and analyzed the relationship between the expression of RPL27A and the clinical features and prognosis of patients with HCC. We evaluated the expression difference of RPL27A in HCC tissues and paired normal adjacent tissues using immunohistochemistry. Furthermore, we analyzed the co-expression genes of RPL27A and used them to explore the possible mechanism of RPL27A and screen hub genes effecting HCC. In addition, we studied the role of RPL27A in immune infiltration and mutation. RESULTS We found that the expression level of RPL27A increased in a variety of cancers, including HCC. In HCC patients, the high expression of RPL27A was related to progression and poor prognosis as an independent predictor. We also constructed a protein interaction network through co-expression gene analysis of RPL27A and screened 9 hub genes. Enrichment analysis showed that co-expression genes were associated with ribosome pathway, viral replication, nuclear-transcribed mRNA catabolic process, and nonsense-mediated decay. We found that the expression level of RPL27A was closely related to TP53 mutation and immune infiltration in HCC. CONCLUSION RPL27A might become a biomarker in the diagnosis, treatment, and follow-up of patients with HCC.
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Affiliation(s)
- Huiwu Xing
- Department of Hepatobiliary Surgery, Children's Hospital of Chongqing Medical University, Chongqing Key Laboratory of Pediatrics, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing, 400010, China
| | - Xiangqi Jiang
- Department of Hepatobiliary Surgery, Children's Hospital of Chongqing Medical University, Chongqing Key Laboratory of Pediatrics, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing, 400010, China
| | - Chenyu Yang
- Department of Hepatobiliary Surgery, Children's Hospital of Chongqing Medical University, Chongqing Key Laboratory of Pediatrics, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing, 400010, China
| | - Bingqian Tan
- Department of Hepatobiliary Surgery, Children's Hospital of Chongqing Medical University, Chongqing Key Laboratory of Pediatrics, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing, 400010, China
| | - Jiqiang Hu
- Department of Hepatobiliary Surgery, Children's Hospital of Chongqing Medical University, Chongqing Key Laboratory of Pediatrics, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing, 400010, China
| | - Mingman Zhang
- Department of Hepatobiliary Surgery, Children's Hospital of Chongqing Medical University, Chongqing Key Laboratory of Pediatrics, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing, 400010, China.
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Antibody Profiling and In Silico Functional Analysis of Differentially Reactive Antibody Signatures of Glioblastomas and Meningiomas. Int J Mol Sci 2023; 24:ijms24021411. [PMID: 36674927 PMCID: PMC9866115 DOI: 10.3390/ijms24021411] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 12/08/2022] [Accepted: 12/22/2022] [Indexed: 01/12/2023] Open
Abstract
Studies on tumor-associated antigens in brain tumors are sparse. There is scope for enhancing our understanding of molecular pathology, in order to improve on existing forms, and discover new forms, of treatment, which could be particularly relevant to immuno-oncological strategies. To elucidate immunological differences, and to provide another level of biological information, we performed antibody profiling, based on a high-density protein array (containing 8173 human transcripts), using IgG isolated from the sera of n = 12 preoperative and n = 16 postoperative glioblastomas, n = 26 preoperative and n = 29 postoperative meningiomas, and n = 27 healthy, cancer-free controls. Differentially reactive antigens were compared to gene expression data from an alternate public GBM data set from OncoDB, and were analyzed using the Reactome pathway browser. Protein array analysis identified approximately 350-800 differentially reactive antigens, and revealed different antigen profiles in the glioblastomas and meningiomas, with approximately 20-30%-similar and 10-15%-similar antigens in preoperative and postoperative sera, respectively. Seroreactivity did not correlate with OncoDB-derived gene expression. Antigens in the preoperative glioblastoma sera were enriched for signaling pathways, such as signaling by Rho-GTPases, COPI-mediated anterograde transport and vesicle-mediated transport, while the infectious disease, SRP-dependent membrane targeting cotranslational proteins were enriched in the meningiomas. The pre-vs. postoperative seroreactivity in the glioblastomas was enriched for antigens, e.g., platelet degranulation and metabolism of lipid pathways; in the meningiomas, the antigens were enriched in infectious diseases, metabolism of amino acids and derivatives, and cell cycle. Antibody profiling in both tumor entities elucidated several hundred antigens and characteristic signaling pathways that may provide new insights into molecular pathology and may be of interest for the development of new treatment strategies.
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Gigic B, van Roekel E, Holowatyj AN, Brezina S, Geijsen AJMR, Ulvik A, Ose J, Koole JL, Damerell V, Kiblawi R, Gumpenberger T, Lin T, Kvalheim G, Koelsch T, Kok DE, van Duijnhoven FJ, Bours MJ, Baierl A, Li CI, Grady W, Vickers K, Habermann N, Schneider M, Kampman E, Ueland PM, Ulrich A, Weijenberg M, Gsur A, Ulrich C. Cohort profile: Biomarkers related to folate-dependent one-carbon metabolism in colorectal cancer recurrence and survival - the FOCUS Consortium. BMJ Open 2022; 12:e062930. [PMID: 36549742 PMCID: PMC9772678 DOI: 10.1136/bmjopen-2022-062930] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 10/07/2022] [Indexed: 12/24/2022] Open
Abstract
PURPOSE The overarching goal of the FOCUS (biomarkers related to folate-dependent one-carbon metabolism in colorectal cancer (CRC) recurrence and survival) Consortium is to unravel the effect of folate and folate-mediated one-carbon metabolism (FOCM) biomarkers on CRC prognosis to provide clinically relevant advice on folate intake to cancer patients and define future tertiary prevention strategies. PARTICIPANTS The FOCUS Consortium is an international, prospective cohort of 2401 women and men above 18 years of age who were diagnosed with a primary invasive non-metastatic (stages I-III) CRC. The consortium comprises patients from Austria, two sites from the Netherlands, Germany and two sites from the USA. Patients are recruited after CRC diagnosis and followed at 6 and 12 months after enrolment. At each time point, sociodemographic data, data on health behaviour and clinical data are collected, blood samples are drawn. FINDINGS TO DATE An increased risk of cancer recurrences was observed among patients with higher compared with lower circulating folic acid concentrations. Furthermore, specific folate species within the FOCM pathway were associated with both inflammation and angiogenesis pathways among patients with CRC. In addition, higher vitamin B6 status was associated with better quality of life at 6 months post-treatment. FUTURE PLANS Better insights into the research on associations between folate and FOCM biomarkers and clinical outcomes in patients with CRC will facilitate the development of guidelines regarding folate intake in order to provide clinically relevant advice to patients with cancer, health professionals involved in patient care, and ultimately further tertiary prevention strategies in the future. The FOCUS Consortium offers an excellent infrastructure for short-term and long-term research projects and for combining additional biomarkers and data resulting from the individual cohorts within the next years, for example, microbiome data, omics and multiomics data or CT-quantified body composition data.
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Affiliation(s)
- Biljana Gigic
- Department of General, Visceral and Transplantation Surgery, University Hospital Heidelberg, Heidelberg, Germany
| | - Eline van Roekel
- Department of Epidemiology, Maastricht University, Maastricht, The Netherlands
| | - Andreana N Holowatyj
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Vanderbilt-Ingram Cancer Center, Nashville, Tennessee, USA
| | - Stefanie Brezina
- Center for Cancer Research, Medical University of Vienna, Wien, Austria
| | - Anne J M R Geijsen
- Division of Human Nutrition and Health, Wageningen University & Research, Wageningen, The Netherlands
| | | | - Jennifer Ose
- Huntsman Cancer Institute, Salt Lake City, Utah, USA
- Department of Population Health Sciences, University of Utah, Salt Lake City, Utah, USA
| | - Janna L Koole
- Department of Epidemiology, Maastricht University, Maastricht, The Netherlands
| | - Victoria Damerell
- Department of General, Visceral and Transplantation Surgery, University Hospital Heidelberg, Heidelberg, Germany
| | - Rama Kiblawi
- Huntsman Cancer Institute, Salt Lake City, Utah, USA
- Department of Population Health Sciences, University of Utah, Salt Lake City, Utah, USA
| | | | - Tengda Lin
- Huntsman Cancer Institute, Salt Lake City, Utah, USA
- Department of Population Health Sciences, University of Utah, Salt Lake City, Utah, USA
| | | | - Torsten Koelsch
- Department of General, Visceral and Transplantation Surgery, University Hospital Heidelberg, Heidelberg, Germany
| | - Dieuwertje E Kok
- Division of Human Nutrition and Health, Wageningen University & Research, Wageningen, The Netherlands
| | - Franzel J van Duijnhoven
- Division of Human Nutrition and Health, Wageningen University & Research, Wageningen, The Netherlands
| | - Martijn J Bours
- Department of Epidemiology, Maastricht University, Maastricht, The Netherlands
| | - Andreas Baierl
- Department of Statistics and Operations Research, University of Vienna, Wien, Austria
| | - Christopher I Li
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - William Grady
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
- Department of Medicine, University of Washington School of Medicine, Seattle, Washington, USA
| | - Kathy Vickers
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Nina Habermann
- Genome Biology, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Martin Schneider
- Department of General, Visceral and Transplantation Surgery, University Hospital Heidelberg, Heidelberg, Germany
| | - Ellen Kampman
- Division of Human Nutrition and Health, Wageningen University & Research, Wageningen, The Netherlands
| | | | - Alexis Ulrich
- Department of General, Visceral and Transplantation Surgery, University Hospital Heidelberg, Heidelberg, Germany
- Surgical Department I, Städtische Kliniken Neuss, Lukaskrankenhaus GmbH, Neuss, Germany
| | - Matty Weijenberg
- Department of Epidemiology, Maastricht University, Maastricht, The Netherlands
| | - Andrea Gsur
- Center for Cancer Research, Medical University of Vienna, Wien, Austria
| | - Cornelia Ulrich
- Huntsman Cancer Institute, Salt Lake City, Utah, USA
- Department of Population Health Sciences, University of Utah, Salt Lake City, Utah, USA
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Abstract
Healthcare is undergoing large transformations, and it is imperative to leverage new technologies to support the advent of personalized medicine and disease prevention. It is now well accepted that the levels of certain biological molecules found in blood and other bodily fluids, as well as in exhaled breath, are an indication of the onset of many human diseases and reflect the health status of the person. Blood, urine, sweat, or saliva biomarkers can therefore serve in early diagnosis of diseases such as cancer, but also in monitoring disease progression, detecting metabolic disfunctions, and predicting response to a given therapy. For most point-of-care sensors, the requirement that patients themselves can use and apply them is crucial not only regarding the diagnostic part, but also at the sample collection level. This has stimulated the development of such diagnostic approaches for the non-invasive analysis of disease-relevant analytes. Considering these timely efforts, this review article focuses on novel, sensitive, and selective sensing systems for the detection of different endogenous target biomarkers in bodily fluids as well as in exhaled breath, which are associated with human diseases.
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Milchram L, Fischer A, Huber J, Soldo R, Sieghart D, Vierlinger K, Blüml S, Steiner G, Weinhäusel A. Functional Analysis of Autoantibody Signatures in Rheumatoid Arthritis. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27041452. [PMID: 35209238 PMCID: PMC8876797 DOI: 10.3390/molecules27041452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 02/11/2022] [Accepted: 02/18/2022] [Indexed: 11/21/2022]
Abstract
For the identification of antigenic protein biomarkers for rheumatoid arthritis (RA), we conducted IgG profiling on high density protein microarrays. Plasma IgG of 96 human samples (healthy controls, osteoarthritis, seropositive and seronegative RA, n = 24 each) and time-series plasma of a pristane-induced arthritis (PIA) rat model (n = 24 total) were probed on AIT’s 16k protein microarray. To investigate the analogy of underlying disease pathways, differential reactivity analysis was conducted. A total of n = 602 differentially reactive antigens (DIRAGs) at a significance cutoff of p < 0.05 were identified between seropositive and seronegative RA for the human samples. Correlation with the clinical disease activity index revealed an inverse correlation of antibodies against self-proteins found in pathways relevant for antigen presentation and immune regulation. The PIA model showed n = 1291 significant DIRAGs within acute disease. Significant DIRAGs for (I) seropositive, (II) seronegative and (III) PIA were subjected to the Reactome pathway browser which also revealed pathways relevant for antigen presentation and immune regulation; of these, seven overlapping pathways had high significance. We therefore conclude that the PIA model reflects the biological similarities of the disease pathogenesis. Our data show that protein array analysis can elucidate biological differences and pathways relevant in disease as well be a useful additional layer of omics information.
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Affiliation(s)
- Lisa Milchram
- Center for Health and Bioresources, Molecular Diagnostics, AIT Austrian Institute of Technology GmbH, Giefinggasse 4, 1210 Vienna, Austria; (L.M.); (J.H.); (R.S.); (K.V.)
| | - Anita Fischer
- Department of Internal Medicine III, Division of Rheumatology, Medical University of Vienna, Währinger Gürtel 18–20, 1090 Vienna, Austria; (A.F.); (D.S.); (S.B.); (G.S.)
| | - Jasmin Huber
- Center for Health and Bioresources, Molecular Diagnostics, AIT Austrian Institute of Technology GmbH, Giefinggasse 4, 1210 Vienna, Austria; (L.M.); (J.H.); (R.S.); (K.V.)
| | - Regina Soldo
- Center for Health and Bioresources, Molecular Diagnostics, AIT Austrian Institute of Technology GmbH, Giefinggasse 4, 1210 Vienna, Austria; (L.M.); (J.H.); (R.S.); (K.V.)
| | - Daniela Sieghart
- Department of Internal Medicine III, Division of Rheumatology, Medical University of Vienna, Währinger Gürtel 18–20, 1090 Vienna, Austria; (A.F.); (D.S.); (S.B.); (G.S.)
| | - Klemens Vierlinger
- Center for Health and Bioresources, Molecular Diagnostics, AIT Austrian Institute of Technology GmbH, Giefinggasse 4, 1210 Vienna, Austria; (L.M.); (J.H.); (R.S.); (K.V.)
| | - Stephan Blüml
- Department of Internal Medicine III, Division of Rheumatology, Medical University of Vienna, Währinger Gürtel 18–20, 1090 Vienna, Austria; (A.F.); (D.S.); (S.B.); (G.S.)
| | - Günter Steiner
- Department of Internal Medicine III, Division of Rheumatology, Medical University of Vienna, Währinger Gürtel 18–20, 1090 Vienna, Austria; (A.F.); (D.S.); (S.B.); (G.S.)
- Ludwig Boltzmann Institute for Arthritis and Rehabilitation, Medical University of Vienna, Währinger Gürtel 18–20, 1090 Vienna, Austria
| | - Andreas Weinhäusel
- Center for Health and Bioresources, Molecular Diagnostics, AIT Austrian Institute of Technology GmbH, Giefinggasse 4, 1210 Vienna, Austria; (L.M.); (J.H.); (R.S.); (K.V.)
- Correspondence:
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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 : THE PREPRINT SERVER FOR BIOLOGY 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] [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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Gsur A, Baierl A, Brezina S. Colorectal Cancer Study of Austria (CORSA): A Population-Based Multicenter Study. BIOLOGY 2021; 10:722. [PMID: 34439954 PMCID: PMC8389216 DOI: 10.3390/biology10080722] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 07/26/2021] [Accepted: 07/26/2021] [Indexed: 12/14/2022]
Abstract
The Colorectal cancer Study of Austria (CORSA) is comprised more than 13,500 newly diagnosed colorectal cancer (CRC) patients, patients with high- and low-risk adenomas as well as population-based controls. The recruitment for the CORSA biobank is performed in close cooperation with the invited two-stage CRC screening project "Burgenland PREvention trial of colorectal Disease with ImmunologiCal Testing" (B-PREDICT). Annually, more than 150,000 inhabitants of the Austrian federal state Burgenland aged between 40 and 80 are invited to participate using FIT-tests as an initial screening. FIT-positive tested participants are offered a diagnostic colonoscopy and are asked to take part in CORSA, sign a written informed consent, complete questionnaires concerning dietary and lifestyle habits and provide an ethylenediaminetetraacetic acid (EDTA) blood sample as well as a stool sample. Additional CRC cases have been recruited at four hospitals in Vienna and a hospital in lower Austria. A major strength of CORSA is the population-based controls who are FIT-positive and colonoscopy-confirmed to be free of polyps and/or CRC.
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Affiliation(s)
- Andrea Gsur
- Institute of Cancer Research, Department of Medicine I, Medical University of Vienna, 1090 Vienna, Austria;
| | - Andreas Baierl
- Department of Statistics and Operations Research, University of Vienna, 1010 Vienna, Austria;
| | - Stefanie Brezina
- Institute of Cancer Research, Department of Medicine I, Medical University of Vienna, 1090 Vienna, Austria;
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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 : THE PREPRINT SERVER FOR BIOLOGY 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] [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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Zeng J, Zhang Y, Zhang H, Zhang Y, Gao L, Tong X, Xie Y, Hu Q, Chen C, Ding S, Lu J. RPL22 Overexpression Promotes Psoriasis-Like Lesion by Inducing Keratinocytes Abnormal Biological Behavior. Front Immunol 2021; 12:699900. [PMID: 34220863 PMCID: PMC8250439 DOI: 10.3389/fimmu.2021.699900] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Accepted: 06/04/2021] [Indexed: 01/23/2023] Open
Abstract
Background Keratinocytes of psoriasis have anti-apoptotic properties including delayed apoptosis process, accelerated proliferation metabolism and postponed differentiation process. However, the specific mechanism leading to the abnormal biological behavior of keratinocytes remains unclear. Objectives We investigated the role of increased RPL22 expression in regulating the abnormal biological behavior of keratinocytes and the mechanism of regulation of RPL22 expression in skin lesions of psoriatic patients. Methods We examined clinical samples and utilized cytokine-induced cell and IMQ-treated mouse models. We determined the expression and functions of RPL22 in vitro and in vivo. Results We showed that RPL22 expression was significantly increased in the skin lesions of psoriasis patients and IMQ-treated psoriatic-like mice. Such increased expression is attributed to hyperacetylation of histone H3K27 in the promoter region of RPL22. Interestingly, overexpression of RPL22 enhanced keratinocyte proliferation by increasing cyclinD1 expression and accelerated CD4+T cells recruitment via upregulating CXCL10 expression. Finally, we demonstrated that RPL22 overexpression promoted psoriasiform phenotypes in IMQ-induced mouse skins. Conclusions These findings suggested that RPL22 regulates keratinocytes abnormal biological behavior and contributes to the development of psoriatic phenotypes. Thus, RPL22 might be a novel potential molecular target for treatment of psoriasis.
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Affiliation(s)
- Jinrong Zeng
- Department of Dermatology, Third Xiangya Hospital, Central South University, Changsha, China
| | - Yue Zhang
- XiangYa School of Medicine, Central South University, Changsha, China
| | - Hanyi Zhang
- XiangYa School of Medicine, Central South University, Changsha, China
| | - Yuezhong Zhang
- XiangYa School of Medicine, Central South University, Changsha, China
| | - Lihua Gao
- Department of Dermatology, Third Xiangya Hospital, Central South University, Changsha, China
| | - Xiaoliang Tong
- Department of Dermatology, Third Xiangya Hospital, Central South University, Changsha, China
| | - Yajie Xie
- Department of Dermatology, Third Xiangya Hospital, Central South University, Changsha, China
| | - Qian Hu
- Department of Dermatology, Third Xiangya Hospital, Central South University, Changsha, China
| | - Chunli Chen
- Department of Dermatology, Third Xiangya Hospital, Central South University, Changsha, China
| | - Shu Ding
- Department of Dermatology, Third Xiangya Hospital, Central South University, Changsha, China
| | - Jianyun Lu
- Department of Dermatology, Third Xiangya Hospital, Central South University, Changsha, China
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11
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Tracking the Antibody Immunome in Sporadic Colorectal Cancer by Using Antigen Self-Assembled Protein Arrays. Cancers (Basel) 2021; 13:cancers13112718. [PMID: 34072782 PMCID: PMC8198956 DOI: 10.3390/cancers13112718] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 05/14/2021] [Accepted: 05/21/2021] [Indexed: 02/07/2023] Open
Abstract
Simple Summary Immunome in Sporadic Colorectal Cancer as source for biomarkers. Hence, a self-assembled protein array has been designed and developed to perform a serum screening to determined specific immune response against tumor antigens proteins as potential diagnostics biomarker panel. Abstract Sporadic Colorectal Cancer (sCRC) is the third leading cause of cancer death in the Western world, and the sCRC patients presenting with synchronic metastasis have the poorest prognosis. Genetic alterations accumulated in sCRC tumor cells translate into mutated proteins and/or abnormal protein expression levels, which contribute to the development of sCRC. Then, the tumor-associated proteins (TAAs) might induce the production of auto-antibodies (aAb) via humoral immune response. Here, Nucleic Acid Programmable Protein Arrays (NAPPArray) are employed to identify aAb in plasma samples from a set of 50 sCRC patients compared to seven healthy donors. Our goal was to establish a systematic workflow based on NAPPArray to define differential aAb profiles between healthy individuals and sCRC patients as well as between non-metastatic (n = 38) and metastatic (n = 12) sCRC, in order to gain insight into the role of the humoral immune system in controlling the development and progression of sCRC. Our results showed aAb profile based on 141 TAA including TAAs associated with biological cellular processes altered in genesis and progress of sCRC (e.g., FSCN1, VTI2 and RPS28) that discriminated healthy donors vs. sCRC patients. In addition, the potential capacity of discrimination (between non-metastatic vs. metastatic sCRC) of 7 TAAs (USP5, ML4, MARCKSL1, CKMT1B, HMOX2, VTI2, TP53) have been analyzed individually in an independent cohort of sCRC patients, where two of them (VTI2 and TP53) were validated (AUC ~75%). In turn, these findings provided novel insights into the immunome of sCRC, in combination with transcriptomics profiles and protein antigenicity characterizations, wich might lead to the identification of novel sCRC biomarkers that might be of clinical utility for early diagnosis of the tumor. These results explore the immunomic analysis as potent source for biomarkers with diagnostic and prognostic value in CRC. Additional prospective studies in larger series of patients are required to confirm the clinical utility of these novel sCRC immunomic biomarkers.
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12
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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 : THE PREPRINT SERVER FOR BIOLOGY 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] [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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13
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Fidelle M, Yonekura S, Picard M, Cogdill A, Hollebecque A, Roberti MP, Zitvogel L. Resolving the Paradox of Colon Cancer Through the Integration of Genetics, Immunology, and the Microbiota. Front Immunol 2020; 11:600886. [PMID: 33381121 PMCID: PMC7768083 DOI: 10.3389/fimmu.2020.600886] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 11/09/2020] [Indexed: 12/13/2022] Open
Abstract
While colorectal cancers (CRC) are paradigmatic tumors invaded by effector memory lymphocytes, the mechanisms accounting for the relative resistance of MSI negative CRC to immunogenic cell death mediated by oxaliplatin and immune checkpoint inhibitors has remained an open conundrum. Here, we propose the viewpoint where its microenvironmental contexture could be explained -at least in part- by macroenvironmental cues constituted by the complex interplay between the epithelial barrier, its microbial ecosystem, and the local immune system. Taken together this dynamic ménage-à-trois offers novel coordinated actors of the humoral and cellular immune responses actionable to restore sensitivity to immune checkpoint inhibition. Solving this paradox involves breaking tolerance to crypt stem cells by inducing the immunogenic apoptosis of ileal cells in the context of an ileal microbiome shifted towards immunogenic bacteria using cytotoxicants. This manoeuver results in the elicitation of a productive Tfh and B cell dialogue in mesenteric lymph nodes culminating in tumor-specific memory CD8+ T cell responses sparing the normal epithelium.
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Affiliation(s)
- Marine Fidelle
- Gustave Roussy, Villejuif, France
- Institut National de la Santé Et de la Recherche Médicale (INSERM) U1015, Villejuif, France
- Equipe Labellisée—Ligue Nationale contre le Cancer, Villejuif, France
- Center of Clinical Investigations in Biotherapies of Cancer (CICBT) 1428, Villejuif, France
- Université Paris-Saclay, Gustave Roussy, Villejuif, France
| | - Satoru Yonekura
- Gustave Roussy, Villejuif, France
- Institut National de la Santé Et de la Recherche Médicale (INSERM) U1015, Villejuif, France
- Equipe Labellisée—Ligue Nationale contre le Cancer, Villejuif, France
- Université Paris-Saclay, Gustave Roussy, Villejuif, France
| | - Marion Picard
- Gustave Roussy, Villejuif, France
- Institut National de la Santé Et de la Recherche Médicale (INSERM) U1015, Villejuif, France
- Equipe Labellisée—Ligue Nationale contre le Cancer, Villejuif, France
- Unit Biology and Genetics of the Bacterial Cell Wall, Institut Pasteur, Paris, France
| | - Alexandria Cogdill
- Department of Immunology, University of Texas, MD Anderson Cancer Center, Houston, TX, United States
- Department of Genomic Medicine, University of Texas, MD Anderson Cancer Center, Houston, TX, United States
| | - Antoine Hollebecque
- Gustave Roussy, Villejuif, France
- Department of Medical Oncology, Gustave Roussy, Villejuif, France
| | - Maria Paula Roberti
- Gustave Roussy, Villejuif, France
- Institut National de la Santé Et de la Recherche Médicale (INSERM) U1015, Villejuif, France
- Equipe Labellisée—Ligue Nationale contre le Cancer, Villejuif, France
| | - Laurence Zitvogel
- Gustave Roussy, Villejuif, France
- Institut National de la Santé Et de la Recherche Médicale (INSERM) U1015, Villejuif, France
- Equipe Labellisée—Ligue Nationale contre le Cancer, Villejuif, France
- Center of Clinical Investigations in Biotherapies of Cancer (CICBT) 1428, Villejuif, France
- Université Paris-Saclay, Gustave Roussy, Villejuif, France
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14
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Chemotherapy-induced ileal crypt apoptosis and the ileal microbiome shape immunosurveillance and prognosis of proximal colon cancer. Nat Med 2020; 26:919-931. [DOI: 10.1038/s41591-020-0882-8] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 04/10/2020] [Indexed: 12/16/2022]
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15
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Krainer J, Siebenhandl S, Weinhäusel A. Systemic autoinflammatory diseases. J Autoimmun 2020; 109:102421. [PMID: 32019685 PMCID: PMC7610735 DOI: 10.1016/j.jaut.2020.102421] [Citation(s) in RCA: 105] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 01/07/2020] [Accepted: 01/13/2020] [Indexed: 12/17/2022]
Abstract
Systemic autoinflammatory diseases (SAIDs) are a growing group of disorders caused by a dysregulation of the innate immune system leading to episodes of systemic inflammation. In 1997, MEFV was the first gene identified as disease causing for Familial Mediterranean Fever, the most common hereditary SAID. In most cases, autoinflammatory diseases have a strong genetic background with mutations in single genes. Since 1997 more than 30 new genes associated with autoinflammatory diseases have been identified, affecting different parts of the innate immune system. Nevertheless, for at least 40-60% of patients with phenotypes typical for SAIDs, a distinct diagnosis cannot be met, leading to undefined SAIDs (uSAIDs). However, SAIDs can also be of polygenic or multifactorial origin, with environmental influence modulating the phenotype. The implementation of a disease continuum model combining the adaptive and the innate immune system with autoinflammatory and autoimmune diseases shows the complexity of SAIDs and the importance of new methods to elucidate molecular changes and causative factors in SAIDs. Diagnosis is often based on clinical presentation and genetic testing. The timeline from onset to diagnosis takes up to 7.3 years, highlighting the indisputable need to identify new treatment and diagnostic targets. Recently, other factors are under investigation as additional contributors to the pathogenesis of SAIDs. This review gives an overview of pathogenesis and etiology of SAIDs, and summarizes recent diagnosis and treatment options.
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Affiliation(s)
- Julie Krainer
- AIT Austrian Institute of Technology GmbH, Center for Health and Bioresources, Molecular Diagnostics, Giefinggasse 4, 1210, Vienna, Austria.
| | - Sandra Siebenhandl
- AIT Austrian Institute of Technology GmbH, Center for Health and Bioresources, Molecular Diagnostics, Giefinggasse 4, 1210, Vienna, Austria
| | - Andreas Weinhäusel
- AIT Austrian Institute of Technology GmbH, Center for Health and Bioresources, Molecular Diagnostics, Giefinggasse 4, 1210, Vienna, Austria
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16
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Kheirkhah R, DeMarshall C, Sieber F, Oh E, Nagele RG. The origin and nature of the complex autoantibody profile in cerebrospinal fluid. Brain Behav Immun Health 2020; 2:100032. [PMID: 38377421 PMCID: PMC8474157 DOI: 10.1016/j.bbih.2019.100032] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 12/19/2019] [Accepted: 12/20/2019] [Indexed: 01/04/2023] Open
Abstract
The present study demonstrates, using human protein microarrays and plasma and cerebrospinal fluid samples obtained pre-surgically and simultaneously from 46 hip fracture repair patients, that CSF exhibits an extraordinarily complex IgG autoantibody profile composed of thousands of autoantibodies. We show that the pattern of expression levels of individual autoantibodies in CSF closely mimics that in the blood, regardless of age, gender or the presence or absence of disease, indicative of a blood-based origin for CSF autoantibodies. In addition, using five longitudinal serum samples obtained from one healthy individual over a span of nine years, we found that blood autoantibody profiles are remarkably stable over a long period of time, and that autoantibody profiles in both blood and CSF show features that are common among different individuals as well as individual-specific. Lastly, we demonstrate that an elevated CSF/plasma autoantibody ratio is more common in elderly hip fracture repair patients that experienced post-operative delirium than in non-delirium subjects, thus highlighting the crucial role that blood-brain and/or blood-CSF barrier compromise may play in the development of post-operative delirium.
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Affiliation(s)
- Rahil Kheirkhah
- Graduate School of Biomedical Sciences (GSBS), Rowan University, Stratford, NJ, USA
| | - Cassandra DeMarshall
- Biomarker Discovery Center, New Jersey Institute for Successful Aging, Rowan University School of Osteopathic Medicine, Stratford, NJ, USA
- Department of Geriatrics and Gerontology, Rowan University School of Osteopathic Medicine, Stratford, NJ, USA
| | - Frederick Sieber
- Department of Anesthesiology and Critical Care Medicine, Johns Hopkins Bayview Medical Center, Baltimore, MD, USA
| | - Esther Oh
- Department of Medicine, Psychiatry and Behavioral Sciences, Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Robert G Nagele
- Biomarker Discovery Center, New Jersey Institute for Successful Aging, Rowan University School of Osteopathic Medicine, Stratford, NJ, USA
- Department of Geriatrics and Gerontology, Rowan University School of Osteopathic Medicine, Stratford, NJ, USA
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17
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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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18
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Palmisano A, Krushkal J, Li MC, Fang J, Sonkin D, Wright G, Yee L, Zhao Y, McShane L. Bioinformatics Tools and Resources for Cancer Immunotherapy Study. Methods Mol Biol 2020; 2055:649-678. [PMID: 31502173 DOI: 10.1007/978-1-4939-9773-2_29] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
In recent years, cancer immunotherapy has emerged as a highly promising approach to treat patients with cancer, as the patient's own immune system is harnessed to attack cancer cells. However, the application of these approaches is still limited to a minority of patients with cancer and it is difficult to predict which patients will derive the greatest clinical benefit.One of the challenges faced by the biomedical community in the search of more effective biomarkers is the fact that translational research efforts involve collecting and accessing data at many different levels: from the type of material examined (e.g., cell line, animal models, clinical samples) to multiple data type (e.g., pharmacodynamic markers, genetic sequencing data) to the scale of a study (e.g., small preclinical study, moderate retrospective study on stored specimen sets, clinical trials with large cohorts).This chapter reviews several publicly available bioinformatics tools and data resources for high throughput molecular analyses applied to a range of data types, including those generated from microarray, whole-exome sequencing (WES), RNA-seq, DNA copy number, and DNA methylation assays, that are extensively used for integrative multidimensional data analysis and visualization.
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Affiliation(s)
- Alida Palmisano
- Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Julia Krushkal
- Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ming-Chung Li
- Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jianwen Fang
- Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Dmitriy Sonkin
- Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - George Wright
- Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Laura Yee
- Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Yingdong Zhao
- Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
| | - Lisa McShane
- Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
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19
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Shao X, Lv N, Liao J, Long J, Xue R, Ai N, Xu D, Fan X. Copy number variation is highly correlated with differential gene expression: a pan-cancer study. BMC MEDICAL GENETICS 2019; 20:175. [PMID: 31706287 PMCID: PMC6842483 DOI: 10.1186/s12881-019-0909-5] [Citation(s) in RCA: 150] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 10/15/2019] [Indexed: 12/13/2022]
Abstract
BACKGROUND Cancer is a heterogeneous disease with many genetic variations. Lines of evidence have shown copy number variations (CNVs) of certain genes are involved in development and progression of many cancers through the alterations of their gene expression levels on individual or several cancer types. However, it is not quite clear whether the correlation will be a general phenomenon across multiple cancer types. METHODS In this study we applied a bioinformatics approach integrating CNV and differential gene expression mathematically across 1025 cell lines and 9159 patient samples to detect their potential relationship. RESULTS Our results showed there is a close correlation between CNV and differential gene expression and the copy number displayed a positive linear influence on gene expression for the majority of genes, indicating that genetic variation generated a direct effect on gene transcriptional level. Another independent dataset is utilized to revalidate the relationship between copy number and expression level. Further analysis show genes with general positive linear influence on gene expression are clustered in certain disease-related pathways, which suggests the involvement of CNV in pathophysiology of diseases. CONCLUSIONS This study shows the close correlation between CNV and differential gene expression revealing the qualitative relationship between genetic variation and its downstream effect, especially for oncogenes and tumor suppressor genes. It is of a critical importance to elucidate the relationship between copy number variation and gene expression for prevention, diagnosis and treatment of cancer.
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Affiliation(s)
- Xin Shao
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Ning Lv
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Jie Liao
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Jinbo Long
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Rui Xue
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Ni Ai
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Donghang Xu
- Department of Pharmacy, The 2nd Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310009, China.
| | - Xiaohui Fan
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China.
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