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Skin genomics

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https://www.readbyqxmd.com/read/28332498/a-genome-wide-screen-identifies-yap-wbp2-interplay-conferring-growth-advantage-on-human-epidermal-stem-cells
#1
Gernot Walko, Samuel Woodhouse, Angela Oliveira Pisco, Emanuel Rognoni, Kifayathullah Liakath-Ali, Beate M Lichtenberger, Ajay Mishra, Stephanie B Telerman, Priyalakshmi Viswanathan, Meike Logtenberg, Lisa M Renz, Giacomo Donati, Sven R Quist, Fiona M Watt
Individual human epidermal cells differ in their self-renewal ability. To uncover the molecular basis for this heterogeneity, we performed genome-wide pooled RNA interference screens and identified genes conferring a clonal growth advantage on normal and neoplastic (cutaneous squamous cell carcinoma, cSCC) human epidermal cells. The Hippo effector YAP was amongst the top positive growth regulators in both screens. By integrating the Hippo network interactome with our data sets, we identify WW-binding protein 2 (WBP2) as an important co-factor of YAP that enhances YAP/TEAD-mediated gene transcription...
March 23, 2017: Nature Communications
https://www.readbyqxmd.com/read/28330499/a-novel-multi-network-approach-reveals-tissue-specific-cellular-modulators-of-fibrosis-in-systemic-sclerosis
#2
Jaclyn N Taroni, Casey S Greene, Viktor Martyanov, Tammara A Wood, Romy B Christmann, Harrison W Farber, Robert A Lafyatis, Christopher P Denton, Monique E Hinchcliff, Patricia A Pioli, J Matthew Mahoney, Michael L Whitfield
BACKGROUND: Systemic sclerosis (SSc) is a multi-organ autoimmune disease characterized by skin fibrosis. Internal organ involvement is heterogeneous. It is unknown whether disease mechanisms are common across all involved affected tissues or if each manifestation has a distinct underlying pathology. METHODS: We used consensus clustering to compare gene expression profiles of biopsies from four SSc-affected tissues (skin, lung, esophagus, and peripheral blood) from patients with SSc, and the related conditions pulmonary fibrosis (PF) and pulmonary arterial hypertension, and derived a consensus disease-associate signature across all tissues...
March 23, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28329662/the-preneoplastic-genome-transcriptomic-drivers-of-squamous-cell-carcinoma-development
#3
Kenneth Y Tsai
Cutaneous squamous cell carcinoma (cuSCC) comprises 15-20% of all skin cancers, accounting for over 700,000 cases in the U.S. annually. Most cuSCC arise in association with a distinct precancerous lesion, the actinic keratosis (AK). In order to identify potential targets for molecularly targeted chemoprevention, we performed integrated cross-species genomic analysis of cuSCC development through the preneoplastic AK stage using matched human samples and a solar UV- driven Hairless mouse model. We performed RNA-seq and microRNA-seq on samples from both patients undergoing Mohs surgery and the mouse model...
September 15, 2016: Dermatology Online Journal
https://www.readbyqxmd.com/read/28327943/whole-genome-sequencing-of-chinese-clearhead-icefish-protosalanx-hyalocranius
#4
Kai Liu, Dongpo Xu, Jia Li, Chao Bian, Jinrong Duan, Yanfeng Zhou, Minying Zhang, Xinxin You, Yang You, Jieming Chen, Hui Yu, Gangchun Xu, Di-An Fang, Jun Qiang, Shulun Jiang, Jie He, Junmin Xu, Qiong Shi, Zhiyong Zhang, Pao Xu
Background: Chinese clearhead icefish, Protosalanx hyalocranius , is a representative icefish species with economic importance and special appearance. Due to its great economic values in China, the fish was introduced into Lake Dianchi and several other lakes from the Lake Taihu half a century ago. Similar to the Sinocyclocheilus cavefish, the clearhead icefish has certain cavefish-like traits, such as transparent body and nearly scaleless skin. Here, we provide the whole genome sequence of this surface-dwelling fish and generated a draft genome assembly, aiming at exploring molecular mechanisms for the biological interests...
February 24, 2017: GigaScience
https://www.readbyqxmd.com/read/28327087/nt5c2-novel-splicing-variant-expands-the-phenotypic-spectrum-of-spastic-paraplegia-spg45-case-report-of-a-new-member-of-thin-corpus-callosum-spg-subgroup
#5
Mahmoud F Elsaid, Khalid Ibrahim, Nader Chalhoub, Ahmed Elsotouhy, Noora El Mudehki, Alice Abdel Aleem
BACKGROUND: Hereditary Spastic Paraplegia (HSP) is a genetically heterogeneous group of neurodegenerative diseases. Thin Corpus Callosum (TCC) associated HSP is a distinguished subgroup of complex forms. Purines and pyrimidine, the basic DNA and RNA components, are regulating the cell metabolism, having roles in signal transduction, energy preservation and cellular repair. Genetic defects in nucleotide metabolism related genes have been only recently implicated in brain and neurodegenerative diseases' pathogenesis...
March 21, 2017: BMC Medical Genetics
https://www.readbyqxmd.com/read/28319090/a-single-copy-sleeping-beauty-transposon-mutagenesis-screen-identifies-new-pten-cooperating-tumor-suppressor-genes
#6
Jorge de la Rosa, Julia Weber, Mathias Josef Friedrich, Yilong Li, Lena Rad, Hannes Ponstingl, Qi Liang, Sandra Bernaldo de Quirós, Imran Noorani, Emmanouil Metzakopian, Alexander Strong, Meng Amy Li, Aurora Astudillo, María Teresa Fernández-García, María Soledad Fernández-García, Gary J Hoffman, Rocío Fuente, George S Vassiliou, Roland Rad, Carlos López-Otín, Allan Bradley, Juan Cadiñanos
The overwhelming number of genetic alterations identified through cancer genome sequencing requires complementary approaches to interpret their significance and interactions. Here we developed a novel whole-body insertional mutagenesis screen in mice, which was designed for the discovery of Pten-cooperating tumor suppressors. Toward this aim, we coupled mobilization of a single-copy inactivating Sleeping Beauty transposon to Pten disruption within the same genome. The analysis of 278 transposition-induced prostate, breast and skin tumors detected tissue-specific and shared data sets of known and candidate genes involved in cancer...
March 20, 2017: Nature Genetics
https://www.readbyqxmd.com/read/28315306/molecular-characterization-of-camelpox-virus-isolates-from-bikaner-india-evidence-of-its-endemicity
#7
Shyam Singh Dahiya, Sachin Kumar, Sharat Chandra Mehta, Raghvendar Singh, Kashi Nath, Shirish D Narnaware, Fateh Chand Tuteja
Camelpox is an important viral disease of camels, which may produce mild skin lesions or severe systemic infections. Camelpox virus (CMLV) isolates retrieved from an incidence of camelpox in camels at Bikaner, India were characterized on the basis of genotype and pathotype. Histopathological examination of the CMLV scab revealed intracytoplasmic-eosinophilic inclusion bodies. The phylogenetic analysis of all eight CMLV isolates for C18L gene nucleotide sequence revealed its clustering with its strains M-96 from Kazakhstan and CMS from Iran...
March 14, 2017: Acta Tropica
https://www.readbyqxmd.com/read/28314921/comparative-genomics-analysis-of-five-psychrobacter-strains-isolated-from-world-wide-habitats-reveal-high-intra-genus-variations
#8
Shan Zhang, Weizhi Song, Min Yu, Xuezheng Lin
Psychrobacter has been regarded as an important genus for bacterial cold adaptation studies. However, members of this genus are highly varied in terms of both cold adaptability and genome content. To get an understanding of the diversity of members of this genus, five Psychrobacter strains (G, K5, 273-4, PAMC21119 and PRwf-1), with publicly available complete/draft genome, were selected and comprehensive comparative genomics analyses were performed among them. The closest phylogenetic relationship, highest average nucleotide identity (96...
March 17, 2017: Extremophiles: Life Under Extreme Conditions
https://www.readbyqxmd.com/read/28314753/transethnic-meta-analysis-identifies-gsdma-and-prdm1-as-susceptibility-genes-to-systemic-sclerosis
#9
Chikashi Terao, Takahisa Kawaguchi, Philippe Dieude, John Varga, Masataka Kuwana, Marie Hudson, Yasushi Kawaguchi, Marco Matucci-Cerinic, Koichiro Ohmura, Gabriela Riemekasten, Aya Kawasaki, Paolo Airo, Tetsuya Horita, Akira Oka, Eric Hachulla, Hajime Yoshifuji, Paola Caramaschi, Nicolas Hunzelmann, Murray Baron, Tatsuya Atsumi, Paul Hassoun, Takeshi Torii, Meiko Takahashi, Yasuharu Tabara, Masakazu Shimizu, Akiko Tochimoto, Naho Ayuzawa, Hidetoshi Yanagida, Hiroshi Furukawa, Shigeto Tohma, Minoru Hasegawa, Manabu Fujimoto, Osamu Ishikawa, Toshiyuki Yamamoto, Daisuke Goto, Yoshihide Asano, Masatoshi Jinnin, Hirahito Endo, Hiroki Takahashi, Kazuhiko Takehara, Shinichi Sato, Hironobu Ihn, Soumya Raychaudhuri, Katherine Liao, Peter Gregersen, Naoyuki Tsuchiya, Valeria Riccieri, Inga Melchers, Gabriele Valentini, Anne Cauvet, Maria Martinez, Tsuneyo Mimori, Fumihiko Matsuda, Yannick Allanore
OBJECTIVES: Systemic sclerosis (SSc) is an autoimmune disease characterised by skin and systemic fibrosis culminating in organ damage. Previous genetic studies including genome-wide association studies (GWAS) have identified 12 susceptibility loci satisfying genome-wide significance. Transethnic meta-analyses have successfully expanded the list of susceptibility genes and deepened biological insights for other autoimmune diseases. METHODS: We performed transethnic meta-analysis of GWAS in the Japanese and European populations, followed by a two-staged replication study comprising a total of 4436 cases and 14 751 controls...
March 17, 2017: Annals of the Rheumatic Diseases
https://www.readbyqxmd.com/read/28300201/identification-of-a-novel-locus-associated-with-skin-colour-in-african-admixed-populations
#10
Natalia Hernandez-Pacheco, Carlos Flores, Santos Alonso, Celeste Eng, Angel C Y Mak, Scott Hunstman, Donglei Hu, Marquitta J White, Sam S Oh, Kelley Meade, Harold J Farber, Pedro C Avila, Denise Serebrisky, Shannon M Thyne, Emerita Brigino-Buenaventura, William Rodriguez-Cintron, Saunak Sen, Rajesh Kumar, Michael Lenoir, Jose R Rodriguez-Santana, Esteban G Burchard, Maria Pino-Yanes
Skin pigmentation is a complex trait that varies largely among populations. Most genome-wide association studies of this trait have been performed in Europeans and Asians. We aimed to uncover genes influencing skin colour in African-admixed individuals. We performed a genome-wide association study of melanin levels in 285 Hispanic/Latino individuals from Puerto Rico, analyzing 14 million genetic variants. A total of 82 variants with p-value ≤1 × 10(-5) were followed up in 373 African Americans. Fourteen single nucleotide polymorphisms were replicated, of which nine were associated with skin colour at genome-wide significance in a meta-analysis across the two studies...
March 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28299865/novel-short-antimicrobial-peptide-isolated-from-xenopus-laevis-skin
#11
Yu Zhang, Songcai Liu, Siming Li, Yunyun Cheng, Linyan Nie, Gang Wang, Chen Lv, Wenzhen Wei, Cheng Cheng, Feng Hou, Linlin Hao
A rich source of bioactive peptides, including a large number of antimicrobial peptides, has been found in amphibian skin. In this study, a novel short antimicrobial peptide was purified from Xenopus laevis skin and characterised through reversed-phase high-performance liquid chromatography, Edman degradation and matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry. The peptide was composed of six amino acids with a sequence of DEDLDE and thus named X. laevis antibacterial peptide-P2 (XLAsp-P2)...
March 16, 2017: Journal of Peptide Science: An Official Publication of the European Peptide Society
https://www.readbyqxmd.com/read/28296509/tp53-and-atm-mrna-expression-in-skin-and-skeletal-muscle-after-low-level-laser-exposure
#12
Luciana Guedes de Almeida, Luiz Philippe da Silva Sergio, Flavia de Paoli, Andre Luiz Mencalha, Adenilson de Souza da Fonseca
Low-level lasers are widespread in regenerative medicine, but the molecular mechanisms involved in their biological effects are not fully understood, particularly those on DNA stability. Therefore, this study aimed to investigate mRNA expression of genes related to DNA genomic stability in skin and skeletal muscle tissue from Wistar rats exposed to low-level red and infrared lasers. For this, TP53 (Tumor Protein 53) and ATM (Ataxia Telangiectasia Mutated gene) mRNA expressions were evaluated by real-time quantitative PCR (RT-qPCR) technique 24 hours after low-level red and infrared laser exposure...
February 16, 2017: Journal of Cosmetic and Laser Therapy: Official Publication of the European Society for Laser Dermatology
https://www.readbyqxmd.com/read/28296353/methodological-considerations-for-detection-of-terrestrial-small-body-salamander-edna-and-implications-for-biodiversity-conservation
#13
Donald M Walker, Jacob E Leys, Kelly E Dunham, Joshua C Oliver, Emily E Schiller, Kelsey S Stephenson, John T Kimrey, Jessica Wooten, Mark W Rogers
Environmental DNA (eDNA) can be used as an assessment tool to detect populations of threatened species and provide fine-scale data required to make management decisions. The objectives of this project were to use quantitative PCR (qPCR) to: 1) detect spiked salamander DNA in soil, 2) quantify eDNA degradation over time, 3) determine detectability of salamander eDNA in a terrestrial environment using soil, feces, and skin swabs, 4) detect salamander eDNA in a mesocosm experiment. Salamander eDNA was positively detected in 100% of skin swabs and 66% of fecal samples and concentrations did not differ between the two sources...
March 15, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28289554/non-coding-rnas-new-players-in-skin-wound-healing
#14
REVIEW
Eva K Herter, Ning Xu Landén
Significance: Wound healing is a basic physiological process that is utilized to keep the integrity of the skin. Impaired wound repair, such as chronic wounds and pathological scars, presents a major health and economic burden worldwide. To date, efficient targeted treatment for these wound disorders is still lacking, which is largely due to our limited understanding of the biological mechanisms underlying these diseases. Research driven around discovering new therapies for these complications is, therefore, an urgent need...
March 1, 2017: Advances in Wound Care
https://www.readbyqxmd.com/read/28285730/new-in-vivo-model-to-analyse-the-expression-of-angiogenic-genes-in-the-borders-of-a-cleft-lip
#15
C François, M L Poli-Merol, C Tournois, P Cornillet-Lefebvre, T Guillard, Z Djerada, M Doco Fenzy, P Nguyen
Defects in the fusion of facial buds can result from an anomaly in tissue development or apoptosis, or both. Our working hypothesis was that anomalies in the development of tissues could be caused by a genetic angiogenic defect. Our main objective was to design a reproducible experimental model to study the expression of angiogenic genes in the borders of cleft lips with or without cleft palate. We therefore prospectively studied seven non-syndromic patients, three with a cleft lip (2 right, 1 left), and four with a cleft lip and palate (1 bilateral, 2 right, 1 left), with no CGH (comparative genomic hybridisation) array, who had primary operations to repair their clefts...
March 9, 2017: British Journal of Oral & Maxillofacial Surgery
https://www.readbyqxmd.com/read/28284627/lumpy-skin-disease-outbreaks-in-greece-during-2015-16-implementation-of-emergency-immunization-and-genetic-differentiation-between-field-isolates-and-vaccine-virus-strains
#16
Eirini I Agianniotaki, Konstantia E Tasioudi, Serafeim C Chaintoutis, Peristera Iliadou, Olga Mangana-Vougiouka, Aikaterini Kirtzalidou, Thomas Alexandropoulos, Achilleas Sachpatzidis, Evangelia Plevraki, Chrysostomos I Dovas, Eleni Chondrokouki
The objective of this study is to present epizootiological data from the lumpy skin disease (LSD) outbreaks in Greece during 2015-16, following the implementation of emergency vaccination and total stamping-out, along with laboratory data regarding the genetic differentiation between field isolates and live attenuated vaccine virus strains. Descriptive geographical chronology analysis was conducted to present the progressive shift of the outbreaks westwards, and at the same time, the absence of further outbreaks in previously affected regional units where high vaccination coverage was achieved...
March 2017: Veterinary Microbiology
https://www.readbyqxmd.com/read/28284619/identification-of-a-novel-species-of-papillomavirus-in-giraffe-lesions-using-nanopore-sequencing
#17
Bert Vanmechelen, Mads Frost Bertelsen, Annabel Rector, Joost J Van den Oord, Lies Laenen, Valentijn Vergote, Piet Maes
Papillomaviridae form a large family of viruses that are known to infect a variety of vertebrates, including mammals, reptiles, birds and fish. Infections usually give rise to minor skin lesions but can in some cases lead to the development of malignant neoplasia. In this study, we identified a novel species of papillomavirus (PV), isolated from warts of four giraffes (Giraffa camelopardalis). The sequence of the L1 gene was determined and found to be identical for all isolates. Using nanopore sequencing, the full sequence of the PV genome could be determined...
March 2017: Veterinary Microbiology
https://www.readbyqxmd.com/read/28282565/genome-wide-identification-and-characterization-of-conserved-and-novel-micrornas-in-grass-carp-ctenopharyngodon-idella-by-deep-sequencing
#18
Wangbao Gong, Yong Huang, Jun Xie, Guangjun Wang, Deguang Yu, Xihong Sun
MicroRNAs (miRNAs) are post-transcriptional regulators which bind to target to regulate protein expression by repressing translation or promoting degradation of the target mRNA. Studies have shown that deep sequencing is a powerful tool for the identification of miRNAs, and it is believed that may more miRNAs remain to be discovered in grass carp. In the present study, a pool of equal amounts of RNA obtained from 8 different adult grass carp tissues (spleen, liver, muscle, kidney, skin, testis, gut and heart) was sequenced using deep sequencing technology...
March 2, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28281550/reduced-h3k27me3-expression-in-merkel-cell-polyoma-virus-positive-tumors
#19
Klaus J Busam, Melissa P Pulitzer, Daniel C Coit, Maria Arcila, Danielle Leng, Achim A Jungbluth, Thomas Wiesner
Merkel cell carcinoma is a primary cutaneous neuroendocrine carcinoma, which once metastatic is difficult to treat. Recent mutation analyses of Merkel cell carcinoma revealed a low number of mutations in Merkel cell polyomavirus-associated tumors, and a high number of mutations in virus-negative combined squamous cell and neuroendocrine carcinomas of chronically sun-damaged skin. We speculated that the paucity of mutations in virus-positive Merkel cell carcinoma may reflect a pathomechanism that depends on derangements of chromatin without alterations in the DNA sequence (epigenetic dysregulation)...
March 10, 2017: Modern Pathology: An Official Journal of the United States and Canadian Academy of Pathology, Inc
https://www.readbyqxmd.com/read/28280007/complete-genome-sequence-of-a-staphylococcus-epidermidis-strain-with-exceptional-antimicrobial-activity
#20
Simon B Lassen, Hans B Lomholt, Holger Brüggemann
Staphylococcus epidermidis is a Gram-positive bacterium that is prevalent on human skin. The species is associated with skin health, as well as with opportunistic infections. Here, we report the complete genome sequence of S. epidermidis 14.1.R1, isolated from human skin. In bacterial interference assays, the strain showed exceptional antimicrobial activity.
March 9, 2017: Genome Announcements
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