Morphological Changes and Durability of Skin and Mucosal Flaps in Intraoral and Pharyngeal Reconstructions: Long-term Follow-up and Literature Review for Potential Second Carcinomas

The long-term changes in tissues implanted in the oral cavity and pharynx after head and neck reconstruction have not been fully evaluated. This study aimed to clarify the morphological changes, long-term durability, and potential for secondary carcinogenesis in such tissues. In our single-center study, the rough morphological changes in 54 cases of intraoral and pharyngeal skin and mucosal flaps were evaluated more than 10 years after flap transfer. In addition, the literature on the development of second carcinomas from skin flaps was reviewed. The mean follow-up period for transferred flaps was 148 months. The reconstruction areas and the probability of morphological changes were significantly correlated (p=0.006), especially in cases with tongue, lower gingiva, and buccal mucosal reconstruction. Free jejunal flap surfaces were well maintained, whereas tubed skin flaps showed severe morphological changes in cases with pharyngeal reconstruction. None of the flaps in our series developed second primary carcinomas. Skin flaps generally had good durability for > 10 years in intraoral environments, while mucosal flaps had better durability for pharyngeal reconstruction. Second squamous carcinomas arising from skin flaps are extremely rare; however, surgeons should take this possibility into consideration and conduct meticulous and long-term follow-up

Independent susceptibility markers for atrial fibrillation on chromosome 4q25

Background-: Genetic variants on chromosome 4q25 are associated with atrial fibrillation (AF). We sought to determine whether there is more than 1 susceptibility signal at this locus. Methods and results-: Thirty-four haplotype-tagging single-nucleotide polymorphisms (SNPs) at the 4q25 locus were genotyped in 790 case and 1177 control subjects from Massachusetts General Hospital and tested for association with AF. We replicated SNPs associated with AF after adjustment for the most significantly associated SNP in 5066 case and 30 661 referent subjects from the German Competence Network for Atrial Fibrillation, Atherosclerosis Risk In Communities Study, Cleveland Clinic Lone AF Study, Cardiovascular Health Study, and Rotterdam Study. All subjects were of European ancestry. A multimarker risk score composed of SNPs that tagged distinct AF susceptibility signals was constructed and tested for association with AF, and all results were subjected to meta-analysis. The previously reported SNP, rs2200733, was most significantly associated with AF (minor allele odds ratio 1.80, 95% confidence interval 1.50 to 2.15, P=1.2×10) in the discovery sample. Adjustment for rs2200733 genotype revealed 2 additional susceptibility signals marked by rs17570669 and rs3853445. A graded risk of AF was observed with an increasing number of AF risk alleles at SNPs that tagged these 3 susceptibility signals. Conclusions-: We identified 2 novel AF susceptibility signals on chromosome 4q25. Consideration of multiple susceptibility signals at chromosome 4q25 identifies individuals with an increased risk of AF and may localize regulatory elements at the locus with biological relevance in the pathogenesis of AF

Cell Specific eQTL Analysis without Sorting Cells

The functional consequences of trait associated SNPs are often investigated using expression quantitative trait locus (eQTL) mapping. While trait-associated variants may operate in a cell-type specific manner, eQTL datasets for such cell-types may not always be available. We performed a genome-environment interaction (GxE) meta-analysis on data from 5,683 samples to infer the cell type specificity of whole blood cis-eQTLs. We demonstrate that this method is able to predict neutrophil and lymphocyte specific cis-eQTLs and replicate these predictions in independent cell-type specific datasets. Finally, we show that SNPs associated with Crohn’s disease preferentially affect gene expression within neutrophils, including the archetypal NOD2 locus

Mutation burden and other molecular markers of prognosis in colorectal cancer treated with curative intent: results from the QUASAR 2 clinical trial and an Australian community-based series

Background Several relatively large studies have assessed molecular indicators of colorectal cancer (CRC) prognosis, but most analyses have been restricted to a handful of markers. Methods In stage II/III CRCs from the QUASAR2 clinical trial and from an Australian community-based series, we assessed gene panels for somatic driver mutations and overall mutation burden. We determined molecular pathways of tumorigenesis, and analysed associations with treatment response and prognosis. Findings In QUASAR2 (N=511), TP53, KRAS, BRAF and GNAS mutations were independently associated with shorter relapse-free survival, whereas total somatic mutation burden was associated with longer survival, even after excluding mismatch repair-deficient (MSI+) and POLE-mutant tumours. We successfully validated these associations in the Australian sample set (N=296). In an extended analysis of 1,752 QUASAR2 and Australian CRCs for which KRAS, BRAF and MSI status was available, we found that KRAS and BRAF mutations were specifically associated with poor prognosis in MSI- cancers. This association was not present in MSI+ cancers, and MSI+ tumours with KRAS or BRAF mutation actually had better prognosis than MSI- cancers that were wildtype for KRAS or BRAF. New rare molecular pathways were also uncovered: mutations in the genes NF1 and NRAS from the MAP kinase pathway co-occurred, mutations in TP53 and ATM appeared to be alternative ways of inactivating the DNA damage response pathway. Interpretation A multi-gene panel has identified two previously unreported prognostic associations in CRC involving both TP53 mutation and total mutation burden, and confirmed associations with KRAS and BRAF. We conclude that even a modest-sized gene panel can provide important information for use in clinical practice and out-perform MSI-based models.</p

Cell Specific eQTL Analysis without Sorting Cells

The functional consequences of trait associated SNPs are often investigated using expression quantitative trait locus (eQTL) mapping. While trait-associated variants may operate in a cell-type specific manner, eQTL datasets for such cell-types may not always be available. We performed a genome-environment interaction (GxE) meta-analysis on data from 5,683 samples to infer the cell type specificity of whole blood cis-eQTLs. We demonstrate that this method is able to predict neutrophil and lymphocyte specific cis-eQTLs and replicate these predictions in independent cell-type specific datasets. Finally, we show that SNPs associated with Crohn's disease preferentially affect gene expression within neutrophils, including the archetypal NOD2 locus.Peer reviewe

Cell Specific eQTL Analysis without Sorting Cells

The functional consequences of trait associated SNPs are often investigated using expression quantitative trait locus (eQTL) mapping. While trait-associated variants may operate in a cell-type specific manner, eQTL datasets for such cell-types may not always be available. We performed a genome-environment interaction (GxE) meta-analysis on data from 5,683 samples to infer the cell type specificity of whole blood cis-eQTLs. We demonstrate that this method is able to predict neutrophil and lymphocyte specific cis-eQTLs and replicate these predictions in independent cell-type specific datasets. Finally, we show that SNPs associated with Crohn's disease preferentially affect gene expression within neutrophils, including the archetypal NOD2 locus.Peer reviewe

Molecular mechanisms of pathogenesis in pathovars of the rice pathogenic bacterial species Xanthomonas oryzae

The pathogenicity of the two closely related phytopathogens Xanthomonas oryzae pv. oryzae and Xanthomonas oryzae pv. oryzicola was studied. These bacteria cause two different diseases with distinct tissue specificities on the same host plant rice. First, X. oryzae pv. oryzicola, the causal agent of bacterial leaf streak of rice, was observed to interfere with resistance gene-mediated defense responses to avirulence genes from X. oryzae pv. oryzae in rice. The expression of two avr genes from X. oryzae pv. oryzae in X. oryzae pv. oryzicola failed to elicit avr gene-mediated plant defense-associated hypersensitive response (HR) in rice cultivars with corresponding R genes and failed to prevent leaf streak development. Co-inoculation of X. oryzae pv. oryzicola quantitatively inhibited HR of blight resistant rice to avirulent X. oryzae pv. oryzae and this inhibition was type III dependent. Second, differential regulation of the type III secretion system required for pathogenesis was explored as a candidate determinant of tissue specificity. Specifically, identification of upstream regulator(s) of HrpG, a regulator of type III secretion, was attempted. Type III genes of the two pathogens are activated by different environmental stimuli, yet the hrpG genes of vascular and non-vascular Xanthomonas strains functioned equivalently in genetic complementation assays. This suggests that activator(s) of HrpG rather than HrpG itself may account for differential regulation and determine the tissue specificity of X. oryzae pv. oryzae and X. oryzae pv. oryzicola. The attempt to identify HrpG activators, based on gain-of-mutagenesis, was unsuccessful but details are presented for reference for future attempts.</p

Investigation of expression quantitative trait loci and regulatory genetic variants in primary human immune cells

The post human genome sequence era has begun to explore various aspects of the functional genome in relation to disease including gene expression, genetic variation and epigenetics. The genetic determinants of common and complex phenotypes are difficult to resolve even though their heritability is recognised. Recent genome-wide association studies (GWAS) for common diseases has identified many new disease susceptibility associated loci. These loci often lie in non-coding regions of the genome and disease associated genetic variants are proposed to act by modulating gene expression. This thesis investigated genetic variation as determinants of gene expression in the context of the immune system especially focused on the innate immune and inflammatory responses. Different primary human immune cell types were collected from healthy volunteers of European ancestry to achieve this. In order to identify genetic variants associating with gene expression, expression quantitative trait loci (eQTL) mapping was conducted in a cell type specific manner. The primary dataset (n=288) consists of CD19+ B-cells from the adaptive immune system and CD14+ monocytes from the innate immune system. 78% of the total cis eQTL were found to be cell type specific and include genes relating to their roles in the immune response. Trans eQTL showed greater cell type specificity and include master regulatory eQTL on the LYZ locus at chromosome 12q15 in monocytes and the KLF4 (9p31) in B-cells. The identified eQTL are implicated in association with autoimmune disease susceptibility including inflammatory bowel disease, diabetes and rheumatoid arthritis. The second analysed dataset (n=64) consists of CD14+ monocytes and macrophages differentiated ex vivo. Macrophages are involved in many inflammatory diseases as well as in the innate immune response. The differential gene expression and eQTL mapping analyses were conducted to investigate macrophages specific gene expression signatures and associations to genetic variants. Macrophage eQTL are involved in signal transduction for the inflammatory response (IL1RN and STAT4) and lipid metabolism (PPARG) with implication for metabolic disease association. The eQTL analyses using primary immune cell types provide insights into genetic variation in association to gene expression which is involved in autoimmunity and disease susceptibility.</p

Investigation of Expression Quantitative Trait Loci and Regulatory Genetic Variants in Primary Human Immune Cells

The post human genome sequence era has begun to explore various aspects of the functional genome in relation to disease including gene expression, genetic variation and epigenetics. The genetic determinants of common and complex phenotypes are difficult to resolve even though their heritability is recognised. Recent genome-wide association studies (GWAS) for common diseases has identified many new disease susceptibility associated loci. These loci often lie in non-coding regions of the genome and disease associated genetic variants are proposed to act by modulating gene expression. This thesis investigated genetic variation as determinants of gene expression in the context of the immune system especially focused on the innate immune and inflammatory responses. Different primary human immune cell types were collected from healthy volunteers of European ancestry to achieve this. In order to identify genetic variants associating with gene expression, expression quantitative trait loci (eQTL) mapping was conducted in a cell type specific manner. The primary dataset (n=288) consists of CD19+ B-cells from the adaptive immune system and CD14+ monocytes from the innate immune system. 78% of the total cis eQTL were found to be cell type specific and include genes relating to their roles in the immune response. Trans eQTL showed greater cell type specificity and include master regulatory eQTL on the LYZ locus at chromosome 12q15 in monocytes and the KLF4 (9p31) in B-cells. The identified eQTL are implicated in association with autoimmune disease susceptibility including inflammatory bowel disease, diabetes and rheumatoid arthritis. The second analysed dataset (n=64) consists of CD14+ monocytes and macrophages differentiated ex vivo. Macrophages are involved in many inflammatory diseases as well as in the innate immune response. The differential gene expression and eQTL mapping analyses were conducted to investigate macrophages specific gene expression signatures and associations to genetic variants. Macrophage eQTL are involved in signal transduction for the inflammatory response (IL1RN and STAT4) and lipid metabolism (PPARG) with implication for metabolic disease association. The eQTL analyses using primary immune cell types provide insights into genetic variation in association to gene expression which is involved in autoimmunity and disease susceptibility.This thesis is not currently available on ORA

Novel Candidate Virulence Factors in Rice Pathogen Xanthomonas oryzae pv. oryzicola as Revealed by Mutational Analysis▿

Bacterial leaf streak, caused by Xanthomonas oryzae pv. oryzicola, is an important disease of rice. Transposon-mediated mutational analysis of the pathogen with a quantitative assay revealed candidate virulence factors including genes involved in the pathogenesis of other phytopathogenic bacteria, virulence factors of animal pathogens, and genes not previously associated with virulence