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Chi-Hua Chen, Yunpeng Wang, Min-Tzu Lo, Andrew Schork, Chun-Chieh Fan, Dominic Holland, Karolina Kauppi, Olav B Smeland, Srdjan Djurovic, Nilotpal Sanyal, Derrek P Hibar, Paul M Thompson, Wesley K Thompson, Ole A Andreassen, Anders M Dale
Discovering genetic variants associated with human brain structures is an on-going effort. The ENIGMA consortium conducted genome-wide association studies (GWAS) with standard multi-study analytical methodology and identified several significant single nucleotide polymorphisms (SNPs). Here we employ a novel analytical approach that incorporates functional genome annotations (e.g., exon or 5'UTR), total linkage disequilibrium (LD) scores and heterozygosity to construct enrichment scores for improved identification of relevant SNPs...
November 16, 2017: Scientific Reports
Chien-Cheng Chen, Alina P Montalbano, Imran Hussain, Wan-Ru Lee, Carole R Mendelson
The mechanisms whereby progesterone (P4 ), acting via the progesterone receptor (PR), inhibits proinflammatory/contractile gene expression during pregnancy are incompletely defined. Using immortalized human myometrial (hTERT-HM) cells stably expressing wild-type PR-A or PR-B (PRWT ), we found that P4 significantly inhibited IL-1β induction of the NF-κB target genes, COX-2 and IL-8 P4 -PRWT transrepression occurred at the level of transcription initiation and was mediated by decreased recruitment of NF-κB p65 and RNA polymerase II to COX-2 and IL-8 promoters...
July 28, 2017: Journal of Biological Chemistry
Karlijn Vermeulen, Anneke de Boer, Joost G E Janzing, David A Koolen, Charlotte W Ockeloen, Marjolein H Willemsen, Floor M Verhoef, Patricia A M van Deurzen, Linde van Dongen, Hans van Bokhoven, Jos I M Egger, Wouter G Staal, Tjitske Kleefstra
Detailed neurobehavioural profiles are of major value for specific clinical management, but have remained underexposed in the population with intellectual disabilities (ID). This was traditionally classified based on IQ level only. Rapid advances in genetics enable etiology based stratification in the majority of patients, which reduces clinical heterogeneity. This paper illustrates that specific profiles can be obtained for rare syndromes with ID. Our main aim was to study (mal)adaptive functioning in Kleefstra Syndrome (KS) by comparing and contrasting our findings to three other subgroups: Koolen-de Vries Syndrome, GATAD2B-related syndrome, and a mixed control group of individuals with ID...
May 12, 2017: American Journal of Medical Genetics. Part A
Thipwimol Tim-Aroon, Natini Jinawath, Weerin Thammachote, Praweena Sinpitak, Anchalee Limrungsikul, Chaiyos Khongkhatithum, Duangrurdee Wattanasirichaigoon
GATAD2B gene is involved in chromatin modification and transcription activity. Loss-of-function mutations of GATAD2B have recently been defined to cause a recognizable syndrome with intellectual disability (ID). Human TPM3 gene encoding thin filament protein is associated with myopathies. Both genes are located on chromosome 1q21.3. We herein report an infant with feeding difficulty, developmental delay, hypotonia, and dysmorphic features including small palpebral fissures, telecanthus, sparse hair and eyebrow, cup-shaped ears, and clinodactyly...
March 2017: American Journal of Medical Genetics. Part A
Xiaomei Luo, Yongyi Zou, Bo Tan, Yue Zhang, Jing Guo, Lanlan Zeng, Rui Zhang, Hu Tan, Xianda Wei, Yiqiao Hu, Yu Zheng, Desheng Liang, Lingqian Wu
GATA zinc finger domain-containing 2B (GATAD2B) is a subunit of the methyl-CpG-binding protein-1 complex (MECP1), which deacetylates methylated nucleosomes and regresses transcriptional activity. Recently, GATAD2B has been elucidated as a candidate gene in patients with intellectual disability (ID). In this study, we identified two novel heterozygous frameshift mutations of GATAD2B in two unrelated ID cases through next-generation sequencing (NGS). Both of the mutations c.80_81insGATGT and c.552_555delGAAA cause truncated proteins that might be detrimental to neurodevelopment...
April 2017: Journal of Human Genetics
Cornelia G Spruijt, Martijn S Luijsterburg, Roberta Menafra, Rik G H Lindeboom, Pascal W T C Jansen, Raghu Ram Edupuganti, Marijke P Baltissen, Wouter W Wiegant, Moritz C Voelker-Albert, Filomena Matarese, Anneloes Mensinga, Ina Poser, Harmjan R Vos, Hendrik G Stunnenberg, Haico van Attikum, Michiel Vermeulen
NuRD (nucleosome remodeling and histone deacetylase) is a versatile multi-protein complex with roles in transcription regulation and the DNA damage response. Here, we show that ZMYND8 bridges NuRD to a number of putative DNA-binding zinc finger proteins. The MYND domain of ZMYND8 directly interacts with PPPLΦ motifs in the NuRD subunit GATAD2A. Both GATAD2A and GATAD2B exclusively form homodimers and define mutually exclusive NuRD subcomplexes. ZMYND8 and NuRD share a large number of genome-wide binding sites, mostly active promoters and enhancers...
October 11, 2016: Cell Reports
Joanna Bednarczyk, Konrad J Dębski, Anna M Bot, Katarzyna Lukasiuk
The aim of the present study was to examine involvement of MBD3 (methyl-CpG-binding domain protein 3), a protein involved in reading DNA methylation patterns, in epileptogenesis and epilepsy. We used a well-characterized rat model of temporal lobe epilepsy that is triggered by status epilepticus, evoked by electrical stimulation of the amygdala. Stimulated and sham-operated animals were sacrificed 14 days after stimulation. We found that MBD3 transcript was present in neurons, oligodendrocytes, and astrocytes in both control and epileptic animals...
2016: Scientific Reports
Morgan P Torchy, Ali Hamiche, Bruno P Klaholz
Transcription regulation through chromatin compaction and decompaction is regulated through various chromatin-remodeling complexes such as nucleosome remodeling and histone deacetylation (NuRD) complex. NuRD is a 1 MDa multi-subunit protein complex which comprises many different subunits, among which histone deacetylases HDAC1/2, ATP-dependent remodeling enzymes CHD3/4, histone chaperones RbAp46/48, CpG-binding proteins MBD2/3, the GATAD2a (p66α) and/or GATAD2b (p66β) and specific DNA-binding proteins MTA1/2/3...
July 2015: Cellular and Molecular Life Sciences: CMLS
Fadi F Hamdan, Myriam Srour, Jose-Mario Capo-Chichi, Hussein Daoud, Christina Nassif, Lysanne Patry, Christine Massicotte, Amirthagowri Ambalavanan, Dan Spiegelman, Ousmane Diallo, Edouard Henrion, Alexandre Dionne-Laporte, Anne Fougerat, Alexey V Pshezhetsky, Sunita Venkateswaran, Guy A Rouleau, Jacques L Michaud
Genetics is believed to have an important role in intellectual disability (ID). Recent studies have emphasized the involvement of de novo mutations (DNMs) in ID but the extent to which they contribute to its pathogenesis and the identity of the corresponding genes remain largely unknown. Here, we report a screen for DNMs in subjects with moderate or severe ID. We sequenced the exomes of 41 probands and their parents, and confirmed 81 DNMs affecting the coding sequence or consensus splice sites (1.98 DNMs/proband)...
October 2014: PLoS Genetics
Yoshitaka Ishihara, Satoshi Tsuno, Satoshi Kuwamoto, Taro Yamashita, Yusuke Endo, Junichi Hasegawa, Norimasa Miura
BACKGROUND: We have previously shown that hsa-miR-520d-5p can convert cancer cells into induced pluripotent stem cells (iPSCs) or mesenchymal stem cells (MSCs) via a dedifferentiation by a demethylation mechanism. METHODS: We tested the effect of miR-520d-5p on human fibroblasts to determine whether it could be safely used in normal cells for future clinical therapeutic applications. After we transfected the microRNA into fibroblasts, we analyzed the phenotypic changes, gene expression levels, and stemness induction in vitro, and we evaluated tumor formation in an in vivo xenograft model...
December 2014: Drugs in R&D
Takashi Fujitomo, Yataro Daigo, Koichi Matsuda, Koji Ueda, Yusuke Nakamura
On the basis of the gene expression profiles of 120 lung cancer cases using a cDNA microarray containing 27,648 genes or expressed sequence tags (ESTs), we identified LRRC42 (Leucine-rich repeat containing 42) to be significantly upregulated in the majority of lung cancers. Northern blot analysis demonstrated that LRRC42 was expressed only in testis among normal tissues examined. Knockdown of LRRC42 expression by siRNA against LRRC42 significantly suppressed the growth of lung cancer cells. On the other hand, stable induction of LRRC42 expression significantly promoted cell growth...
July 2014: International Journal of Oncology
Marjolein H Willemsen, Bonnie Nijhof, Michaela Fenckova, Willy M Nillesen, Ernie M H F Bongers, Anna Castells-Nobau, Lenke Asztalos, Erika Viragh, Bregje W M van Bon, Emre Tezel, Joris A Veltman, Han G Brunner, Bert B A de Vries, Joep de Ligt, Helger G Yntema, Hans van Bokhoven, Bertrand Isidor, Cédric Le Caignec, Elsa Lorino, Zoltan Asztalos, David A Koolen, Lisenka E L M Vissers, Annette Schenck, Tjitske Kleefstra
BACKGROUND: GATA zinc finger domain containing 2B (GATAD2B) encodes a subunit of the MeCP1-Mi-2/nucleosome remodelling and deacetylase complex involved in chromatin modification and regulation of transcription. We recently identified two de novo loss-of-function mutations in GATAD2B by whole exome sequencing in two unrelated individuals with severe intellectual disability. METHODS: To identify additional individuals with GATAD2B aberrations, we searched for microdeletions overlapping with GATAD2B in inhouse and international databases, and performed targeted Sanger sequencing of the GATAD2B locus in a selected cohort of 80 individuals based on an overlap with the clinical features in the two index cases...
August 2013: Journal of Medical Genetics
Laura K Schenk, Steven J Bolger, Kelli Luginbuhl, Patricia A Gonzales, Markus M Rinschen, Ming-Jiun Yu, Jason D Hoffert, Trairak Pisitkun, Mark A Knepper
Vasopressin controls transport in the renal collecting duct, in part, by regulating transcription. This complex process, which can involve translocation and/or modification of transcriptional regulators, is not completely understood. Here, we applied a method for large-scale profiling of nuclear proteins to quantify vasopressin-induced changes in the nuclear proteome of cortical collecting duct (mpkCCD) cells. Using stable isotope labeling and tandem mass spectrometry, we quantified 3987 nuclear proteins and identified significant changes in the abundance of 65, including previously established targets of vasopressin signaling in the collecting duct...
June 2012: Journal of the American Society of Nephrology: JASN
Jeong-Dan Cha, Hyung Jun Kim, In-Ho Cha
BACKGROUND: Oral squamous cell carcinoma (OSCC), the most common malignancy of the oral cavity, has been shown to occur via a multistep process driven by the accumulation of carcinogen-induced genetic changes. STUDY DESIGN: Array-based comparative genomic hybridization (aCGH) and multiplex ligation-dependent probe amplification (MLPA) were conducted to screen human genomewide alterations on fresh tissues of the cancer area, the dysplastic transitional area, and the resection margin (normal) free of tumor; these samples were obtained from 7 OSCC patients...
May 2011: Oral Surgery, Oral Medicine, Oral Pathology, Oral Radiology, and Endodontics
Shoji Ichikawa, Daniel L Koller, Leah R Curry, Dongbing Lai, Xiaoling Xuei, Elizabeth W Pugh, Ya-Yu Tsai, Kimberly F Doheny, Howard J Edenberg, Siu L Hui, Tatiana Foroud, Munro Peacock, Michael J Econs
Osteoporosis is a complex disease with both genetic and environmental risk factors. A major determinant of osteoporotic fractures is peak BMD obtained during young adulthood. We previously reported linkage of chromosome 1q (LOD = 4.3) with variation in spinal areal BMD in healthy premenopausal white women. In this study, we used a two-stage genotyping approach to identify genes in the linked region that contributed to the variation of femoral neck and lumbar spine areal BMD. In the first stage, 654 SNPs across the linked region were genotyped in a sample of 1309 premenopausal white women...
October 2008: Journal of Bone and Mineral Research: the Official Journal of the American Society for Bone and Mineral Research
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