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Sherry Bhalla, Kumardeep Chaudhary, Ritesh Kumar, Manika Sehgal, Harpreet Kaur, Suresh Sharma, Gajendra P S Raghava
In this study, an attempt has been made to identify expression-based gene biomarkers that can discriminate early and late stage of clear cell renal cell carcinoma (ccRCC) patients. We have analyzed the gene expression of 523 samples to identify genes that are differentially expressed in the early and late stage of ccRCC. First, a threshold-based method has been developed, which attained a maximum accuracy of 71.12% with ROC 0.67 using single gene NR3C2. To improve the performance of threshold-based method, we combined two or more genes and achieved maximum accuracy of 70...
March 28, 2017: Scientific Reports
Kuo Wang, Man Gao, Mingyue Yang, Fanzheng Meng, Deli Li, Ruihua Lu, Yan Wang, Huadong Zhuang, Mengyao Li, Genhong Cheng, Xiaosong Wang
BACKGROUND: A growing number of severe Mycoplasma pneumoniae pneumonia (MPP) cases have been reported recently. However, the pathogenesis of severe MPP is not clear. In the current study, transcriptome sequencing was used to identify gene expression and alternative splicing profiles to provide insights into the pathogenesis of severe MPP. METHODS: RNAs of bronchoalveolar lavage fluid (BALF) samples from three severe MPP children and three mild MPP children were analyzed respectively by deep sequencing followed by computational annotation and quantification...
March 16, 2017: Human Genomics
Hongyan Sun
BACKGROUND: Avian pathogenic E. coli (APEC) can lead to a loss in millions of dollars in poultry annually because of mortality and produce contamination. Studies have verified that many immune-related genes undergo changes in alternative splicing (AS), along with nonsense mediated decay (NMD), to regulate the immune system under different conditions. Therefore, the splicing profiles of primary lymphoid tissues with systemic APEC infection need to be comprehensively examined. RESULTS: Gene expression in RNAseq data were obtained for three different immune tissues (bone marrow, thymus, and bursa) from three phenotype birds (non-challenged, resistant, and susceptible birds) at two time points...
March 7, 2017: BMC Genetics
Aleksander Lenert, David W Fardo
OBJECTIVES: To identify novel risk genes by gene-based association analysis in rheumatoid arthritis (RA). METHODS: We performed gene-based association testing with GATES (Gene-based Association Test using Extended Simes procedure) to augment the power of genomewide-association study (GWAS) results from the largest meta-GWAS by Okada et al. in 14,361 RA cases and 43,923 controls of European ancestry using 8,694,488 SNPs. RESULTS: We identified 115 genes significantly associated with RA by gene-based association testing corresponding to 43 RA risk loci; 23 risk loci contained a single top risk gene, while 20 risk loci contained two or more risk genes...
January 27, 2017: Clinical and Experimental Rheumatology
J P A Rego, J M Martins, C A Wolf, M van Tilburg, F Moreno, A C Monteiro-Moreira, R A Moreira, D O Santos, A A Moura
The objective of the present study was to describe the relationship of seminal plasma and total sperm cell proteins with the semen freezability parameters of Guzerat bulls. Thirteen bulls were subjected to breeding soundness evaluation. Semen samples were collected, cryopreserved, and then post-thawing sperm kinetics were assessed, where high ( = 7) and low ( = 6) freezability groups were defined. Seminal plasma and total sperm proteins from the 2 groups were separated by 2-dimensional SDS-PAGE, and spots were identified by mass spectrometry...
December 2016: Journal of Animal Science
Qi Zhao, Chunshu Yang, Jianing Wang, Yujia Li, Pingting Yang
DNase1l3 is an endonuclease to degrade the chromatin of apoptotic or necrotic cells. Serum DNase1l3 may fulfill the function of clearance of chromatin released into the circulation by dying cells, which can trigger autoimmune responses. To date, it remains unclear whether serum DNase1l3 level associates with the pathogenesis of autoimmune diseases. Sixty-eight patients with dermatomyositis/polymyositis (DM/PM, n = 30), systemic lupus erythematosus (SLE, n = 20) and rheumatoid arthritis (RA, n = 18), as well as 26 healthy blood donors were enrolled in the present study...
December 30, 2016: Clinical and Experimental Medicine
A Carbonella, G Mancano, E Gremese, F S Alkuraya, N Patel, F Gurrieri, G Ferraccioli
We describe the third family in the world, after Arabian and Turkish ones, displaying an autosomal recessive autoimmune disease (AID), mimicking systemic lupus erythematosus (SLE), with unusual manifestations due to a homozygous frame-shift variant in DNASE1L3. SLE is a complex AID characterized by multiple organ involvement. Genetic risk variants identified account for only 15% of SLE heritability. Rare Mendelian forms have been reported, including DNASE1L3-related SLE. Through specific genetic tests we identified a homozygous 2 bp-deletion c...
January 1, 2016: Lupus
Mindy S Lo
PURPOSE OF REVIEW: Systemic lupus erythematosus (SLE) is a multisystem autoimmune disease known for its clinical heterogeneity. Over time, new insights into the complex genetic origin of SLE have started to explain some of this clinical variability. These findings, reviewed here, have also yielded important understanding in the immune mechanisms behind SLE pathogenesis. RECENT FINDINGS: Several new monogenic disorders with lupus-like phenotype have been described...
December 2016: Current Rheumatology Reports
Hanna Kim, Gina A Montealegre Sanchez, Raphaela Goldbach-Mansky
Autoinflammatory disorders are sterile inflammatory conditions characterized by episodes of early-onset fever and disease-specific patterns of organ inflammation. Recently, the discoveries of monogenic disorders with strong type I interferon (IFN) signatures caused by mutations in proteasome degradation and cytoplasmic RNA and DNA sensing pathways suggest a pathogenic role of IFNs in causing autoinflammatory phenotypes. The IFN response gene signature (IGS) has been associated with systemic lupus erythematosus (SLE) and other autoimmune diseases...
October 2016: Journal of Molecular Medicine: Official Organ of the "Gesellschaft Deutscher Naturforscher und Ärzte"
Sarah Onuora
No abstract text is available yet for this article.
August 2016: Nature Reviews. Rheumatology
Vanja Sisirak, Benjamin Sally, Vivette D'Agati, Wilnelly Martinez-Ortiz, Z Birsin Özçakar, Joseph David, Ali Rashidfarrokhi, Ada Yeste, Casandra Panea, Asiya Seema Chida, Milena Bogunovic, Ivaylo I Ivanov, Francisco J Quintana, Inaki Sanz, Keith B Elkon, Mustafa Tekin, Fatoş Yalçınkaya, Timothy J Cardozo, Robert M Clancy, Jill P Buyon, Boris Reizis
Antibodies to DNA and chromatin drive autoimmunity in systemic lupus erythematosus (SLE). Null mutations and hypomorphic variants of the secreted deoxyribonuclease DNASE1L3 are linked to familial and sporadic SLE, respectively. We report that DNASE1L3-deficient mice rapidly develop autoantibodies to DNA and chromatin, followed by an SLE-like disease. Circulating DNASE1L3 is produced by dendritic cells and macrophages, and its levels inversely correlate with anti-DNA antibody response. DNASE1L3 is uniquely capable of digesting chromatin in microparticles released from apoptotic cells...
June 30, 2016: Cell
F David Carmona, Ahmet Mesut Onat, Tamara Fernández-Aranguren, Alberto Serrano-Fernández, Gema Robledo, Haner Direskeneli, Amr H Sawalha, Sule Yavuz, Javier Martín
OBJECTIVE: To evaluate the genetic background of systemic sclerosis (SSc) in the Turkish population. METHODS: There were 354 cases and 718 unaffected controls from Turkey genotyped for the most relevant SSc genetic markers (IRF5-rs10488631, STAT4-rs3821236, CD247-rs2056626, DNASE1L3-rs35677470, IL12A-rs77583790, and ATG5-rs9373839). Association tests were conducted to identify possible associations. RESULTS: Except for ATG5, all the analyzed genes showed either significant associations (IRF5: p = 1...
July 2016: Journal of Rheumatology
Junko Fujihara, Misuzu Ueki, Kaori Kimura-Kataoka, Reiko Iida, Haruo Takeshita, Toshihiro Yasuda
OBJECTIVE: To continue our previous investigations, we have extensively investigated the function of the 61, 41, and 35 non-synonymous single nucleotide polymorphisms (SNPs) in the human genes encoding DNASE1, DNASE1L3, and DNASE2, respectively, potentially relevant to autoimmune diseases. METHODS: The site-directed mutagenesis was employed to amino acid-substituted constructs corresponding to each SNP. The COS-7 cells were transfected with each vector and DNase activity was assayed by the single radial enzyme diffusion method...
July 2016: Immunological Investigations
Yun Ju Sung, Jacob Basson, Dabeeru C Rao
Analysis of longitudinal family data is challenging because of 2 sources of correlations: correlations across longitudinal measurements and correlations among related individuals. We investigated whether analysis using long-term average (average of all 3 visits) can enhance gene discovery compared with a single-visit analysis. We analyzed all 200 replicates of simulated systolic blood pressure (SBP) in Genetic Analysis Workshop 18 (GAW18) family data using both single-marker and collapsing methods. We considered 2 collapsing approaches: collapsing all variants and collapsing low-frequency variants...
2014: BMC Proceedings
Jane Zochling, Felicity Newell, Jac C Charlesworth, Paul Leo, Jim Stankovich, Adrian Cortes, Yuan Zhou, Wendy Stevens, Joanne Sahhar, Janet Roddy, Peter Nash, Kathleen Tymms, Maureen Rischmueller, Sue Lester, Susanna Proudman, Matthew A Brown
INTRODUCTION: The aim of the study was to interrogate the genetic architecture and autoimmune pleiotropy of scleroderma susceptibility in the Australian population. METHODS: We genotyped individuals from a well-characterized cohort of Australian scleroderma patients with the Immunochip, a custom array enriched for single nucleotide polymorphisms (SNPs) at immune loci. Controls were taken from the 1958 British Birth Cohort. After data cleaning and adjusting for population stratification the final dataset consisted of 486 cases, 4,458 controls and 146,525 SNPs...
2014: Arthritis Research & Therapy
Marek Malecki, Christine LaVanne, Dominique Alhambra, Chaitanya Dodivenaka, Sarah Nagel, Raf Malecki
INTRODUCTION: The worst possible complication of using stem cells for regenerative therapy is iatrogenic cancerogenesis. The ultimate goal of our work is to develop a self-triggering feedback mechanism aimed at causing death of all stem cells, which resist directed differentiation, keep proliferating, and can grow into tumors. SPECIFIC AIM: The specific aim was threefold: (1) to genetically engineer the DNA constructs for the human, recombinant DNASE1, DNASE1L3, DNASE2, DFFB controlled by POLA promoter; (2) to bioengineer anti-SSEA-4 antibody guided vectors delivering transgenes to human undifferentiated and proliferating pluripotent stem cells; (3) to cause death of proliferating and directed differentiation resisting stem cells by transgenic expression of the human recombinant the DNases (hrDNases)...
July 22, 2013: Journal of Stem Cell Research & Therapy
Marek Malecki, Jessica Dahlke, Melissa Haig, Lynn Wohlwend, Raf Malecki
INTRODUCTION: Ovarian cancer is the most deadly among all gynecological cancers. Patients undergoing systemic therapies of advanced ovarian cancers suffer from horrendous side effects. Cancer survivors and their offspring suffer from iatrogenic consequences of systemic therapies: genetic mutations. The ultimate goal of our work is development of therapies, which selectively and completely eliminate cancer cells, but do not harm healthy cells. An important consideration for attaining this goal is the fact that ovarian cancer cells over-express EGFR or its mutants, what becomes the factor discriminating them from healthy cells - a potential facilitator of personalized therapy...
July 21, 2013: Journal of Genetic Syndrome & Gene Therapy
Katherine J Baines, Jodie L Simpson, Lisa G Wood, Rodney J Scott, Naomi L Fibbens, Heather Powell, Douglas C Cowan, D Robin Taylor, Jan O Cowan, Peter G Gibson
BACKGROUND: Airway inflammation is associated with asthma exacerbation risk, treatment response, and disease mechanisms. OBJECTIVE: This study aimed to identify and validate a sputum gene expression signature that discriminates asthma inflammatory phenotypes. METHODS: An asthma phenotype biomarker discovery study generated gene expression profiles from induced sputum of 47 asthmatic patients. A clinical validation study (n = 59 asthmatic patients) confirmed differential expression of key genes...
April 2014: Journal of Allergy and Clinical Immunology
Maureen D Mayes, Lara Bossini-Castillo, Olga Gorlova, José Ezequiel Martin, Xiaodong Zhou, Wei V Chen, Shervin Assassi, Jun Ying, Filemon K Tan, Frank C Arnett, John D Reveille, Sandra Guerra, María Teruel, Francisco David Carmona, Peter K Gregersen, Annette T Lee, Elena López-Isac, Eguzkine Ochoa, Patricia Carreira, Carmen Pilar Simeón, Iván Castellví, Miguel Ángel González-Gay, Alexandra Zhernakova, Leonid Padyukov, Marta Alarcón-Riquelme, Cisca Wijmenga, Matthew Brown, Lorenzo Beretta, Gabriela Riemekasten, Torsten Witte, Nicolas Hunzelmann, Alexander Kreuter, Jörg H W Distler, Alexandre E Voskuyl, Annemie J Schuerwegh, Roger Hesselstrand, Annika Nordin, Paolo Airó, Claudio Lunardi, Paul Shiels, Jacob M van Laar, Ariane Herrick, Jane Worthington, Christopher Denton, Fredrick M Wigley, Laura K Hummers, John Varga, Monique E Hinchcliff, Murray Baron, Marie Hudson, Janet E Pope, Daniel E Furst, Dinesh Khanna, Kristin Phillips, Elena Schiopu, Barbara M Segal, Jerry A Molitor, Richard M Silver, Virginia D Steen, Robert W Simms, Robert A Lafyatis, Barri J Fessler, Tracy M Frech, Firas Alkassab, Peter Docherty, Elzbieta Kaminska, Nader Khalidi, Henry Niall Jones, Janet Markland, David Robinson, Jasper Broen, Timothy R D J Radstake, Carmen Fonseca, Bobby P Koeleman, Javier Martin
In this study, 1,833 systemic sclerosis (SSc) cases and 3,466 controls were genotyped with the Immunochip array. Classical alleles, amino acid residues, and SNPs across the human leukocyte antigen (HLA) region were imputed and tested. These analyses resulted in a model composed of six polymorphic amino acid positions and seven SNPs that explained the observed significant associations in the region. In addition, a replication step comprising 4,017 SSc cases and 5,935 controls was carried out for several selected non-HLA variants, reaching a total of 5,850 cases and 9,401 controls of European ancestry...
January 2, 2014: American Journal of Human Genetics
Misuzu Ueki, Kaori Kimura-Kataoka, Haruo Takeshita, Junko Fujihara, Reiko Iida, Rie Sano, Tamiko Nakajima, Yoshihiko Kominato, Yasuyuki Kawai, Toshihiro Yasuda
The objectives of this study were to evaluate all the non-synonymous single nucleotide polymorphisms (SNPs) in the DNase I and DNase I-like 3 (1L3) genes potentially implicated in autoimmune diseases as a functional SNP in terms of alteration of the activity levels. We examined the genotype distributions of the 32 and 20 non-synonymous SNPs in DNASE1 and DNASE1L3, respectively, in three ethnic groups, and the effect of these SNPs on the DNase activities. Among a total of 44 and 25 SNPs including those characterized in our previous studies [Yasuda et al...
January 2014: FEBS Journal
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