3D chromatin conformation correlates with replication timing and is conserved in resting cells.
AuthorsMoindrot B, Audit B, Klous P, Baker A, Thermes C, de Laat W, Bouvet P, Mongelard F, Arneodo A,
JournalNucleic Acids Res
PubMed ID22879376
'Although chromatin folding is known to be of functional importance to control the gene expression program, less is known regarding its interplay with DNA replication. Here, using Circular Chromatin Conformation Capture combined with high-throughput sequencing, we identified megabase-sized self-interacting domains in the nucleus of a human lymphoblastoid cell line, as ... More
A significant effect of the TSPY1 copy number on spermatogenesis efficiency and the phenotypic expression of the gr/gr deletion.
AuthorsShen Y, Yan Y, Liu Y, Zhang S, Yang D, Zhang P, Li L, Wang Y, Ma Y, Tao D, Yang Y,
JournalHum Mol Genet
PubMed ID23307928
'AZFc deletions cause a significant phenotypic heterogeneity with respect to spermatogenesis; however, the reason for this is poorly understood. Recently, testis-specific protein Y-encoded 1 (TSPY1) copy number variation (CNV) was determined to be a potential genetic modifier of spermatogenesis. We performed a large-scale cohort study to investigate the effect of ... More
Gene expression profiling in insulinomas of Men1 beta-cell mutant mice reveals early genetic and epigenetic events involved in pancreatic beta-cell tumorigenesis.
AuthorsFontanière S, Tost J, Wierinckx A, Lachuer J, Lu J, Hussein N, Busato F, Gut I, Wang ZQ, Zhang CX,
JournalEndocr Relat Cancer
PubMed ID17158767
'Mutations of the MEN1 gene lead to the occurrence of multiple endocrine neoplasia type 1 (MEN1). To gain insights into the mechanisms of the tumorigenesis related to MEN1 inactivation, we have used mice in which the Men1 gene was specifically disrupted in pancreatic beta-cells. In these mice, we observed full ... More
Effects of essential oils on methane production and fermentation by, and abundance and diversity of, rumen microbial populations.
AuthorsPatra AK, Yu Z,
JournalAppl Environ Microbiol
PubMed ID22492451
'Five essential oils (EOs), namely, clove oil (CLO), eucalyptus oil (EUO), garlic oil (GAO), origanum oil (ORO), and peppermint oil (PEO), were tested in vitro at 3 different doses (0.25, 0.50, and 1.0 g/liter) for their effect on methane production, fermentation, and select groups of ruminal microbes, including total bacteria, ... More
Normal variants of Microcephalin and ASPM do not account for brain size variability.
AuthorsWoods RP, Freimer NB, De Young JA, Fears SC, Sicotte NL, Service SK, Valentino DJ, Toga AW, Mazziotta JC,
JournalHum Mol Genet
PubMed ID16687438
'Normal human brain volume is heritable. The genes responsible for variation in brain volume are not known. Microcephalin (MCPH1) and ASPM (abnormal spindle-like microcephaly associated) have been proposed as candidate genes as mutations in both genes are associated with microcephaly, and common variants of each gene are apparently under strong ... More
Colonic mucosa-associated microbiota is influenced by an interaction of Crohn disease and FUT2 (Secretor) genotype.
AuthorsRausch P, Rehman A, Künzel S, Häsler R, Ott SJ, Schreiber S, Rosenstiel P, Franke A, Baines JF,
JournalProc Natl Acad Sci U S A
PubMed ID22068912
The FUT2 (Secretor) gene is responsible for the presence of ABO histo-blood group antigens on the gastrointestinal mucosa and in bodily secretions. Individuals lacking a functional copy of FUT2 are known as ... More
Introduction of phospholipids to cultured cells with cyclodextrin.
AuthorsKainu V, Hermansson M, Somerharju P,
JournalJ Lipid Res
PubMed ID20881052
Previous studies indicate that methyl-ß-cyclodextrin (meß-CD) can greatly enhance translocation of long-chain phospholipids from vesicles to cells in culture, which is very useful when studying, e.g., phospholipid metabolism and trafficking. However, the parameters affecting the transfer have not been systematically studied. Therefore, we studied the relevant parameters including meß-CD and ... More
A comparison of the roles of peroxisome proliferator-activated receptor and retinoic acid receptor on CYP26 regulation.
AuthorsTay S, Dickmann L, Dixit V, Isoherranen N,
JournalMol Pharmacol
PubMed ID19884280
The cytochrome P450 26 family is believed to be responsible for all-trans-retinoic acid (atRA) metabolism and elimination in the human fetus and adults. CYP26A1 and CYP26B1 mRNA is expressed in a tissue-specific manner, and mice in which the CPY26 isoform has been knocked out show distinct malformations and lethality. The ... More
Hypermethylation of the IGF2 differentially methylated region 2 is a specific event in insulinomas leading to loss-of-imprinting and overexpression.
AuthorsDejeux E, Olaso R, Dousset B, Audebourg A, Gut IG, Terris B, Tost J,
JournalEndocr Relat Cancer
PubMed ID19502451
Prediction of the evolution of endocrine pancreatic tumors remains difficult based on histological criteria alone. We have previously demonstrated that epigenetic changes are an early event in a mouse model developing insulinomas. Particularly, overexpression of the imprinted IGF2 was caused by the hypermethylation of CpGs in the differentially methylated region ... More
Cigarette smoke extract reduces VEGF in primary human airway epithelial cells.
AuthorsThaikoottathil JV, Martin RJ, Zdunek J, Weinberger A, Rino JG, Chu HW,
JournalEur Respir J
PubMed ID19129286
Reduced vascular endothelial growth factor (VEGF) has been reported in bronchoalveolar lavage fluid and lungs of severe emphysema patients. Airway epithelial cells (AEC) are exposed to various environmental insults like cigarette smoke and bacterial infections, but their direct effect on VEGF production in well-differentiated primary human AEC remains unclear. The ... More
Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases.
AuthorsLloyd-Price J, Arze C, Ananthakrishnan AN, Schirmer M, Avila-Pacheco J, Poon TW, Andrews E, Ajami NJ, Bonham KS, Brislawn CJ, Casero D, Courtney H, Gonzalez A, Graeber TG, Hall AB, Lake K, Landers CJ, Mallick H, Plichta DR, Prasad M, Rahnavard G, Sauk J, Shungin D, Vázquez-Baeza Y, White RA, Braun J, Denson LA, Jansson JK, Knight R, Kugathasan S, McGovern DPB, Petrosino JF, Stappenbeck TS, Winter HS, Clish CB, Franzosa EA, Vlamakis H, Xavier RJ, Huttenhower C
JournalNature
PubMed ID31142855
'Inflammatory bowel diseases, which include Crohn''s disease and ulcerative colitis, affect several million individuals worldwide. Crohn''s disease and ulcerative colitis are complex diseases that are heterogeneous at the clinical, immunological, molecular, genetic, and microbial levels. Individual contributing factors have been the focus of extensive research. As part of the Integrative ... More
Locus-specific concordance of genomic alterations between tissue and plasma circulating tumor DNA in metastatic melanoma.
AuthorsCalapre L, Giardina T, Robinson C, Reid AL, Al-Ogaili Z, Pereira MR, McEvoy AC, Warburton L, Hayward NK, Khattak MA, Meniawy TM, Millward M, Amanuel B, Ziman M, Gray ES
JournalMol Oncol
PubMed ID30312528
'Circulating tumor DNA (ctDNA) may serve as a surrogate to tissue biopsy for noninvasive identification of mutations across multiple genetic loci and for disease monitoring in melanoma. In this study, we compared the mutation profiles of tumor biopsies and plasma ctDNA from metastatic melanoma patients using custom sequencing panels targeting 30 ... More
A synthetic-diploid benchmark for accurate variant-calling evaluation.
AuthorsLi H, Bloom JM, Farjoun Y, Fleharty M, Gauthier L, Neale B, MacArthur D
JournalNat Methods
PubMed ID30013044
Existing benchmark datasets for use in evaluating variant-calling accuracy are constructed from a consensus of known short-variant callers, and they are thus biased toward easy regions that are accessible by these algorithms. We derived a new benchmark dataset from the de novo PacBio assemblies of two fully homozygous human cell ... More
A 1204-single nucleotide polymorphism and insertion-deletion polymorphism panel for massively parallel sequencing analysis of DNA mixtures.
AuthorsHwa HL, Chung WC, Chen PL, Lin CP, Li HY, Yin HI, Lee JC
JournalForensic Sci Int Genet
PubMed ID29128546
Massively parallel sequencing (MPS) technology enables the simultaneous analysis of a huge number of single nucleotide polymorphisms (SNPs) and insertion-deletion polymorphisms (indels). MPS also enables the detection of the alleles of minor contributors in a highly unbalanced DNA mixture. In this study, we established a 1204-marker panel optimized for MPS ... More
The Genomic and Immune Landscapes of Lethal Metastatic Breast Cancer.
AuthorsDe Mattos-Arruda L, Sammut SJ, Ross EM, Bashford-Rogers R, Greenstein E, Markus H, Morganella S, Teng Y, Maruvka Y, Pereira B, Rueda OM, Chin SF, Contente-Cuomo T, Mayor R, Arias A, Ali HR, Cope W, Tiezzi D, Dariush A, Dias Amarante T, Reshef D, Ciriaco N, Martinez-Saez E, Peg V, Ramon Y Cajal S, Cortes J, Vassiliou G, Getz G, Nik-Zainal S, Murtaza M, Friedman N, Markowetz F, Seoane J, Caldas C
JournalCell Rep
PubMed ID31141692
The detailed molecular characterization of lethal cancers is a prerequisite to understanding resistance to therapy and escape from cancer immunoediting. We performed extensive multi-platform profiling of multi-regional metastases in autopsies from 10 patients with therapy-resistant breast cancer. The integrated genomic and immune landscapes show that metastases propagate and evolve as ... More
Analysis of error profiles in deep next-generation sequencing data.
AuthorsMa X, Shao Y, Tian L, Flasch DA, Mulder HL, Edmonson MN, Liu Y, Chen X, Newman S, Nakitandwe J, Li Y, Li B, Shen S, Wang Z, Shurtleff S, Robison LL, Levy S, Easton J, Zhang J
JournalGenome Biol
PubMed ID30867008
Sequencing errors are key confounding factors for detecting low-frequency genetic variants that are important for cancer molecular diagnosis, treatment, and surveillance using deep next-generation sequencing (NGS). However, there is a lack of comprehensive understanding of errors introduced at various steps of a conventional NGS workflow, such as sample handling, library ... More