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https://www.readbyqxmd.com/read/29346770/integrative-analyses-of-de-novo-mutations-provide-deeper-biological-insights-into-autism-spectrum-disorder
#1
Atsushi Takata, Noriko Miyake, Yoshinori Tsurusaki, Ryoko Fukai, Satoko Miyatake, Eriko Koshimizu, Itaru Kushima, Takashi Okada, Mako Morikawa, Yota Uno, Kanako Ishizuka, Kazuhiko Nakamura, Masatsugu Tsujii, Takeo Yoshikawa, Tomoko Toyota, Nobuhiko Okamoto, Yoko Hiraki, Ryota Hashimoto, Yuka Yasuda, Shinji Saitoh, Kei Ohashi, Yasunari Sakai, Shouichi Ohga, Toshiro Hara, Mitsuhiro Kato, Kazuyuki Nakamura, Aiko Ito, Chizuru Seiwa, Emi Shirahata, Hitoshi Osaka, Ayumi Matsumoto, Saoko Takeshita, Jun Tohyama, Tomoko Saikusa, Toyojiro Matsuishi, Takumi Nakamura, Takashi Tsuboi, Tadafumi Kato, Toshifumi Suzuki, Hirotomo Saitsu, Mitsuko Nakashima, Takeshi Mizuguchi, Fumiaki Tanaka, Norio Mori, Norio Ozaki, Naomichi Matsumoto
Recent studies have established important roles of de novo mutations (DNMs) in autism spectrum disorders (ASDs). Here, we analyze DNMs in 262 ASD probands of Japanese origin and confirm the "de novo paradigm" of ASDs across ethnicities. Based on this consistency, we combine the lists of damaging DNMs in our and published ASD cohorts (total number of trios, 4,244) and perform integrative bioinformatics analyses. Besides replicating the findings of previous studies, our analyses highlight ATP-binding genes and fetal cerebellar/striatal circuits...
January 16, 2018: Cell Reports
https://www.readbyqxmd.com/read/29346705/effect-of-dys-1-mutation-on-gene-expression-profile-in-space-flown-c-elegans
#2
Dan Xu, Ying Gao, Lin Guo, Chenggang Lin, Yeqing Sun
INTRODUCTION: Dystrophin-like dys-1 gene expression increases in the body-wall muscles of Caenorhabditis elegans (C. elegans) after spaceflight. Here, we utilized a dys-1(cx18) mutant to analyze the molecular adaptive responses of C. elegans to spaceflight. METHODS: DNA microarrays were performed to identify differentially expressed genes between wild-type and dys-1 mutant worms after spaceflight. We performed Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses, predicted human diseases and screened out key genes for human muscle diseases with NextBio...
January 18, 2018: Muscle & Nerve
https://www.readbyqxmd.com/read/29346646/the-evolutionary-history-of-nebraska-deer-mice-local-adaptation-in-the-face-of-strong-gene-flow
#3
Susanne P Pfeifer, Stefan Laurent, Vitor C Sousa, Catherine R Linnen, Matthieu Foll, Laurent Excoffier, Hopi E Hoekstra, Jeffrey D Jensen
The interplay of gene flow, genetic drift, and local selective pressure is a dynamic process that has been well studied from a theoretical perspective over the last century. Wright and Haldane laid the foundation for expectations under an island-continent model, demonstrating that an island-specific beneficial allele may be maintained locally if the selection coefficient is larger than the rate of migration of the ancestral allele from the continent. Subsequent extensions of this model have provided considerably more insight...
January 15, 2018: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29346610/novel-mutations-in-the-lipase-h-gene-lead-to-secretion-defects-of-liph-in-chinese-patients-with-autosomal-recessive-woolly-hair-hypotrichosis-arwh-ht
#4
Xiao-Dan Chang, Ya-Juan Gu, Shan Dai, Xue-Rong Chen, Chun-Lei Zhang, Hong-Shan Zhao, Qing-Hua Song
Autosomal recessive woolly hair/hypotrichosis (ARWH/HT: OMIM #278150/604379) is a rare hereditary hair disease characterized by tightly curled hair at birth which can lead to sparse hair later in life. The mutations in both LIPH and LPAR6/P2RY5 are responsible for autosomal recessive woolly hair with or without hypotrichosis (ARWH/HT). To conduct clinical and genetic investigations in four patients from three unrelated Chinese Han families with ARWH/HT, we performed mutation screening of LIPH and LPAR6/P2RY5 gene and identified four mutations in LIPH: c...
January 13, 2018: Mutagenesis
https://www.readbyqxmd.com/read/29346604/unique-genetic-profiles-from-cerebrospinal-fluid-cell-free-dna-in-leptomeningeal-metastases-of-egfr-mutant-non-small-cell-lung-cancer-a-new-medium-of-liquid-biopsy
#5
Y S Li, B Y Jiang, J J Yang, X C Zhang, Z Zhang, J Y Ye, W Z Zhong, H Y Tu, H J Chen, Z Wang, C R Xu, B C Wang, H J Du, S Chuai, H Han-Zhang, J Su, Q Zhou, X N Yang, W B Guo, H H Yan, Y H Liu, L X Yan, B Huang, M M Zheng, Y L Wu
Background: Leptomeningeal metastases (LM) are more frequent in non-small cell lung cancer (NSCLC) with epidermal growth factor receptor (EGFR) mutations. Due to limited access to leptomeningeal lesions, the purpose of this study was to explore the potential role of cerebrospinal fluid (CSF) as a source of liquid biopsy in patients with LM. Patients and methods: Primary tumor, CSF, and plasma in NSCLC with LM were tested by next-generation sequencing. In total, 45 patients with suspected LM underwent lumbar puncture, and those with EGFR mutations diagnosed with LM were enrolled...
January 15, 2018: Annals of Oncology: Official Journal of the European Society for Medical Oncology
https://www.readbyqxmd.com/read/29346549/transcriptome-and-functional-analysis-in-a-drosophila-model-of-ngly1-deficiency-provides-insight-into-therapeutic-approaches
#6
Katie G Owings, Joshua B Lowry, Yiling Bi, Matthew Might, Clement Y Chow
Autosomal recessive loss-of-function mutations in N-Glycanase 1 (NGLY1) cause NGLY1 deficiency, the only known human disease of deglycosylation. Patients present with developmental delay, movement disorder, seizures, liver dysfunction, and alacrima. NGLY1 is a conserved cytoplasmic component of the Endoplasmic Reticulum Associated Degradation (ERAD) pathway. ERAD clears misfolded proteins from the ER lumen. However, it is unclear how loss of NGLY1 function impacts ERAD and other cellular processes and results in the constellation of problems associated with NGLY1 deficiency...
January 15, 2018: Human Molecular Genetics
https://www.readbyqxmd.com/read/29346513/pancancer-analysis-identifies-prognostic-high-apobec1-expression-level-implicated-in-cancer-in-frame-insertions-and-deletions
#7
Ahmadreza Niavarani, Asieh Shahrabi Farahani, Maryam Sharafkhah, Minoo Rassoulzadegan
Genome insertions and deletions (indels) show tremendous functional impacts despite they are much less common than single nucleotide variants, which are at the center of studies assessing cancer mutational signatures. We studied 8,891 tumor samples of 32 types from The Cancer Genome Atlas in order to explore those genes which are potentially implicated in cancer indels. Survival analysis identified in-frame indels as the most important variants predicting adverse outcome. Transcriptome-wide association study identified 16 genes overexpressed in both tumor samples and tumor types with high number of in-frame indels, of whom four (APOBEC1, BCL2L15, FOXL1, and PDX1) were identified with gene products distributed within the nucleus...
January 13, 2018: Carcinogenesis
https://www.readbyqxmd.com/read/29346447/pik3ca-is-required-for-mouse-uterine-gland-development-and-pregnancy
#8
Hye Jin Chang, Hee Sung Shin, Tae Hoon Kim, Jung-Yoon Yoo, Hanna E Teasley, Jean J Zhao, Un-Hwan Ha, Jae-Wook Jeong
The PI3K/AKT signaling pathway plays a critical role in the maintenance of equilibrium between cell survival and apoptosis. The Pik3ca gene is mutated in a range of human cancers. It has been found to be oncogenic, and mutations lead to constitutive activation of the PI3K/AKT pathway. The expression patterns of PIK3CA proteins in the uterus of mice during early pregnancy indicate that it may play a role in the regulation of glandular epithelial cells, which is required to support uterine receptivity. To further investigate the role of Pik3ca in uterine function, Pik3ca was conditionally ablated only in the PGR-positive cells (Pgrcre/+Pik3caf/f; Pik3cad/d)...
2018: PloS One
https://www.readbyqxmd.com/read/29346445/transcriptome-analysis-of-skin-fibroblasts-with-dominant-negative-col3a1-mutations-provides-molecular-insights-into-the-etiopathology-of-vascular-ehlers-danlos-syndrome
#9
Nicola Chiarelli, Giulia Carini, Nicoletta Zoppi, Marco Ritelli, Marina Colombi
Vascular Ehlers-Danlos syndrome (vEDS) is a dominantly inherited connective tissue disorder caused by mutations in the COL3A1 gene that encodes type III collagen (COLLIII), which is the major expressed collagen in blood vessels and hollow organs. The majority of disease-causing variants in COL3A1 are glycine substitutions and in-frame splice mutations in the triple helix domain that through a dominant negative effect are associated with the severe clinical spectrum potentially lethal of vEDS, characterized by fragility of soft connective tissues with arterial and organ ruptures...
2018: PloS One
https://www.readbyqxmd.com/read/29346421/the-absence-of-specific-yeast-heat-shock-proteins-leads-to-abnormal-aggregation-and-compromised-autophagic-clearance-of-mutant-huntingtin-proteins
#10
Ryan Higgins, Marie-Helene Kabbaj, Alexa Hatcher, Yanchang Wang
The functionality of a protein depends on its correct folding, but newly synthesized proteins are susceptible to aberrant folding and aggregation. Heat shock proteins (HSPs) function as molecular chaperones that aid in protein folding and the degradation of misfolded proteins. Trinucleotide (CAG) repeat expansion in the Huntingtin gene (HTT) results in the expression of misfolded Huntingtin protein (Htt), which contributes to the development of Huntington's disease. We previously found that the degradation of mutated Htt with polyQ expansion (Htt103QP) depends on both ubiquitin proteasome system and autophagy...
2018: PloS One
https://www.readbyqxmd.com/read/29346415/acute-multi-sgrna-knockdown-of-keops-complex-genes-reproduces-the-microcephaly-phenotype-of-the-stable-knockout-zebrafish-model
#11
Tilman Jobst-Schwan, Johanna Magdalena Schmidt, Ronen Schneider, Charlotte A Hoogstraten, Jeremy F P Ullmann, David Schapiro, Amar J Majmundar, Amy Kolb, Kaitlyn Eddy, Shirlee Shril, Daniela A Braun, Annapurna Poduri, Friedhelm Hildebrandt
Until recently, morpholino oligonucleotides have been widely employed in zebrafish as an acute and efficient loss-of-function assay. However, off-target effects and reproducibility issues when compared to stable knockout lines have compromised their further use. Here we employed an acute CRISPR/Cas approach using multiple single guide RNAs targeting simultaneously different positions in two exemplar genes (osgep or tprkb) to increase the likelihood of generating mutations on both alleles in the injected F0 generation and to achieve a similar effect as morpholinos but with the reproducibility of stable lines...
2018: PloS One
https://www.readbyqxmd.com/read/29346382/6-ohda-induced-dopaminergic-neurodegeneration-in-caenorhabditis-elegans-is-promoted-by-the-engulfment-pathway-and-inhibited-by-the-transthyretin-related-protein-ttr-33
#12
Sarah-Lena Offenburger, Xue Yan Ho, Theresa Tachie-Menson, Sean Coakley, Massimo A Hilliard, Anton Gartner
Oxidative stress is linked to many pathological conditions including the loss of dopaminergic neurons in Parkinson's disease. The vast majority of disease cases appear to be caused by a combination of genetic mutations and environmental factors. We screened for genes protecting Caenorhabditis elegans dopaminergic neurons from oxidative stress induced by the neurotoxin 6-hydroxydopamine (6-OHDA) and identified the transthyretin-related gene ttr-33. The only described C. elegans transthyretin-related protein to date, TTR-52, has been shown to mediate corpse engulfment as well as axon repair...
January 2018: PLoS Genetics
https://www.readbyqxmd.com/read/29346364/mutations-in-caenorhabditis-elegans-neuroligin-like-glit-1-the-apoptosis-pathway-and-the-calcium-chaperone-crt-1-increase-dopaminergic-neurodegeneration-after-6-ohda-treatment
#13
Sarah-Lena Offenburger, Elisabeth Jongsma, Anton Gartner
The loss of dopaminergic neurons is a hallmark of Parkinson's disease, the aetiology of which is associated with increased levels of oxidative stress. We used C. elegans to screen for genes that protect dopaminergic neurons against oxidative stress and isolated glit-1 (gliotactin (Drosophila neuroligin-like) homologue). Loss of the C. elegans neuroligin-like glit-1 causes increased dopaminergic neurodegeneration after treatment with 6-hydroxydopamine (6-OHDA), an oxidative-stress inducing drug that is specifically taken up into dopaminergic neurons...
January 2018: PLoS Genetics
https://www.readbyqxmd.com/read/29346284/double-heterozygosity-for-brca1-pathogenic-variant-and-brca2-polymorphic-stop-codon-k3326x-a-case-report-in-a-southern-italian-family
#14
Raffaele Palmirotta, Domenica Lovero, Luigia Stefania Stucci, Erica Silvestris, Davide Quaresmini, Angela Cardascia, Franco Silvestris
Here, we describe a patient with bilateral breast cancer and melanoma, and with a concomitant double variant, namely p.Gln563Ter in BRCA1 and p.Lys3326Ter in BRCA2. The BRCA2 p.Lys3326Ter (K3326X) (rs11571833) mutation identified in our patient is a debated substitution of thymidine for adenine which is currently regarded as benign polymorphism in main gene databases. Recent studies, however, describe this variant as associated with breast and ovarian tumors. Based on the observation of the cancer's earliest age of onset in this subject, our purpose was to reevaluate this variant according to recent papers indicating a role of powerful modifier of the genetic penetrance...
January 18, 2018: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29346025/linkage-of-metabolic-defects-to-activated-pik3ca-alleles-in-endothelial-cells-derived-from-lymphatic-malformation
#15
Kathryn Glaser, Peter Dickie, Derek Neilson, Alexander Osborn, Belinda Hsi Dickie
BACKGROUND: Lymphatic endothelial cells (LECs) derived from lymphatic malformations (LMs) bear activated PIK3CA alleles yet display an inflammatory gene expression profile. A basis for the inflammatory phenotype was sought by screening for coexisting somatic mutations. METHODS AND RESULTS: Fourteen independent LEC populations bearing activated PIK3CA alleles were isolated from LM. These were characterized by the expression of growth and inflammatory genes (VEGFC, IL-6, COX-2, IL-8, HO-1, E-SEL) by qRT-PCR...
January 18, 2018: Lymphatic Research and Biology
https://www.readbyqxmd.com/read/29345973/r-spondin-2-is-upregulated-in-idiopathic-pulmonary-fibrosis-and-affects-fibroblasts-behavior
#16
Adrián Munguía-Reyes, Yalbi I Balderas-Martínez, Carina Becerril, Marco Checa, Remedios Ramírez, Blanca Ortíz-Quintero, Jorge Meléndez-Zajgla, Annie Pardo, Moisés Selman
Idiopathic pulmonary fibrosis (IPF) is characterized by the expansion of the myofibroblasts population, excessive extracellular matrix accumulation, and destruction of the lung parenchyma. The R-spondins family (RSPO) comprises a group of proteins essential for development. From them, RSPO2 is expressed primarily in the lungs and its mutations cause severe defects in the respiratory tract. Interestingly, RSPO2 participates in the canonical WNT pathway, a critical route in the pathogenesis of IPF. Thus, the aim of this study was to examine the expression and putative role of RSPO2 in this disease...
January 18, 2018: American Journal of Respiratory Cell and Molecular Biology
https://www.readbyqxmd.com/read/29345728/analytical-performance-of-the-thyroseq-v3-genomic-classifier-for-cancer-diagnosis-in-thyroid-nodules
#17
Marina N Nikiforova, Stephanie Mercurio, Abigail I Wald, Michelle Barbi de Moura, Keith Callenberg, Lucas Santana-Santos, William E Gooding, Linwah Yip, Robert L Ferris, Yuri E Nikiforov
BACKGROUND: Molecular tests have clinical utility for thyroid nodules with indeterminate fine-needle aspiration (FNA) cytology, although their performance requires further improvement. This study evaluated the analytical performance of the newly created ThyroSeq v3 test. METHODS: ThyroSeq v3 is a DNA- and RNA-based next-generation sequencing assay that analyzes 112 genes for a variety of genetic alterations, including point mutations, insertions/deletions, gene fusions, copy number alterations, and abnormal gene expression, and it uses a genomic classifier (GC) to separate malignant lesions from benign lesions...
January 18, 2018: Cancer
https://www.readbyqxmd.com/read/29345621/the-circulating-t-helper-subsets-and-regulatory-t-cells-in-patients-with-common-variable-immunodeficiency-with-no-known-monogenic-disease
#18
G Azizi, A Mirshafiey, H Abolhassani, R Yazdani, F J Ansariha, M Shaghaghi, S S Mortazavi-Jahromi, F Noorbakhsh, N Rezaei, A Aghamohammadi
BACKGROUND: Common variable immunodeficiency (CVID) is the most common symptomatic primary immunodeficiency (PID), characterized by heterogeneous clinical manifestations and defects in B- and T- cells. In the present study, we investigated the T helper (Th) cell subsets and regulatory T (Treg) cells, and their related cytokines and transcription factors in the CVID patients with no definite genetic diagnosis. METHODS: The study population comprised 13 CVID patients and 13 healthy controls (HC)...
January 18, 2018: Journal of Investigational Allergology & Clinical Immunology
https://www.readbyqxmd.com/read/29345446/the-first-south-american-case-of-pre-implantation-genetic-diagnosis-to-select-compatible-embryo-for-cord-blood-transplantation-as-treatment-for-sickle-cell-anemia
#19
Ciro D Martinhago, Kalina Rn Endo, Mariana A Oliveira, Alex Mm Dias, Gislaine S Pereira, Augusto M Azzolini, Paula Rq Estrada, Caio G Bruzaca, Ana Carolina N Martinhago
Sickle cell anemia is an inherited systemic hemoglobinopathy that affects hemoglobin production in red blood cells, leading to early morbidity and mortality. It is caused by a homozygous nucleotide substitution (c.20A>T) in the β-globin gene (HBB) that changes a glutamic acid to a valine in the protein. We present a case report of a fertile couple, both carriers of the sickle cell anemia mutation, with one affected daughter. Six cycles of assisted reproductive techniques were performed, resulting in 53 embryos in cleavage stage...
January 18, 2018: JBRA Assisted Reproduction
https://www.readbyqxmd.com/read/29345357/the-prognostic-value-of-pi3k-mutational-status-in-breast-cancer-a-meta-analysis
#20
N Sobhani, G Roviello, S P Corona, M Scaltriti, A Ianza, M Bortul, F Zanconati, D Generali
Breast cancer (BC) is the second most common cause of cancer-related deaths in women worldwide. The availability of reliable biomarkers of response/resistance to cancer treatments would benefit patients and clinicians allowing for a better selection of BC patients most likely to respond to a specific treatment. Phosphatidylinositol 3-kinase (PI3K) enzymes are involved in numerous cellular- functions and processes. The gene encoding for PI3K catalytic subunit p110α is mutated in 20-40% of BC. We performed a meta-analysis of the current literature on randomized clinical trials, investigating the role of PIK3CA mutational status as prognostic factor and predictor of response to anti-cancer treatments...
January 18, 2018: Journal of Cellular Biochemistry
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