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Ye Jin Ha, Ka Hee Tak, Chan Wook Kim, Seon Ae Roh, Eun Kyung Choi, Dong Hyung Cho, Jeong Hwan Kim, Seon Kyu Kim, Seon Young Kim, Yong Sung Kim, Jin Cheon Kim
PURPOSE: The ability to predict individual responsiveness to cancer therapy is urgently needed. This is particularly true for patients with locally advanced rectal cancer (LARC) because a large proportion are resistant to preoperative chemoradiation therapy (CRT). In this study, we sought to identify markers that could predict response by comparing the gene expression profiles of the tumors of patients who received preoperative CRT. METHODS AND MATERIALS: The basal gene expression profiles of tumors from 22 LARC patients who were responders (n=9) and nonresponders (n=13) to preoperative CRT were analyzed using RNA sequencing (RNA-Seq)...
August 1, 2017: International Journal of Radiation Oncology, Biology, Physics
Martin H Pedersen, Brian L Hood, Hans Christian Beck, Thomas P Conrads, Henrik J Ditzel, Rikke Leth-Larsen
Triple-negative breast cancer (TNBC) is a heterogeneous subtype with varying disease outcomes. Tumor-infiltrating lymphocytes (TILs) are frequent in TNBC and have been shown to correlate with outcome, suggesting an immunogenic component in this subtype. However, other factors intrinsic to the cancer cells may also influence outcome. To identify proteins and molecular pathways associated with recurrence in TNBC, 34 formalin-fixed paraffin-embedded (FFPE) primary TNBC tumors were investigated by global proteomic profiling using mass spectrometry...
2017: Oncoimmunology
Cathrin Ritter, Kaiji Fan, Annette Paschen, Sine Reker Hardrup, Soldano Ferrone, Paul Nghiem, Selma Ugurel, David Schrama, Jürgen C Becker
Merkel cell carcinoma (MCC) is a rare and aggressive, yet highly immunogenic skin cancer. The latter is due to its viral or UV-associated carcinogenesis. For tumor progression MCC has to escape the host's immuno-surveillance, e.g. by loss of HLA class-I expression. Indeed, a reduced HLA class-I expression was observed in MCC tumor tissues and MCC cell lines. This reduced HLA class-I surface expression is caused by an impaired expression of key components of the antigen processing machinery (APM), including LMP2 and LMP7 as well as TAP1 and TAP2...
May 23, 2017: Scientific Reports
Y Al Khaled, S Tierling, M Laqqan, C Lo Porto, M E Hammadeh
DNA methylation plays important roles in genome stability and regulation of gene expression. This study was designed to determine the influence of cigarette smoking on sperm DNA methylation. From a genome-wide survey on sperm samples, differentially methylated target CpGs should be selected and subjected to local deep bisulphite sequencing. Obtained methylation data are compared to sperm parameters and (ICSI) outcome. Similar to pilot study, samples were subjected to Infinium 450K BeadChip arrays to identify alterations in sperm DNA methylation between smokers and nonsmokers males...
May 14, 2017: Andrologia
Yufeng Qian, Genlin Wang, Feng Xue, Lianghui Chen, Yan Wang, Liang Tang, Huilin Yang
OBJECTIVES: Ankylosing spondylitis (AS) is a chronic inflammatory joint disease. The transporter associated with antigen processing (TAP) has been identified to play an important role in immune response as well as the HLA-associated diseases. The aim of our meta-analysis was to investigate the contribution of TAP (TAP1 and TAP2) polymorphisms to the risk of AS. METHODS: Meta-analyses were performed between 2 polymorphisms in TAP1 (TAP1-333, -637) and 3 polymorphisms in TAP2 (TAP2-379, -565, and -665) and AS...
August 2017: Inflammation Research: Official Journal of the European Histamine Research Society ... [et Al.]
Seolhee Park, Hyeon-Jun Shin, Masaud Shah, Hey-Young Cho, Muhammad Ayaz Anwar, Asma Achek, Hyuk-Kwon Kwon, Byugsung Lee, Tae Hyeon Yoo, Sangdun Choi
Negative regulation of Toll-like receptor-4 (TLR4) is anticipated to control the pathogen-induced exaggerated immune response. However, effective TLR4 antagonists with scarce off-target effects are yet to be developed. To fill this void, we sought to design small peptide-inhibitors of the TLR4/MD2-LPS interaction. Here we report novel TLR4-antagonistic peptides (TAP), identified through phage display, endowed with the LPS-induced proinflammation inhibition, and confirmed in mice. TAPs-attributed TLR4-antagonism were initially evaluated through NF-κB inhibition in HEK-blue hTLR4 and RAW264...
February 20, 2017: Biomaterials
Liao Chang, Shiyang He, Danqing Mao, Yuanhong Liu, Zijun Xiong, Dongke Fu, Bo Li, Shuguang Wei, Xun Xu, Shengbin Li, Hui Yuan
Whole-genome shotgun (WGS) sequencing has become a routine method in genome research over the past decade. However, the assembly of highly polymorphic regions in WGS projects remains a challenge, especially for large genomes. Employing BAC library constructing, PCR screening and Sanger sequencing, traditional strategy is laborious and expensive, which hampers research on polymorphic genomic regions. As one of the most highly polymorphic regions, the major histocompatibility complex (MHC) plays a central role in the adaptive immunity of all jawed vertebrates...
2016: PloS One
Antonio Lapenna, Ibrahim Omar, Michael Berger
We report a new mouse strain with a single point mutation in the type 2 transporter associated with antigen processing (TAP2). This strain randomly arose in one of our C57BL/6J mouse colonies and was initially discovered because of the lack of CD8(+) T cells in the periphery. Following our observation, we subsequently revealed a lack of cell surface MHC-I expression, derived from TAP2 protein deficiency. Our strain, named eightless, has a C to T substitution in exon 5 resulting in a glutamine to stop codon substitution at position 285 in the TAP2 protein...
April 2017: Immunology
Katelyn M Mika, Vincent J Lynch
Variation in female reproductive traits, such as fertility, fecundity, and fecundability, is heritable in humans, but identifying and functionally characterizing genetic variants associated with these traits has been challenging. Here, we explore the functional significance and evolutionary history of a T/C polymorphism of SNP rs2071473, which we have previously shown is an eQTL for TAP2 and significantly associated with fecundability (time to pregnancy). We replicated the association between the rs2071473 genotype and TAP2 expression by using GTEx data and demonstrated that TAP2 is expressed by decidual stromal cells at the maternal-fetal interface...
November 3, 2016: American Journal of Human Genetics
Manuel Albanese, Takanobu Tagawa, Mickaël Bouvet, Liridona Maliqi, Dominik Lutter, Jonathan Hoser, Maximilian Hastreiter, Mitch Hayes, Bill Sugden, Larissa Martin, Andreas Moosmann, Wolfgang Hammerschmidt
Infection with Epstein-Barr virus (EBV) affects most humans worldwide and persists life-long in the presence of robust virus-specific T-cell responses. In both immunocompromised and some immunocompetent people, EBV causes several cancers and lymphoproliferative diseases. EBV transforms B cells in vitro and encodes at least 44 microRNAs (miRNAs), most of which are expressed in EBV-transformed B cells, but their functions are largely unknown. Recently, we showed that EBV miRNAs inhibit CD4(+) T-cell responses to infected B cells by targeting IL-12, MHC class II, and lysosomal proteases...
October 18, 2016: Proceedings of the National Academy of Sciences of the United States of America
Kimberly Mayes, Suehyb G Alkhatib, Kristen Peterson, Aiman Alhazmi, Carolyn Song, Vivian Chan, Tana Blevins, Mark Roberts, Catherine I Dumur, Xiang-Yang Wang, Joseph W Landry
Genetic studies in fruit flies have implicated the chromatin remodeling complex nucleosome remodeling factor (NURF) in immunity, but it has yet to be studied in mammals. Here we show that its targeting in mice enhances antitumor immunity in two syngeneic models of cancer. NURF was disabled by silencing of bromodomain PHD-finger containing transcription factor (BPTF), the largest and essential subunit of NURF. We found that both CD8(+) and CD4(+) T cells were necessary for enhanced antitumor activity, with elevated numbers of activated CD8(+) T cells observed in BPTF-deficient tumors...
November 1, 2016: Cancer Research
Sean C McConnell, Kyle M Hernandez, Dustin J Wcisel, Ross N Kettleborough, Derek L Stemple, Jeffrey A Yoder, Jorge Andrade, Jill L O de Jong
Antigen processing and presentation genes found within the MHC are among the most highly polymorphic genes of vertebrate genomes, providing populations with diverse immune responses to a wide array of pathogens. Here, we describe transcriptome, exome, and whole-genome sequencing of clonal zebrafish, uncovering the most extensive diversity within the antigen processing and presentation genes of any species yet examined. Our CG2 clonal zebrafish assembly provides genomic context within a remarkably divergent haplotype of the core MHC region on chromosome 19 for six expressed genes not found in the zebrafish reference genome: mhc1uga, proteasome-β 9b (psmb9b), psmb8f, and previously unknown genes psmb13b, tap2d, and tap2e We identify ancient lineages for Psmb13 within a proteasome branch previously thought to be monomorphic and provide evidence of substantial lineage diversity within each of three major trifurcations of catalytic-type proteasome subunits in vertebrates: Psmb5/Psmb8/Psmb11, Psmb6/Psmb9/Psmb12, and Psmb7/Psmb10/Psmb13...
August 23, 2016: Proceedings of the National Academy of Sciences of the United States of America
Courtney K Burrows, Gülüm Kosova, Catherine Herman, Kristen Patterson, Katherine E Hartmann, Digna R Velez Edwards, Mary D Stephenson, Vincent J Lynch, Carole Ober
Fertility traits in humans are heritable, however, little is known about the genes that influence reproductive outcomes or the genetic variants that contribute to differences in these traits between individuals, particularly women. To address this gap in knowledge, we performed an unbiased genome-wide expression quantitative trait locus (eQTL) mapping study to identify common regulatory (expression) single nucleotide polymorphisms (eSNPs) in mid-secretory endometrium. We identified 423 cis-eQTLs for 132 genes that were significant at a false discovery rate (FDR) of 1%...
July 2016: PLoS Genetics
X Xiao, J Hao, Y Wen, W Wang, X Guo, F Zhang
OBJECTIVES: The molecular mechanism of rheumatoid arthritis (RA) remains elusive. We conducted a protein-protein interaction network-based integrative analysis of genome-wide association studies (GWAS) and gene expression profiles of RA. METHODS: We first performed a dense search of RA-associated gene modules by integrating a large GWAS meta-analysis dataset (containing 5539 RA patients and 20 169 healthy controls), protein interaction network and gene expression profiles of RA synovium and peripheral blood mononuclear cells (PBMCs)...
July 2016: Bone & Joint Research
Wing Fuk Chan, Julie A Parks-Dely, Brad G Magor, Katharine E Magor
In many nonmammalian vertebrates, the genomic organization of the MHC class I region leads to biased expression of a single classical MHC class I gene coevolving with TAP transporters, whereas class I genes are poorly expressed. This contrasts to the three codominantly expressed classical MHC class I genes in humans and mice. In a sequenced haplotype from White Pekin duck, Anas platyrhynchos, there is one predominantly expressed MHC class I, UAA, although they have five MHC class I genes in the complex, arranged TAP1-TAP2-UAA-UBA-UCA-UDA-UEA The UAA gene, situated proximal to the TAP2 gene, is expressed at levels 10-fold greater than that of another expressed gene, UDA...
August 15, 2016: Journal of Immunology: Official Journal of the American Association of Immunologists
Ximena Fleming-Canepa, Shawna M Jensen, Christine M Mesa, Laura Diaz-Satizabal, Alexa J Roth, Julie A Parks-Dely, Debra A Moon, Janet P Wong, Danyel Evseev, Desolie A Gossen, David G Tetrault, Katharine E Magor
MHC class I is critically involved in defense against viruses, and diversity from polygeny and polymorphism contributes to the breadth of the immune response and health of the population. In this article, we examine MHC class I diversity in wild mallard ducks, the natural host and reservoir of influenza A viruses. We previously showed domestic ducks predominantly use UAA, one of five MHC class I genes, but whether biased expression is also true for wild mallards is unknown. Using RT-PCR from blood, we examined expressed MHC class I alleles from 38 wild mallards (Anas platyrhynchos) and identified 61 unique alleles, typically 1 or 2 expressed alleles in each individual...
August 1, 2016: Journal of Immunology: Official Journal of the American Association of Immunologists
Kaung Si Thu, Noriko Sato, Shinobu Ikeda, Makiko Naka-Mieno, Tomio Arai, Seijiro Mori, Motoji Sawabe, Masaaki Muramatsu, Masashi Tanaka
The transporter associated with antigen processing 2 (TAP2) gene is involved in the immunological response to tuberculosis (TB) infection. Variations in the TAP2 gene have been associated with TB infection in small population studies in India, Columbia, and Korea. We investigated the association of TAP2 polymorphisms with TB susceptibility in an elderly Japanese population. We analyzed samples from consecutive autopsy cases (n = 1850) registered in the Japanese Geriatric SNP Research database. TB was diagnosed pathologically by TB granuloma on autopsy samples...
August 2016: APMIS: Acta Pathologica, Microbiologica, et Immunologica Scandinavica
James W Wynne, Amanda P Woon, Nadine L Dudek, Nathan P Croft, Justin H J Ng, Michelle L Baker, Lin-Fa Wang, Anthony W Purcell
Bats are a major reservoir of emerging and re-emerging infectious diseases, including severe acute respiratory syndrome-like coronaviruses, henipaviruses, and Ebola virus. Although highly pathogenic to their spillover hosts, bats harbor these viruses, and a large number of other viruses, with little or no clinical signs of disease. How bats asymptomatically coexist with these viruses is unknown. In particular, little is known about bat adaptive immunity, and the presence of functional MHC molecules is mostly inferred from recently described genomes...
June 1, 2016: Journal of Immunology: Official Journal of the American Association of Immunologists
Ming-Shu Mo, Wei Huang, Cong-Cong Sun, Li-Min Zhang, Luan Cen, You-Sheng Xiao, Guo-Fei Li, Xin-Ling Yang, Shao-Gang Qu, Ping-Yi Xu
BACKGROUND: Proteasome subunits (PSMB) and transporter associated with antigen processing (TAP) loci are located in the human leukocyte antigen (HLA) Class II region play important roles in immune response and protein degradation in neurodegenerative diseases. This study aimed to explore the association between single nucleotide polymorphisms (SNPs) of PSMB and TAP and Parkinson's disease (PD). METHODS: A case-control study was conducted by genotyping SNPs in PSMB8, PSMB9, TAP1, and TAP2 genes in the Chinese population...
May 5, 2016: Chinese Medical Journal
Mohammad Naderi, Mohammad Hashemi, Shadi Amininia
TAP1 and TAP2 genes encode heterodimeric molecule involved in endogenous antigen processing. The present study was undertaken to find out the possible association between TAP1 and TAP2 polymorphisms and risk of pulmonary tuberculosis (PTB) in a sample of Iranian population. Polymorphisms of TAP1 (rs1057141, rs1135216) and TAP2 (rs2228396, rs241447, rs67511411, rs141555015) were determined in 173 PTB patients and 164 healthy subjects. Our findings showed that rs1135216 AG, GG and AG+GG genotypes increased the risk of PTB in comparison with AA (OR=2...
February 2016: Iranian Journal of Allergy, Asthma, and Immunology
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