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Hagn-Meincke R, Yadav D, Andersen DK, Vege SS, Fogel EL, Serrano J, Bellin MD, Topazian MD, Conwell DL, Li L, Van Den Eeden SK, Drewes AM, Pandol SJ, Forsmark CE, Fisher WE, Hart PA, Olesen SS, Park WG. Circulating immune signatures in chronic pancreatitis with and without preceding acute pancreatitis: A pilot study. Pancreatology 2024; 24:384-393. [PMID: 38461145 PMCID: PMC11023786 DOI: 10.1016/j.pan.2024.02.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 02/05/2024] [Accepted: 02/21/2024] [Indexed: 03/11/2024]
Abstract
OBJECTIVE To investigate profiles of circulating immune signatures in healthy controls and chronic pancreatitis patients (CP) with and without a preceding history of acute pancreatitis (AP). METHODS We performed a phase 1, cross-sectional analysis of prospectively collected serum samples from the PROspective Evaluation of Chronic Pancreatitis for EpidEmiologic and Translation StuDies (PROCEED) study. All samples were collected during a clinically quiescent phase. CP subjects were categorized into two subgroups based on preceding episode(s) of AP. Healthy controls were included for comparison. Blinded samples were analyzed using an 80-plex Luminex assay of cytokines, chemokines, and adhesion molecules. Group and pairwise comparisons of analytes were performed between the subgroups. RESULTS In total, 133 patients with CP (111 with AP and 22 without AP) and 50 healthy controls were included. Among the 80 analytes studied, CP patients with a history of AP had significantly higher serum levels of pro-inflammatory cytokines (interleukin (IL)-6, IL-8, IL-1 receptor antagonist, IL-15) and chemokines (Cutaneous T-Cell Attracting Chemokine (CTACK), Monokine induced Gamma Interferon (MIG), Macrophage-derived Chemokine (MDC), Monocyte Chemoattractant Protein-1 (MCP-1)) compared to CP without preceding AP and controls. In contrast, CP patients without AP had immune profiles characterized by low systemic inflammation and downregulation of anti-inflammatory mediators, including IL-10. CONCLUSION CP patients with a preceding history of AP have signs of systemic inflammatory activity even during a clinically quiescent phase. In contrast, CP patients without a history of AP have low systemic inflammatory activity. These findings suggest the presence of two immunologically diverse subtypes of CP.
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Affiliation(s)
- Rasmus Hagn-Meincke
- Centre for Pancreatic Diseases and Mech-Sense, Department of Gastroenterology & Hepatology, Aalborg University Hospital, Aalborg, Denmark; Division of Gastroenterology and Hepatology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Dhiraj Yadav
- Division of Gastroenterology, Hepatology and Nutrition, University of Pittsburgh, Pittsburgh, PA, USA
| | - Dana K Andersen
- Division of Digestive Diseases and Nutrition, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Santhi Swaroop Vege
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
| | - Evan L Fogel
- Division of Gastroenterology and Hepatology, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Jose Serrano
- Division of Digestive Diseases and Nutrition, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Melena D Bellin
- Division of Pediatric Endocrinology, University of Minnesota, Minnesota, MN, USA
| | - Mark D Topazian
- Division of Digestive Diseases and Nutrition, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Darwin L Conwell
- Department of Medicine, University of Kentucky, Lexington, KY, USA
| | - Liang Li
- Department of Biostatistics, MD Anderson Cancer Center, Houston, TX, USA
| | | | - Asbjørn M Drewes
- Centre for Pancreatic Diseases and Mech-Sense, Department of Gastroenterology & Hepatology, Aalborg University Hospital, Aalborg, Denmark
| | - Stephen J Pandol
- Division of Digestive and Liver Diseases, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Chris E Forsmark
- Division of Gastroenterology, Hepatology, and Nutrition. University of Florida, Gainesville, FL, USA
| | - William E Fisher
- Division of General Surgery, Baylor College of Medicine, Houston, TX, USA
| | - Phil A Hart
- Division of Gastroenterology, Hepatology, and Nutrition, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Søren S Olesen
- Centre for Pancreatic Diseases and Mech-Sense, Department of Gastroenterology & Hepatology, Aalborg University Hospital, Aalborg, Denmark
| | - Walter G Park
- Division of Gastroenterology and Hepatology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA.
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Meeks JJ, Black PC, Galsky M, Grivas P, Hahn NM, Hussain SA, Milowsky MI, Steinberg GD, Svatek RS, Rosenberg JE. Checkpoint Inhibitors in Urothelial Carcinoma-Future Directions and Biomarker Selection. Eur Urol 2023; 84:473-483. [PMID: 37258363 DOI: 10.1016/j.eururo.2023.05.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 04/22/2023] [Accepted: 05/13/2023] [Indexed: 06/02/2023]
Abstract
CONTEXT Several recent phase 2 and 3 trials have evaluated the efficacy and toxicity of checkpoint inhibitor (CPI) therapy for urothelial carcinoma (UC) in the metastatic, localized muscle-invasive UC (MIUC), upper tract UC, and non-muscle-invasive bladder cancer (NMIBC) disease state. OBJECTIVE To assess the outcomes and toxicity of CPIs across the treatment landscape of UC and contextualize their application to current real-world treatment. EVIDENCE ACQUISITION We queried PubMed, Web of Science, and EMBASE databases and conference abstracts to identify prospective trials examining CPIs in UC. The primary endpoints included overall survival, recurrence-free survival, and toxicity (when available). A secondary analysis included biomarker evaluation of response. EVIDENCE SYNTHESIS We identified 21 trials, 12 phase 2 and nine phase 3 trials, in which a CPI was used for metastatic UC (seven), MIUC (nine), and NMIBC (five). For first-line (1L) metastatic UC, concurrent chemotherapy with CPIs failed to show superiority. Improved overall and progression-free survival for switch maintenance avelumab (after achieving stable disease or response with induction systemic chemotherapy) has established the current standard of care for 1L metastatic UC. A single-agent CPI is a consideration for patients unable to tolerate chemotherapy. CPIs in the perioperative setting are limited to only the adjuvant treatment with nivolumab after radical surgery for MIUC in patients at a higher risk of recurrence based on pathologic stage. Only pembrolizumab is approved by the Food and Drug Administration for carcinoma in situ unresponsive to bacillus Calmette-Guérin (BCG) in patients who are not fit for or who refuse radical cystectomy. Trials investigating CPIs in combination with multiple immune regulators, antibody drug conjugates, targeted therapies, antiangiogenic agents, chemotherapy, and radiotherapy are enrolling patients and may shape the future treatment of patients with UC. CONCLUSIONS CPIs have an established role across multiple states of UC, with broadened applications likely to occur in the future. Several combinations are being evaluated, while the development of predictive biomarkers and their validation may help identify patients who are most likely to respond. PATIENT SUMMARY Our findings highlight the broad activity of checkpoint inhibitors in urothelial carcinoma, noting the need for further investigation for the best application of combinations and patient selection to patient care.
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Affiliation(s)
- Joshua J Meeks
- Department of Urology, Feinberg School of Medicine, Chicago, IL, USA; Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Chicago, IL, USA; Jesse Brown VAMC, Chicago, IL, USA.
| | - Peter C Black
- Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Petros Grivas
- Department of Medicine, Division of Medical Oncology, University of Washington, Seattle, WA, USA; Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Noah M Hahn
- Greenberg Bladder Cancer Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Syed A Hussain
- Department of Oncology and Metabolism, University of Sheffield, Sheffield, UK
| | - Matthew I Milowsky
- University of North Carolina Lineberger Comprehensive Cancer Center, Chapel Hill, NC, USA
| | | | - Robert S Svatek
- Department of Urology, University of Texas Health San Antonio (UTHSA), San Antonio, TX, USA
| | - Jonathan E Rosenberg
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Weill Cornell Medical College, New York, NY, USA
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Liu Q, Wang X. Classification of triple-negative breast cancer based on pathway enrichment levels. Med Oncol 2023; 40:157. [PMID: 37093316 DOI: 10.1007/s12032-023-02021-w] [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] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 04/02/2023] [Indexed: 04/25/2023]
Abstract
Triple-negative breast cancer (TNBC) is highly heterogeneous in the stromal and immune microenvironment, genome integrity, oncogenic signatures, and metabolic processes. However, a classification of TNBC by combining these features remains lacking. Here we classified TNBC based on the enrichment levels of 14 pathways related to immune, stromal, oncogenic and metabolic signatures by unsupervised clustering. In three bulk tumor transcriptome datasets and a single cell RNA-Seq (scRNA-seq) dataset, we consistently identified four TNBC subtypes: Imm-E, Str-E, DR-E, and Met-E. Imm-E displayed the strongest immune signatures, the lowest intratumor heterogeneity (ITH), the highest global methylation levels, the lowest tumor purity, and the best prognosis. Str-E showed the strongest stromal signatures and TGF-β signaling. DR-E had the highest DNA repair activity, cell cycle activity, and genomic instability. Met-E demonstrated the strongest hormone metabolism and signaling, the highest ITH, the lowest genomic instability, and the worst prognosis. The subtyping of TNBC provides novel insights into tumor biology and clinical implications for this disease.
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Affiliation(s)
- Qian Liu
- Biomedical Informatics Research Lab, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
- Cancer Genomics Research Center, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
- Big Data Research Institute, China Pharmaceutical University, Nanjing, 211198, China
| | - Xiaosheng Wang
- Biomedical Informatics Research Lab, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, 211198, China.
- Cancer Genomics Research Center, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, 211198, China.
- Big Data Research Institute, China Pharmaceutical University, Nanjing, 211198, China.
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Kim SY, Yin J, Bohlman S, Walker P, Dacic S, Kim C, Khan H, Liu SV, Ma PC, Nagasaka M, Reckamp KL, Abraham J, Uprety D, Wang F, Xiu J, Zhang J, Cheng H, Halmos B. Characterization of MET Exon 14 Skipping Alterations (in NSCLC) and Identification of Potential Therapeutic Targets Using Whole Transcriptome Sequencing. JTO Clin Res Rep 2022; 3:100381. [PMID: 36082279 PMCID: PMC9445394 DOI: 10.1016/j.jtocrr.2022.100381] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 07/06/2022] [Accepted: 07/07/2022] [Indexed: 11/26/2022] Open
Abstract
Introduction Genomic alterations in the juxtamembrane exon 14 splice sites in NSCLC lead to increased MET stability and oncogenesis. We present the largest cohort study of MET Exon 14 (METex14) using whole transcriptome sequencing. Methods A total of 21,582 NSCLC tumor samples underwent complete genomic profiling with next-generation sequencing of DNA (592 Gene Panel, NextSeq, whole exome sequencing, NovaSeq) and RNA (NovaSeq, whole transcriptome sequencing). Clinicopathologic information including programmed death-ligand 1 and tumor mutational burden were collected and RNA expression for mutation subtypes and MET amplification were quantified. Immunogenic signatures and potential pathways of invasion were characterized using single-sample gene set enrichment analysis and mRNA gene signatures. Results A total of 533tumors (2.47%) with METex14 were identified. The most common alterations were point mutations (49.5%) at donor splice sites. Most alterations translated to increased MET expression, with MET co-amplification resulting in synergistic increase in expression (q < 0.05). Common coalterations were amplifications of MDM2 (19.0% versus 1.8% wild-type [WT]), HMGA2 (13.2% versus 0.98% WT), and CDK4 (10.0% versus 1.5% WT) (q < 0.05). High programmed death-ligand 1 > 50% (52.5% versus 27.3% WT, q < 0.0001) and lower proportion of high tumor mutational burden (>10 mutations per megabase, 8.3% versus 36.7% WT, p < 0.0001) were associated with METex14, which were also enriched in both immunogenic signatures and immunosuppressive checkpoints. Pathways associated with METex14 included angiogenesis and apical junction pathways (q < 0.05). Conclusions METex14 splicing alterations and MET co-amplification translated to higher and synergistic MET expression at the transcriptomic level. High frequencies of MDM2 and CDK4 co-amplifications and association with multiple immunosuppressive checkpoints and angiogenic pathways provide insight into potential actionable targets for combination strategies in METex14 NSCLC.
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Affiliation(s)
- So Yeon Kim
- Department of Medical Oncology, Montefiore Medical Center, Albert Einstein Cancer Center, Bronx, New York
- Yale School of Medicine, New Haven, Connecticut
| | - Jun Yin
- Caris Life Sciences, Phoenix, Arizona
| | - Stephen Bohlman
- Department of Medical Oncology, Montefiore Medical Center, Albert Einstein Cancer Center, Bronx, New York
| | | | - Sanja Dacic
- Yale School of Medicine, New Haven, Connecticut
| | - Chul Kim
- Georgetown Lombardi Comprehensive Cancer Center, Washington, District of Columbia
| | - Hina Khan
- Warren Alpert Medical School of Brown University, Providence, Rhode Island
| | - Stephen V. Liu
- Georgetown Lombardi Comprehensive Cancer Center, Washington, District of Columbia
| | | | | | | | | | | | - Feng Wang
- Department of Medical Oncology, Montefiore Medical Center, Albert Einstein Cancer Center, Bronx, New York
| | | | | | - Haiying Cheng
- Department of Medical Oncology, Montefiore Medical Center, Albert Einstein Cancer Center, Bronx, New York
| | - Balazs Halmos
- Department of Medical Oncology, Montefiore Medical Center, Albert Einstein Cancer Center, Bronx, New York
- Corresponding author. Address for correspondence: Balazs Halmos, MD, Montefiore Medical Center, Albert Einstein Cancer Center, Bronx, New York.
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Zhang J, Liu W, Feng S, Zhong B. The possible role of SRMS in colorectal cancer by bioinformatics analysis. World J Surg Oncol 2021; 19:326. [PMID: 34781983 PMCID: PMC8594183 DOI: 10.1186/s12957-021-02431-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] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 10/24/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Src-related kinase lacking C-terminal regulatory tyrosine and N-terminal myristoylation sites (SRMS) is a non-receptor tyrosine kinase that has been found to be overexpressed in various tumors. However, the role of SRMS in colorectal cancer (CRC) has not been well established. METHODS We evaluated the expression levels of SRMS in CRC using GEPIA, Oncomine, and HPA datasets. Survival information and gene expression data of CRC were obtained from The Cancer Genome Atlas (TCGA). Then, the association between SRMS and clinicopathological features was analyzed using UALCAN dataset. LinkedOmics was used to determine co-expression and functional networks associated with SRMS. Besides, we used TISIDB to assess the correlation between SRMS and immune signatures, including tumor-infiltrating immune cells and immunomodulators. Lastly, protein-protein interaction network (PPI) was established and the function enrichment analysis of the SRMS-associated immunomodulators and immune cell marker genes were performed using the STRING portal. RESULTS Compared to normal colorectal tissues, SRMS was found to be overexpressed in CRC tissues, which was correlated with a poor prognosis. In colon adenocarcinoma (COAD), the expression levels of SRMS are significantly correlated with pathological stages and nodal metastasis status. Functional network analysis suggested that SRMS regulates intermediate filament-based processes, protein autophosphorylation, translational initiation, and elongation signaling through pathways involving ribosomes, proteasomes, oxidative phosphorylation, and DNA replication. In addition, SRMS expression was correlated with infiltrating levels of CD4+ T cells, CD56dim, MEM B, Neutrophils, Th2, Th17, and Act DC. The gene ontology (GO) analysis of SRMS-associated immunomodulators and immune cell marker genes showed that they were mainly enriched in the immune microenvironment molecule-related signals. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of these genes indicated that they are involved in multiple cancer-related pathways. CONCLUSIONS SRMS is a promising prognostic biomarker and potential therapeutic target for CRC patients. In particular, SRMS regulates CRC progression by modulating cytokine-cytokine receptor interaction, chemokines, IL-17, and intestinal immune networks for IgA production signaling pathways among others. However, more studies are needed to validate these findings.
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Affiliation(s)
- Jie Zhang
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, 87 Xiangya Road, Kaifu District, Changsha, 410008, China
| | - Weidong Liu
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, 87 Xiangya Road, Kaifu District, Changsha, 410008, China
| | - Sisi Feng
- Department of Essential Surgery, Xiangya Hospital, Central South University, Changsha, China
| | - Baiyun Zhong
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, 87 Xiangya Road, Kaifu District, Changsha, 410008, China.
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Elsayed I, Li L, Sheahan K, Moran B, Bakheit S, Wang X. Adenoma to carcinoma: A portrait of molecular and immunological profiles of colorectal sporadic tumors. Int Immunopharmacol 2021; 100:108168. [PMID: 34562842 DOI: 10.1016/j.intimp.2021.108168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 09/08/2021] [Accepted: 09/15/2021] [Indexed: 12/24/2022]
Abstract
An in-depth investigation of the molecular and immunologic properties of colorectal adenoma is important for understanding the mechanisms of colorectal cancer (CRC) initiation and development through the adenoma pathway. We performed a meta-analysis of the gene expression data from seven CRC and colorectal sporadic conventional adenoma datasets. We compared the enrichment levels of immune signatures between adenoma, normal colon, and CRC, then applied immunohistochemistry to compare the CD3 + and CD8 + T cells infiltration using samples of adenoma, contiguous adenoma, and CRC. We identified differentially expressed genes (DEGs) between adenoma, normal colon, and CRC, then performed pathway, network, immune correlation, and survival analyses on the DEGs. Adenoma had lower enrichment levels of antitumor immune signatures (CD8 + T cells, NK cells, and MHC Class I) while higher levels of TGF-β and Th17 signatures. Immunohistochemistry revealed variations in CD3 + and CD8 + T cells infiltration between low-grade and high-grade adenomas and between adenoma, normal colon, and CRC. We identified two groups of genes, which we named (NACupGs and NACdownGs), with consistent expression elevation and reduction respectively across the normal, precancerous, and cancerous stages. 48% of the NACupGs had expression levels highly correlated with Treg and TGF-β immune signatures, of which 39% were inversely correlated with CRC survival. We conclude that anti-tumor immune response is reduced at the precancerous (adenoma) stage which is characterized by prominent TGF-β and Th17 activity. The alterations of molecular and immunological profiles in adenoma can provide new insights into the initiation and development of CRC.
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Affiliation(s)
- Inas Elsayed
- Biomedical Informatics Research Lab, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 211198, China; Cancer Genomics Research Center, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 211198, China; Big Data Research Institute, China Pharmaceutical University, Nanjing 211198, China; Department of Pharmacology, Faculty of Pharmacy, University of Gezira, Wad Madani 20, Sudan
| | - Lin Li
- Biomedical Informatics Research Lab, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 211198, China; Cancer Genomics Research Center, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 211198, China; Big Data Research Institute, China Pharmaceutical University, Nanjing 211198, China
| | - Kieran Sheahan
- Centre for Colorectal Disease, St. Vincent's University Hospital, Elm Park Dublin 4, Ireland; School of Medicine and Medical Sciences, University College Dublin, Belfield Dublin 4, Ireland
| | - Bruce Moran
- Department of Pathology, St. Vincent's University Hospital, Elm Park Dublin 4, Ireland
| | - Salih Bakheit
- Hull Royal Infirmary, Hull University Hospital NHS Trust, Hull, East Yorkshire, UK
| | - Xiaosheng Wang
- Biomedical Informatics Research Lab, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 211198, China; Cancer Genomics Research Center, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 211198, China; Big Data Research Institute, China Pharmaceutical University, Nanjing 211198, China.
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Cao W, Feng Q, Wang X. Computational analysis of TMPRSS2 expression in normal and SARS-CoV-2-infected human tissues. Chem Biol Interact 2021; 346:109583. [PMID: 34284028 PMCID: PMC8285370 DOI: 10.1016/j.cbi.2021.109583] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 07/05/2021] [Accepted: 07/16/2021] [Indexed: 12/13/2022]
Abstract
The transmembrane serine protease 2 (TMPRSS2) is a key molecule for SARS-CoV-2 invading human host cells. To provide insights into SARS-CoV-2 infection of various human tissues and understand the potential mechanism of SARS-CoV-2 infection, we investigated TMPRSS2 expression in various normal human tissues and SARS-CoV-2-infected human tissues. Using publicly available datasets, we performed computational analyses of TMPRSS2 expression levels in 30 normal human tissues, and compared them between males and females and between younger (ages ≤ 49 years) and older (ages > 49 years) populations in these tissues. We found that TMPRSS2 expression levels were the highest in the prostate, stomach, pancreas, lungs, small intestine, and salivary gland. The TMPRSS2 protein had relatively high expression levels in the parathyroid gland, stomach, small intestine, pancreas, kidneys, seminal vesicle, epididymis, and prostate. However, TMPRSS2 expression levels were not significantly different between females and males or between younger and older populations in these tissues. The pathways enriched in TMPRSS2-upregulated pan-tissue were mainly involved in immune, metabolism, cell growth and proliferation, stromal signatures, and cancer and other diseases. Many cytokine genes displayed positive expression correlations with TMPRSS2 in pan-tissue, including TNF-α, IL-1, IL-2, IL-4, IL-7, IL-8, IL-12, IL-18, IFN-α, MCP-1, G-CSF, and IP-10. We further analyzed TMPRSS2 expression levels in nasopharyngeal swabs from SARS-CoV-2-infected patients. TMPRSS2 expression levels showed no significant difference between males and females or between younger and older patients. However, they were significantly lower in SARS-CoV-2-infected than in healthy individuals and patients with other viral acute respiratory illnesses. Interestingly, TMPRSS2 expression levels were positively correlated with the enrichment levels of four immune signatures (B cells, CD8+ T cells, NK cells, and interferon response) in SARS-CoV-2-infected patients but likely to be negatively correlated with them in the normal lung tissue. Our data may provide insights into the mechanism of SARS-CoV-2 infection.
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Affiliation(s)
- Wenxiu Cao
- Biomedical Informatics Research Lab, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, 211198, China; Big Data Research Institute, China Pharmaceutical University, Nanjing, 211198, China
| | - Qiushi Feng
- Biomedical Informatics Research Lab, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, 211198, China; Big Data Research Institute, China Pharmaceutical University, Nanjing, 211198, China
| | - Xiaosheng Wang
- Biomedical Informatics Research Lab, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, 211198, China; Big Data Research Institute, China Pharmaceutical University, Nanjing, 211198, China.
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Yu S, Hu C, Liu L, Cai L, Du X, Yu Q, Lin F, Zhao J, Zhao Y, Zhang C, Liu X, Li W. Comprehensive analysis and establishment of a prediction model of alternative splicing events reveal the prognostic predictor and immune microenvironment signatures in triple negative breast cancer. J Transl Med 2020; 18:286. [PMID: 32723333 PMCID: PMC7388537 DOI: 10.1186/s12967-020-02454-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [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: 04/04/2020] [Accepted: 07/21/2020] [Indexed: 12/15/2022] Open
Abstract
Background Triple-negative breast cancer (TNBC) is widely concerning because of high malignancy and poor prognosis. There is increasing evidence that alternative splicing (AS) plays an important role in the development of cancer and the formation of the tumour microenvironment. However, comprehensive analysis of AS signalling in TNBC is still lacking and urgently needed. Methods Transcriptome and clinical data of 169 TNBC tissues and 15 normal tissues were obtained and integrated from the cancer genome atlas (TCGA), and an overview of AS events was downloaded from the SpliceSeq database. Then, differential comparative analysis was performed to obtain cancer-associated AS events (CAAS). Metascape was used to perform parent gene enrichment analysis based on CAAS. Unsupervised cluster analysis was performed to analyse the characteristics of immune infiltration in the microenvironment. A splicing network was established based on the correlation between CAAS events and splicing factors (SFs). We then constructed prediction models and assessed the accuracy of these models by receiver operating characteristic (ROC) curve and Kaplan–Meier survival analyses. Furthermore, a nomogram was adopted to predict the individualized survival rate of TNBC patients. Results We identified 1194 cancer-associated AS events (CAAS) and evaluated the enrichment of 981 parent genes. The top 20 parent genes with significant differences were mostly related to cell adhesion, cell component connection and other pathways. Furthermore, immune-related pathways were also enriched. Unsupervised clustering analysis revealed the heterogeneity of the immune microenvironment in TNBC. The splicing network also suggested an obvious correlation between SFs expression and CAAS events in TNBC patients. Univariate and multivariate Cox regression analyses showed that the survival-related AS events were detected, including some significant participants in the carcinogenic process. A nomogram incorporating risk, AJCC and radiotherapy showed good calibration and moderate discrimination. Conclusion Our study revealed AS events related to tumorigenesis and the immune microenvironment, elaborated the potential correlation between SFs and CAAS, established a prognostic model based on survival-related AS events, and created a nomogram to better predict the individual survival rate of TNBC patients, which improved our understanding of the relationship between AS events and TNBC.
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Affiliation(s)
- Shanshan Yu
- Department of Chemoradiation Oncology, The First Affiliated Hospital of Wenzhou Medical University, 2 Fuxue Road, Wenzhou, Zhejiang, 325000, People's Republic of China
| | - Chuan Hu
- Department of Orthopaedic Surgery, the Affiliated Hospital of Qingdao University, Qingdao, 266071, China
| | - Lixiao Liu
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, People's Republic of China
| | - Luya Cai
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, People's Republic of China
| | - Xuedan Du
- Department of Chemoradiation Oncology, The First Affiliated Hospital of Wenzhou Medical University, 2 Fuxue Road, Wenzhou, Zhejiang, 325000, People's Republic of China
| | - Qiongjie Yu
- Department of Chemoradiation Oncology, The First Affiliated Hospital of Wenzhou Medical University, 2 Fuxue Road, Wenzhou, Zhejiang, 325000, People's Republic of China
| | - Fan Lin
- Department of Dermatology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, People's Republic of China
| | - Jinduo Zhao
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, People's Republic of China
| | - Ye Zhao
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, People's Republic of China
| | - Cheng Zhang
- Department of Dermatology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, People's Republic of China
| | - Xuan Liu
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, People's Republic of China
| | - Wenfeng Li
- Department of Chemoradiation Oncology, The First Affiliated Hospital of Wenzhou Medical University, 2 Fuxue Road, Wenzhou, Zhejiang, 325000, People's Republic of China.
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Robertson AG, Groeneveld CS, Jordan B, Lin X, McLaughlin KA, Das A, Fall LA, Fantini D, Taxter TJ, Mogil LS, Lindskrog SV, Dyrskjøt L, McConkey DJ, Svatek RS, de Reyniès A, Castro MAA, Meeks JJ. Identification of Differential Tumor Subtypes of T1 Bladder Cancer. Eur Urol 2020; 78:533-7. [PMID: 32684305 DOI: 10.1016/j.eururo.2020.06.048] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Accepted: 06/22/2020] [Indexed: 11/24/2022]
Abstract
Stage T1 bladder cancers have the highest progression and recurrence rates of all non-muscle-invasive bladder cancers (NMIBCs). Most T1 cancers are treated with bacillus Calmette-Guérin (BCG), but many will progress or recur, and some T1 patients will die from bladder cancer. Particularly aggressive tumors could be treated with early cystectomy. To better understand the molecular heterogeneity of T1 cancers, we performed transcriptome profiling and unsupervised clustering, and identified five consensus subtypes of T1 tumors treated with repeat transurethral resection (reTUR) and induction and maintenance BCG. The T1-LumGU subtype was associated with carcinoma in situ (CIS; six/13, 46% of all CIS), had high E2F1 and EZH2 expression, and was enriched in E2F target and G2M checkpoint hallmarks. The T1-Inflam subtype was inflamed and infiltrated with immune cells. While most T1 tumors were classified as luminal papillary, the T1-TLum subtype had the highest median luminal papillary score and FGFR3 expression, no recurrence events, and the fewest copy number gains. T1-Myc and T1-Early subtypes had the most recurrences (14/30 within 24 mo), the highest median MYC expression, and, when combined, had significantly worse recurrence-free survival than the other three subtypes. T1-Early had five (38%) recurrences within the first 6 mo of BCG, and repressed IFN-α and IFN-γ hallmarks and inflammation. We developed a single-patient T1 classifier and validated our subtype biology in a second cohort of T1 tumors. Future research will be necessary to validate the proposed T1 subtypes and to determine if therapies can be individualized for each subtype. PATIENT SUMMARY: We identified and characterized expression subtypes of high-grade stage T1 bladder cancer that are biologically heterogeneous and have variable responses to bacillus Calmette-Guérin treatment. We validated the subtypes and describe a single-patient classifier.
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Mao S, Li Y, Lu Z, Che Y, Huang J, Lei Y, Wang Y, Wang X, Liu C, Zheng S, Li N, Li J, Sun N, He J. Systematic profiling of immune signatures identifies prognostic predictors in lung adenocarcinoma. Cell Oncol (Dordr) 2020; 43:681-694. [PMID: 32462608 DOI: 10.1007/s13402-020-00515-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/03/2020] [Indexed: 02/06/2023] Open
Abstract
PURPOSE Lung adenocarcinoma (LUAD) is the predominant subtype of lung cancer, with increasing evidence showing clinical benefits of immunotherapy. However, a lack of integrated profiles of complex LUAD immune microenvironments hampers the application of immunotherapy, resulting in limited eligible patient populations as well as drug resistance problems. Here, we aimed to systematically profile the immune signatures of LUADs and to assess the role of the immune microenvironment in patient outcome. METHODS We systematically profiled the immune signatures of LUADs deposited in the TCGA and GEO databases using a total of 730 immune-related genes. Differential expression analysis was used to identify dysregulated genes. Univariate Cox analysis followed by robust likelihood-based survival analysis and multivariate Cox analysis were applied to construct an immune-related prognostic model. RESULTS We found that differentially expressed immune genes were mainly enriched in immune cell proliferation, migration, activation and the NF-κB and TNF signaling pathways. The 10-immune gene predictive model that we constructed could differentiate LUAD patients with different overall survival times in several datasets, with areas under the curve (AUCs) of 0.67, 0.69, 0.72 and 0.74. LUAD patients with high- or low-risk scores exhibited distinct immune cell compositions, which may explain the prognostic significance of our model. CONCLUSIONS Our results add to the current knowledge of immune processes in LUADs and underscore the critical role of the immune microenvironment in LUAD patient outcome.
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Affiliation(s)
- Shuangshuang Mao
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Yuan Li
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Zhiliang Lu
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Yun Che
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Jianbing Huang
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Yuanyuan Lei
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Yalong Wang
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Xinfeng Wang
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Chengming Liu
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Sufei Zheng
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Ning Li
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Jiagen Li
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Nan Sun
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
| | - Jie He
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
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11
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Watanabe T, Firat E, Scholber J, Gaedicke S, Heinrich C, Luo R, Ehrat N, Multhoff G, Schmitt-Graeff A, Grosu AL, Abdollahi A, Hassel JC, von Bubnoff D, Meiss F, Niedermann G. Deep abscopal response to radiotherapy and anti-PD-1 in an oligometastatic melanoma patient with unfavorable pretreatment immune signature. Cancer Immunol Immunother 2020; 69:1823-1832. [PMID: 32350591 PMCID: PMC7413872 DOI: 10.1007/s00262-020-02587-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 04/17/2020] [Indexed: 12/11/2022]
Abstract
Radiotherapy can elicit abscopal effects in non-irradiated metastases, particularly under immune checkpoint blockade (ICB). We report on two elderly patients with oligometastatic melanoma treated with anti-PD-1 and stereotactic body radiation therapy (SBRT). Before treatment, patient 1 showed strong tumor infiltration with exhausted CD8+ T cells and high expression of T cell-attracting chemokines. This patient rapidly mounted a complete response, now ongoing for more than 4.5 years. Patient 2 exhibited low CD8+ T cell infiltration and high expression of immunosuppressive arginase. After the first SBRT, his non-irradiated metastases did not regress and new metastases occurred although neoepitope-specific and differentiation antigen-specific CD8+ T cells were detected in the blood. A second SBRT after 10 months on anti-PD-1 induced a radiologic complete response correlating with an increase in activated PD-1-expressing CD8 T cells. Apart from a new lung lesion, which was also irradiated, this deep abscopal response lasted for more than 2.5 years. However, thereafter, his disease progressed and the activated PD-1-expressing CD8 T cells dropped. Our data suggest that oligometastatic patients, where a large proportion of the tumor mass can be irradiated, are good candidates to improve ICB responses by RT, even in the case of an unfavorable pretreatment immune signature, after progression on anti-PD-1, and despite advanced age. Besides repeated irradiation, T cell epitope-based immunotherapies (e.g., vaccination) may prolong antitumor responses even in patients with unfavorable pretreatment immune signature.
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Affiliation(s)
- Tsubasa Watanabe
- Department of Radiation Oncology, Faculty of Medicine, University of Freiburg, Robert-Koch-Strasse 3, 79106, Freiburg, Germany
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Osaka, Japan
| | - Elke Firat
- Department of Radiation Oncology, Faculty of Medicine, University of Freiburg, Robert-Koch-Strasse 3, 79106, Freiburg, Germany
| | - Jutta Scholber
- Department of Radiation Oncology, Faculty of Medicine, University of Freiburg, Robert-Koch-Strasse 3, 79106, Freiburg, Germany
| | - Simone Gaedicke
- Department of Radiation Oncology, Faculty of Medicine, University of Freiburg, Robert-Koch-Strasse 3, 79106, Freiburg, Germany
| | - Corinne Heinrich
- Department of Dermatology and Venerology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Ren Luo
- Department of Radiation Oncology, Faculty of Medicine, University of Freiburg, Robert-Koch-Strasse 3, 79106, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Nicolas Ehrat
- Department of Radiation Oncology, Faculty of Medicine, University of Freiburg, Robert-Koch-Strasse 3, 79106, Freiburg, Germany
| | - Gabriele Multhoff
- Department of Radiation Oncology, Technical University Munich, Munich, Germany
- German Cancer Consortium (DKTK), Partner Site Munich, and German Cancer Research Center, Heidelberg, Germany
| | | | - Anca-Ligia Grosu
- Department of Radiation Oncology, Faculty of Medicine, University of Freiburg, Robert-Koch-Strasse 3, 79106, Freiburg, Germany
- German Cancer Consortium (DKTK), Partner Site Freiburg, and German Cancer Research Center, Heidelberg, Germany
| | - Amir Abdollahi
- Department of Radiation Oncology, Heidelberg University Medical School, Heidelberg Institute of Radiation Oncology (HIRO), National Center for Radiation Research in Oncology (NCOR), Heidelberg, Germany
- German Cancer Consortium (DKTK), Partner Site Heidelberg, and German Cancer Research Center, Heidelberg, Germany
| | - Jessica C Hassel
- Skin Cancer Center, Department of Dermatology and National Center for Tumor Diseases (NCT), University Hospital Heidelberg, Heidelberg, Germany
| | - Dagmar von Bubnoff
- Department of Dermatology, Allergy, and Venereology, University of Lübeck, Lübeck, Germany
| | - Frank Meiss
- Department of Dermatology and Venerology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Gabriele Niedermann
- Department of Radiation Oncology, Faculty of Medicine, University of Freiburg, Robert-Koch-Strasse 3, 79106, Freiburg, Germany.
- German Cancer Consortium (DKTK), Partner Site Freiburg, and German Cancer Research Center, Heidelberg, Germany.
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12
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Abstract
BACKGROUND Since its discovery in December 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has infected more than 2 180 000 people worldwide and has caused more than 150 000 deaths as of April 16, 2020. SARS-CoV-2, which is the virus causing coronavirus disease 2019 (COVID-19), uses the angiotensin-converting enzyme 2 (ACE2) as a cell receptor to invade human cells. Thus, ACE2 is the key to understanding the mechanism of SARS-CoV-2 infection. This study is to investigate the ACE2 expression in various human tissues in order to provide insights into the mechanism of SARS-CoV-2 infection. METHODS We compared ACE2 expression levels across 31 normal human tissues between males and females and between younger (ages ≤ 49 years) and older (ages > 49 years) persons using two-sided Student's t test. We also investigated the correlations between ACE2 expression and immune signatures in various tissues using Pearson's correlation test. RESULTS ACE2 expression levels were the highest in the small intestine, testis, kidneys, heart, thyroid, and adipose tissue, and were the lowest in the blood, spleen, bone marrow, brain, blood vessels, and muscle. ACE2 showed medium expression levels in the lungs, colon, liver, bladder, and adrenal gland. ACE2 was not differentially expressed between males and females or between younger and older persons in any tissue. In the skin, digestive system, brain, and blood vessels, ACE2 expression levels were positively associated with immune signatures in both males and females. In the thyroid and lungs, ACE2 expression levels were positively and negatively associated with immune signatures in males and females, respectively, and in the lungs they had a positive and a negative correlation in the older and younger groups, respectively. CONCLUSIONS Our data indicate that SARS-CoV-2 may infect other tissues aside from the lungs and infect persons with different sexes, ages, and races equally. The different host immune responses to SARS-CoV-2 infection may partially explain why males and females, young and old persons infected with this virus have markedly distinct disease severity. This study provides new insights into the role of ACE2 in the SARS-CoV-2 pandemic.
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Affiliation(s)
- Meng-Yuan Li
- Biomedical Informatics Research Lab, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
- Big Data Research Institute, China Pharmaceutical University, Nanjing, 211198, China
| | - Lin Li
- Biomedical Informatics Research Lab, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
- Big Data Research Institute, China Pharmaceutical University, Nanjing, 211198, China
| | - Yue Zhang
- Pinghu hospital of Shenzhen University, Shenzhen, 440307, China
- Futian Hospital for Rheumatic Diseases, Shenzhen, 518000, China
- Department of Rheumatology and Immunology, The First Clinical College of Harbin Medical University, Harbin, 150001, China
| | - Xiao-Sheng Wang
- Biomedical Informatics Research Lab, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, 211198, China.
- Big Data Research Institute, China Pharmaceutical University, Nanjing, 211198, China.
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13
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Isnaldi E, Ferraioli D, Ferrando L, Brohée S, Ferrando F, Fregatti P, Bedognetti D, Ballestrero A, Zoppoli G. Schlafen-11 expression is associated with immune signatures and basal-like phenotype in breast cancer. Breast Cancer Res Treat 2019; 177:335-43. [PMID: 31222709 DOI: 10.1007/s10549-019-05313-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 06/05/2019] [Indexed: 12/21/2022]
Abstract
PURPOSE Breast cancer (BC) is a heterogeneous disorder, with variable response to systemic chemotherapy. Likewise, BC shows highly complex immune activation patterns, only in part reflecting classical histopathological subtyping. Schlafen-11 (SLFN11) is a nuclear protein we independently described as causal factor of sensitivity to DNA damaging agents (DDA) in cancer cell line models. SLFN11 has been reported as a predictive biomarker for DDA and PARP inhibitors in human neoplasms. SLFN11 has been implicated in several immune processes such as thymocyte maturation and antiviral response through the activation of interferon signaling pathway, suggesting its potential relevance as a link between immunity and cancer. In the present work, we investigated the transcriptional landscape of SLFN11, its potential prognostic value, and the clinico-pathological associations with its variability in BC. METHODS We assessed SLFN11 determinants in a gene expression meta-set of 5061 breast cancer patients annotated with clinical data and multigene signatures. RESULTS We found that 537 transcripts are highly correlated with SLFN11, identifying "immune response", "lymphocyte activation", and "T cell activation" as top Gene Ontology processes. We established a strong association of SLFN11 with stromal signatures of basal-like phenotype and response to chemotherapy in estrogen receptor negative (ER-) BC. We identified a distinct subgroup of patients, characterized by high SLFN11 levels, ER- status, basal-like phenotype, immune activation, and younger age. Finally, we observed an independent positive predictive role for SLFN11 in BC. CONCLUSIONS Our findings are suggestive of a relevant role for SLFN11 in BC and its immune and molecular variability.
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14
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Wittenbrink N, Herrmann S, Blazquez-Navarro A, Bauer C, Lindberg E, Wolk K, Sabat R, Reinke P, Sawitzki B, Thomusch O, Hugo C, Babel N, Seitz H, Or-Guil M. A novel approach reveals that HLA class 1 single antigen bead-signatures provide a means of high-accuracy pre-transplant risk assessment of acute cellular rejection in renal transplantation. BMC Immunol 2019; 20:11. [PMID: 31029086 PMCID: PMC6486998 DOI: 10.1186/s12865-019-0291-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 04/08/2019] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Acute cellular rejection (ACR) is associated with complications after kidney transplantation, such as graft dysfunction and graft loss. Early risk assessment is therefore critical for the improvement of transplantation outcomes. In this work, we retrospectively analyzed a pre-transplant HLA antigen bead assay data set that was acquired by the e:KID consortium as part of a systems medicine approach. RESULTS The data set included single antigen bead (SAB) reactivity profiles of 52 low-risk graft recipients (negative complement dependent cytotoxicity crossmatch, PRA < 30%) who showed detectable pre-transplant anti-HLA 1 antibodies. To assess whether the reactivity profiles provide a means for ACR risk assessment, we established a novel approach which differs from standard approaches in two aspects: the use of quantitative continuous data and the use of a multiparameter classification method. Remarkably, it achieved significant prediction of the 38 graft recipients who experienced ACR with a balanced accuracy of 82.7% (sensitivity = 76.5%, specificity = 88.9%). CONCLUSIONS The resultant classifier achieved one of the highest prediction accuracies in the literature for pre-transplant risk assessment of ACR. Importantly, it can facilitate risk assessment in non-sensitized patients who lack donor-specific antibodies. As the classifier is based on continuous data and includes weak signals, our results emphasize that not only strong but also weak binding interactions of antibodies and HLA 1 antigens contain predictive information. TRIAL REGISTRATION ClinicalTrials.gov NCT00724022 . Retrospectively registered July 2008.
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Affiliation(s)
- Nicole Wittenbrink
- Systems Immunology Lab, Department of Biology, Humboldt University Berlin, Berlin, Germany
| | - Sabrina Herrmann
- Fraunhofer Institute for Cell Therapy and Immunology, Bioanalytics und Bioprocesses, Potsdam, Germany
| | - Arturo Blazquez-Navarro
- Systems Immunology Lab, Department of Biology, Humboldt University Berlin, Berlin, Germany
- Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Berlin, Germany
| | | | | | - Kerstin Wolk
- Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Berlin, Germany
- Psoriasis Research and Treatment Center, Institute of Medical Immunology, Department of Dermatology and Allergy, Charité University Medicine Berlin, Berlin, Germany
| | - Robert Sabat
- Psoriasis Research and Treatment Center, Institute of Medical Immunology, Department of Dermatology and Allergy, Charité University Medicine Berlin, Berlin, Germany
- Interdisciplinary Group of Molecular Immunopathology, Institute of Medical Immunology, Department of Dermatology and Allergy, Charité University Medicine Berlin, Berlin, Germany
| | - Petra Reinke
- Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Berlin, Germany
- Department of Nephrology and Internal Intensive Care, Charité University Medicine Berlin, Campus Virchow Clinic, Berlin, Germany
- Berlin Center for Advanced Therapies (BeCAT), Charité University Medicine Berlin, Campus Virchow Clinic, Berlin, Germany
| | - Birgit Sawitzki
- Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Berlin, Germany
- Molecular Immune Modulation, Institute for Medical Immunology, Charité University Medicine Berlin, Campus Virchow Clinic, Berlin, Germany
| | - Oliver Thomusch
- Klinik für Allgemein- und Viszeralchirurgie, Universitätsklinikum Freiburg, Freiburg, Germany
| | - Christian Hugo
- University Hospital Carl Gustav Carus, Dresden University of Technology, Dresden, Germany
| | - Nina Babel
- Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Berlin, Germany
- Medical Clinic I, Marien Hospital Herne, Ruhr University Bochum, Herne, Germany
| | - Harald Seitz
- Fraunhofer Institute for Cell Therapy and Immunology, Bioanalytics und Bioprocesses, Potsdam, Germany
| | - Michal Or-Guil
- Systems Immunology Lab, Department of Biology, Humboldt University Berlin, Berlin, Germany
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15
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Eid RS, Gobinath AR, Galea LAM. Sex differences in depression: Insights from clinical and preclinical studies. Prog Neurobiol 2019; 176:86-102. [PMID: 30721749 DOI: 10.1016/j.pneurobio.2019.01.006] [Citation(s) in RCA: 186] [Impact Index Per Article: 37.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 12/21/2018] [Accepted: 01/28/2019] [Indexed: 12/22/2022]
Abstract
Depression represents a global mental health concern, and disproportionally affects women as they are twice more likely to be diagnosed than men. In this review, we provide a summary of evidence to support the notion that differences in depression between men and women span multiple facets of the disease, including epidemiology, symptomology, treatment, and pathophysiology. Through a lens of biological sex, we overview depression-related transcriptional patterns, changes in neuroanatomy and neuroplasticity, and immune signatures. We acknowledge the unique physiological and behavioral demands of pregnancy and motherhood by devoting special attention to depression occurring in the peripartum period. Specifically, we discuss issues surrounding the presentation, time course, treatment, and neurobiology of peripartum depression. We write this review with the intention of highlighting the encouraging advancements in our understanding of sex differences in depression, while underscoring the gaps that remain. A more systematic consideration of biological sex as a variable in depression research will be critical in the discovery and development of pharmacotherapies that are efficacious for both men and women.
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Affiliation(s)
- Rand S Eid
- Graduate Program in Neuroscience, University of British Columbia, Vancouver, BC, Canada; Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, BC, Canada
| | - Aarthi R Gobinath
- Graduate Program in Neuroscience, University of British Columbia, Vancouver, BC, Canada; Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, BC, Canada
| | - Liisa A M Galea
- Graduate Program in Neuroscience, University of British Columbia, Vancouver, BC, Canada; Department of Psychology, University of British Columbia, Vancouver, BC, Canada; Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, BC, Canada.
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Abstract
BACKGROUND Tumor mutation burden (TMB) has been associated with cancer immunotherapeutic response and cancer prognosis. Although many explorations have revealed that high TMB may yield many neoantigens to incite antitumor immune response, a systematic exploration of the correlation between TMB and immune signatures in different cancer types is lacking. RESULTS We classified cancer into the lower-TMB subtype and the higher-TMB subtype for each of 32 cancer types based on their somatic mutation data from the Cancer Genome Atlas (TCGA), and compared the expression levels of immune-related genes and gene-sets between both subtypes of cancers in each cancer type. In some cancer types most of the immune signatures analyzed were upregulated in the lower-TMB subtype, while in some other cancer types the immune signatures were prone to be upregulated in the higher-TMB subtype. However, the regulatory T cells, immune cell infiltrate, tumor-infiltrating lymphocytes, and cytokine signatures tended to be upregulated in the lower-TMB subtype, and the cancer-testis antigen (CTA) and pro-inflammatory signatures were inclined to be upregulated in the higher-TMB subtype. Importantly, high TMB was associated with elevated expression of PD-L1 in diverse prevailing cancers. Furthermore, we found that higher TMB was associated with better survival prognosis in numerous cancer types while was associated with worse prognosis in a few cancer types. CONCLUSIONS High TMB may inhibit immune cell infiltrations while promote CTAs expression and inflammatory response in cancer. In many common cancer types, higher TMB may respond favorably to anti-PD-1/PD-L1 immunotherapy. Our data implicate that higher-TMB patients could gain a more favorable prognosis in diverse cancer types if treated with immunotherapy, otherwise would have a poorer prognosis compared to lower-TMB patients.
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Affiliation(s)
- Xiaosheng Wang
- Biomedical Informatics Research Lab, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, 211198 China
- Cancer Genomics Research Center, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, 211198 China
- Big Data Research Institute, China Pharmaceutical University, Nanjing, 211198 China
| | - Mengyuan Li
- Biomedical Informatics Research Lab, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, 211198 China
- Cancer Genomics Research Center, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, 211198 China
- Big Data Research Institute, China Pharmaceutical University, Nanjing, 211198 China
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Heimes AS, Madjar K, Edlund K, Battista MJ, Almstedt K, Elger T, Krajnak S, Rahnenführer J, Brenner W, Hasenburg A, Hengstler JG, Schmidt M. Subtype-specific prognostic impact of different immune signatures in node-negative breast cancer. Breast Cancer Res Treat 2017; 165:293-300. [PMID: 28585074 DOI: 10.1007/s10549-017-4327-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Accepted: 06/01/2017] [Indexed: 10/19/2022]
Abstract
BACKGROUND The role of different subtypes of immune cells is still a matter of debate. METHODS We compared the prognostic relevance for metastasis-free survival (MFS) of a B-cell signature (BS), a T-cell signature (TS), and an immune checkpoint signature (CPS) in node-negative breast cancer (BC) using mRNA expression. Microarray-based gene-expression data were analyzed in six previously published cohorts of node-negative breast cancer patients not treated with adjuvant therapy (n = 824). The prognostic relevance of the individual immune markers was assessed using univariate analysis. The amount of independent prognostic information provided by each immune signature was then compared using a likelihood ratio statistic in the whole cohort as well as in different molecular subtypes. RESULTS Univariate Cox regression in the whole cohort revealed prognostic significance of CD4 (HR 0.66, CI 0.50-0.87, p = 0.004), CXCL13 (HR 0.86, CI 0.81-0.92, p < 0.001), CD20 (HR 0.76, CI 0.64-0.89, p = 0.001), IgκC (HR 0.81, CI 0.75-0.88, p < 0.001), and CTLA-4 (HR 0.67, CI 0.46-0.97, p = 0.032). Multivariate analyses of the immune signatures showed that both TS (p < 0.001) and BS (p < 0.001) showed a significant prognostic information in the whole cohort. After accounting for clinical-pathological variables, TS (p < 0.001), BS (p < 0.05), and CPS (p < 0.05) had an independent effect for MFS. In subgroup analyses, the prognostic effect of immune cells was most pronounced in HER2+ BC: BS as well as TS showed a strong association with MFS when included first in the model (p < 0.001). CONCLUSION Immune signatures provide subtype-specific additional prognostic information over clinical-pathological variables in node-negative breast cancer.
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Chifman J, Pullikuth A, Chou JW, Bedognetti D, Miller LD. Conservation of immune gene signatures in solid tumors and prognostic implications. BMC Cancer 2016; 16:911. [PMID: 27871313 DOI: 10.1186/s12885-016-2948-z] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 11/03/2016] [Indexed: 12/20/2022] Open
Abstract
Background Tumor-infiltrating leukocytes can either limit cancer growth or facilitate its spread. Diagnostic strategies that comprehensively assess the functional complexity of tumor immune infiltrates could have wide-reaching clinical value. In previous work we identified distinct immune gene signatures in breast tumors that reflect the relative abundance of infiltrating immune cells and exhibited significant associations with patient outcomes. Here we hypothesized that immune gene signatures agnostic to tumor type can be identified by de novo discovery of gene clusters enriched for immunological functions and possessing internal correlation structure conserved across solid tumors from different anatomic sites. Methods We assembled microarray expression datasets encompassing 5,295 tumors of the breast, colon, lung, ovarian and prostate. Unsupervised clustering methods were used to determine number and composition of gene clusters within each dataset. Immune-enriched gene clusters (signatures) identified by gene ontology enrichment were analyzed for internal correlation structure and conservation across tumors then compared against expression profiles of: 1) flow-sorted leukocytes from peripheral blood and 2) >300 cancer cell lines from solid and hematologic cancers. Cox regression analysis was used to identify signatures with significant associations with clinical outcome. Results We identified nine distinct immune-enriched gene signatures conserved across all five tumor types. The signatures differentiated specific leukocyte lineages with moderate discernment overall, and naturally organized into six discrete groups indicative of admixed lineages. Moreover, seven of the signatures exhibit minimal and uncorrelated expression in cancer cell lines, suggesting that these signatures derive predominantly from infiltrating immune cells. All nine immune signatures achieved statistically significant associations with patient prognosis (p<0.05) in one or more tumor types with greatest significance observed in breast and skin cancers. Several signatures indicative of myeloid lineages exhibited poor outcome associations that were most apparent in brain and colon cancers. Conclusions These findings suggest that tumor infiltrating immune cells can be differentiated by immune-specific gene expression patterns that quantify the relative abundance of multiple immune infiltrates across a range of solid tumor types. That these markers of immune involvement are significantly associated with patient prognosis in diverse cancers suggests their clinical utility as pan-cancer markers of tumor behavior and immune responsiveness. Electronic supplementary material The online version of this article (doi:10.1186/s12885-016-2948-z) contains supplementary material, which is available to authorized users.
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