Major Candidate Genes Research Articles

The differences in brain stem transcriptional profiling in hypertensive ISIAH and normotensive WAG rats

BackgroundThe development of essential hypertension is associated with a wide range of mechanisms. The brain stem neurons are essential for the homeostatic regulation of arterial pressure as they control baroreflex and sympathetic nerve activity. The ISIAH (Inherited Stress Induced Arterial Hypertension) rats reproduce the human stress-sensitive hypertensive disease with predominant activation of the neuroendocrine hypothalamic-pituitary-adrenal and sympathetic adrenal axes. RNA-Seq analysis of the brain stems from the hypertensive ISIAH and normotensive control WAG (Wistar Albino Glaxo) rats was performed to identify the differentially expressed genes (DEGs) and the main central mechanisms (biological processes and metabolic pathways) contributing to the hypertensive state in the ISIAH rats.ResultsThe study revealed 224 DEGs. Their annotation in databases showed that 22 of them were associated with hypertension and blood pressure (BP) regulation, and 61 DEGs were associated with central nervous system diseases. In accordance with the functional annotation of DEGs, the key role of hormonal metabolic processes and, in particular, the enhanced biosynthesis of aldosterone in the brain stem of ISIAH rats was proposed. Multiple DEGs associated with several Gene Ontology (GO) terms essentially related to modulation of BP were identified. Abundant groups of DEGs were related to GO terms associated with responses to different stimuli including response to organic (hormonal) substance, to external stimulus, and to stress. Several DEGs making the most contribution to the inter-strain differences were detected including the Ephx2, which was earlier defined as a major candidate gene in the studies of transcriptional profiles in different tissues/organs (hypothalamus, adrenal gland and kidney) of ISIAH rats.ConclusionsThe results of the study showed that inter-strain differences in ISIAH and WAG brain stem functioning might be a result of the imbalance in processes leading to the pathology development and those, exerting the compensatory effects. The data obtained in this study are useful for a better understanding of the genetic mechanisms underlying the complexity of the brain stem processes in ISIAH rats, which are a model of stress-sensitive form of hypertension.

Tbx1 regulates extracellular matrix-cell interactions in the second heart field.

Tbx1, the major candidate gene for DiGeorge or 22q11.2 deletion syndrome, is required for efficient incorporation of cardiac progenitors of the second heart field (SHF) into the heart. However, the mechanisms by which TBX1 regulates this process are still unclear. Here, we have used two independent models, mouse embryos and cultured cells, to define the role of TBX1 in establishing morphological and dynamic characteristics of SHF in the mouse. We found that loss of TBX1 impairs extracellular matrix (ECM)-integrin-focal adhesion (FA) signaling in both models. Mosaic analysis in embryos suggested that this function is non-cell autonomous, and, in cultured cells, loss of TBX1 impairs cell migration and FAs. Additionally, we found that ECM-mediated integrin signaling is disrupted upon loss of TBX1. Finally, we show that interfering with the ECM-integrin-FA axis between E8.5 and E9.5 in mouse embryos, corresponding to the time window within which TBX1 is required in the SHF, causes outflow tract dysmorphogenesis. Our results demonstrate that TBX1 is required to maintain the integrity of ECM-cell interactions in the SHF and that this interaction is critical for cardiac outflow tract development. More broadly, our data identifies a novel TBX1 downstream pathway as an important player in SHF tissue architecture and cardiac morphogenesis.

Identification and classification of differentially expressed genes in pyrethroid-resistant Culex pipiens pallens.

Culex pipiens pallens is an important vector that transmits Bancroftian filariasis, Japanese encephalitis and other diseases that pose a serious threat to human health. Extensive and improper use of insecticides has caused insecticide resistance in mosquitoes, which has become an important obstacle to the control of mosquito-borne diseases. It is crucial to investigate the underlying mechanism of insecticide resistance. The aims of this study were to identify genes involved in insecticide resistance based on the resistance phenotype, gene expression profile and single-nucleotide polymorphisms (SNPs) and to screen for major genes controlling insecticide resistance. Using a combination of SNP and transcriptome data, gene expression quantitative trait loci (eQTLs) were studied in deltamethrin-resistant mosquitoes. The most differentially expressed pathway in the resistant group was identified, and a regulatory network was built using these SNPs and the differentially expressed genes (DEGs) in this pathway. The major candidate genes involved in the control of insecticide resistance were analyzed by qPCR, siRNA microinjection and CDC bottle bioassays. A total of 85 DEGs that encoded putative detoxification enzymes (including 61 P450s) were identified in this pathway. The resistance regulatory network was built using SNPs, and these metabolic genes, and a major gene, CYP9AL1, were identified. The functional role of CYP9AL1 in insecticide resistance was confirmed by siRNA microinjection and CDC bottle bioassays. Using the eQTL approach, we identified important genes in pyrethroid resistance that may aid in understanding the mechanism underlying insecticide resistance and in targeting new measures for resistance monitoring and management.

Identification of Early Tomato Fruit Ripening Loci by QTL-seq

QTL-seq has been successfully studied in identifying major QTLs, markers, and candidate genes associated with traits that are important for crop improvement. Tomato earliness is an economically important trait and is a major current research focus recently. This paper reports the identification of tomato early ripening fruit locus facilitated by QTL-seq using a novel next-generation sequencing technology. Two DNA pools of phenotypes of F2 offspring from crosses between the Bone ММ (early ripening fruit, P1) and 071-440 (late ripening fruit, P2) cultivars of (Solanum lycopersicum) were bulked for sequencing and alignment analysis. Sequencing results revealed 434 SNP markers on chromosome 11, a candidate QTL at position 52,048,208 bp (named er-fruit) and a candidate gene, Solyc11g071510.1.1. The “er-fruit” as confirmed by the traditional QTL method was related to the early fruit ripening trait in tomato. Additionally, BLAST analysis to known homologies for Solyc11g071510.1.1 gene encodes glycoside hydrolases (GHs). GHs are functionally associated with cell wall degradation, fruit softening and ripening. Thus, GHs may be important in fruit softening, stimulating early fruit ripening in tomato. Our results confirmed that QTL-seq is effective method to identify candidate QTL loci, candidate genes and candidate markers.

Next Generation Sequencing Analysis in Early Onset Dementia Patients.

Background: Early onset dementias (EOD) are rare neurodegenerative dementias that present before 65 years. Genetic factors have a substantially higher pathogenetic contribution in EOD patients than in late onset dementia.Objective: To identify known and/or novel rare variants in major candidate genes associated to EOD by high-throughput sequencing. Common-risk variants of apolipoprotein E (APOE) and prion protein (PRNP) genes were also assessed.Methods: We studied 22 EOD patients recruited in Memory Clinics, in the context of studies investigating genetic forms of dementia. Two methodological approaches were applied for the target-Next Generation Sequencing (NGS) analysis of these patients. In addition, we performed progranulin plasma dosage, C9Orf72 hexanucleotide repeat expansion analysis, and APOE genotyping.Results: We detected three rare known pathogenic mutations in the GRN and PSEN2 genes and eleven unknown-impact mutations in the GRN, VCP, MAPT, FUS, TREM2, and NOTCH3 genes. Six patients were carriers of only common risk variants (APOE and PRNP), and one did not show any risk mutation/variant. Overall, 69% (n = 9) of our early onset Alzheimer’s disease (EAOD) patients, compared with 34% (n = 13) of sporadic late onset Alzheimer’s disease (LOAD) patients and 27% (n = 73) of non-affected controls (ADNI, whole genome data), were carriers of at least two rare/common risk variants in the analyzed candidate genes panel, excluding the full penetrant mutations.Conclusion: This study suggests that EOD patients without full penetrant mutations are characterized by higher probability to carry polygenic risk alleles that patients with LOAD forms. This finding is in line with recently reported evidence, thus suggesting that the genetic risk factors identified in LOAD might modulate the risk also in EOAD.

Detection of Snps in the Melanocortin 1-Receptor (MC1R) and Its Association with Shank Color Trait in Hs Chicken

ABSTRACT The melanocortin 1 receptor (MC1R) gene plays a key role in controlling the deposition of melanin. In mammals, the MC1Rgene is regarded as a major candidate gene in the control of melanin formation. In domestic animals, the MC1R gene mainly controls the expression of coat, skin, and plumage color in mammals and birds. In order to breed chickens with dark-green shank faster, we screened the molecular markers for shank color in a HS chicken population by exploring the relationship between polymorphism of the MC1R gene and three different shank colors (light green, dark green and yellow). Two primer pairs for code region of the MC1R gene were designed in the basic of chicken genomic sequence. DNA sequencing was performed to detect the polymorphisms and PCR was used to amplify DNA fragment. Sequences analysis indicated that 7 SNPs were predominant the three HS chicken populations with different shank color, including g.18,287,945C>T, g.18,288,088T>C, g.18,288,150G>A, g.18,288,303A>G, g.18,288,512G>A, g.18,288,513T>C, and g.18,288,520A>C. Association analysis revealed that the dark-green shank population showed moderate polymorphism, whereas the light-green shank population showed low polymorphism among overall 7 SNPs and that SNP6 (g.18,288,513T>C) may be significantly associated with three different shank colors in HS chickens. The haplotype CTGGACA had the largest haplotype frequencies, accounting for 56.22%, and the haplotype combination H1H1 is mainly distributed in the dark-green shank population, and may be used as molecular maker for marker-assisted selection of shank color in HS chickens.

A Review on the Genetic Basis of Growth and Prolificacy Traits in Sheep

The performance of an animal for a particular trait is the result of its genetic merit and the effects of the environment where it exists. To set up genetic improvement in sheep, the genetic component attributed to the trait of interest need to be defined. The aim of this review was to describe major candidate genes influencing growth traits and prolificacy in sheep. Although growth and prolificacy are quantitative traits and are expected to be influenced by many genes with individual genes contributing small effects, there are major genes that have been identified with significant influence on growth and prolificacy. The CLPG, GDF8 and CAST genes are some of the major genes that have strong influence on sheep growth and carcass quality. The CLPG mutation can cause pronounced effect in the muscle found in the hindquarter and is responsible for the muscular hypertrophy phenotype in sheep. The GDF8 gene also play important role in increasing muscle depth due to mutation in the regulatory region and coding sequences. The CAST gene is an endogenous and specific inhibitor of calpain enzyme and thereby regulates the rate and extent of muscle tenderization following slaughtering. For prolificacy, BMP15, GDF9 and BMPR1B have been shown to exert significant influence on ovulation rate and litter size in various sheep breeds in the world. Both of the three genes are member of the TGF-beta family protein that encode protein product responsible for growth, differentiation and proliferation of ovarian follicles. The mechanism of action for such major genes are associated with the existence of mutation in the coding sequence resulting amino acid change as well as in the regulatory region that vary the expression level and inheritance of the genes. Up to now, better attempts have been made to describe the genetic basis of growth and prolificacy in sheep. However, more works are needed to characterize other genes influencing these traits. More importantly, making use of the identified genes in sheep breeding program through marker assisted and genomic selection should receive due attentions.

THE GENETIC SUSCEPTIBILITY TO ATHEROSCLEROSIS

Atherosclerosis is a complex multifocal arterial disease involving interactions of multiple genetic and environmental factors. Atherosclerosis is the main cause of death and disability in developed countries, while in developing countries the incidence of this pathology is growing rapidly. Advances in techniques of molecular genetics have revealed that genetic polymorphisms significantly influence susceptibility to atherosclerotic vascular diseases. A large number of candidate genes, genetic polymorphisms and susceptibility loci associated with atherosclerotic diseases have been identified in recent years and their number is rapidly increasing. In recent years, there is significant interest in identifying additional factors of genetic risk for atherosclerosis. In recent years, a large number of genetic studies have been carried out to prove the genetic effect on the atherosclerotic process. Rapid progress in the sequencing of the human genome and molecular genetic methods have helped in the definition of susceptibility loci and associated candidate genes with atherosclerosis and concomitant diseases. The association of a large number of susceptibility genes with atherosclerosis reflects the enormous complexity of the disease. Multiple factors, including endothelial dysfunction, lipid metabolism defects, inflammation and immune responses, oxidative stress, cell proliferation, tissue remodeling and hemostatic defects are involved in the pathogenesis of atherosclerosis. In this review we focus and discuss on some of the major candidate genes and genetic polymorphisms associated with human atherosclerotic vascular diseases.

Vesicular trafficking in abscission zone cells during ethylene-promoted fruit abscission in citrus

Abscission is a cell separation process by which plants are able to shed aerial organs. This physiological process proceeds through a breakdown in adhesion between a group of specialized cells that usually differentiate in particular positions of the plant body named abscission zones (AZs). The occurrence of fruit abscission has special relevance in fruit tree crops such as citrus since it may have negative consequences on yield. To identify AZ-specifically expressed genes involved in citrus fruit abscission, we used a combined strategy of laser microdissection and microarray analysis to compare the global expression profiles of calyx abscission zone (AZ-C) cells of citrus fruits and adjacent fruit rind cells during ethylene-promoted fruit abscission. The comparison enabled to identify a set of potentially specific genes including those associated with vesicular transport and intracellular transport vesicles. The first ultrastructural observations on AZ-C cells during fruit abscission (Iwahori and van Steveninck, 1976) showed an increase in rough endoplasmic reticulum profiles and dictyosome stacks with associated vesicles that fused with the plasma membrane to release their contents to the cell wall. In this comparative transcriptomic survey, we highlighted specific over-expression in AZ-C cells of genes belonging to the major transport steps along the secretory and the endocytic pathways of vesicle trafficking. In particular, it is likely that some of the genes identified in this study would represent major candidate genes for further biotechnological approaches aimed at trying to solve or at least mitigate agronomic issues regarding citrus fruit abscission.

A major QTL and candidate genes for capsaicinoid biosynthesis in the pericarp of Capsicum chinense revealed using QTL-seq and RNA-seq.

A major QTL and candidate genes controlling capsaicinoid content in the pericarp were identified by QTL-seq and RNA-seq in Capsicum chinense. Capsaicinoid biosynthesis was previously thought to be restricted to the placental tissue; however, the recent discovery of their biosynthesis in the pericarp provides new opportunities to increase the capsaicinoid content in pepper fruits. Currently, the genetic mechanisms regulating capsaicinoid biosynthesis in the pericarp remain unknown. Here, we performed quantitative trait loci (QTL) mapping and RNA sequencing (RNA-seq) to reveal the genes controlling capsaicinoid biosynthesis in the pericarp. A whole-genome sequencing-based QTL-seq strategy was employed, identifying a major QTL on chromosome 6. To validate the QTL on chromosome 6, we performed traditional QTL mapping using the same population in QTL-seq with an additional biparental population. A total of 15 QTLs for capsaicinoid content distributed on chromosomes 3, 6, and 11 were newly identified. Among these QTLs, the genetic loci on the lower arm of chromosome 6 were commonly detected in the two mapping populations, corresponding to the location of the major QTL detected using whole-genome sequencing-based QTL-seq. Our RNA-seq analysis identified candidate genes within the common QTL that were differentially expressed in the pungent and non-pungent pericarp tissues. Our results are expected to contribute to the elucidation of the regulation of capsaicinoid biosynthesis. We also demonstrated that a combination of QTL mapping and RNA-seq is helpful for refining the candidate genes of a complicated trait of interest.

Isolation and characterization of Aquaporin 1 (AQP1), sodium/potassium-transporting ATPase subunit alpha-1 (Na/K-ATPase α1), Heat Shock Protein 90 (HSP90), Heat Shock Cognate 71 (HSC71), Osmotic Stress Transcription Factor 1 (OSTF1) and Transcription Factor II B (TFIIB) genes from a euryhaline fish, Etroplus suratensis.

The present study reports the complete sequences of Aquaporin 1 (AQP1) gene and partial sequences of genes, Sodium/potassium-transporting ATPase subunit alpha-1 (Na/K-ATPase α1 subunit), Osmotic Stress Transcription Factor 1 (OSTF1), Transcription Factor II B (TFIIB), Heat Shock Cognate 71 (HSC71) and Heat Shock Protein 90 (HSP90) obtained from mRNA and genomic DNA of Etroplus suratensis. They are candidate genes involved in stress responses of fishes. AQP1 gene was 2163bp long. Its mRNA sequence has 55bp 5' UTR, 783bp open reading frame (ORF), 119bp 3' UTR, three intronic regions and 90% identity with AQP1 of Oreochromis niloticus. The partial Na/K-ATPase α1subunit gene obtained 5998bp length with an ORF of 2213bp and 12 intronic regions. The partial OSTF1, TF IIB, HSC71 and HSP90 mRNA sequences obtained were 1473bp, 587bp, 1708bp and 151bp in length respectively. All the genes showed a high sequence similarity with respective genes reported from fishes. Comparison of AQP1 and Na/K-ATPase α1 genomic DNA sequence of E. suratensis collected from different water system showed two type of AQP1 with one synonymous mutation in exon-1 and higher sequence difference in intronic regions (including addition, deletion, transition and transversion mutations) with few synonymous and non-synonymous mutations in the exons of Na/K-ATPase α1. The sequence information of these major candidate genes involved in stress responses will help in further studies on population genetics, adaptive variations and genetic improvement programs of this cichlid species having aquaculture, ornamental and evolutionary importance.

Abstract 028: Susceptibility to Strokes in Spontaneously Hypertensive Rats Due to a Mutation in Stim1

Stroke-prone spontaneously hypertensive rats (SHR-A3/SHRSP) develop cerebrovascular disease as a result of naturally occurring genetic variation. We recently identified a novel truncating mutation in the SHR-A3 line affecting the C-terminus of STIM1, a protein involved in the store-operated Ca 2+ entry (SOCE) pathway. The SHR-B2 line, which is also hypertensive but resists end organ injury, expresses the ‘wild type’ Stim1 . Here, we test whether the emergence of cerebrovascular disease in SHR-A3 is prevented by gene rescue of Stim1 . We created a Stim1 congenic line (SHR-A3( Stim1 -B2)), in which the functional Stim1 allele was transferred from the SHR-B2 line into the stroke-prone SHR-A3 genome. SHR-A3 and SHR-A3( Stim1 -B2) rats were salt loaded (1% NaCl in drinking water) for 8 weeks starting at 20 weeks of age to induce strokes. Baseline BP measured by telemetry before salt loading was not different between SHR-A3 and SHR-A3( Stim1 -B2) rats (199.5±6.49 vs 196.26±2.431 mmHg, ns). Salt loading resulted in a progressive increase in BP in SHR-A3 rats, but was blunted in SHR-A3( Stim1 -B2) rats. Compared to SHR-A3 rats, Stim1 -rescue congenic rats had improved survival (% survival: 100 (9 of 9) vs 22.2% (2 of 9) at the end of 8 weeks) and lower neurological deficit scores (2.45±0.412 vs 1±0.00, p<0.01). Salt loading resulted in significant cerebral edema in SHR-A3 rats but not in the SHR-A3( Stim1 -B2) rats (% brain wt/body wt: 0.805±0.045 vs 0.617±0.009, p<0.01). Gross morphology of the brain revealed microbleeds and hemorrhages in 5 of 9 SHR-A3 rats. These lesions were absent in SHR-A3( Stim1 -B2) rats. Stim1 gene rescue in the congenic line was also associated with decreased susceptibility to renal injury assessed histologically at 40 weeks of age (glomerular injury: 1.915±0.086 vs 1.355±0.071, p<0.001; tubulointerstitial injury: 3.2±0.102 vs 1.69±0.112, p<0.001). Our findings identify Stim1 as a major candidate gene that promotes susceptibility to strokes as well as renal injury in spontaneously hypertensive rats.

Signatures of human-commensalism in the house sparrow genome.

House sparrows (Passer domesticus) are a hugely successful anthrodependent species; occurring on nearly every continent. Yet, despite their ubiquity and familiarity to humans, surprisingly little is known about their origins. We sought to investigate the evolutionary history of the house sparrow and identify the processes involved in its transition to a human-commensal niche. We used a whole genome resequencing dataset of 120 individuals from three Eurasian species, including three populations of Bactrianus sparrows, a non-commensal, divergent house sparrow lineage occurring in the Near East. Coalescent modelling supports a split between house and Bactrianus sparrow 11 Kya and an expansion in the house sparrow at 6 Kya, consistent with the spread of agriculture following the Neolithic revolution. Commensal house sparrows therefore likely moved into Europe with the spread of agriculture following this period. Using the Bactrianus sparrow as a proxy for a pre-commensal, ancestral house population, we performed a comparative genome scan to identify genes potentially involved with adaptation to an anthropogenic niche. We identified potential signatures of recent, positive selection in the genome of the commensal house sparrow that are absent in Bactrianus populations. The strongest selected region encompasses two major candidate genes; COL11A-which regulates craniofacial and skull development and AMY2A, part of the amylase gene family which has previously been linked to adaptation to high-starch diets in humans and dogs. Our work examines human-commensalism in an evolutionary framework, identifies genomic regions likely involved in rapid adaptation to this new niche and ties the evolution of this species to the development of modern human civilization.

Mutation Survey of Candidate Genes and Genotype–Phenotype Analysis in 20 Southeastern Chinese Patients with Axenfeld–Rieger Syndrome

ABSTRACTPurpose/aim of the study: To conduct a survey spectrum of the PITX2, FOXC1, and PRDM5 genes to reveal genotype–phenotype correlations in a cohort of Southeastern Chinese patients with Axenfeld–Rieger syndrome (ARS).Materials and methods: A total of 20 probands with ARS were recruited in Southeast China. All patients underwent full ocular and systemic examinations. Sanger sequencing was used to analyze all coding regions of and regions adjacent to PITX2, FOXC1, and PRDM5 and 13 upstream regulatory elements of PITX2. Multiplex ligation-dependent probe amplification was performed to detect gross insertions and deletions in PITX2 and FOXC1. Quantitative polymerase chain reaction was used to detect copy number variations in regulatory elements of PITX2. A bioinformatics analysis was conducted to evaluate the pathogenicity of variants.Results: Eleven mutations, including eight novel mutations, were identified in PITX2. Seven of the mutations were truncations. A genotype–phenotype correlation analysis showed that 81.8% (9/11) of patients with mutations in PITX2 developed glaucoma before reaching 10 years old. The proportion of patients without detected mutations was only 33.3% (3/9, P = 0.0399). In patient G1399, ultrasound biomicroscopy revealed that the left eye exhibited a phenotype similar to aniridia with complete angle closure and a remaining stub of iris tissue.Conclusion: This is the first genetic study of a cohort of Southeastern Chinese patients with ARS. Eight novel mutations were detected, expanding the mutation spectrum of PITX2. PITX2 may be a major candidate gene for ARS in Southeastern Chinese patients. Truncations may be the primary mutation type in PITX2. Glaucoma onset may be earlier in patients with mutations in PITX2 than in those without mutations in PITX2 and FOXC1. A block of the anterior chamber angle by the end of the iris might represent the main factor influencing the development of glaucoma in ARS patients with an asymmetric aniridia phenotype.

PO-490 Expression of cortactin and focal adhesion kinase in early stages of laryngeal tumorigenesis and clinical application for cancer risk-stratification

IntroductionCortactin (CTTN) and the Focal Adhesion Kinase (FAK) are two major candidate genes to respectively drive 11q13- and 8q24-associated aggressive behaviour in various cancers. Recent evidence uncovered their clinical relevance in early stages of tumorigenesis as promising biomarkers for cancer risk assessment.Material and methodsUsing a multicenter validation study CTTN and FAK expression was evaluated by immunohistochemistry in a cohort of 109 patients with laryngeal precancerous lesions, and correlated with clinicopathologic parameters and laryngeal cancer risk. The pathophysiological role of CTTN and FAK was further investigated using functional studies in cellular models.Results and discussionsIncreased CTTN and FAK expression was detected in 49 (41%) and 35 (32%) laryngeal dysplasias, respectively. Univariate Cox analysis showed that CTTN and FAK expression but not histological grading were significantly associated with both recurrence risk and laryngeal cancer risk. Patients carrying strong CTTN- or FAK-expressing lesions experienced the highest laryngeal cancer incidence (log-rank p<0.001). In multivariate stepwise analysis, FAK expression (HR=13.91, 95% CI 4.82–40.15; p<0.001) and alcohol consumption (HR=2.22, 95% CI 1.17–4.20; p=0.014) were significant independent predictors of laryngeal cancer development. Targeting FAK by either RNAi or pharmacological inhibitors effectively blocked cell growth, colony formation and invasion into 3D collagen matrices.ConclusionCTTN and FAK emerge as powerful predictors of laryngeal cancer risk beyond histological grading, thus encouraging their clinical application as complementary markers for risk-stratification. Furthermore, our findings unveil that pharmacological targeting of FAK could constitute a promising therapeutic strategy for HNSCC prevention and treatment.

Immunohistochemical Expression of Cortactin and Focal Adhesion Kinase Predicts Recurrence Risk and Laryngeal Cancer Risk Beyond Histologic Grading.

Background: Cortactin (CTTN) and the focal adhesion kinase (FAK) are two major candidate genes to, respectively, drive 11q13- and 8q24-associated aggressive behavior in various cancers. Recent evidence uncovered their clinical relevance in early stages of tumorigenesis as promising biomarkers for cancer risk assessment.Methods: Using a multicenter validation study, CTTN and FAK expression was evaluated by immunohistochemistry (IHC) in a cohort of 109 patients with laryngeal precancerous lesions, and correlated with clinicopathologic parameters and laryngeal cancer risk. The pathophysiologic role of CTTN and FAK was further investigated using functional studies in cellular models.Results: Positive CTTN and FAK expression (scores 2 and 3) was detected in 49 (41%) and 35 (32%) laryngeal dysplasias, respectively. Univariate Cox analysis showed that CTTN and FAK expression but not histologic grading was significantly associated with both recurrence risk and laryngeal cancer risk. Patients carrying strong CTTN- or FAK-expressing lesions (score 3) experienced the highest laryngeal cancer incidence (log-rank P < 0.001). In multivariate stepwise analysis, FAK expression [HR = 13.91; 95% CI, 4.82-40.15; P < 0.001] and alcohol consumption (HR = 2.22; 95% confidence interval, 1.17-4.20; P = 0.014) were significant independent predictors of laryngeal cancer development. Targeting FAK by either RNAi or pharmacologic inhibitors effectively blocked cell growth, colony formation, and invasion into 3D collagen matrices.Conclusions: CTTN and FAK emerge as powerful predictors of laryngeal cancer risk and recurrence risk beyond histologic grading.Impact: Our work supports the applicability of IHC CTTN and FAK as complementary markers for risk stratification in patients with laryngeal precancerous lesions. Cancer Epidemiol Biomarkers Prev; 27(7); 805-13. ©2018 AACR.

Prospects of Zinc Supplementation in Autism Spectrum Disorders and Shankopathies Such as Phelan McDermid Syndrome.

The loss of one copy of SHANK3 (SH3 and multiple ankyrin repeat domains 3) in humans highly contributes to Phelan McDermid syndrome (PMDS). In addition, SHANK3 was identified as a major autism candidate gene. Interestingly, the protein encoded by the SHANK3 gene is regulated by zinc. While zinc deficiency depletes synaptic pools of Shank3, increased zinc levels were shown to promote synaptic scaffold formation. Therefore, the hypothesis arises that patients with PMDS and Autism caused by Shankopathies, having one intact copy of SHANK3 left, may benefit from zinc supplementation, as elevated zinc may drive remaining Shank3 into the post-synaptic density (PSD) and may additional recruit Shank2, a second zinc-dependent member of the SHANK gene family. Further, elevated synaptic zinc levels may modulate E/I ratios affecting other synaptic components such as NMDARs. However, several factors need to be considered in relation to zinc supplementation such as the role of Shank3 in the gastrointestinal (GI) system—the location of zinc absorption in humans. Therefore, here, we briefly discuss the prospect and impediments of zinc supplementation in disorders affecting Shank3 such as PMDS and propose a model for most efficacious supplementation.

Genomic differentiation between swamp and river buffalo using a cattle high-density single nucleotide polymorphisms panel

Buffalo (Bubalus bubalis) is an important livestock species in many tropical and subtropical regions. In recent decades, the interest in buffalo’s milk have expanded and intensive buffalo farms start to emerge. However, breeding programs and population genetics information for this species is scarce or inexistent. The present study aims to test the suitability of the commercial high-density single nucleotide polymorphisms (SNP) genotyping panel, the Illumina BovineHD BeadChip, to estimate population genetics parameters, pedigree control and identification of common variants in major production candidate genes. From a total of 777 962 SNPs included in the panel, 20 479 were polymorphic in water buffalo at a call rate of 86% and an average expected heterozygosity (HE) of 0.306. From these, 357 were mapped within or around the flanking regions of several major candidate genes. A principal components analysis identified three different clusters, each representing pure swamp buffalo type, pure river buffalo type and admixed river buffalo. The hybrids between swamp and river buffalo were clearly identified as an intermediary cluster. The suitability of these SNPs data set for parentage and identity testing demonstrated that the combination of just 30 to 50 SNPs were enough to attain high probabilities of parentage exclusion (0.9999) in both types and identity (2.3×10−5 and 2.0×10−7) for river and swamp buffalo, respectively. Our analysis confirms the suitability of the BovineHD BeadChip to assess population structure, hybridization and identity of the water buffalo populations.

Association analysis between genetic diversity of the melanocortin4 receptor (MC4R) gene and production traits in turkey

Melanocortin receptor (MC4R) plays an important role in central melanocortin system and regulating feeding behavior in humans and birds. The current study was designed to estimate the frequency of MC4R gene polymorphism and investigate if their polymorphisms have association with production traits Turkeys (Meleagris gallopavo) by PCR-SSCP method. For this purpose, a number of 100 turkeys were randomly chosen and blood samples were collected. DNA were extracted from blood samples, and amplified a fragment of 469 bp in size from MC4R gene. Single strand conformation polymorphism technique (SSCP) was used to determine genotypes. Electrophoresis of SSCP-PCR products on 6% polyacrylamide gel indicated that the polymorphism of the MC4R gene. Also, results of electrophoresis showed that three genotypes AA, and BB, with frequencies of 0.2397, 0.4998 and 0.2605, respectively. Shanon index, Nei index and observed heterozygosity with frequencies of 0.6929, 0.4998 and 0.5208, respectively. Significant associations (P&lt;0.01) were obtained for genotypes with live body weight. But no significant relationship between the genotypes with egg performance (egg mass, mean egg weight and the number of eggs) is found. These results suggest that, the turkey MC4R gene can be selected as the major candidate gene for the carcass traits such as body weight, and at future more study is required to confirm these results in Turkey.

The molecular basis of non-syndromic orofacial clefts and tooth agenesis

Non-syndromic orofacial clefts and tooth agenesis are two of the most common craniofacial birth defects. Both of them have a complex etiology, with genetic and environmental factors involved. Additionally, the epigenetic modifications have been implicated in the pathogenesis of these structural malformations. Despite an increasing number of research studies, using a variety of methodological approaches, the role of genetic factors in the etiology of orofacial clefts and tooth agenesis is still not well elucidated. The most consistent findings across studies concerning the genetic factors influencing the risk to orofacial clefts include the association of polymorphic variants of the IRF6 gene and the chromosomal locus 8q24.21. The major candidate gene for tooth agenesis in the European populations is WNT10A; its pathogenic mutations are present in more than 50% of patients with this dental anomaly. It has been found that both orofacial clefts and tooth agenesis, which co-occurrence is often reported, may share common candidate genes.