Microbiomic subprofiles and MDR1 promoter methylation in head and neck squamous cell carcinoma.

Abstract:

:Clinical observations and epidemiologic studies suggest that the incidence of head and neck squamous cell carcinoma (HNSCC) correlates with dental hygiene, implying a role for bacteria-induced inflammation in its pathogenesis. Here we begin to explore the pilot hypothesis that specific microbial populations may contribute to HNSCC pathogenesis via epigenetic modifications in inflammatory- and HNSCC-associated genes. Microbiomic profiling by 16S rRNA sequencing of matched tumor and adjacent normal tissue specimens in 42 individuals with HNSCC demonstrate a significant association of specific bacterial subpopulations with HNSCC over normal tissue (P < 0.01). Furthermore, microbial populations can separate tumors by tobacco status (P < 0.008), but not by alcohol status (P = 0.41). If our subhypothesis regarding a mechanistic link from microorganism to carcinogenesis via inflammation and consequent aberrant DNA methylation is correct, then we should see hypermethylation of relevant genes associate with specific microbiomic profiles. Methylation analysis in four genes (MDR1, IL8, RARB, TGFBR2) previously linked to HNSCC or inflammation shows significantly increased methylation in tumor samples compared with normal oral mucosa. Of these, MDR1 promoter methylation associates with specific microbiomic profiles in tumor over normal mucosa. Additionally, we report that MDR1 methylation correlates with regional nodal metastases in the context of two specific bacterial subpopulations, Enterobacteriaceae and Tenericutes (P < 0.001 for each). These associations may lead to a different, and potentially more comprehensive, perspective on the pathogenesis of HNSCC, and support further exploration of mechanistic linkage and, if so, novel therapeutic strategies such as demethylating agents and probiotic adjuncts, particularly for patients with advanced or refractory disease.

journal_name

Hum Mol Genet

journal_title

Human molecular genetics

authors

Bebek G,Bennett KL,Funchain P,Campbell R,Seth R,Scharpf J,Burkey B,Eng C

doi

10.1093/hmg/ddr593

subject

Has Abstract

pub_date

2012-04-01 00:00:00

pages

1557-65

issue

7

eissn

0964-6906

issn

1460-2083

pii

ddr593

journal_volume

21

pub_type

杂志文章
  • N88S seipin mutant transgenic mice develop features of seipinopathy/BSCL2-related motor neuron disease via endoplasmic reticulum stress.

    abstract::Heterozygosity for mutations (N88S and P90L) in the N-glycosylation site of seipin/BSCL2 is associated with the autosomal dominant motor neuron diseases, spastic paraplegia 17 and distal hereditary motor neuropathy type V, referred to as 'seipinopathies'. Previous in vitro studies have shown that seipinopathy-linked m...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddr304

    authors: Yagi T,Ito D,Nihei Y,Ishihara T,Suzuki N

    更新日期:2011-10-01 00:00:00

  • An L1 element intronic insertion in the black-eyed white (Mitf[mi-bw]) gene: the loss of a single Mitf isoform responsible for the pigmentary defect and inner ear deafness.

    abstract::Waardenburg syndrome type 2 (WS2) is an autosomal dominant disorder characterized by a combination of pigmentary and auditory abnormalities. Approximately 20% of WS2 cases are associated with mutations in the gene encoding microphthalmia-associated transcription factor (MITF). MITF plays a critical role in the develop...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/8.8.1431

    authors: Yajima I,Sato S,Kimura T,Yasumoto K,Shibahara S,Goding CR,Yamamoto H

    更新日期:1999-08-01 00:00:00

  • A novel X gene with a widely transcribed Y-linked homologue escapes X-inactivation in mouse and human.

    abstract::A new gene, designated Smcx, was cloned from the mouse X chromosome by its homology to the Y located gene Smcy. Using direct in situ hybridisation Smcx was mapped to the distal end of the mouse X chromosome (XF2-XF4) and its human homologue, SMCX, was mapped to proximal Xp (Xp11.1-Xp11.2). Further meiotic mapping in t...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/3.6.879

    authors: Agulnik AI,Mitchell MJ,Mattei MG,Borsani G,Avner PA,Lerner JL,Bishop CE

    更新日期:1994-06-01 00:00:00

  • Multiple evidence strands suggest that there may be as few as 19,000 human protein-coding genes.

    abstract::Determining the full complement of protein-coding genes is a key goal of genome annotation. The most powerful approach for confirming protein-coding potential is the detection of cellular protein expression through peptide mass spectrometry (MS) experiments. Here, we mapped peptides detected in seven large-scale prote...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddu309

    authors: Ezkurdia I,Juan D,Rodriguez JM,Frankish A,Diekhans M,Harrow J,Vazquez J,Valencia A,Tress ML

    更新日期:2014-11-15 00:00:00

  • A human homologue of Drosophila minibrain (MNB) is expressed in the neuronal regions affected in Down syndrome and maps to the critical region.

    abstract::The minibrain (mnb) gene of Drosophila melanogaster encodes a serine-threonine protein kinase with an essential role in postembryonic neurogenesis. A corresponding human gene with similar function to mnb could provide important insights into both normal brain development and the abnormal brain development and mental r...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/5.9.1305

    authors: Guimerá J,Casas C,Pucharcòs C,Solans A,Domènech A,Planas AM,Ashley J,Lovett M,Estivill X,Pritchard MA

    更新日期:1996-09-01 00:00:00

  • Blepharophimosis syndrome is linked to chromosome 3q.

    abstract::Blepharophimosis syndrome (BPES, blepharophimosis eyelid syndrome) is a distinctive congenital eyelid malformation which can occur sporadically or be inherited in an autosomal dominant fashion. Previous reports have described associated cytogenetic abnormalities on chromosome 3q. We have ascertained and sampled two BP...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/4.3.443

    authors: Small KW,Stalvey M,Fisher L,Mullen L,Dickel C,Beadles K,Reimer R,Lessner A,Lewis K,Pericak-Vance MA

    更新日期:1995-03-01 00:00:00

  • A mouse model for kinesin family member 11 (Kif11)-associated familial exudative vitreoretinopathy.

    abstract::During mitosis, Kif11, a kinesin motor protein, promotes bipolar spindle formation and chromosome movement, and during interphase, Kif11 mediates diverse trafficking processes in the cytoplasm. In humans, inactivating mutations in KIF11 are associated with (1) retinal hypovascularization with or without microcephaly a...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddaa018

    authors: Wang Y,Smallwood PM,Williams J,Nathans J

    更新日期:2020-05-08 00:00:00

  • Loss of thymidine kinase 2 alters neuronal bioenergetics and leads to neurodegeneration.

    abstract::Mutations of thymidine kinase 2 (TK2), an essential component of the mitochondrial nucleotide salvage pathway, can give rise to mitochondrial DNA (mtDNA) depletion syndromes (MDS). These clinically heterogeneous disorders are characterized by severe reduction in mtDNA copy number in affected tissues and are associated...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddq043

    authors: Bartesaghi S,Betts-Henderson J,Cain K,Dinsdale D,Zhou X,Karlsson A,Salomoni P,Nicotera P

    更新日期:2010-05-01 00:00:00

  • Localization of a gene for oculodentodigital syndrome to human chromosome 6q22-q24.

    abstract::Oculodentodigital syndrome (ODD) is a congenital, autosomal dominant disorder which affects the development of the face, eyes, limbs and dentition. Spastic paraparesis is thought to be an occasional manifestation of the disorder. Type III syndactyly, which occurs as part of ODD, has also been reported to occur as an i...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/6.1.123

    authors: Gladwin A,Donnai D,Metcalfe K,Schrander-Stumpel C,Brueton L,Verloes A,Aylsworth A,Toriello H,Winter R,Dixon M

    更新日期:1997-01-01 00:00:00

  • A genome scan for loci influencing total serum immunoglobulin levels: possible linkage of IgA to the chromosome 13 atopy locus.

    abstract::Immunoglobulins play an essential part in the immune system, and immunoglobulin deficiencies can have profound medical consequences. The genetic control and regulation of the immunoglobulin response is therefore of interest. Previous investigations have identified a number of loci influencing total and specific IgE le...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/7.1.27

    authors: Wiltshire S,Bhattacharyya S,Faux JA,Leaves NI,Daniels SE,Moffatt MF,James A,Musk AW,Cookson WO

    更新日期:1998-01-01 00:00:00

  • ATRX promotes gene expression by facilitating transcriptional elongation through guanine-rich coding regions.

    abstract::ATRX is a chromatin remodeling protein involved in deposition of the histone variant H3.3 at telomeres and pericentromeric heterochromatin. It also influences the expression level of specific genes; however, deposition of H3.3 at transcribed genes is currently thought to occur independently of ATRX. We focused on a se...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddu596

    authors: Levy MA,Kernohan KD,Jiang Y,Bérubé NG

    更新日期:2015-04-01 00:00:00

  • Haploinsufficiency of RCBTB1 is associated with Coats disease and familial exudative vitreoretinopathy.

    abstract::Familial exudative vitreoretinopathy (FEVR) belongs to a group of genetically and clinically heterogeneous disorders in retinal vascular development. To date, in approximately 50% of patients with FEVR, pathogenic mutations have been detected in FZD4, LRP5, TSPAN12, NDP and ZNF408. In this study, we identified two het...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddw041

    authors: Wu JH,Liu JH,Ko YC,Wang CT,Chung YC,Chu KC,Liu TT,Chao HM,Jiang YJ,Chen SJ,Chung MY

    更新日期:2016-04-15 00:00:00

  • Mutations in the diastrophic dysplasia sulfate transporter (DTDST) gene: correlation between sulfate transport activity and chondrodysplasia phenotype.

    abstract::The diastrophic dysplasia sulfate transporter (DTDST) gene encodes a transmembrane protein that transports sulfate into chondrocytes to maintain adequate sulfation of proteoglycans. Mutations in this gene are responsible for four recessively inherited chondrodysplasias that include diastrophic dysplasia, multiple epip...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/10.14.1485

    authors: Karniski LP

    更新日期:2001-07-01 00:00:00

  • Functional assessment of variants associated with Wolfram syndrome.

    abstract::Wolfram syndrome (WS) is a heterogeneous multisystem neurodegenerative disorder with two allelic variations in addition to a separate subtype known as WS type 2. The wide phenotypic spectrum of WS includes diabetes mellitus and optic atrophy which is often accompanied by diabetes insipidus, deafness, urological and ne...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddz212

    authors: Riachi M,Yilmaz S,Kurnaz E,Aycan Z,Çetinkaya S,Tranebjærg L,Rendtorff ND,Bitner-Glindzicz M,Bockenhauer D,Hussain K

    更新日期:2019-11-15 00:00:00

  • Abnormal interaction between the mitochondrial fission protein Drp1 and hyperphosphorylated tau in Alzheimer's disease neurons: implications for mitochondrial dysfunction and neuronal damage.

    abstract::We recently reported increased mitochondrial fission and decreased fusion, increased amyloid beta (Aβ) interaction with the mitochondrial fission protein Drp1, increased mitochondrial fragmentation, impaired axonal transport of mitochondria and synaptic degeneration in neurons affected by AD. In the present study, we ...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/dds072

    authors: Manczak M,Reddy PH

    更新日期:2012-06-01 00:00:00

  • Partial loss of Tip60 slows mid-stage neurodegeneration in a spinocerebellar ataxia type 1 (SCA1) mouse model.

    abstract::Spinocerebellar ataxia type 1 (SCA1) is one of nine dominantly inherited neurodegenerative diseases caused by polyglutamine tract expansion. In SCA1, the expanded polyglutamine tract is in the ataxin-1 (ATXN1) protein. ATXN1 is part of an in vivo complex with retinoid acid receptor-related orphan receptor alpha (Rora)...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddr108

    authors: Gehrking KM,Andresen JM,Duvick L,Lough J,Zoghbi HY,Orr HT

    更新日期:2011-06-01 00:00:00

  • Huntingtin facilitates polycomb repressive complex 2.

    abstract::Huntington's disease (HD) is caused by expansion of the polymorphic polyglutamine segment in the huntingtin protein. Full-length huntingtin is thought to be a predominant HEAT repeat alpha-solenoid, implying a role as a facilitator of macromolecular complexes. Here we have investigated huntingtin's domain structure an...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddp524

    authors: Seong IS,Woda JM,Song JJ,Lloret A,Abeyrathne PD,Woo CJ,Gregory G,Lee JM,Wheeler VC,Walz T,Kingston RE,Gusella JF,Conlon RA,MacDonald ME

    更新日期:2010-02-15 00:00:00

  • Identification of Btk mutations in 20 unrelated patients with X-linked agammaglobulinaemia (XLA).

    abstract::X-linked agammaglobulinaemia (XLA) is an inherited immunodeficiency resulting from mutations in the gene for a cytoplasmic protein tyrosine kinase (Btk). We have utilised reverse-transcription-based PCR in combination with the chemical cleavage and mismatch technique (CCM) to screen for Btk mutations in 42 unrelated p...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/4.4.693

    authors: Jin H,Webster AD,Vihinen M,Sideras P,Vorechovsky I,Hammarstróm L,Bernatowska-Matuszkiewicz E,Smith CI,Bobrow M,Vetrie D

    更新日期:1995-04-01 00:00:00

  • An extended genome-wide association study identifies novel susceptibility loci for nasopharyngeal carcinoma.

    abstract::To further identify novel susceptibility loci of nasopharyngeal carcinoma (NPC), we here extended our previous genome-wide association study (GWAS) by boosting statistical power with larger sample size and validating more SNPs in the ranking list based on the GWAS P-values. The discovery stage consisting of 463,250 SN...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddw200

    authors: Cui Q,Feng QS,Mo HY,Sun J,Xia YF,Zhang H,Foo JN,Guo YM,Chen LZ,Li M,Liu WS,Xu M,Zhou G,He F,Yu X,Jia WH,Liu J,Zeng YX,Bei JX

    更新日期:2016-08-15 00:00:00

  • Oncogenic conversion of a novel orphan nuclear receptor by chromosome translocation.

    abstract::A recurrent t(9;22) (q22;q12) chromosome translocation has been described in extraskeletal myxoid chondrosarcoma (EMC). Fluorescent in situ hybridization experiments performed on one EMC tumour indicated that the chromosome 22 breakpoint occurred in the EWS gene. Northern blot analysis revealed an aberrant EWS transcr...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/4.12.2219

    authors: Labelle Y,Zucman J,Stenman G,Kindblom LG,Knight J,Turc-Carel C,Dockhorn-Dworniczak B,Mandahl N,Desmaze C,Peter M

    更新日期:1995-12-01 00:00:00

  • Ataxin-2 repeat-length variation and neurodegeneration.

    abstract::Expanded glutamine repeats of the ataxin-2 (ATXN2) protein cause spinocerebellar ataxia type 2 (SCA2), a rare neurodegenerative disorder. More recent studies have suggested that expanded ATXN2 repeats are a genetic risk factor for amyotrophic lateral sclerosis (ALS) via an RNA-dependent interaction with TDP-43. Given ...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddr227

    authors: Ross OA,Rutherford NJ,Baker M,Soto-Ortolaza AI,Carrasquillo MM,DeJesus-Hernandez M,Adamson J,Li M,Volkening K,Finger E,Seeley WW,Hatanpaa KJ,Lomen-Hoerth C,Kertesz A,Bigio EH,Lippa C,Woodruff BK,Knopman DS,White CL 3r

    更新日期:2011-08-15 00:00:00

  • Epileptogenic Q555X SYN1 mutant triggers imbalances in release dynamics and short-term plasticity.

    abstract::Synapsin I (SynI) is a synaptic vesicle (SV) phosphoprotein playing multiple roles in synaptic transmission and plasticity by differentially affecting crucial steps of SV trafficking in excitatory and inhibitory synapses. SynI knockout (KO) mice are epileptic, and nonsense and missense mutations in the human SYN1 gene...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddt071

    authors: Lignani G,Raimondi A,Ferrea E,Rocchi A,Paonessa F,Cesca F,Orlando M,Tkatch T,Valtorta F,Cossette P,Baldelli P,Benfenati F

    更新日期:2013-06-01 00:00:00

  • Pathway-driven gene stability selection of two rheumatoid arthritis GWAS identifies and validates new susceptibility genes in receptor mediated signalling pathways.

    abstract::Rheumatoid arthritis (RA) is the commonest chronic, systemic, inflammatory disorder affecting ∼1% of the world population. It has a strong genetic component and a growing number of associated genes have been discovered in genome-wide association studies (GWAS), which nevertheless only account for 23% of the total gene...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddr248

    authors: Eleftherohorinou H,Hoggart CJ,Wright VJ,Levin M,Coin LJ

    更新日期:2011-09-01 00:00:00

  • Non-manifesting AHI1 truncations indicate localized loss-of-function tolerance in a severe Mendelian disease gene.

    abstract::Determination of variant pathogenicity represents a major challenge in the era of high-throughput sequencing. Erroneous categorization may result if variants affect genes that are in fact dispensable. We demonstrate that this also applies to rare, apparently unambiguous truncating mutations of an established disease g...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddv022

    authors: Elsayed SM,Phillips JB,Heller R,Thoenes M,Elsobky E,Nürnberg G,Nürnberg P,Seland S,Ebermann I,Altmüller J,Thiele H,Toliat M,Körber F,Hu XJ,Wu YD,Zaki MS,Abdel-Salam G,Gleeson J,Boltshauser E,Westerfield M,Bolz HJ

    更新日期:2015-05-01 00:00:00

  • DNA mismatch repair gene mutations in 55 kindreds with verified or putative hereditary non-polyposis colorectal cancer.

    abstract::The DNA mismatch repair genes MSH2 and MLH1 have been shown to account for a major share of hereditary non-polyposis colorectal cancer (HNPCC). We searched for germline mutations in these genes in 35 HNPCC kindreds fulfilling the Amsterdam diagnostic criteria and in a further 20 kindreds with an average of four affect...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/5.6.763

    authors: Nyström-Lahti M,Wu Y,Moisio AL,Hofstra RM,Osinga J,Mecklin JP,Järvinen HJ,Leisti J,Buys CH,de la Chapelle A,Peltomäki P

    更新日期:1996-06-01 00:00:00

  • Low levels of microsatellite instability characterize MLH1 and MSH2 HNPCC carriers before tumor diagnosis.

    abstract::Microsatellite instability (MSI) characterizes tumors arising in patients with hereditary non-polyposis colorectal cancer (HNPCC) syndrome. HNPCC is a hereditary autosomal dominant disease caused by germline mutations in genes from the DNA (MMR) mismatch repair system. In these tumors, the loss of MMR compromises the ...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddi021

    authors: Alazzouzi H,Domingo E,González S,Blanco I,Armengol M,Espín E,Plaja A,Schwartz S,Capella G,Schwartz S Jr

    更新日期:2005-01-15 00:00:00

  • Genome-wide association study identifies novel loci association with fasting insulin and insulin resistance in African Americans.

    abstract::Insulin resistance (IR) is a key determinant of type 2 diabetes (T2D) and other metabolic disorders. This genome-wide association study (GWAS) was designed to shed light on the genetic basis of fasting insulin (FI) and IR in 927 non-diabetic African Americans. 5 396 838 single-nucleotide polymorphisms (SNPs) were test...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/dds282

    authors: Chen G,Bentley A,Adeyemo A,Shriner D,Zhou J,Doumatey A,Huang H,Ramos E,Erdos M,Gerry N,Herbert A,Christman M,Rotimi C

    更新日期:2012-10-15 00:00:00

  • Gtf2i and Gtf2ird1 mutation do not account for the full phenotypic effect of the Williams syndrome critical region in mouse models.

    abstract::Williams syndrome (WS) is a neurodevelopmental disorder caused by a 1.5-1.8 Mbp deletion on chromosome 7q11.23, affecting the copy number of 26-28 genes. Phenotypes of WS include cardiovascular problems, craniofacial dysmorphology, deficits in visual-spatial cognition and a characteristic hypersocial personality. Ther...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddz176

    authors: Kopp N,McCullough K,Maloney SE,Dougherty JD

    更新日期:2019-10-15 00:00:00

  • A mutation affecting polycystin-1 mediated heterotrimeric G-protein signaling causes PKD.

    abstract::Autosomal dominant polycystic kidney disease (ADPKD) is characterized by the growth of renal cysts that ultimately destroy kidney function. Mutations in the PKD1 and PKD2 genes cause ADPKD. Their protein products, polycystin-1 (PC1) and polycystin-2 (PC2) have been proposed to form a calcium-permeable receptor-channel...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddy223

    authors: Parnell SC,Magenheimer BS,Maser RL,Pavlov TS,Havens MA,Hastings ML,Jackson SF,Ward CJ,Peterson KR,Staruschenko A,Calvet JP

    更新日期:2018-10-01 00:00:00

  • SRY interference of normal regulation of the RET gene suggests a potential role of the Y-chromosome gene in sexual dimorphism in Hirschsprung disease.

    abstract::The Hirschsprung disease (HSCR) is a complex congenital disorder, arising from abnormalities in enteric nervous system (ENS) development. There is a gender disparity among the patients, with the male to female ratio as high as 5 : 1. Loss-of-function mutations of HSCR genes and haploinsufficiency of their gene product...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddu488

    authors: Li Y,Kido T,Garcia-Barcelo MM,Tam PK,Tabatabai ZL,Lau YF

    更新日期:2015-02-01 00:00:00