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Skin genomics

Juntao Hu, Felipe Pérez-Jvostov, Léa Blondel, Rowan D H Barrett
Epigenetic modification, especially DNA methylation, can play an important role in mediating gene regulatory response to environmental stressors, and may be a key process affecting phenotypic plasticity and adaptation. Parasites are potent stressors with profound physiological and ecological effects on their hosts, yet it remains unclear how parasites influence host methylation patterns. Here, we used a well-studied host-parasite system, the guppy Poecilia reticulata and its ectoparasitic monogenean Gyrodactylus turnbulli to gain mechanistic insight into the dynamics of DNA methylation in host-parasite interactions...
June 19, 2018: Molecular Ecology
Dalong Sun, Jing Chen, Longzi Liu, Guangxi Zhao, Pingping Dong, Bingrui Wu, Jun Wang, Ling Dong
A robust and accurate gene expression signature is essential to assist oncologists to determine which subset of patients at similar Tumor-Lymph Node-Metastasis (TNM) stage has high recurrence risk and could benefit from adjuvant therapies. Here we applied a two-step supervised machine-learning method and established a 12-gene expression signature to precisely predict colon adenocarcinoma (COAD) prognosis by using COAD RNA-seq transcriptome data from The Cancer Genome Atlas (TCGA). The predictive performance of the 12-gene signature was validated with two independent gene expression microarray datasets: GSE39582 includes 566 COAD cases for the development of six molecular subtypes with distinct clinical, molecular and survival characteristics; GSE17538 is a dataset containing 232 colon cancer patients for the generation of a metastasis gene expression profile to predict recurrence and death in COAD patients...
2018: PeerJ
Lili Tang, Yuyan Cheng, Caihong Zhu, Chao Yang, Lu Liu, Yuanjing Zhang, Leilei Wen, Xuejun Zhang, Fusheng Zhou, Sen Yang
BACKGROUND: Recent studies have revealed that DNA methylation (DNAm) could modulate gene expression in psoriasis (Ps). However, the relationship between whole-genome DNAm and gene expression in Ps has not been studied yet. OBJECTIVES: To better characterize the relationship between DNAm and gene expression, and to identify biological pathways triggered by changes in methylation involved in the pathogenesis of Ps. METHODS: Differentially methylated sites (DMSs) and differentially expressed genes (DEGs) were analysed by comparing 20 involved psoriatic (PP) skin, 20 uninvolved psoriatic (PN) skin and 20 normal (NN) skin biopsies...
June 9, 2018: Journal of Dermatological Science
Valérie Haydont, Véronique Neiveyans, Hélène Zucchi, Nicolas O Fortunel, Daniel Asselineau
Deciphering the characteristics of dermal fibroblasts is critical to further understand skin ageing. We have conducted a genome-wide transcriptomic characterization of papillary (Fp) and reticular (Fr) fibroblasts extracted from human skin samples corresponding to younger and older adult ages. From this screen, biomarkers suitable for the assessment of chronological ageing were identified, and extrapolated to the context of photo-damaged skin. In particular, KANK4, ACAN, Col XI α1, and PSG1, were expressed at an increased level in both chronologically-aged and photo-damaged skin...
June 15, 2018: Mechanisms of Ageing and Development
P Zhan, K Dukik, D Li, J Sun, J B Stielow, B Gerrits van den Ende, B Brankovics, S B J Menken, H Mei, W Bao, G Lv, W Liu, G S de Hoog
Trichophyton rubrum and T. violaceum are prevalent agents of human dermatophyte infections, the former being found on glabrous skin and nail, while the latter is confined to the scalp. The two species are phenotypically different but are highly similar phylogenetically. The taxonomy of dermatophytes is currently being reconsidered on the basis of molecular phylogeny. Molecular species definitions do not always coincide with existing concepts which are guided by ecological and clinical principles. In this article, we aim to bring phylogenetic and ecological data together in an attempt to develop new species concepts for anthropophilic dermatophytes...
March 2018: Studies in Mycology
Boyang Qiu, Kait Al, Ana M Pena-Diaz, George S Athwal, Darren Drosdowech, Kenneth J Faber, Jeremy P Burton, David B O'Gorman
BACKGROUND: Advances in DNA sequencing technologies have made it possible to detect microbial genome sequences (microbiomes) within tissues once thought to be sterile. We used this approach to gain insights into the likely sources of Cutibacterium acnes (formerly Propionibacterium acnes) infections within the shoulder. METHODS: Tissue samples were collected from the skin, subcutaneous fat, anterior supraspinatus tendon, middle glenohumeral ligament, and humeral head cartilage of 23 patients (14 male and 9 female patients) during primary arthroplasty surgery...
June 13, 2018: Journal of Shoulder and Elbow Surgery
P Haines Ely
The gut is the largest lymphoid organ in the body. The human microbiome is composed of trillions of bacteria. The DNA of these bacteria dwarfs the human genome. Diet and ethanol can cause rapid shifts in the number and types of bacteria in the gut. The psoriatic microbiome is similar to that seen in alcoholics; there is a decrease in bacterial diversity and overgrowth of bacteria in the small bowel. Psoriatics often have liver disease and deficiencies in bile acids. Psoriasis is a disease characterized by a leaky gut...
May 2018: Clinics in Dermatology
Randy W Loftus, Franklin Dexter, Alysha D M Robinson
BACKGROUND: Increased awareness of the epidemiology of transmission of pathogenic bacterial strain characteristics may help to improve compliance with intraoperative infection control measures. Our aim was to characterize the epidemiology of intraoperative transmission of high-risk Staphylococcus aureus sequence types (STs). METHODS: S aureus isolates collected from 3 academic medical centers underwent whole cell genome analysis, analytical profile indexing, and biofilm absorbance...
June 12, 2018: American Journal of Infection Control
Aurelie Chauffour, Emmanuel Lecorche, Florence Reibel, Faiza Mougari, Laurent Raskine, Alexandra Aubry, Vincent Jarlier, Emmanuelle Cambau
OBJECTIVES: Antimicrobial resistance (AMR) in leprosy is mostly unknown since Mycobacterium leprae does not grow in vitro and bacteriological investigations were abandoned. However, molecular detection of resistance can be applied to multibacillary (MB) cases. METHODS: Patients living in France mainland or in French territories and diagnosed for leprosy from 2001 to 2015 were prospectively studied for AMR by detecting mutations in rpoB for rifampicin resistance, in folP1 for dapsone and in gyrA for ofloxacin...
June 12, 2018: Clinical Microbiology and Infection
Salih Kumru, Hasan C Tekedar, Matt J Griffin, Geoffrey C Waldbieser, Mark R Liles, Tad Sonstegard, Steven G Schroeder, Mark L Lawrence, Attila Karsi
Aeromonas bestiarum is a Gram-negative mesophilic motile bacterium causing acute hemorrhagic septicemia or chronic skin ulcers in fish. Here, we report the draft genome sequence of A. bestiarum strain GA97-22, which was isolated from rainbow trout in 1997. This genome sequence will improve our understanding of the complex taxonomy of motile aeromonads.
June 14, 2018: Genome Announcements
Beatriz Mengual-Chuliá, Gudrun Wibbelt, Marc Gottschling, Ignacio G Bravo
We report the complete genome sequences of Rusa timorensis papillomavirus 1 (RtimPV1) and Rusa timorensis papillomavirus 2 (RtimPV2), isolated from hair follicles of asymptomatic skin from the same Timor deer specimen. RtimPV1 and RtimPV2 are evolutionarily only distantly related. RtimPV1 lacks a canonical E2-binding site, and RtimPV2 does not carry an E6 gene.
June 14, 2018: Genome Announcements
Lucy C Fox, Costas K Yannakou, Georgina Ryland, Stephen Lade, Michael Dickinson, Belinda A Campbell, Henry Miles Prince
Primary cutaneous diffuse large B-cell lymphoma, leg type (PCDLBCL-LT) is one of the well-recognized extranodal lymphomas commonly addicted to the B-cell receptor-MYD88 superpathway. We aimed to describe the genomic changes in a patient who progressed through treatment with ibrutinib, a Bruton’s tyrosine kinase (BTK) inhibitor. An 80-year-old woman presented with multiply relapsed PCDLBCL-LT after multiple lines of chemoimmunotherapy and radiotherapy. Pre-treatment testing of the localized cutaneous tumor lesion on a lymphoid amplicon panel demonstrated an MYD88 p...
June 13, 2018: International Journal of Molecular Sciences
Hyun Joo Park, Jung-Hoon Bae, Hyeok-Jin Ko, Sun-Hee Lee, Bong Hyun Sung, Jong-In Han, Jung-Hoon Sohn
Lactic acid is a platform chemical for the sustainable production of various materials. To develop a robust yeast platform for low-pH production of D-lactic acid, an acid-tolerant yeast strain was isolated from grape skins and named Pichia kudriavzevii NG7 by ribosomal RNA sequencing. This strain was able to grow at pH 2.0 and 50°C. For the commercial application of P. kudriavzevii NG7 as a lactic acid producer, the ethanol fermentation pathway was redirected to lactic acid by replacing pyruvate decarboxylase 1 gene (PDC1) with D-lactate dehydrogenase gene (D-LDH) derived from Lactobacillus plantarum...
June 13, 2018: Biotechnology and Bioengineering
Yuqiang Lyu, Chuankui Shi, Kaihui Zhang, Min Gao, Yi Liu
OBJECTIVE: To explore the genetic cause and clinical features of a neonate with bullous congenital ichthyosiform erythroderma. METHODS: The patient was examined thoroughly. Following the extraction of genomic DNA, next generation sequencing was performed to analyze the genetic cause. RESULTS: The patient manifested generalized erythema, blistering, and extensive exfoliation of the skin. A heterozygous missence 482T>G mutation was found in the first exon of KRT10 gene, which led to a p...
June 10, 2018: Zhonghua Yi Xue Yi Chuan Xue za Zhi, Zhonghua Yixue Yichuanxue Zazhi, Chinese Journal of Medical Genetics
Chihiro Endo, Todd A Johnson, Ryoko Morino, Kazuyuki Nakazono, Shigeo Kamitsuji, Masanori Akita, Maiko Kawajiri, Tatsuya Yamasaki, Azusa Kami, Yuria Hoshi, Asami Tada, Kenichi Ishikawa, Maaya Hine, Miki Kobayashi, Nami Kurume, Yuichiro Tsunemi, Naoyuki Kamatani, Makoto Kawashima
Skin trait variation impacts quality-of-life, especially for females from the viewpoint of beauty. To investigate genetic variation related to these traits, we conducted a GWAS of various skin phenotypes in 11,311 Japanese women and identified associations for age-spots, freckles, double eyelids, straight/curly hair, eyebrow thickness, hairiness, and sweating. In silico annotation with RoadMap Epigenomics epigenetic state maps and colocalization analysis of GWAS and GTEx Project eQTL signals provided information about tissue specificity, candidate causal variants, and functional target genes...
June 12, 2018: Scientific Reports
Christiane Querfeld, Samantha Leung, Patricia L Myskowski, Shane A Curran, Debra A Goldman, Glenn Heller, Xiwei Wu, Sung Hee Kil, Sneh Sharma, Kathleen J Finn, Steven Horwitz, Alison Moskowitz, Babak Mehrara, Steven T Rosen, Allan C Halpern, James W Young
Cutaneous T-cell lymphoma (CTCL) develops from clonally expanded CD4+ T cells in a background of chronic inflammation. Although dendritic cells (DCs) stimulate T cells and are present in skin, cutaneous T cells in CTCL do not respond with effective antitumor immunity. We evaluated primary T-cell and DC émigrés from epidermal and dermal explant cultures of skin biopsies from CTCL patients (n = 37) and healthy donors (n = 5). Compared with healthy skin, CD4+ CTCL populations contained more T cells expressing PD-1, CTLA-4, and LAG-3...
June 12, 2018: Cancer Immunology Research
Hiroto Nakano, Yohei Kirino, Mitsuhiro Takeno, Kana Higashitani, Hideto Nagai, Ryusuke Yoshimi, Yukie Yamaguchi, Ikuma Kato, Ichiro Aoki, Hideaki Nakajima
BACKGROUND: Low C-C chemokine receptor 1 (CCR1) and interleukin (IL)-10 expression is associated with risk of Behçet's disease (BD). The objective of the present study was to clarify the pathological roles of CCR1 and IL10 loci identified by previous BD genome-wide association studies (GWASs). METHODS: M1 and M2 macrophages (Mφ) were differentiated with granulocyte-macrophage colony-stimulating factor or macrophage colony-stimulating factor (M-CSF) from peripheral monocytes of healthy control subjects (HC) and patients with BD...
June 12, 2018: Arthritis Research & Therapy
B Dréno, S Pécastaings, S Corvec, S Veraldi, A Khammari, C Roques
While the commensal bacterium Propionibacterium acnes (P. acnes) is involved in the maintenance of a healthy skin, it can also act as an opportunistic pathogen in acne vulgaris. The latest findings on P. acnes shed light on the critical role of a tight equilibrium between members of its phylotypes and within the skin microbiota in the development of this skin disease. Indeed, contrary to what was previously thought, proliferation of P. acnes is not the trigger of acne as patients with acne do not harbour more P...
June 2018: Journal of the European Academy of Dermatology and Venereology: JEADV
Abdelmalik I Khalafalla, Annabel Rector, Ahmed K Elfadl
Cases of wart-like lesions in humans and dromedary camels occurred in eastern Sudan in 2015 were described. Involvement of papillomavirus (PV) in causing these cases was affirmed by PCR and immunoperoxidase test. Mostly, the lesions were observed on the skin of the chest and forearms in addition to lips and mandible. Sequence analysis revealed Camelus dromedarius PV types 1 and 2 genotypes as the causative genotypes. We also observed cases of wart-like lesions on hands and legs of two herders attending the infected camel herd...
June 12, 2018: Vector Borne and Zoonotic Diseases
C Tacheau, F Weisgerber, D Fagot, P Bastien, M P Verdier, M Liboutet, G Sore, B A Bernard
OBJECTIVE: To study the effects of the very high minerality Vichy thermal spring water (VTSW) on human keratinocytes grown in vitro. METHODS: The effect of VTSW was monitored by full genome transcriptomic technology and immunofluorescence microscopy. RESULTS: In the presence of 50% VTSW, the expression of a number of skin homeostasis related genes is increased, specifically with respect to dermal-epidermal junction, epidermal cohesion and communication, keratinocyte proliferation-differentiation balance, antioxidant mechanisms and DNA repair...
June 7, 2018: International Journal of Cosmetic Science
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