1
|
Zhu W, Wu J, Huang J, Xiao D, Li F, Wu C, Li X, Zeng H, Zheng J, Lai W, Wen X. Multi-omics analysis reveals a macrophage-related marker gene signature for prognostic prediction, immune landscape, genomic heterogeneity, and drug choices in prostate cancer. Front Immunol 2023; 14:1122670. [PMID: 37122696 PMCID: PMC10140525 DOI: 10.3389/fimmu.2023.1122670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 04/03/2023] [Indexed: 05/02/2023] Open
Abstract
Introduction Macrophages are components of the innate immune system and can play an anti-tumor or pro-tumor role in the tumor microenvironment owing to their high heterogeneity and plasticity. Meanwhile, prostate cancer (PCa) is an immune-sensitive tumor, making it essential to investigate the value of macrophage-associated networks in its prognosis and treatment. Methods Macrophage-related marker genes (MRMGs) were identified through the comprehensive analysis of single-cell sequencing data from GSE141445 and the impact of macrophages on PCa was evaluated using consensus clustering of MRMGs in the TCGA database. Subsequently, a macrophage-related marker gene prognostic signature (MRMGPS) was constructed by LASSO-Cox regression analysis and grouped based on the median risk score. The predictive ability of MRMGPS was verified by experiments, survival analysis, and nomogram in the TCGA cohort and GEO-Merged cohort. Additionally, immune landscape, genomic heterogeneity, tumor stemness, drug sensitivity, and molecular docking were conducted to explore the relationship between MRMGPS and the tumor immune microenvironment, therapeutic response, and drug selection. Results We identified 307 MRMGs and verified that macrophages had a strong influence on the development and progression of PCa. Furthermore, we showed that the MRMGPS constructed with 9 genes and the predictive nomogram had excellent predictive ability in both the TCGA and GEO-Merged cohorts. More importantly, we also found the close relationship between MRMGPS and the tumor immune microenvironment, therapeutic response, and drug selection by multi-omics analysis. Discussion Our study reveals the application value of MRMGPS in predicting the prognosis of PCa patients. It also provides a novel perspective and theoretical basis for immune research and drug choices for PCa.
Collapse
Affiliation(s)
- Weian Zhu
- Department of Urology, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Jianjie Wu
- Department of Urology, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Jiongduan Huang
- Department of Urology, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Dongming Xiao
- Department of Urology, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Fengao Li
- Department of Urology, Anqing First People’s Hospital of Anhui Medical University, Anqing, China
| | - Chenglun Wu
- Department of Urology, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Xiaojuan Li
- Department of Health Care, Shenzhen Hospital, Southern Medical University, Shenzhen, China
| | - Hengda Zeng
- Department of Urology, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Jiayu Zheng
- Department of Urology, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Wenjie Lai
- Department of Urology, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Laboratory of Biomaterials and Translational Medicine, Center for Nanomedicine, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- *Correspondence: Xingqiao Wen, ; Wenjie Lai,
| | - Xingqiao Wen
- Department of Urology, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- *Correspondence: Xingqiao Wen, ; Wenjie Lai,
| |
Collapse
|
2
|
Fry SE, Kaye M, Missan DS, Becker C, Shabilla M, Martinez D, Bossert E, Ellis J. Microbial community profiling by next-generation DNA sequencing of adenocarcinoma of the prostate with evidence of ochratoxin A producing fungi. Exp Mol Pathol 2022; 128:104831. [PMID: 36100037 DOI: 10.1016/j.yexmp.2022.104831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 07/12/2022] [Accepted: 08/30/2022] [Indexed: 12/15/2022]
Abstract
BACKGROUND Prostatic carcinomas are a leading cancer and leading cause of mortality in the developed world. The etiology is diverse with underlying patient genetics, environmental factors, and microbial associations. Sequencing DNA for microbes allows the detection of potential disease relationships. OBJECTIVE Targeted 16S (prokaryotic) and 18S (eukaryotic) rDNA sequencing was performed to map the tumor microbial flora. DESIGN Twelve patients undergoing elective laparoscopic prostatectomy for biopsy proven adenocarcinoma of the prostate were enrolled. PCR and amplicon based sequencing was conducted; a portion of the sequencing results were confirmed by special stains. SETTING Patients were recruited by the urologist were prospectively scheduled for radical prostatectomy by 'Da Vinci' robotically assisted procedure in an outpatient setting. Samples were portioned in the hospital surgical suite at the time of prostatectomy. PARTICIPANTS Male patients were requested to enter the study on a first come basis. OUTCOME MEASUREMENT AND STATISTICAL ANALYSIS Average age of the 12 participants was 64.3 years. RESULTS AND LIMITATIONS DNA reads were detected and by 'best match' were identified belonging to Perkinsus, Hydrurus, Diversispora and Funneliformis genera, few samples displayed bacteria. Out of the 12 total patients, 11 patients had detectable DNA sequences matching arbuscular mycorrhizal fungi in the Glomeromycetes Class; Funneliformis mosseae and Diversasporum versiformis. Specific PCR for arbuscular mycorrhizal fungi failed to confirm Glomeromycetes Class; in-depth taxonomic analysis suggests a newer fungal grouping, not falling within an accepted Phylum of fungi. Calcoflour white staining of histological sections confirmed potential fungal markers in all 12 cases. Ochratoxin A antigen was identified by immunofluorescence in all 12 patient samples. The study was limited by the low sample volume and disease free normal controls. CONCLUSIONS Fungi may play a significant role in adenocarcinoma of the prostate.
Collapse
Affiliation(s)
- Stephen E Fry
- Fry Laboratories, LLC, Scottsdale, AZ, United States of America.
| | - Mitchell Kaye
- Scottsdale Urology, Scottsdale, AZ, United States of America
| | - Dara S Missan
- Mayo Clinic, Scottsdale, AZ, United States of America
| | | | | | - Delyn Martinez
- Tricore Laboratory, Albuquerque Community Hospital, Albuquerque, NM, United States of America
| | - Erin Bossert
- Mayo Clinic, Scottsdale, AZ, United States of America
| | - Jeremy Ellis
- Fry Laboratories, LLC, Scottsdale, AZ, United States of America
| |
Collapse
|
3
|
Wang X, Zhou Z, Turner D, Lilly M, Ou T, Jiang W. Differential Circulating Fungal Microbiome in Prostate Cancer Patients Compared to Healthy Control Individuals. J Immunol Res 2022; 2022:2574964. [PMID: 35155686 PMCID: PMC8831061 DOI: 10.1155/2022/2574964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 12/23/2021] [Indexed: 11/17/2022] Open
Abstract
BACKGROUNDS Infection and inflammation play an important role in prostate cancer (PCa) etiology and pathogenesis. However, the environmental drivers for PCa are not fully understood. METHODS In a cross-sectional study, we analyzed circulating fungal microbiome in plasma samples from age and race-matched healthy control men (n = 34) and preoperative PCa patients (n = 31). RESULTS The fungal community in the plasma exhibited differences between individuals with PCa and healthy controls according to the beta diversity; there was no difference in the alpha diversity. Moreover, the relative abundance of several fungi differed between the two study groups from the class to species levels. The most significant differences were Filobasidiales family, Pyronemataceae family, and Cryptococcus ater species, which were enriched in PCa patients compared to controls. The increased Bipolaris genus was associated with low prostate-specific antigen (PSA) levels, increased Sordariomycetes class was associated with severe pathological stage, and decreased Phoma herbarum species was associated with disease relapse, compared to corresponding controls. Several fungi from class to species levels were increased in the controls compared to patients. CONCLUSION This is the first study to show plasma distinct fungal microbiome and its associations with PSA levels, relapse, and pathology stages in PCa patients.
Collapse
Affiliation(s)
- Xu Wang
- Department of Microbiology and Immunology, Medical University of South Carolina, Charleston, 29425 SC, USA
- Department of Urology, Capital Medical University Affiliated XuanWu Hospital, 45 Changchun Street, Xicheng District, Beijing 100053, China
| | - Zejun Zhou
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha 410081, China
| | - David Turner
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, SC, USA
| | - Michael Lilly
- Division of Hematology and Oncology, Department of Medicine, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Tongwen Ou
- Department of Urology, Capital Medical University Affiliated XuanWu Hospital, 45 Changchun Street, Xicheng District, Beijing 100053, China
| | - Wei Jiang
- Department of Microbiology and Immunology, Medical University of South Carolina, Charleston, 29425 SC, USA
- Division of Infectious Diseases, Department of Medicine, Medical University of South Carolina, Charleston, SC 29425, USA
| |
Collapse
|
4
|
El Atab O, Ekim Kocabey A, Asojo OA, Schneiter R. Prostate secretory protein 94 (PSP94) inhibits sterol-binding and export by the mammalian CAP protein CRISP2 in a calcium-sensitive manner. J Biol Chem 2022; 298:101600. [PMID: 35063506 PMCID: PMC8857485 DOI: 10.1016/j.jbc.2022.101600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Revised: 01/07/2022] [Accepted: 01/08/2022] [Indexed: 11/30/2022] Open
Abstract
Members of the CAP protein superfamily are present in all kingdoms of life and have been implicated in many different processes, including pathogen defense, immune evasion, sperm maturation, and cancer progression. Most CAP proteins are secreted glycoproteins and share a unique conserved αβα sandwich fold. The precise mode of action of this class of proteins, however, has remained elusive. Saccharomyces cerevisiae has three CAP family members, termed pathogen related in yeast (Pry). We have previously shown that Pry1 and Pry2 export sterols in vivo and that they bind sterols in vitro. This sterol binding and export function of yeast Pry proteins is conserved in the mammalian CRISP proteins and other CAP superfamily members. CRISP3 is an abundant protein of the human seminal plasma and interacts with prostate secretory protein of 94 amino acids (PSP94), another major protein component in the seminal plasma. Here we examine whether the interaction between CRISP proteins and PSP94 affects the sterol binding function of CAP family members. We show that coexpression of PSP94 with CAP proteins in yeast abolished their sterol export function and the interaction between PSP94 and CAP proteins inhibits sterol binding in vitro. In addition, mutations that affect the formation of the PSP94–CRISP2 heteromeric complex restore sterol binding. Of interest, we found the interaction of PSP94 with CRISP2 is sensitive to high calcium concentrations. The observation that PSP94 modulates the sterol binding function of CRISP2 in a calcium-dependent manner has potential implications for the role of PSP94 and CRISP2 in prostate physiology and progression of prostate cancer.
Collapse
|
5
|
The human fungal pathogen Malassezia and its role in cancer. FUNGAL BIOL REV 2021. [DOI: 10.1016/j.fbr.2021.08.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
6
|
RNA-Seq transcriptome analysis of ileum in Taiping chicken supplemented with the dietary probiotic. Trop Anim Health Prod 2021; 53:131. [PMID: 33462736 DOI: 10.1007/s11250-021-02566-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Accepted: 01/06/2021] [Indexed: 12/11/2022]
Abstract
Taiping chicken is indigenous chickens (Gallus gallus domesticus), which was one of China's excellent poultry species. As the problems caused by the overuse of antibiotics become more and more concern, people begin to look for ways to replace them. Among them, probiotics and their preparations are the research hotspot to replace antibiotics. Probiotics can promote the absorption of nutrients, improve the ratio of meat to meat, resist and prevent diseases, and improve the intestinal tissue morphology. Here, we performed transcriptome profiling of Taiping chicken ileum which was given probiotics by using the Hiseq™ 2500 sequencing platform. A total of 18 genes were differentially expressed in the ileum under control group and probiotics group. Thirteen genes were upregulated with a range of fold change from 1.02 to 8.61, and 5 were downregulated with a range of fold change from - 1.06 to - 2.29. Ten of the differently expressed genes were further validated by qRT-PCR. In addition, Gene ontology and Kyoto Encyclopedia of Genes and Genomes analyses revealed that these differentially expressed genes were mainly enriched to bile secretion, alpha-linolenic acid metabolism, linoleic acid metabolism, ether lipid metabolism, and arachidonic acid metabolism. This study will help us to understand the role of probiotics in indigenous chicken production and provide theoretical basis for the genetic development of indigenous chickens.
Collapse
|
7
|
LMTK2 as Potential Biomarker for Stratification between Clinically Insignificant and Clinically Significant Prostate Cancer. JOURNAL OF ONCOLOGY 2021; 2021:8820366. [PMID: 33488712 PMCID: PMC7803409 DOI: 10.1155/2021/8820366] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 12/15/2020] [Accepted: 12/18/2020] [Indexed: 12/14/2022]
Abstract
A set of prostate tumors tend to grow slowly and do not require active treatment. Therefore, stratification between patients with clinically significant and clinically insignificant prostate cancer (PC) remains a vital issue to avoid overtreatment. Fast development of genetic technologies accelerated development of next-generation molecular tools for reliable PC diagnosis. The aim of this study is to evaluate the diagnostic value of molecular biomarkers (CRISP3, LMTK2, and MSMB) for separation of PC cases from benign prostatic changes and more specifically for identification of clinically significant PC from all pool of PC cases in patients with rising PSA levels. Patients (n = 200) who had rising PSA (PSA II) after negative transrectal systematic prostate biopsy due to elevated PSA (PSA I) were eligible to the study. In addition to PSA concentration, PSA density was calculated for each patient. Gene expression level was measured in peripheral blood samples of cases applying RT-PCR, while MSMB (−57 C/T) polymorphism was identified by pyrosequencing. LMTK2 and MSMB significantly differentiated control group from both BPD and PC groups. MSMB expression tended to increase from the major alleles of the CC genotype to the minor alleles of the TT genotype. PSA density was the only clinical characteristic that significantly differentiated clinically significant PC from clinically insignificant PC. Therefore, LMTK2 expression and PSA density were significantly distinguished between clinically significant PC and clinically insignificant PC. PSA density rather than PSA can differentiate PC from the benign prostate disease and, in combination with LMTK2, assist in stratification between clinically insignificant and clinically significant PC.
Collapse
|
8
|
Feng Z, Ren X, Fang Y, Yin Y, Huang C, Zhao Y, Wang Y. scTIM: seeking cell-type-indicative marker from single cell RNA-seq data by consensus optimization. Bioinformatics 2020; 36:2474-2485. [PMID: 31845960 DOI: 10.1093/bioinformatics/btz936] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 11/26/2019] [Accepted: 12/13/2019] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION Single cell RNA-seq data offers us new resource and resolution to study cell type identity and its conversion. However, data analyses are challenging in dealing with noise, sparsity and poor annotation at single cell resolution. Detecting cell-type-indicative markers is promising to help denoising, clustering and cell type annotation. RESULTS We developed a new method, scTIM, to reveal cell-type-indicative markers. scTIM is based on a multi-objective optimization framework to simultaneously maximize gene specificity by considering gene-cell relationship, maximize gene's ability to reconstruct cell-cell relationship and minimize gene redundancy by considering gene-gene relationship. Furthermore, consensus optimization is introduced for robust solution. Experimental results on three diverse single cell RNA-seq datasets show scTIM's advantages in identifying cell types (clustering), annotating cell types and reconstructing cell development trajectory. Applying scTIM to the large-scale mouse cell atlas data identifies critical markers for 15 tissues as 'mouse cell marker atlas', which allows us to investigate identities of different tissues and subtle cell types within a tissue. scTIM will serve as a useful method for single cell RNA-seq data mining. AVAILABILITY AND IMPLEMENTATION scTIM is freely available at https://github.com/Frank-Orwell/scTIM. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Zhanying Feng
- CEMS, NCMIS, MDIS, Academy of Mathematics and System Science, Chinese Academy of Sciences, Beijing 100190, China.,School of Mathematical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xianwen Ren
- School of Life Sciences, Peking University, Beijing 100871, China
| | - Yuan Fang
- School of Mathematics and Statistics, Wuhan University, Wuhan 430072, China
| | - Yining Yin
- School of Mathematics and Statistics, Wuhan University, Wuhan 430072, China
| | - Chutian Huang
- School of Mathematics and Statistics, Wuhan University, Wuhan 430072, China
| | - Yimin Zhao
- School of Mathematics and Statistics, Wuhan University, Wuhan 430072, China
| | - Yong Wang
- CEMS, NCMIS, MDIS, Academy of Mathematics and System Science, Chinese Academy of Sciences, Beijing 100190, China.,School of Mathematical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
| |
Collapse
|
9
|
Wu Y, Jiang H, Tan M, Lu X. Screening for chronic prostatitis pathogens using high-throughput next-generation sequencing. Prostate 2020; 80:577-587. [PMID: 32162709 PMCID: PMC7187444 DOI: 10.1002/pros.23971] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 02/24/2020] [Indexed: 01/26/2023]
Abstract
BACKGROUND The pathogens responsible for chronic prostatitis/chronic pelvic pain syndrome (CP/CPPS; NIH category III) are not currently known. the present study utilized high-throughput next-generation sequencing to screen for potential pathogens associated with NIH category III CP (CP III). METHODS This study included 33 patients with CP III and 30 healthy men, from which one sample each of urethral secretions and expressed prostatic secretion (EPS) was collected. High-throughput next-generation sequencing was performed to detect the sequence variations and the relative abundance of the bacterial 16S ribosomal variable region and fungal internal transcribed spacer region in all samples. Bioinformatics software and databases were used for data analysis, and differences with P < .05 were considered statistically significant. RESULTS Unweighted pair group method with arithmetic mean (UPGMA) cluster analysis, principal component analysis (PCA), and Spearman's rank correlation showed that the microbial compositions of the urethral secretions and EPS collected from the same subject were essentially the same. CONCLUSIONS No potential pathogens were identified in diagnosed patients with CP III. The EPS may be free from bacteria before and after infection. Changes in the urinary tract microbiome may disrupt the microecological balance of the urinary system, thereby leading to CP III. Conversely, the true pathogens of CP III may not be prokaryotic or eukaryotic microorganisms, Future research may involve the evaluation of noncellular microbes.
Collapse
Affiliation(s)
- Yi Wu
- Department of Clinical Laboratory ScienceShenzhen Seventh People's HospitalShenzhenChina
| | - Haiyang Jiang
- Department of UrologyThe Eighth Affiliated Hospital of Sun Yat‐Sen UniversityShenzhenChina
| | - Mingbo Tan
- Department of UrologyThe Eighth Affiliated Hospital of Sun Yat‐Sen UniversityShenzhenChina
| | - Xuedong Lu
- Department of Laboratory MedicineThe Eighth Affiliated Hospital of Sun Yat‐Sen UniversityShenzhenChina
| |
Collapse
|
10
|
Smith Byrne K, Appleby PN, Key TJ, Holmes MV, Fensom GK, Agudo A, Ardanaz E, Boeing H, Bueno-de-Mesquita HB, Chirlaque MD, Kaaks R, Larrañaga N, Palli D, Perez-Cornago A, Quirós JR, Ricceri F, Sánchez MJ, Tagliabue G, Tsilidis KK, Tumino R, Fortner RT, Ferrari P, Riboli E, Lilja H, Travis RC. The role of plasma microseminoprotein-beta in prostate cancer: an observational nested case-control and Mendelian randomization study in the European prospective investigation into cancer and nutrition. Ann Oncol 2019; 30:983-989. [PMID: 31089709 PMCID: PMC6594452 DOI: 10.1093/annonc/mdz121] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Microseminoprotein-beta (MSP), a protein secreted by the prostate epithelium, may have a protective role in the development of prostate cancer. The only previous prospective study found a 2% reduced prostate cancer risk per unit increase in MSP. This work investigates the association of MSP with prostate cancer risk using observational and Mendelian randomization (MR) methods. PATIENTS AND METHODS A nested case-control study was conducted with the European Prospective Investigation into Cancer and Nutrition (EPIC) with 1871 cases and 1871 matched controls. Conditional logistic regression analysis was used to investigate the association of pre-diagnostic circulating MSP with risk of incident prostate cancer overall and by tumour subtype. EPIC-derived estimates were combined with published data to calculate an MR estimate using two-sample inverse-variance method. RESULTS Plasma MSP concentrations were inversely associated with prostate cancer risk after adjusting for total prostate-specific antigen concentration [odds ratio (OR) highest versus lowest fourth of MSP = 0.65, 95% confidence interval (CI) 0.51-0.84, Ptrend = 0.001]. No heterogeneity in this association was observed by tumour stage or histological grade. Plasma MSP concentrations were 66% lower in rs10993994 TT compared with CC homozygotes (per allele difference in MSP: 6.09 ng/ml, 95% CI 5.56-6.61, r2=0.42). MR analyses supported a potentially causal protective association of MSP with prostate cancer risk (OR per 1 ng/ml increase in MSP for MR: 0.96, 95% CI 0.95-0.97 versus EPIC observational: 0.98, 95% CI 0.97-0.99). Limitations include lack of complete tumour subtype information and more complete information on the biological function of MSP. CONCLUSIONS In this large prospective European study and using MR analyses, men with high circulating MSP concentration have a lower risk of prostate cancer. MSP may play a causally protective role in prostate cancer.
Collapse
Affiliation(s)
| | | | | | - M V Holmes
- Medical Research Council Population Health Research Unit, University of Oxford, Oxford; Clinical Trial Service Unit & Epidemiological Studies Unit (CTSU), Oxford; National Institute for Health Research Oxford Biomedical Research Centre, Oxford University Hospital, Oxford; Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | | | - A Agudo
- Unit of Nutrition and Cancer, Catalan Institute of Oncology-IDIBELL, Barcelona
| | - E Ardanaz
- CIBER of Epidemiology and Public Health (CIBERESP), Madrid; Navarra Public Health Institute, Pamplona; Navarra Institute for Health Research (IdiSNA), Pamplona, Spain
| | - H Boeing
- Department of Epidemiology, German Institute of Human Nutrition (DIfE), Potsdam-Rehbrücke, Germany
| | - H B Bueno-de-Mesquita
- Department for Determinants of Chronic Diseases (DCD), National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands; Department of Epidemiology and Biostatistics, Imperial College London, London, UK; Department of Social & Preventive Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - M D Chirlaque
- CIBER of Epidemiology and Public Health (CIBERESP), Madrid; Department of Epidemiology, IMIB-Arrixaca, Murcia; Department of Health and Social Sciences, University of Murcia, Murcia, Spain
| | - R Kaaks
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - N Larrañaga
- CIBER of Epidemiology and Public Health (CIBERESP), Madrid; Public Health Division of Gipuzkoa, Regional Government of the Basque Country, Vitoria-Gasteiz, Spain
| | - D Palli
- Cancer Risk Factors and Life-style Epidemiology Unit, Institute for Cancer Research, Prevention and Clinical Network (ISPRO), Florence, Italy
| | | | - J R Quirós
- Public Health Directorate, Asturias, Spain
| | - F Ricceri
- Unit of Epidemiology, Regional Health Service Azienda Sanitaria Locale Torino 3 (ASL TO3), Grugliasco; Unit of Cancer Epidemiology, Department of Medical Sciences, University of Turin, Turin, Italy
| | - M J Sánchez
- CIBER of Epidemiology and Public Health (CIBERESP), Madrid; Escuela Andaluza de Salud Pública, Instituto de Investigación Biosanitaria ibs.GRANADA, Hospitales Universitarios de Granada/Universidad de Granada, Granada, Spain
| | - G Tagliabue
- Department of Preventative and Predictive Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - K K Tsilidis
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK; Department of Hygiene and Epidemiology, University of Ioannina School of Medicine, Ioannina, Greece
| | - R Tumino
- Cancer Registry and Histopathology Unit, "Civic M.P. Arezzo" Hospital, Ragusa, Italy
| | - R T Fortner
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - P Ferrari
- Nutritional Methodology and Biostatistics Group, International Agency for Research on Cancer (IARC/WHO), Lyon, France
| | - E Riboli
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK
| | - H Lilja
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK; Department of Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, USA; Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, USA; Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, USA; Department of Translational Medicine, Lund University, Malmö, Sweden
| | | |
Collapse
|
11
|
Shabelnikov SV, Bobkov DE, Sharlaimova NS, Petukhova OA. Injury affects coelomic fluid proteome of the common starfish, Asterias rubens. ACTA ACUST UNITED AC 2019; 222:jeb.198556. [PMID: 30877231 DOI: 10.1242/jeb.198556] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 02/11/2019] [Indexed: 01/04/2023]
Abstract
Echinoderms, possessing outstanding regenerative capabilities, provide a unique model system for the study of response to injury. However, little is known about the proteomic composition of coelomic fluid, an important biofluid circulating throughout the animal's body and reflecting the overall biological status of the organism. In this study, we used LC-MALDI tandem mass spectrometry to characterize the proteome of the cell-free coelomic fluid of the starfish Asterias rubens and to follow the changes occurring in response to puncture wound and blood loss. In total, 91 proteins were identified, of which 61 were extracellular soluble and 16 were bound to the plasma membrane. The most represented functional terms were 'pattern recognition receptor activity' and 'peptidase inhibitor activity'. A series of candidate proteins involved in early response to injury was revealed. Ependymin, β-microseminoprotein, serum amyloid A and avidin-like proteins, which are known to be involved in intestinal regeneration in the sea cucumber, were also identified as injury-responsive proteins. Our results expand the list of proteins potentially involved in defense and regeneration in echinoderms and demonstrate dramatic effects of injury on the coelomic fluid proteome.
Collapse
Affiliation(s)
- Sergey V Shabelnikov
- Laboratory of Regulation of Gene Expression, Institute of Cytology, Russian Academy of Sciences, 194064 St Petersburg, Russia
| | - Danila E Bobkov
- Department of Cell Cultures, Institute of Cytology, Russian Academy of Sciences, 194064 St Petersburg, Russia
| | - Natalia S Sharlaimova
- Department of Cell Cultures, Institute of Cytology, Russian Academy of Sciences, 194064 St Petersburg, Russia
| | - Olga A Petukhova
- Department of Cell Cultures, Institute of Cytology, Russian Academy of Sciences, 194064 St Petersburg, Russia
| |
Collapse
|
12
|
van der Toom EE, Axelrod HD, de la Rosette JJ, de Reijke TM, Pienta KJ, Valkenburg KC. Prostate-specific markers to identify rare prostate cancer cells in liquid biopsies. Nat Rev Urol 2019; 16:7-22. [PMID: 30479377 DOI: 10.1038/s41585-018-0119-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Despite improvements in early detection and advances in treatment, patients with prostate cancer continue to die from their disease. Minimal residual disease after primary definitive treatment can lead to relapse and distant metastases, and increasing evidence suggests that circulating tumour cells (CTCs) and bone marrow-derived disseminated tumour cells (BM-DTCs) can offer clinically relevant biological insights into prostate cancer dissemination and metastasis. Using epithelial markers to accurately detect CTCs and BM-DTCs is associated with difficulties, and prostate-specific markers are needed for the detection of these cells using rare cell assays. Putative prostate-specific markers have been identified, and an optimized strategy for staining rare cancer cells from liquid biopsies using these markers is required. The ideal prostate-specific marker will be expressed on every CTC or BM-DTC throughout disease progression (giving high sensitivity) and will not be expressed on non-prostate-cancer cells in the sample (giving high specificity). Some markers might not be specific enough to the prostate to be used as individual markers of prostate cancer cells, whereas others could be truly prostate-specific and would make ideal markers for use in rare cell assays. The goal of future studies is to use sensitive and specific prostate markers to consistently and reliably identify rare cancer cells.
Collapse
Affiliation(s)
| | - Haley D Axelrod
- The James Buchanan Brady Urological Institute, Baltimore, MD, USA.,Graduate Program in Cellular and Molecular Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | | | - Kenneth J Pienta
- The James Buchanan Brady Urological Institute, Baltimore, MD, USA
| | | |
Collapse
|
13
|
Trujillo-Cáceres SJ, Torres-Sánchez L, Burguete-García AI, Orbe Orihuela YC, Vázquez-Salas RA, Álvarez-Topete E, Gómez R. Contribution of MSMB promoter region gene polymorphism to early-onset prostate cancer risk in Mexican males. Oncotarget 2019; 10:738-748. [PMID: 30774776 PMCID: PMC6366823 DOI: 10.18632/oncotarget.26592] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 12/16/2018] [Indexed: 11/25/2022] Open
Abstract
Sexually transmitted infections and its contribution to prostate cancer (PC) development have been relevant in different populations. MSMB gene polymorphism (rs10993994) has exhibited an association both with PC as well as the susceptibility to sexually transmitted infections. Hitherto, these conditions have been not studied in Mexico yet, neither if sexually transmitted infections could modify the MSMB and PC association. Herein, socio-demographic features, sexually transmitted infections records, the reproductive backgrounds, and the genetic characterisation were analysed in 322 incident PC cases and 628 population healthy controls from Mexico City. Whole PC, early-onset PC (PC at < 60 years old), late-onset PC (≥ 60 years old), and PC aggressiveness were used to evaluate the genetic variants contribution to PC risk using unconditional logistic regression models. Overall, none associations between the allelic variants of rs10993994 polymorphisms with whole and PC aggressiveness were found. Howbeit, the TT genotype carriers presented the highest susceptibility to develop early-onset PC (OR = 2.66; 95% CI = 1.41, 5.04; p = 0.03) than CC+CT carriers, both with codominant and recessive models. Although none association between whole PC and MSMB gene polymorphism was found, our results were reinforced by prior studies in European descendent populations, suggesting a contribution between rs10993994 and early-onset PC development.
Collapse
Affiliation(s)
| | - Luisa Torres-Sánchez
- Centro de Investigación en Salud Poblacional, Instituto Nacional de Salud Pública (INSP), Cuernavaca, Morelos, Mexico
| | - Ana I Burguete-García
- Centro de Investigación en Enfermedades Infecciosas, INSP, Cuernavaca, Morelos, Mexico
| | | | | | | | - Rocío Gómez
- Departamento de Toxicología, Cinvestav-IPN, Mexico City, Mexico
| |
Collapse
|
14
|
Farashi S, Kryza T, Clements J, Batra J. Post-GWAS in prostate cancer: from genetic association to biological contribution. Nat Rev Cancer 2019; 19:46-59. [PMID: 30538273 DOI: 10.1038/s41568-018-0087-3] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Genome-wide association studies (GWAS) have been successful in deciphering the genetic component of predisposition to many human complex diseases including prostate cancer. Germline variants identified by GWAS progressively unravelled the substantial knowledge gap concerning prostate cancer heritability. With the beginning of the post-GWAS era, more and more studies reveal that, in addition to their value as risk markers, germline variants can exert active roles in prostate oncogenesis. Consequently, current research efforts focus on exploring the biological mechanisms underlying specific susceptibility loci known as causal variants by applying novel and precise analytical methods to available GWAS data. Results obtained from these post-GWAS analyses have highlighted the potential of exploiting prostate cancer risk-associated germline variants to identify new gene networks and signalling pathways involved in prostate tumorigenesis. In this Review, we describe the molecular basis of several important prostate cancer-causal variants with an emphasis on using post-GWAS analysis to gain insight into cancer aetiology. In addition to discussing the current status of post-GWAS studies, we also summarize the main molecular mechanisms of potential causal variants at prostate cancer risk loci and explore the major challenges in moving from association to functional studies and their implication in clinical translation.
Collapse
Affiliation(s)
- Samaneh Farashi
- Cancer Program, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Queensland, Australia
- Australian Prostate Cancer Research Centre - Queensland, Queensland University of Technology, Translational Research Institute, Woolloongabba, Queensland, Australia
| | - Thomas Kryza
- Cancer Program, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Queensland, Australia
- Australian Prostate Cancer Research Centre - Queensland, Queensland University of Technology, Translational Research Institute, Woolloongabba, Queensland, Australia
| | - Judith Clements
- Cancer Program, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Queensland, Australia
- Australian Prostate Cancer Research Centre - Queensland, Queensland University of Technology, Translational Research Institute, Woolloongabba, Queensland, Australia
| | - Jyotsna Batra
- Cancer Program, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Queensland, Australia.
- Australian Prostate Cancer Research Centre - Queensland, Queensland University of Technology, Translational Research Institute, Woolloongabba, Queensland, Australia.
| |
Collapse
|
15
|
Mancuso N, Gayther S, Gusev A, Zheng W, Penney KL, Kote-Jarai Z, Eeles R, Freedman M, Haiman C, Pasaniuc B. Large-scale transcriptome-wide association study identifies new prostate cancer risk regions. Nat Commun 2018; 9:4079. [PMID: 30287866 PMCID: PMC6172280 DOI: 10.1038/s41467-018-06302-1] [Citation(s) in RCA: 99] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 08/28/2018] [Indexed: 12/16/2022] Open
Abstract
Although genome-wide association studies (GWAS) for prostate cancer (PrCa) have identified more than 100 risk regions, most of the risk genes at these regions remain largely unknown. Here we integrate the largest PrCa GWAS (N = 142,392) with gene expression measured in 45 tissues (N = 4458), including normal and tumor prostate, to perform a multi-tissue transcriptome-wide association study (TWAS) for PrCa. We identify 217 genes at 84 independent 1 Mb regions associated with PrCa risk, 9 of which are regions with no genome-wide significant SNP within 2 Mb. 23 genes are significant in TWAS only for alternative splicing models in prostate tumor thus supporting the hypothesis of splicing driving risk for continued oncogenesis. Finally, we use a Bayesian probabilistic approach to estimate credible sets of genes containing the causal gene at a pre-defined level; this reduced the list of 217 associations to 109 genes in the 90% credible set. Overall, our findings highlight the power of integrating expression with PrCa GWAS to identify novel risk loci and prioritize putative causal genes at known risk loci.
Collapse
Affiliation(s)
- Nicholas Mancuso
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, 90095, CA, USA.
| | - Simon Gayther
- The Center for Bioinformatics and Functional Genomics, Cedars-Sinai Medical Center, Los Angeles, 90048, CA, USA
| | | | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, 37232, TN, USA
| | - Kathryn L Penney
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, 02115, MA, USA
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital/Harvard Medical School, Boston, 02115, MA, USA
| | - Zsofia Kote-Jarai
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
- Royal Marsden NHS Foundation Trust, London, SW3 6JJ, UK
| | - Rosalind Eeles
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
- Royal Marsden NHS Foundation Trust, London, SW3 6JJ, UK
| | - Matthew Freedman
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, 02215, MA, USA
| | - Christopher Haiman
- Department of Preventive Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, 90015, CA, USA
| | - Bogdan Pasaniuc
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, 90095, CA, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, 90095, CA, USA
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, 90095, CA, USA
| |
Collapse
|
16
|
Dias A, Kote-Jarai Z, Mikropoulos C, Eeles R. Prostate Cancer Germline Variations and Implications for Screening and Treatment. Cold Spring Harb Perspect Med 2018; 8:a030379. [PMID: 29101112 PMCID: PMC6120689 DOI: 10.1101/cshperspect.a030379] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Prostate cancer (PCa) is a highly heritable disease, and rapid evolution of sequencing technologies has enabled marked progression of our understanding of its genetic inheritance. A complex polygenic model that involves common low-penetrance susceptibility alleles causing individually small but cumulatively significant risk and rarer genetic variants causing greater risk represent the current most accepted model. Through genome-wide association studies, more than 100 single-nucleotide polymorphisms (SNPs) associated with PCa risk have been identified. Consistent reports have identified germline mutations in the genes BRCA1, BRCA2, MMR, HOXB13, CHEK2, and NBS1 as conferring moderate risks, with some leading to a more aggressive disease behavior. Considering this knowledge, several research strategies have been developed to determine whether targeted prostate screening using genetic information can overcome the limitations of population-based prostate-specific antigen (PSA) screening. Germline DNA-repair mutations are more frequent in men with metastatic disease than previously thought, and these patients have a more favorable response to therapy with poly(adenosine diphosphate [ADP]-ribose) polymerase (PARP) inhibitors. Genomic information is a practical tool that has the potential to enable the concept of precision medicine to become a reality in all steps of PCa patient care.
Collapse
Affiliation(s)
- Alexander Dias
- The Institute of Cancer Research, Sutton, Surrey SM2 5NG, United Kingdom
- The Institute of Cancer Research and Royal Marsden National Health Service (NHS) Foundation Trust, Academic Urology Unit and The Oncogenetics Team, London SW3 6JJ, United Kingdom
| | - Zsofia Kote-Jarai
- The Institute of Cancer Research, Sutton, Surrey SM2 5NG, United Kingdom
| | | | - Ros Eeles
- The Institute of Cancer Research, Sutton, Surrey SM2 5NG, United Kingdom
- The Institute of Cancer Research and Royal Marsden National Health Service (NHS) Foundation Trust, Academic Urology Unit and The Oncogenetics Team, London SW3 6JJ, United Kingdom
| |
Collapse
|
17
|
Laurence M, Asquith M, Rosenbaum JT. Spondyloarthritis, Acute Anterior Uveitis, and Fungi: Updating the Catterall-King Hypothesis. Front Med (Lausanne) 2018; 5:80. [PMID: 29675414 PMCID: PMC5895656 DOI: 10.3389/fmed.2018.00080] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 03/09/2018] [Indexed: 12/12/2022] Open
Abstract
Spondyloarthritis is a common type of arthritis which affects mostly adults. It consists of idiopathic chronic inflammation of the spine, joints, eyes, skin, gut, and prostate. Inflammation is often asymptomatic, especially in the gut and prostate. The HLA-B*27 allele group, which presents intracellular peptides to CD8+ T cells, is by far the strongest risk factor for spondyloarthritis. The precise mechanisms and antigens remain unknown. In 1959, Catterall and King advanced a novel hypothesis explaining the etiology of spondyloarthritis: an as-yet-unrecognized sexually acquired microbe would be causing all spondyloarthritis types, including acute anterior uveitis. Recent studies suggest an unrecognized sexually acquired fungal infection may be involved in prostate cancer and perhaps multiple sclerosis. This warrants reanalyzing the Catterall-King hypothesis based on the current literature. In the last decade, many links between spondyloarthritis and fungal infections have been found. Antibodies against the fungal cell wall component mannan are elevated in spondyloarthritis. Functional polymorphisms in genes regulating the innate immune response against fungi have been associated with spondyloarthritis (CARD9 and IL23R). Psoriasis and inflammatory bowel disease, two common comorbidities of spondyloarthritis, are both strongly associated with fungi. Evidence reviewed here lends credence to the Catterall-King hypothesis and implicates a common fungal etiology in prostate cancer, benign prostatic hyperplasia, multiple sclerosis, psoriasis, inflammatory bowel disease, and spondyloarthritis. However, the evidence available at this time is insufficient to definitely confirm this hypothesis. Future studies investigating the microbiome in relation to these conditions should screen specimens for fungi in addition to bacteria. Future clinical studies of spondyloarthritis should consider antifungals which are effective in psoriasis and multiple sclerosis, such as dimethyl fumarate and nystatin.
Collapse
Affiliation(s)
| | - Mark Asquith
- Division of Arthritis and Rheumatic Diseases, Oregon Health & Science University, Portland, OR, United States
| | - James T Rosenbaum
- Department of Ophthalmology, Oregon Health and Science University, Portland, OR, United States.,Department of Medicine, Oregon Health and Science University, Portland, OR, United States.,Department of Cell Biology, Oregon Health and Science University, Portland, OR, United States.,Legacy Devers Eye Institute, Portland, OR, United States
| |
Collapse
|
18
|
Xin X, Gu Y, Chen Y, Huang Y, Mo Z, Hu Y. Functional analysis implicating the SNP rs61552325 in ERBB2 as an effector for androgen-insensitive prostate cancer cell invasion. Oncotarget 2018; 8:33745-33755. [PMID: 28422721 PMCID: PMC5464908 DOI: 10.18632/oncotarget.16807] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2016] [Accepted: 03/11/2017] [Indexed: 11/25/2022] Open
Abstract
Background As one of the most common cancers in men, the pathogenesis of prostate cancer has been widely researched. Aberrant activation of the erb-b2 receptor tyrosine kinase 2 (ERBB2) has been found to play a critical role in metastatic prostate cancer. In our previous study, we demonstrated that rs61552325 (Pro1140Ala) located in ERBB2 is strongly correlated to prostate cancer. Therefore, we initially studied the effect of rs61552325 on androgen-independent prostate cancer cell metastasis. Results Bioinformatic results demonstrated that the mutant Pro1140Ala likely decrease the stability of the ERBB2 protein and its interactions. The mean migration rate after 6 h for PC3 minor variant cells which carried the G allele was 1.28-fold higher than major variant PC3 cells that carried the C allele (P = 0.016). The mean invasion rate of DU145 putative minor variant cells was 0.40 reducer than negative control cells (P = 5.9E-04). Methods rs61552325 major variant (C allele) and minor variant (G allele) were produced by site directed mutagenesis and transfected into DU145 and PC3 cells. A wound healing assay was performed to compare migration abilities between alleles. After knocking down endogenous ERBB2 and then expressing the rs61552325 minor variant, invasion abilities were evaluated with a transwell assay using DU145 and PC3 cells. Conclusions Our data showed that the rs61552325 major variant decreases PC3 cell migration and its minor variant depresses DU145 cell invasion, suggesting that rs61552325 is likely an important change during prostate cancer invasion.
Collapse
Affiliation(s)
- Xianxiang Xin
- Experimental Centre of Medical Sciences, Guangxi Medical University, Nanning, Guangxi, China.,Commission for Discipline Inspection, Yantai Affiliated Hospital of Binzhou Medical University, Yantai, China
| | - Yinmin Gu
- Experimental Centre of Medical Sciences, Guangxi Medical University, Nanning, Guangxi, China
| | - Yang Chen
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi, China
| | - Yuanjie Huang
- Experimental Centre of Medical Sciences, Guangxi Medical University, Nanning, Guangxi, China
| | - Zengnan Mo
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi, China
| | - Yanling Hu
- Experimental Centre of Medical Sciences, Guangxi Medical University, Nanning, Guangxi, China.,Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi, China.,Guangxi Colleges and Universities Key Laboratory of Biological Molecular Medicine Research, Guangxi Medical University, Nanning, Guangxi, China
| |
Collapse
|
19
|
Shah SI, Bui H, Velasco N, Rungta S. Incidental Finding of Cryptococcus on Prostate Biopsy for Prostate Adenocarcinoma Following Cardiac Transplant: Case Report and Review of the Literature. AMERICAN JOURNAL OF CASE REPORTS 2017; 18:1171-1180. [PMID: 29104281 PMCID: PMC5687115 DOI: 10.12659/ajcr.905528] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
BACKGROUND Cryptococcus is the third most common invasive fungal organism in immunocompromised patients, including transplant patients, and usually involves the central nervous system and lungs, with a median time to infection of 25 months. We report a case of Cryptococcus of the prostate gland, found as an incidental finding on prostate biopsy for prostate adenocarcinoma, four months following cardiac transplantation. CASE REPORT A 62-year-old male African-American who had a cardiac transplant four months previously, underwent a six-core prostate biopsy for a two-year history of increasing prostate-specific antigen (PSA) levels, and a recent history of non-specific urinary tract symptoms. A prostatic adenocarcinoma, Gleason grade 4+4=8, was diagnosed on histopathology, and 'foamy' cells were seen in the biopsies. Histochemical stains, including Grocott methenamine silver (GMS), and periodic acid-Schiff (PAS) showed abundant round and oval 5-7 µm diameter fungal elements; mucicarmine highlighted the fungal polysaccharide capsule, diagnostic for Cryptococcus. Cryptococcal antigen detection was made by the latex agglutination test and cultures. We reviewed the literature and found 70 published cases (from 1946-2008) of Cryptococcus of the prostate gland, with only one previous case presenting five years following cardiac transplantation. CONCLUSIONS Fungal infections of the prostate are rare, and occur mainly in immunocompromised patients. We present a unique case of prostatic Cryptococcus found incidentally at four months following cardiac transplantation. This case report highlights the need to consider atypical fungal infection as a differential diagnosis for prostatitis in immunosuppressed patients, including transplant patients.
Collapse
Affiliation(s)
- Sujal I Shah
- Department of Pathology, University of Cincinnati Medical Center, Cincinnati, OH, USA.,Department of Pathology, Cincinnati VA Medical Center, Cincinnati, OH, USA
| | - Hai Bui
- Department of Pathology, University of Cincinnati Medical Center, Cincinnati, OH, USA.,Department of Pathology, Cincinnati VA Medical Center, Cincinnati, OH, USA
| | - Nelson Velasco
- Department of Pathology, University of Cincinnati Medical Center, Cincinnati, OH, USA.,Department of Primary Care, Veterans Affairs, Southern Oregon Rehabilitation Center and Clinics, White City, OR, USA
| | - Shilpa Rungta
- Department of Pathology, University of Cincinnati Medical Center, Cincinnati, OH, USA.,Department of Pathology, Cincinnati VA Medical Center, Cincinnati, OH, USA
| |
Collapse
|
20
|
Larson NB, McDonnell SK, Fogarty Z, Larson MC, Cheville J, Riska S, Baheti S, Weber AM, Nair AA, Wang L, O’Brien D, Davila J, Schaid DJ, Thibodeau SN. Network-directed cis-mediator analysis of normal prostate tissue expression profiles reveals downstream regulatory associations of prostate cancer susceptibility loci. Oncotarget 2017; 8:85896-85908. [PMID: 29156765 PMCID: PMC5689655 DOI: 10.18632/oncotarget.20717] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 07/29/2017] [Indexed: 12/19/2022] Open
Abstract
Large-scale genome-wide association studies have identified multiple single-nucleotide polymorphisms associated with risk of prostate cancer. Many of these genetic variants are presumed to be regulatory in nature; however, follow-up expression quantitative trait loci (eQTL) association studies have to-date been restricted largely to cis-acting associations due to study limitations. While trans-eQTL scans suffer from high testing dimensionality, recent evidence indicates most trans-eQTL associations are mediated by cis-regulated genes, such as transcription factors. Leveraging a data-driven gene co-expression network, we conducted a comprehensive cis-mediator analysis using RNA-Seq data from 471 normal prostate tissue samples to identify downstream regulatory associations of previously identified prostate cancer risk variants. We discovered multiple trans-eQTL associations that were significantly mediated by cis-regulated transcripts, four of which involved risk locus 17q12, proximal transcription factor HNF1B, and target trans-genes with known HNF response elements (MIA2, SRC, SEMA6A, KIF12). We additionally identified evidence of cis-acting down-regulation of MSMB via rs10993994 corresponding to reduced co-expression of NDRG1. The majority of these cis-mediator relationships demonstrated trans-eQTL replicability in 87 prostate tissue samples from the Gene-Tissue Expression Project. These findings provide further biological context to known risk loci and outline new hypotheses for investigation into the etiology of prostate cancer.
Collapse
Affiliation(s)
- Nicholas B. Larson
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Shannon K. McDonnell
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Zach Fogarty
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Melissa C. Larson
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - John Cheville
- Division of Anatomic Pathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Shaun Riska
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Saurabh Baheti
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Alexandra M. Weber
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Asha A. Nair
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Liang Wang
- Department of Pathology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Daniel O’Brien
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Jaime Davila
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Daniel J. Schaid
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Stephen N. Thibodeau
- Division of Laboratory Genetics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| |
Collapse
|
21
|
Benito-León J, Laurence M. The Role of Fungi in the Etiology of Multiple Sclerosis. Front Neurol 2017; 8:535. [PMID: 29085329 PMCID: PMC5650687 DOI: 10.3389/fneur.2017.00535] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2017] [Accepted: 09/25/2017] [Indexed: 01/07/2023] Open
Abstract
Multiple sclerosis (MS) is a chronic inflammatory disorder of the central nervous system. Infectious triggers of MS are being actively investigated. Substantial evidence supports the involvement of the Epstein-Barr virus (EBV), though other viruses, bacteria, protists, and fungi are also being considered. Many links between fungi and diseases involving chronic inflammation have been found recently. Evidence linking MS and fungi is reviewed here. The HLA-DRB1*15 allele group is the most important genetic risk factor of MS, and is a risk factor in several other conditions linked to fungal infections. Many biomarkers of MS are consistent with fungal infections, such as IL-17, chitotriosidase, and antibodies against fungi. Dimethyl fumarate (DMF), first used as an industrial fungicide, was recently repurposed to reduce MS symptoms. Its mechanisms of action in MS have not been firmly established. The low risk of MS during childhood and its moderate association with herpes simplex virus type 2 suggest genital exposure to microbes (including fungi) should be investigated as a possible trigger. Molecular and epidemiological evidence support a role for infections such as EBV in MS. Though fungal infections have not been widely studied in MS, many lines of evidence are consistent with a fungal etiology. Future microbiome and serological studies should consider fungi as a possible risk factor for MS, and future clinical studies should consider the effect of fungicides other than DMF on MS symptoms.
Collapse
Affiliation(s)
- Julián Benito-León
- Department of Neurology, University Hospital “12 de Octubre”, Madrid, Spain
- Department of Medicine, Faculty of Medicine, Complutense University, Madrid, Spain
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
| | | |
Collapse
|
22
|
The sea cucumber genome provides insights into morphological evolution and visceral regeneration. PLoS Biol 2017; 15:e2003790. [PMID: 29023486 PMCID: PMC5638244 DOI: 10.1371/journal.pbio.2003790] [Citation(s) in RCA: 134] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 09/11/2017] [Indexed: 11/25/2022] Open
Abstract
Apart from sharing common ancestry with chordates, sea cucumbers exhibit a unique morphology and exceptional regenerative capacity. Here we present the complete genome sequence of an economically important sea cucumber, A. japonicus, generated using Illumina and PacBio platforms, to achieve an assembly of approximately 805 Mb (contig N50 of 190 Kb and scaffold N50 of 486 Kb), with 30,350 protein-coding genes and high continuity. We used this resource to explore key genetic mechanisms behind the unique biological characters of sea cucumbers. Phylogenetic and comparative genomic analyses revealed the presence of marker genes associated with notochord and gill slits, suggesting that these chordate features were present in ancestral echinoderms. The unique shape and weak mineralization of the sea cucumber adult body were also preliminarily explained by the contraction of biomineralization genes. Genome, transcriptome, and proteome analyses of organ regrowth after induced evisceration provided insight into the molecular underpinnings of visceral regeneration, including a specific tandem-duplicated prostatic secretory protein of 94 amino acids (PSP94)-like gene family and a significantly expanded fibrinogen-related protein (FREP) gene family. This high-quality genome resource will provide a useful framework for future research into biological processes and evolution in deuterostomes, including remarkable regenerative abilities that could have medical applications. Moreover, the multiomics data will be of prime value for commercial sea cucumber breeding programs. Echinoderms, ubiquitous in the marine environment, are important from evolutionary, ecological, and socioeconomic perspectives. Together with chordates and hemichordates, they form the deuterostome clade, making them a crucial node in the study of chordate ancestry. Within echinoderms, class Holothuroidea is unique; its members (the sea cucumbers) display remarkable regenerative abilities and play key roles as sediment bioturbators and symbiotic hosts, and many are prized in the seafood and pharmaceutical industries. The sea cucumber genome therefore has the potential to significantly contribute to our understanding of important evolutionary and biological processes and help enhance aquaculture programs. Here we present a high-quality genome sequence for the economically important species Apostichopus japonicus. Through comparative analyses, we identified 763 echinoderm-specific gene families enriched in genes encoding membrane proteins, ion channels, and signal transduction proteins. Marker genes associated with the notochord and gill slits were also found, providing valuable insight into the origin of chordates. The reduced number and low expression levels of biomineralization genes reflect the skeletal degeneration seen in sea cucumbers. Importantly, 2 gene families appeared to be expanded in A. japonicus and may play crucial roles in its heightened regenerative potential. Together, findings from the sea cucumber genome provide important and novel insights into echinoderm and deuterostome biology.
Collapse
|
23
|
Terenina E, Fabre S, Bonnet A, Monniaux D, Robert-Granié C, SanCristobal M, Sarry J, Vignoles F, Gondret F, Monget P, Tosser-Klopp G. Differentially expressed genes and gene networks involved in pig ovarian follicular atresia. Physiol Genomics 2017; 49:67-80. [DOI: 10.1152/physiolgenomics.00069.2016] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 11/28/2016] [Accepted: 12/02/2016] [Indexed: 01/08/2023] Open
Abstract
Ovarian folliculogenesis corresponds to the development of follicles leading to either ovulation or degeneration, this latter process being called atresia. Even if atresia involves apoptosis, its mechanism is not well understood. The objective of this study was to analyze global gene expression in pig granulosa cells of ovarian follicles during atresia. The transcriptome analysis was performed on a 9,216 cDNA microarray to identify gene networks and candidate genes involved in pig ovarian follicular atresia. We found 1,684 significantly regulated genes to be differentially regulated between small healthy follicles and small atretic follicles. Among them, 287 genes had a fold-change higher than two between the two follicle groups. Eleven genes ( DKK3, GADD45A, CAMTA2, CCDC80, DAPK2, ECSIT, MSMB, NUPR1, RUNX2, SAMD4A, and ZNF628) having a fold-change higher than five between groups could likely serve as markers of follicular atresia. Moreover, automatic confrontation of deregulated genes with literature data highlighted 93 genes as regulatory candidates of pig granulosa cell atresia. Among these genes known to be inhibitors of apoptosis, stimulators of apoptosis, or tumor suppressors INHBB, HNF4, CLU, different interleukins ( IL5, IL24), TNF-associated receptor ( TNFR1), and cytochrome-c oxidase ( COX) were suggested as playing an important role in porcine atresia. The present study also enlists key upstream regulators in follicle atresia based on our results and on a literature review. The novel gene candidates and gene networks identified in the current study lead to a better understanding of the molecular regulation of ovarian follicular atresia.
Collapse
Affiliation(s)
- Elena Terenina
- GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Castanet Tolosan, France
| | - Stephane Fabre
- GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Castanet Tolosan, France
| | - Agnès Bonnet
- GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Castanet Tolosan, France
| | - Danielle Monniaux
- INRA UMR 0085, CNRS UMR 7247, Université Francois Rabelais de Tours, IFCE, Physiologie de la Reproduction et des Comportements, Nouzilly, France
| | | | - Magali SanCristobal
- GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Castanet Tolosan, France
| | - Julien Sarry
- GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Castanet Tolosan, France
| | - Florence Vignoles
- GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Castanet Tolosan, France
| | - Florence Gondret
- INRA, UMR1348 Pegase, Saint‐Gilles, France; and
- AgroCampus-Ouest, UMR1348 Pegase, Saint‐Gilles, France
| | - Philippe Monget
- INRA UMR 0085, CNRS UMR 7247, Université Francois Rabelais de Tours, IFCE, Physiologie de la Reproduction et des Comportements, Nouzilly, France
| | | |
Collapse
|
24
|
Malik E, Dennison SR, Harris F, Phoenix DA. pH Dependent Antimicrobial Peptides and Proteins, Their Mechanisms of Action and Potential as Therapeutic Agents. Pharmaceuticals (Basel) 2016; 9:ph9040067. [PMID: 27809281 PMCID: PMC5198042 DOI: 10.3390/ph9040067] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Revised: 10/25/2016] [Accepted: 10/26/2016] [Indexed: 12/16/2022] Open
Abstract
Antimicrobial peptides (AMPs) are potent antibiotics of the innate immune system that have been extensively investigated as a potential solution to the global problem of infectious diseases caused by pathogenic microbes. A group of AMPs that are increasingly being reported are those that utilise pH dependent antimicrobial mechanisms, and here we review research into this area. This review shows that these antimicrobial molecules are produced by a diverse spectrum of creatures, including vertebrates and invertebrates, and are primarily cationic, although a number of anionic examples are known. Some of these molecules exhibit high pH optima for their antimicrobial activity but in most cases, these AMPs show activity against microbes that present low pH optima, which reflects the acidic pH generally found at their sites of action, particularly the skin. The modes of action used by these molecules are based on a number of major structure/function relationships, which include metal ion binding, changes to net charge and conformational plasticity, and primarily involve the protonation of histidine, aspartic acid and glutamic acid residues at low pH. The pH dependent activity of pore forming antimicrobial proteins involves mechanisms that generally differ fundamentally to those used by pH dependent AMPs, which can be described by the carpet, toroidal pore and barrel-stave pore models of membrane interaction. A number of pH dependent AMPs and antimicrobial proteins have been developed for medical purposes and have successfully completed clinical trials, including kappacins, LL-37, histatins and lactoferrin, along with a number of their derivatives. Major examples of the therapeutic application of these antimicrobial molecules include wound healing as well as the treatment of multiple cancers and infections due to viruses, bacteria and fungi. In general, these applications involve topical administration, such as the use of mouth washes, cream formulations and hydrogel delivery systems. Nonetheless, many pH dependent AMPs and antimicrobial proteins have yet to be fully characterized and these molecules, as a whole, represent an untapped source of novel biologically active agents that could aid fulfillment of the urgent need for alternatives to conventional antibiotics, helping to avert a return to the pre-antibiotic era.
Collapse
Affiliation(s)
- Erum Malik
- School of Forensic and Applied Sciences, University of Central Lancashire, Preston PR1 2HE, UK.
| | - Sarah R Dennison
- School of Pharmacy and Biological Sciences, University of Central Lancashire, Preston PR1 2HE, UK.
| | - Frederick Harris
- School of Forensic and Applied Sciences, University of Central Lancashire, Preston PR1 2HE, UK.
| | - David A Phoenix
- Office of the Vice Chancellor, London South Bank University, 103 Borough Road, London SE1 0AA, UK.
| |
Collapse
|
25
|
El Mubarak MA, Leontari I, Danika C, Katsila T, Sivolapenko G. Development and validation of a UHPLC-UV method for the determination of a prostate secretory protein 94-derived synthetic peptide (PCK3145) in human plasma and assessment of its stability in human plasma. Biomed Chromatogr 2016; 30:1476-80. [DOI: 10.1002/bmc.3708] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Revised: 01/26/2016] [Accepted: 02/09/2016] [Indexed: 12/25/2022]
Affiliation(s)
- Mohamed A. El Mubarak
- Department of Pharmacy, Laboratory of Pharmacokinetics; University of Patras; Patras Greece
| | - Iliana Leontari
- Department of Pharmacy, Laboratory of Pharmacokinetics; University of Patras; Patras Greece
| | - Charikleia Danika
- Department of Pharmacy, Laboratory of Pharmacokinetics; University of Patras; Patras Greece
| | - Theodora Katsila
- Department of Pharmacy, Laboratory of Pharmacokinetics; University of Patras; Patras Greece
| | - Gregory Sivolapenko
- Department of Pharmacy, Laboratory of Pharmacokinetics; University of Patras; Patras Greece
| |
Collapse
|
26
|
Overexpression and purification of folded domain of prostate cancer related proteins MSMB and PSA. Mol Biol Rep 2016; 43:349-58. [PMID: 27038170 DOI: 10.1007/s11033-016-3956-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 02/12/2016] [Indexed: 10/22/2022]
Abstract
Overexpression of domains of a human protein using recombinant DNA technology has been challenging because individual domains intend to accumulate as non-soluble aggregate when expressed separately. Studies on identifying right sequences for a domain to be able to fold independently may help understand the folding pattern and underlying protein-engineering events to isolate the functional domains of a protein. In this report, individual domains of prostate cancer related biomarkers; MSMB and PSA were overexpressed in bacterial system and purified in their folded forms using affinity chromatography. The western blotting experiment using domain specific antibodies further confirmed these proteins. The designed nucleotide sequences domains were truncated using fold index software and folding were predicted by phyre2 and I-TASSER software. Other parameters were optimized for their overexpression and purification using Co-NTA affinity chromatography. Purified domains of each protein showed secondary structures such as α + β type for PSA, α/β and β type for the each domains of PSA and MSMB respectively. This is the first report on producing PSA and MSMB individual domains in functional folded forms. This study may help produce the folded domain of many such proteins to be used for better diagnostic purpose.
Collapse
|
27
|
Pisa D, Alonso R, Rábano A, Carrasco L. Corpora Amylacea of Brain Tissue from Neurodegenerative Diseases Are Stained with Specific Antifungal Antibodies. Front Neurosci 2016; 10:86. [PMID: 27013948 PMCID: PMC4781869 DOI: 10.3389/fnins.2016.00086] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 02/22/2016] [Indexed: 11/13/2022] Open
Abstract
The origin and potential function of corpora amylacea (CA) remains largely unknown. Low numbers of CA are detected in the aging brain of normal individuals but they are abundant in the central nervous system of patients with neurodegenerative diseases. In the present study, we show that CA from patients diagnosed with Alzheimer's disease (AD) contain fungal proteins as detected by immunohistochemistry analyses. Accordingly, CA were labeled with different anti-fungal antibodies at the external surface, whereas the central portion composed of calcium salts contain less proteins. Detection of fungal proteins was achieved using a number of antibodies raised against different fungal species, which indicated cross-reactivity between the fungal proteins present in CA and the antibodies employed. Importantly, these antibodies do not immunoreact with cellular proteins. Additionally, CNS samples from patients diagnosed with amyotrophic lateral sclerosis (ALS) and Parkinson's disease (PD) also contained CA that were immunoreactive with a range of antifungal antibodies. However, CA were less abundant in ALS or PD patients as compared to CNS samples from AD. By contrast, CA from brain tissue of control subjects were almost devoid of fungal immunoreactivity. These observations are consistent with the concept that CA associate with fungal infections and may contribute to the elucidation of the origin of CA.
Collapse
Affiliation(s)
- Diana Pisa
- Centro de Biología Molecular "Severo Ochoa," Universidad Autónoma de Madrid Madrid, Spain
| | - Ruth Alonso
- Centro de Biología Molecular "Severo Ochoa," Universidad Autónoma de Madrid Madrid, Spain
| | - Alberto Rábano
- Department of Neuropathology and Tissue Bank, Unidad de Investigación Proyecto Alzheimer, Fundación Centro de Investigación de Enfermedades Neurologicas, Instituto de Salud Carlos III Madrid, Spain
| | - Luis Carrasco
- Centro de Biología Molecular "Severo Ochoa," Universidad Autónoma de Madrid Madrid, Spain
| |
Collapse
|
28
|
|
29
|
Veilleux A, Mayeur S, Bérubé JC, Beaulieu JF, Tremblay E, Hould FS, Bossé Y, Richard D, Levy E. Altered intestinal functions and increased local inflammation in insulin-resistant obese subjects: a gene-expression profile analysis. BMC Gastroenterol 2015; 15:119. [PMID: 26376914 PMCID: PMC4574092 DOI: 10.1186/s12876-015-0342-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Accepted: 08/25/2015] [Indexed: 03/15/2023] Open
Abstract
BACKGROUND Metabolic alterations relevant to postprandial dyslipidemia were previously identified in the intestine of obese insulin-resistant subjects. The aim of the study was to identify the genes deregulated by systemic insulin resistance in the intestine of severely obese subjects. METHODS Transcripts from duodenal samples of insulin-sensitive (HOMA-IR < 3, n = 9) and insulin-resistant (HOMA-IR > 7, n = 9) obese subjects were assayed by microarray (Illumina HumanHT-12). RESULTS A total of 195 annotated genes were identified as differentially expressed between these two groups (Fold change > 1.2). Of these genes, 36 were found to be directly involved in known intestinal functions, including digestion, extracellular matrix, endocrine system, immunity and cholesterol metabolism. Interestingly, all differentially expressed genes (n = 8) implicated in inflammation and oxidative stress were found to be upregulated in the intestine of insulin-resistant compared to insulin-sensitive subjects. Metabolic pathway analysis revealed that several signaling pathways involved in immunity and inflammation were significantly enriched in differently expressed genes and were predicted to be activated in the intestine of insulin-resistant subjects. Using stringent criteria (Fold change > 1.5; FDR < 0.05), three genes were found to be significantly and differently expressed in the intestine of insulin-resistant compared to insulin-sensitive subjects: the transcripts of the insulinotropic glucose-dependant peptide (GIP) and of the β-microseminoprotein (MSMB) were significantly reduced, but that of the humanin like-1 (MTRNR2L1) was significantly increased. CONCLUSION These results underline that systemic insulin resistance is associated with remodeling of key intestinal functions. Moreover, these data indicate that small intestine metabolic dysfunction is accompanied with a local amplification of low-grade inflammatory process implicating several pathways. Genes identified in this study are potentially triggered throughout the development of intestinal metabolic abnormalities, which could contribute to dyslipidemia, a component of metabolic syndrome and diabetes.
Collapse
Affiliation(s)
- Alain Veilleux
- Department of Nutrition, Université de Montréal and Research center of CHU Sainte-Justine, 3175 Côte Ste-Catherine, Montréal, Qc, Canada.
| | - Sylvain Mayeur
- Department of Nutrition, Université de Montréal and Research center of CHU Sainte-Justine, 3175 Côte Ste-Catherine, Montréal, Qc, Canada.
| | - Jean-Christophe Bérubé
- Institut universitaire de cardiologie et de pneumologie de Québec (CRIUCPQ), Université Laval, Québec, Qc, Canada.
| | - Jean-François Beaulieu
- Departement of Anatomy and cellular biology, Université de Sherbrooke, Sherbrooke, Qc, Canada. .,Canada Research Chair in Intestinal Physiopathology, Sherbrooke, Québec, Canada.
| | - Eric Tremblay
- Departement of Anatomy and cellular biology, Université de Sherbrooke, Sherbrooke, Qc, Canada.
| | - Frédéric-Simon Hould
- Institut universitaire de cardiologie et de pneumologie de Québec (CRIUCPQ), Université Laval, Québec, Qc, Canada. .,Departement of surgery, Université Laval, Québec, Qc, Canada.
| | - Yohan Bossé
- Institut universitaire de cardiologie et de pneumologie de Québec (CRIUCPQ), Université Laval, Québec, Qc, Canada. .,Department of Molecular Medicine, Université Laval, Quebec, Qc, Canada.
| | - Denis Richard
- Institut universitaire de cardiologie et de pneumologie de Québec (CRIUCPQ), Université Laval, Québec, Qc, Canada. .,Department of Molecular Medicine, Université Laval, Quebec, Qc, Canada. .,Chaire de Recherche Merck Frosst/IRSC Research Chair on Obesity, Québec, Qc, Canada.
| | - Emile Levy
- Department of Nutrition, Université de Montréal and Research center of CHU Sainte-Justine, 3175 Côte Ste-Catherine, Montréal, Qc, Canada. .,JA. deSève Research Chair in nutrition, Montréal, Qc, Canada.
| |
Collapse
|
30
|
Gruber K. Here, there, and everywhere: From PCRs to next-generation sequencing technologies and sequence databases, DNA contaminants creep in from the most unlikely places. EMBO Rep 2015; 16:898-901. [PMID: 26150097 DOI: 10.15252/embr.201540822] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
|
31
|
Promoter Polymorphism (rs12770170, -184C/T) of Microseminoprotein, Beta as a Risk Factor for Benign Prostatic Hyperplasia in Korean Population. Int Neurourol J 2014; 18:63-7. [PMID: 24987558 PMCID: PMC4076482 DOI: 10.5213/inj.2014.18.2.63] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2014] [Accepted: 06/14/2014] [Indexed: 12/26/2022] Open
Abstract
Purpose Benign prostatic hyperplasia (BPH) is the most common prostate disease in aging men. Microseminoprotein-beta (MSMB) is abundant in semen. In this study, we investigated association between single nucleotide polymorphisms (SNPs) at the promoter of the MSMB gene and the risk for developing BPH in a Korean population. Methods We genotyped two promoter polymorphisms (rs12770171, -184C/T and rs10993994, -2C/T) of the MSMB gene by direct sequencing. Ninety-five BPH patients and 78 control subjects were recruited for this study. SNPStats and Haploview version 4.2 were used for genetic analyses. Multiple logistic regression models (codominant, dominant, recessive, and log-additive models) were applied to determine the odds ratio (OR), 95% confidence interval (CI), and P-value. Results Genotype frequency of the rs12770171 SNP showed significant difference between BPH patients and controls (OR, 2.14; 95% CI, 1.07-4.27; P=0.032 in the codominant 1 model; OR, 2.31; 95% CI, 1.19-4.47; P=0.011 in the dominant model; and OR, 2.05; 95% CI, 1.17-3.61; P=0.009 in the log-additive model). Moreover, the SNP also showed association between the two groups (OR, 2.05; 95% CI, 1.19-3.52; P=0.009). The rs10993994 SNP was not associated with BPH. In haplotype analysis, CC and TT haplotypes were associated with BPH (P<0.05). Conclusions This result indicates that a promoter polymorphism (rs12770170, -184C/T) in the MSMB gene may be associated with BPH development in a Korean population.
Collapse
|
32
|
Mhatre DR, Mahale SD, Khatkhatay MI, Desai SS, Jagtap DD, Dhabalia JV, Tongaonkar HB, Desai MP, Dandekar SP, Varadkar AM. Development of an ELISA for sPSP94 and utility of the sPSP94/sPSA ratio as a diagnostic indicator to differentiate between benign prostatic hyperplasia and prostate cancer. Clin Chim Acta 2014; 436:256-62. [PMID: 24952364 DOI: 10.1016/j.cca.2014.06.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Revised: 06/05/2014] [Accepted: 06/07/2014] [Indexed: 10/25/2022]
Abstract
BACKGROUND The serum PSA (sPSA) test has low specificity for prostate cancer (PCa), since sPSA also rises in benign prostatic hyperplasia (BPH). Serum PSP94 (sPSP94), a major secreted prostate protein, is indicated as a PCa marker. The potential of sPSP94 and sPSA in conjunction with each other to improve specificity of diagnostic test for PCa needs to be evaluated. METHODS PCa patients (n=33), BPH patients (n=44) and healthy controls (n=50) were recruited. A serum-based sandwich ELISA was developed to measure sPSP94 concentrations. Utility of sPSP94 in improving specificity of sPSA test was evaluated by studying sPSP94/sPSA ratios of study participants. RESULTS Considerable decrease in overlap among sPSP94/sPSA ratio values of BPH and PCa patients was observed, as compared to sPSP94 or sPSA alone. For differentiating between BPH and PCa patients, this ratio had a maximum area under the curve (AUC) of 0.859 (P=0.0132) and had a comparable sensitivity (90.91%) to sPSA with an increased specificity of 70.45%. Further, decision curve analysis (DCA) showed that sPSP94/sPSA ratio had a superior net benefit in identifying PCa, in patients opting for biopsy. CONCLUSION The sPSP94/sPSA ratio can be a better differentiating marker between BPH and PCa, than sPSP94 or sPSA alone.
Collapse
Affiliation(s)
- Deepa R Mhatre
- Department of Biochemistry & Clinical Nutrition, Seth G.S. Medical College & K.E.M Hospital, Parel, Mumbai, India.
| | - Smita D Mahale
- Division of Structural Biology, National Institute for Research in Reproductive Health, Jehangir Merwanji Street, Parel, Mumbai, India
| | - Mohammed I Khatkhatay
- Department of Molecular Immunodiagnostics, National Institute for Research in Reproductive Health, Jehangir Merwanji Street, Parel, Mumbai, India
| | - Swapna S Desai
- Division of Structural Biology, National Institute for Research in Reproductive Health, Jehangir Merwanji Street, Parel, Mumbai, India
| | - Dhanashree D Jagtap
- Division of Structural Biology, National Institute for Research in Reproductive Health, Jehangir Merwanji Street, Parel, Mumbai, India
| | - Jayesh V Dhabalia
- Department of Urology, Seth G.S. Medical College & K.E.M Hospital, Parel, Mumbai, India
| | - Hemant B Tongaonkar
- Department of Genitourinary Oncology, Tata Memorial Hospital, Parel, Mumbai, India
| | - Meena P Desai
- Department of Molecular Immunodiagnostics, National Institute for Research in Reproductive Health, Jehangir Merwanji Street, Parel, Mumbai, India
| | - Sucheta P Dandekar
- Department of Biochemistry & Clinical Nutrition, Seth G.S. Medical College & K.E.M Hospital, Parel, Mumbai, India
| | - Anand M Varadkar
- Department of Biochemistry & Clinical Nutrition, Seth G.S. Medical College & K.E.M Hospital, Parel, Mumbai, India
| |
Collapse
|
33
|
Laurence M, Hatzis C, Brash DE. Common contaminants in next-generation sequencing that hinder discovery of low-abundance microbes. PLoS One 2014; 9:e97876. [PMID: 24837716 PMCID: PMC4023998 DOI: 10.1371/journal.pone.0097876] [Citation(s) in RCA: 204] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Accepted: 04/25/2014] [Indexed: 12/17/2022] Open
Abstract
Unbiased high-throughput sequencing of whole metagenome shotgun DNA libraries is a promising new approach to identifying microbes in clinical specimens, which, unlike other techniques, is not limited to known sequences. Unlike most sequencing applications, it is highly sensitive to laboratory contaminants as these will appear to originate from the clinical specimens. To assess the extent and diversity of sequence contaminants, we aligned 57 "1000 Genomes Project" sequencing runs from six centers against the four largest NCBI BLAST databases, detecting reads of diverse contaminant species in all runs and identifying the most common of these contaminant genera (Bradyrhizobium) in assembled genomes from the NCBI Genome database. Many of these microorganisms have been reported as contaminants of ultrapure water systems. Studies aiming to identify novel microbes in clinical specimens will greatly benefit from not only preventive measures such as extensive UV irradiation of water and cross-validation using independent techniques, but also a concerted effort to sequence the complete genomes of common contaminants so that they may be subtracted computationally.
Collapse
Affiliation(s)
| | - Christos Hatzis
- Yale Comprehensive Cancer Center, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Douglas E. Brash
- Department of Therapeutic Radiology, Yale School of Medicine, New Haven, Connecticut, United States of America
| |
Collapse
|