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https://www.readbyqxmd.com/read/29360682/ontogeny-related-pharmacogene-changes-in-the-pediatric-liver-transcriptome
#1
Richard Meier, Chengpeng Bi, Roger Gaedigk, Daniel P Heruth, Shui Qing Ye, J Steven Leeder, Brooke L Fridley
OBJECTIVES: The majority of drug dosing studies are based on adult populations, with modification of the dosing for children based on size and weight. This rudimentary approach for drug dosing children is limited, as biologically a child can differ from an adult in far more aspects than just size and weight. Specifically, understanding the ontogeny of childhood liver development is critical in dosing drugs that are metabolized through the liver, as the rate of metabolism determines the duration and intensity of a drug's pharmacologic action...
January 22, 2018: Pharmacogenetics and Genomics
https://www.readbyqxmd.com/read/29230811/whole-exome-sequencing-of-oral-mucosal-melanoma-reveals-mutational-profile-and-therapeutic-targets
#2
Jiong Lyu, Zhijian Song, Jianhua Chen, Matthew J Shepard, Hao Song, Guoxin Ren, Zhiqiang Li, Wei Guo, Zhengping Zhuang, Yongyong Shi
Oral mucosal melanoma (OMM) is rare and aggressive subtype of melanoma with little known about its pathogenesis carcinogenesis. We therefore performed whole-exome sequencing (WES) on 19 matched OMM tumor/normal pairs in order to gain insight on potential genetic drivers of tumor formation. For the first time we describe the comprehensive mutational profile of OMM. Our data suggests that the genetic background of OMM differs from those of other melanoma subtypes. We identified recurrent mutations involving KIT, POLE,PTPRD, PTCHD2 and DMXL2...
December 12, 2017: Journal of Pathology
https://www.readbyqxmd.com/read/29228728/protein-tyrosine-phosphatase-receptor-type-%C3%AE-acts-as-a-negative-regulator-suppressing-breast-cancer
#3
Xiaotang Yu, Fan Zhang, Jun Mao, Ying Lu, Jiazhi Li, Wei Ma, Shujun Fan, Chunying Zhang, Qing Li, Bo Wang, Bo Song, Lianhong Li
Protein tyrosine phosphatase receptor-type δ (PTPRD) is frequently inactivated in human cancers. This study investigated the role of PTPRD in the regulation of stemness, epithelial-mesenchymal transition (EMT), and migration and invasion in breast cancer cells. In vitro, PTPRD silencing using siRNA enhanced the stem cell-like properties of breast cancer cells, including their mammosphere- and holoclone-forming abilities, and it promoted tumorigenicity in vivo. PTPRD knockdown also increased the CD44+/CD24- breast cancer stem cell (BCSC) population and the expression of the stem cell markers ALDH1 and OCT4...
November 17, 2017: Oncotarget
https://www.readbyqxmd.com/read/29187730/genome-wide-analysis-in-uk-biobank-identifies-four-loci-associated-with-mood-instability-and-genetic-correlation-with-major-depressive-disorder-anxiety-disorder-and-schizophrenia
#4
Joey Ward, Rona J Strawbridge, Mark E S Bailey, Nicholas Graham, Amy Ferguson, Donald M Lyall, Breda Cullen, Laura M Pidgeon, Jonathan Cavanagh, Daniel F Mackay, Jill P Pell, Michael O'Donovan, Valentina Escott-Price, Daniel J Smith
Mood instability is a core clinical feature of affective and psychotic disorders. In keeping with the Research Domain Criteria approach, it may be a useful construct for identifying biology that cuts across psychiatric categories. We aimed to investigate the biological validity of a simple measure of mood instability and evaluate its genetic relationship with several psychiatric disorders, including major depressive disorder (MDD), bipolar disorder (BD), schizophrenia, attention deficit hyperactivity disorder (ADHD), anxiety disorder and post-traumatic stress disorder (PTSD)...
November 30, 2017: Translational Psychiatry
https://www.readbyqxmd.com/read/29033051/genetics-of-restless-legs-syndrome-an-update
#5
REVIEW
Félix J Jiménez-Jiménez, Hortensia Alonso-Navarro, Elena García-Martín, José A G Agúndez
A major role of genetic factors in the risk of developing restless legs syndrome (RLS) is supported by the high frequency of positive family history of RLS in patients affected with this disease, and the higher concordance rates in monozygotic twins compared with dizygotic ones in twin studies. In this review we have focused on those reports describing inheritance patterns of RLS, genetic anticipation, the results of studies performed on positivity of family history of RLS, twin studies, linkage studies in familial RLS, genome-wide association studies (GWAS), exome sequencing studies, and case-control association studies on candidate genes in RLS...
August 31, 2017: Sleep Medicine Reviews
https://www.readbyqxmd.com/read/28977839/genetic-defects-of-the-irf1-mediated-major-histocompatibility-complex-class-i-antigen-presentation-pathway-occur-prevalently-in-the-jak2-gene-in-non-small-cell-lung-cancer
#6
Tao Shen, Zhengming Chen, Zhizhuang Joe Zhao, Jie Wu
Recognition of major histocompatibility complex (MHC) class I antigens on tumor cells by cytotoxic T cells is involved in T cell-mediated tumor immune surveillance and immune checkpoint therapy. The interferon-γ (IFNγ)-IRF1 signaling pathway regulates MHC class I antigen presentation. To examine genetic defects of the IFNγ-IRF1 pathway in non-small cell lung cancer (NSCLC), we analyzed The Cancer Genome Atlas (TCGA) lung adenocarcinoma (LuAd) and lung squamous cell carcinoma (LuSc) data. Loss-of-function (LOF) genetic alterations of the IFNγ-IRF1 pathway genes (IFNGR1, IFNGR2, JAK1, JAK2, STAT1, IRF1) were found in 64 (6...
September 22, 2017: Oncotarget
https://www.readbyqxmd.com/read/28968711/spectrum-of-germline-mutations-in-smokers-and-non-smokers-in-brazilian-non-small-cell-lung-cancer-nsclc-patients
#7
Patrícia P Couto, Luciana Bastos-Rodrigues, Hagit Schayek, Flavia M Melo, Raony G C Lisboa, Debora M Miranda, Alyne Vilhena, Allen E Bale, Eitan Friedman, Luiz De Marco
Lung cancer (LC) is a leading cause of cancer-related mortality. Although smoking is the major risk factor, ~15% of all cases occur in never-smokers, suggesting that genetic factors play a role in LC predisposition. Indeed, germline mutations in the TP53 gene predispose to multiple cancer types, including LC. To date, few studies compared the somatic and germline mutational profiles of LC cases by smoking status, and none was reported in Brazilians. Whole-exome sequencing (WES) was performed on two pools (seven smokers and six non-smokers) of tumor-derived DNA using the Illumina HiSeq2000 platform...
October 26, 2017: Carcinogenesis
https://www.readbyqxmd.com/read/28859360/targeted-next-generation-sequencing-of-commonly-mutated-genes-in-esophageal-adenocarcinoma-patients-with-long-term-survival
#8
E Visser, I A Franken, L A A Brosens, W W J de Leng, E Strengman, J A Offerhaus, J P Ruurda, R van Hillegersberg
Survival of patients with esophageal adenocarcinoma remains poor and individual differences in prognosis remain unexplained. This study investigated whether gene mutations can explain why patients with high-risk (pT3-4, pN+) esophageal adenocarcinoma survive past 5 years after esophagectomy. Six long-term survivors (LTS) (≥5 years survival without recurrence) and six short-term survivors (STS) (<2 years survival due to recurrence) who underwent resection without neoadjuvant therapy for high-risk esophageal adenocarcinoma were included...
September 1, 2017: Diseases of the Esophagus: Official Journal of the International Society for Diseases of the Esophagus
https://www.readbyqxmd.com/read/28802642/prognostic-value-of-tert-alterations-mutational-and-copy-number-alterations-burden-in-urothelial-carcinoma
#9
Sumit Isharwal, François Audenet, Esther Drill, Eugene J Pietzak, Gopa Iyer, Irina Ostrovnaya, Eugene Cha, Timothy Donahue, Maria Arcila, Gowtham Jayakumaran, Michael F Berger, Jonathan E Rosenberg, Dean F Bajorin, Jonathan Coleman, Guido Dalbagni, Victor E Reuter, Bernard H Bochner, David B Solit, Hikmat A Al-Ahmadie
Point mutations in the TERT gene promoter occur at high frequency in multiple cancers, including urothelial carcinoma (UC). However, the relationship between TERT promoter mutations and UC patient outcomes is unclear due to conflicting reports in the literature. In this study, we examined the association of TERT alterations, tumor mutational burden per megabase (Mb), and copy number alteration (CNA) burden with clinical parameters and their prognostic value in a cohort of 398 urothelial tumors. The majority of TERT mutations were located at two promoter region hotspots (chromosome 5, 1 295 228 C>T and 1 295 250 C>T)...
August 10, 2017: European Urology Focus
https://www.readbyqxmd.com/read/28761083/revealing-the-complex-genetic-architecture-of-obsessive-compulsive-disorder-using-meta-analysis
#10
(no author information available yet)
Two obsessive-compulsive disorder (OCD) genome-wide association studies (GWASs) have been published by independent OCD consortia, the International Obsessive-Compulsive Disorder Foundation Genetics Collaborative (IOCDF-GC) and the OCD Collaborative Genetics Association Study (OCGAS), but many of the top-ranked signals were supported in only one study. We therefore conducted a meta-analysis from the two consortia, investigating a total of 2688 individuals of European ancestry with OCD and 7037 genomically matched controls...
August 1, 2017: Molecular Psychiatry
https://www.readbyqxmd.com/read/28615674/meta-analysis-of-genome-wide-snp-and-pathway-based-associations-for-facets-of-neuroticism
#11
Song E Kim, Han-Na Kim, Yeo-Jun Yun, Seong Gu Heo, Juhee Cho, Min-Jung Kwon, Yoosoo Chang, Seungho Ryu, Hocheol Shin, Chol Shin, Nam H Cho, Yeon Ah Sung, Hyung-Lae Kim
Neuroticism is a heritable personality trait that is comprised of distinct sub-factors, or facets. Sub-factors of neuroticism are linked to different emotional states or psychiatric symptoms and studying the genetic variants associated with these facets may help reveal the biological mechanisms underlying psychiatric disorders. In the present study, a meta-analysis of genome-wide association studies for six facets of neuroticism was performed in 5584 participants from three cohorts. Additionally, a Gene Set Enrichment Analysis was conducted to find biological pathways associated with each facet...
October 2017: Journal of Human Genetics
https://www.readbyqxmd.com/read/28537924/genetic-defects-of-the-irf1-mediated-major-histocompatibility-complex-class-i-antigen-presentation-pathway-occur-prevalently-in-the-jak2-gene-in-non-small-cell-lung-cancer
#12
Tao Shen, Zhengming Chen, Zhizhuang Joe Zhao, Jie Wu
Recognition of major histocompatibility complex (MHC) class I antigens on tumor cells by cytotoxic T cells is involved in T cell-mediated tumor immune surveillance and immune checkpoint therapy. The interferon-γ (IFNγ)-IRF1 signaling pathway regulates MHC class I antigen presentation. To examine genetic defects of the IFNγ-IRF1 pathway in non-small cell lung cancer (NSCLC), we analyzed The Cancer Genome Atlas (TCGA) lung adenocarcinoma (LuAd) and lung squamous cell carcinoma (LuSc) data. Loss-of-function (LOF) genetic alterations of the IFNγ-IRF1 pathway genes (IFNGR1, IFNGR2, JAK1, JAK2, STAT1, IRF1) were found in 64 (6...
May 8, 2017: Oncotarget
https://www.readbyqxmd.com/read/28497593/polymorphism-of-receptor-type-tyrosine-protein-phosphatase-delta-gene-in-the-development-of-non-alcoholic-fatty-liver-disease
#13
Shunsuke Nakajima, Hiroki Tanaka, Koji Sawada, Hidemi Hayashi, Takumu Hasebe, Masami Abe, Chitomi Hasebe, Mikihiro Fujiya, Toshikatsu Okumura
BACKGROUND AND AIM: Some single nucleotide polymorphisms (SNPs) are associated with the development of non-alcoholic fatty liver disease (NAFLD). As one of the genetic factors, PNPLA3 rs738409 (I148M) is important to associate with pathogenesis of NAFLD. Since other SNPs remain unclear in Japan, we performed high-throughput sequencing, which targeted more than 1,000 genes to identify a novel genetic variant in Japanese patients with NAFLD. METHODS: The present study in 36 NAFLD patients and 27 healthy volunteers (HVs) was performed...
May 11, 2017: Journal of Gastroenterology and Hepatology
https://www.readbyqxmd.com/read/28433457/spatial-and-temporal-expression-patterns-of-genes-around-nine-neuroticism-associated-loci
#14
Kazutaka Ohi, Takamitsu Shimada, Toshiki Yasuyama, Kohei Kimura, Takashi Uehara, Yasuhiro Kawasaki
Neuroticism is a high-order personality trait. Individuals with higher neuroticism have increased risks of various psychiatric disorders and physical health outcomes. Neuroticism is related to physiological differences in the brain. A recent genome-wide association study identified nine distinct genomic loci that contribute to neuroticism. Brain development and function depend on the precise regulation of gene expression, which is differentially regulated across brain regions and developmental stages. Using multiple publicly available human post-mortem databases, we investigated, in brain and non-brain tissues and across several developmental life stages, the spatial and temporal expression patterns of genes arising from nine neuroticism-associated loci...
April 19, 2017: Progress in Neuro-psychopharmacology & Biological Psychiatry
https://www.readbyqxmd.com/read/28431800/genetic-predictors-of-antipsychotic-response-to-lurasidone-identified-in-a-genome-wide-association-study-and-by-schizophrenia-risk-genes
#15
Jiang Li, Akane Yoshikawa, Mark D Brennan, Timothy L Ramsey, Herbert Y Meltzer
Biomarkers which predict response to atypical antipsychotic drugs (AAPDs) increases their benefit/risk ratio. We sought to identify common variants in genes which predict response to lurasidone, an AAPD, by associating genome-wide association study (GWAS) data and changes (Δ) in Positive And Negative Syndrome Scale (PANSS) scores from two 6-week randomized, placebo-controlled trials of lurasidone in schizophrenia (SCZ) patients. We also included SCZ risk SNPs identified by the Psychiatric Genomics Consortium using a polygenic risk analysis...
April 18, 2017: Schizophrenia Research
https://www.readbyqxmd.com/read/28426752/somatic-copy-number-alterations-in-gastric-adenocarcinomas-among-asian-and-western-patients
#16
Steven E Schumacher, Byoung Yong Shim, Giovanni Corso, Min-Hee Ryu, Yoon-Koo Kang, Franco Roviello, Gordon Saksena, Shouyong Peng, Ramesh A Shivdasani, Adam J Bass, Rameen Beroukhim
Gastric cancer, a leading worldwide cause of cancer mortality, shows high geographic and ethnic variation in incidence rates, which are highest in East Asia. The anatomic locations and clinical behavior also differ by geography, leading to the controversial idea that Eastern and Western forms of the disease are distinct. In view of these differences, we investigated whether gastric cancers from Eastern and Western patients show distinct genomic profiles. We used high-density profiling of somatic copy-number aberrations to analyze the largest collection to date of gastric adenocarcinomas and utilized genotyping data to rigorously annotate ethnic status...
2017: PloS One
https://www.readbyqxmd.com/read/28345455/recurrent-epigenetic-silencing-of-the-ptprd-tumor-suppressor-in-laryngeal-squamous-cell-carcinoma
#17
Marcin Szaumkessel, Sonia Wojciechowska, Joanna Janiszewska, Natalia Zemke, Ewa Byzia, Katarzyna Kiwerska, Magdalena Kostrzewska-Poczekaj, Adam Ustaszewski, Malgorzata Jarmuz-Szymczak, Reidar Grenman, Malgorzata Wierzbicka, Anna Bartochowska, Krzysztof Szyfter, Maciej Giefing
Cellular processes like differentiation, mitotic cycle, and cell growth are regulated by tyrosine kinases with known oncogenic potential and tyrosine phosphatases that downmodulate the first. Therefore, tyrosine phosphatases are recurrent targets of gene alterations in human carcinomas. We and others suggested recently a tumor suppressor function of the PTPRD tyrosine phosphatase and reported homozygous deletions of the PTPRD locus in laryngeal squamous cell carcinoma. In this study, we investigated other gene-inactivating mechanisms potentially targeting PTPRD, including loss-of-function mutations and also epigenetic alterations like promoter DNA hypermethylation...
March 2017: Tumour Biology: the Journal of the International Society for Oncodevelopmental Biology and Medicine
https://www.readbyqxmd.com/read/28329290/association-of-btbd9-and-map2k5-skor1-with-restless-legs-syndrome-in-chinese-population
#18
Gen Li, Huidong Tang, Cheng Wang, Xuemei Qi, Jie Chen, Shengdi Chen, Jianfang Ma
Study Objectives: The aim of the study was to investigate the relationship between genetic factors and primary restless legs syndrome (RLS) in Chinese population. Methods: A total of 116 RLS patients and 200 controls were recruited and the diagnosis of RLS was based on the criteria of International RLS Study Group. Polymer chain reaction (PCR) and sequencing were used to detect 19 single nucleotide polymorphisms (SNPs) in six genetic loci (MEIS1, BTBD9, PTPRD, MAP2K5/SKOR1, TOX3, and Intergenic region of 2p14)...
April 1, 2017: Sleep
https://www.readbyqxmd.com/read/28322283/susceptibility-to-neurofibrillary-tangles-role-of-the-ptprd-locus-and-limited-pleiotropy-with-other-neuropathologies
#19
L B Chibnik, C C White, S Mukherjee, T Raj, L Yu, E B Larson, T J Montine, C D Keene, J Sonnen, J A Schneider, P K Crane, J M Shulman, D A Bennett, P L De Jager
Tauopathies, including Alzheimer's disease (AD) and other neurodegenerative conditions, are defined by a pathological hallmark: neurofibrillary tangles (NFTs). NFT accumulation is thought to be closely linked to cognitive decline in AD. Here, we perform a genome-wide association study for NFT pathologic burden and report the association of the PTPRD locus (rs560380, P=3.8 × 10(-8)) in 909 prospective autopsies. The association is replicated in an independent data set of 369 autopsies. The association of PTPRD with NFT is not dependent on the accumulation of amyloid pathology...
March 21, 2017: Molecular Psychiatry
https://www.readbyqxmd.com/read/28235956/genomic-complexity-and-targeted-genes-in-anaplastic-thyroid-cancer-cell-lines
#20
Eleanor L Woodward, Andrea Biloglav, Naveen Ravi, Minjun Yang, Lars Ekblad, Johan Wennerberg, Kajsa Paulsson
Anaplastic thyroid cancer (ATC) is a highly malignant disease with a very short median survival time. Few studies have addressed the underlying somatic mutations, and the genomic landscape of ATC thus remains largely unknown. In the present study, we have ascertained copy number aberrations, gene fusions, gene expression patterns, and mutations in early-passage cells from ten newly established ATC cell lines using single nucleotide polymorphism (SNP) array analysis, RNA sequencing and whole exome sequencing...
May 2017: Endocrine-related Cancer
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