Identification Of New Candidate Genes Research Articles

Identifying genetic determinants of forage sorghum [Sorghum bicolor (Moench)] adaptation through GWAS

BackgroundForage sorghum is a highly valued crop in livestock feed production due to its versatility, adaptability, high productivity, and resilience under adverse environmental conditions, making it a crucial option for sustainable forage production. This study aimed to investigate ninety-five forage sorghum genotypes and identify the marker – trait associations (MTAs) in adaptive traits, including yield and flowering through genome-wide association studies (GWAS).ResultsUsing 41,854 polymorphic SNPs, a GWAS involving the GLM, MLM, and FarmCPU models was performed to analyse fourteen adaptive traits. The population structure revealed the presence of two subpopulation groups. Linkage disequilibrium (LD) plots showed varying degrees of LD decay across the chromosomes, with an average LD decay of 19.49 kbp. Twelve common significant QTNs, encoding 17 putative candidate genes, were simultaneously co-detected and studied by at least two or more GWAS methods. Three QTNs were associated to days to 50% flowering; two each to leaf-to-stem ratio and number of nodes per plant; and one each to plant height, leaf width, number of leaves per plant, stem girth, and internodal length. Six candidate genes were associated with days to 50% flowering, two each with leaf width, stem girth, leaf-to-stem ratio, and number of nodes per plant, and one each with plant height, number of leaves per plant, and internodal length.ConclusionFarmCPU was identified as the most suitable and effective among all the models for controlling both false positives and false negatives. Further in-depth analysis of the newly discovered QTNs may lead to the identification of new candidate genes for the trait of interest. These studies elucidate gene functions and could transform forage sorghum breeding through marker-assisted selection and transgenic approaches, accelerating the development of superior forage sorghum varieties and enhancing global food security.

Challenges in molecular diagnosis of multiple endocrine neoplasia.

Multiple endocrine neoplasia (MEN) is a group of rare genetic diseases characterized by the occurrence of multiple tumors of the endocrine system in the same patient. The first MEN described was MEN1, followed by MEN2A, and MEN2B. The identification of the genes responsible for these syndromes led to the introduction of family genetic screening programs. More than twenty years later, not all cases of MENs have been resolved from a genetic point of view, and new clinicogenetic entities have been described. In this review, we will discuss the strategies and difficulties of genetic screening for classic and newly described MENs in a clinical setting, from limitations in sequencing, to problems in classifying variants, to the identification of new candidate genes. In the era of genomic medicine, characterization of new candidate genes and their specific tumor risk is essential for inclusion of patients in personalized medicine programs as well as to permit accurate genetic counseling to be proposed for families.

Human Exome Sequencing and Prospects for Predictive Medicine: Analysis of International Data and Own Experience.

Today, whole-exome sequencing (WES) is used to conduct the massive screening of structural and regulatory genes in order to identify the allele frequencies of disease-associated polymorphisms in various populations and thus detect pathogenic genetic changes (mutations or polymorphisms) conducive to malfunctional protein sequences. With its extensive capabilities, exome sequencing today allows both the diagnosis of monogenic diseases (MDs) and the examination of seemingly healthy populations to reveal a wide range of potential risks prior to disease manifestation (in the future, exome sequencing may outpace costly and less informative genome sequencing to become the first-line examination technique). This review establishes the human genetic passport as a new WES-based clinical concept for the identification of new candidate genes, gene variants, and molecular mechanisms in the diagnosis, prediction, and treatment of monogenic, oligogenic, and multifactorial diseases. Various diseases are addressed to demonstrate the extensive potential of WES and consider its advantages as well as disadvantages. Thus, WES can become a general test with a broad spectrum pf applications, including opportunistic screening.

Identification of New Candidate Genes Related to Semen Traits in Duroc Pigs through Weighted Single-Step GWAS.

Semen traits play a key role in the pig industry because boar semen is widely used in purebred and crossbred pigs. The production of high-quality semen is crucial to ensuring a good result in artificial insemination. With the wide application of artificial insemination in the pig industry, more and more attention has been paid to the improvement of semen traits by genetic selection. The purpose of this study was to identify the genetic regions and candidate genes associated with semen traits of Duroc boars. We used weighted single-step GWAS to identify candidate genes associated with sperm motility, sperm progressive motility, sperm abnormality rate and total sperm count in Duroc pigs. In Duroc pigs, the three most important windows for sperm motility-sperm progressive motility, sperm abnormality rate, and total sperm count-explained 12.45%, 9.77%, 15.80%, and 12.15% of the genetic variance, respectively. Some genes that are reported to be associated with spermatogenesis, testicular function and male fertility in mammals have been detected previously. The candidate genes CATSPER1, STRA8, ZSWIM7, TEKT3, UBB, PTBP2, EIF2B2, MLH3, and CCDC70 were associated with semen traits in Duroc pigs. We found a common candidate gene, STRA8, in sperm motility and sperm progressive motility, and common candidate genes ZSWIM7, TEKT3 and UBB in sperm motility and sperm abnormality rate, which confirms the hypothesis of gene pleiotropy. Gene network enrichment analysis showed that STRA8, UBB and CATSPER1 were enriched in the common biological process and participated in male meiosis and spermatogenesis. The SNPs of candidate genes can be given more weight in genome selection to improve the ability of genome prediction. This study provides further insight into the understanding the genetic structure of semen traits in Duroc boars.

A comprehensive WGS-based pipeline for the identification of new candidate genes in inherited retinal dystrophies

To enhance the use of Whole Genome Sequencing (WGS) in clinical practice, it is still necessary to standardize data analysis pipelines. Herein, we aimed to define a WGS-based algorithm for the accurate interpretation of variants in inherited retinal dystrophies (IRD). This study comprised 429 phenotyped individuals divided into three cohorts. A comparison of 14 pathogenicity predictors, and the re-definition of its cutoffs, were performed using panel-sequencing curated data from 209 genetically diagnosed individuals with IRD (training cohort). The optimal tool combinations, previously validated in 50 additional IRD individuals, were also tested in patients with hereditary cancer (n = 109), and with neurological diseases (n = 47) to evaluate the translational value of this approach (validation cohort). Then, our workflow was applied for the WGS-data analysis of 14 individuals from genetically undiagnosed IRD families (discovery cohort). The statistical analysis showed that the optimal filtering combination included CADDv1.6, MAPP, Grantham, and SIFT tools. Our pipeline allowed the identification of one homozygous variant in the candidate gene CFAP20 (c.337 C > T; p.Arg113Trp), a conserved ciliary gene, which was abundantly expressed in human retina and was located in the photoreceptors layer. Although further studies are needed, we propose CFAP20 as a candidate gene for autosomal recessive retinitis pigmentosa. Moreover, we offer a translational strategy for accurate WGS-data prioritization, which is essential for the advancement of personalized medicine.

Hearing Function: Identification of New Candidate Genes Further Explaining the Complexity of This Sensory Ability.

To date, the knowledge of the genetic determinants behind the modulation of hearing ability is relatively limited. To investigate this trait, we performed Genome-Wide Association Study (GWAS) meta-analysis using genotype and audiometric data (hearing thresholds at 0.25, 0.5, 1, 2, 4, and 8 kHz, and pure-tone averages of thresholds at low, medium, and high frequencies) collected in nine cohorts from Europe, South-Eastern USA, Caucasus, and Central Asia, for an overall number of ~9000 subjects. Three hundred seventy-five genes across all nine analyses were tagged by single nucleotide polymorphisms (SNPs) reaching a suggestive p-value (p < 10−5). Amongst these, 15 were successfully replicated using a gene-based approach in the independent Italian Salus in the Apulia cohort (n = 1774) at the nominal significance threshold (p < 0.05). In addition, the expression level of the replicated genes was assessed in published human and mouse inner ear datasets. Considering expression patterns in humans and mice, eleven genes were considered particularly promising candidates for the hearing function: BNIP3L, ELP5, MAP3K20, MATN2, MTMR7, MYO1E, PCNT, R3HDM1, SLC9A9, TGFB2, and YTHDC2. These findings represent a further contribution to our understanding of the genetic basis of hearing function and its related diseases.

A graph centrality-based approach for candidate gene prediction for type 1 diabetes.

Type 1 diabetes mellitus (T1DM) or insulin-dependent diabetes is an autoimmune disease that may pose life-threatening situations to individuals. In most cases, cytotoxic T lymphocytes (CTLs) promotes killing of islets of Langerhans in the pancreas, which harbour insulin-producing beta cells. The trigger for autoimmune attack is still unclear; therefore, identifying and targeting candidate genes are imperative to hinder its deleterious effects. In the present study, we focused on identification of new candidate genes for T1DM. For our study, we exclusively selected immune-related genes as they play a crucial role in T1DM. We constructed and analysed a human immunome signalling network (directed network) to identify the new candidate genes through various graph centrality measures combining with Gene Ontology (GO). As a result, we identified 4 new candidate genes which may act as potential drug targets for T1DM. We further validated for their disease relevance through literature survey and pathway analysis and found that 3 out of 4 predicted genes mirrored their well-established roles as potential targets for T1DM.

Identification of new candidate genes for spina bifida through exome sequencing.

Neural tube defects are a group of birth defects caused by failure of neural tube closure during development. The etiology of NTD, requiring a complex interaction between environmental and genetic factors, is not well understood. We performed whole-exome sequencing (WES) in six trios, with a single affected proband with spina bifida, to identify rare/novel variants as potential causes of the NTD. Our analysis identified four de novo and ten X-linked recessive variants in four of the six probands, all of them in genes previously never implicated in NTD. Among the 14 variants, we ruled out six of them, based on different criteria and pursued the evaluation of eight potential candidates in the following genes: RXRγ, DTX1, COL15A1, ARHGAP36, TKTL1, AMOT, GPR50, and NKRF. The de novo variants where located in the RXRγ, DTX1, and COL15A1 genes while ARHGAP36, TKTL1, AMOT, GPR50, and NKRF carry X-linked recessive variants. This analysis also revealed that four patients presented multiple variants, while we were unable to identify any significant variant in two patients. Our preliminary conclusion support a major role for the de novo variants with respect to the X-linked recessive variants where the X-linked could represent a contribution to the phenotype in an oligogenic model.

Genome wide associations study of single nucleotide polymorphisms with productivity parameters in Jalgin merino for identification of new candidate genes

A genome-wide association study (GWAS) was conducted on the frequency of occurrence of individual SNPs using the Ovine Infinium HD BeadChip 600K in sheep of the Jalgin merino breed with different class evaluations according to the phenotype determining productive qualities. Twenty-three single nucleotide polymorphisms with high significant differences in occurrence between groups of examined animals were identified. Annotation of closely located genes to determine candidate genes for productivity showed that 10 substitutions were in the introns of the protein-coding genes, and three in the intron of one gene. Two polymorphisms were located next to the genes of long non-coding RNAs, one next to the microRNA gene, and two more to the spliceosomal RNA gene. The remaining substitutions related to intergenic variants. As a result of the study, we identified the following candidate genes: FOXN3, CNTN3, FTO, CFAP73, ARPP21, ADAMTS9, FRMPD4, RBM45, SHC4, ZFP36L1, ACTN1, ASTN1, RAB21. Most of these genes are regulatory, determining the intensity of growth and development of cells and tissues. The detected substitutions, significantly differing in frequency between the groups of animals examined, can be used as genetic markers of productivity in breeding work to improve the quality of Jalgin merino and other sheep breeds.

Manipulating Amino Acid Metabolism to Improve Crop Nitrogen Use Efficiency for a Sustainable Agriculture.

In a context of a growing worldwide food demand coupled to the need to develop a sustainable agriculture, it is crucial to improve crop nitrogen use efficiency (NUE) while reducing field N inputs. Classical genetic approaches based on natural allelic variations existing within crops have led to the discovery of quantitative trait loci controlling NUE under low nitrogen conditions; however, the identification of candidate genes from mapping studies is still challenging. Amino acid metabolism is the cornerstone of plant N management, which involves N uptake, assimilation, and remobilization efficiencies, and it is finely regulated during acclimation to low N conditions and other abiotic stresses. Over the last two decades, biotechnological engineering of amino acid metabolism has led to promising results for the improvement of crop NUE, and more recently under low N conditions. This review summarizes current work carried out in crops and provides perspectives on the identification of new candidate genes and future strategies for crop improvement.

A Profile of Candidate Causal Genes of Spontaneous Coronary Artery Dissection Identified Through Machine Learning

Background: Spontaneous coronary artery dissection (SCAD), defined as the dissection of coronary arterial intima and media, is a genetic disorder but currently only two genes, PHACTR1 and TSR1, have been reported as it is not strongly familial. Given the limitations of association tests such as genome wide association test and gene based association test, we applied a new strategy of machine learning for identification of new candidate genes. Methods: Whole exome sequencing (WES) was performed on 85 SCAD cases and 285 controls, as well as 60 SCAD cases in replication cohort, recruited from Tongji Hospital, Wuhan, China. Accumulated gene burden scores were computed based on average scores of VEST3, MetaLR and M-CAP annotated by ANNOVAR. A machine learning model was constructed to identify candidate causal genes of SCAD by logistic regression with penalty. Findings: The machine learning model identified 116 genes associated with SCAD, whose mutational burden was elevated in cases relative to controls and yielded an area under curve area of 0.83 in cross validation. Compared to control group, patients with SCAD carried more rare deleterious variants of machine learning identified genes. Multiple variants in different machine learning identified genes were more prevalent in SCAD cohort. In a replication cohort, 73 genes were confirmed, with FBN3 ranking the top. Specifically, two deleterious variants of FBN3 were exactly the same as in discovery cohort. Interpretation: We built a machine learning model and identified a profile of candidate genes associated with SCAD where rare deleterious and multiple variants were enriched in patients with SCAD. Funding Statement: This work was supported in part by key grants from National Key R&D Program of China (No. 2017YFC0909400), National Nature Science Foundation of China (No. 91839302 and 81790624), Shanghai Municipal Science and Technology Major Project (No. 2017SHZDZX01) and Major Project of Technological Innovation of Hubei province (No. 2017ACA170). Declaration of Interests: All authors declares no conflict of interests Ethics Approval Statement: The study protocol was approved by the Tongji Hospital Review Board and all participants have signed written informed content.

Identification of new candidate genes and signalling pathways associated with the development of neuroendocrine pancreatic tumours based on next generation sequencing data.

Despite advances in classification, treatment, and imaging, neuroendocrine tumours remain a clinically complex subject. In this work, we studied the genetic profile of well-differentiated pancreatic neuroendocrine tumours (PanNETs) in a cohort of Caucasian patients and analysed the signalling pathways and candidate genes potentially associated with the development of this oncological disease. Twenty-four formalin-fixed paraffin-embedded (FFPE) samples of well-differentiated PanNETs were subjected to massive parallel sequencing using the targeted gene panel (409 genes) of the Illumina NextSeq 550 platform (San Diego, USA). In 24 patients, 119 variants were identified in 54 genes. The median mutation rate per patient was 5 (2.8-7). The detected genetic changes were dominated by missense mutations (67%) and nonsense mutations (29%). 18% of the mutations were activating, 35% of the variants led to a loss of function of the encoded protein, and 52% were not classified. Twenty-six variants were described as new. Functionally significant changes in the tertiary structure and activity of the protein molecules in an in silico assay were predicted for 5 new genetic variants. The 5 highest priority candidate genes were selected: CREB1, TCF12, PRKAR1A, BCL11A, and BUB1B. Genes carrying the identified mutations participate in signalling pathways known to be involved in PanNETs; in addition, 38% of the cases showed genetic changes in the regulation of the SMAD2/3 signalling pathway. Well-differentiated PanNETs in a Russian cohort demonstrate various molecular genetic features, including new genetic variations and potential driver genes. The highlighted molecular genetic changes in the SMAD2/3 signalling pathway suggest new prospects for targeted therapy.

Dynamics of the transcriptional landscape during human fetal testis and ovary development.

Which transcriptional program triggers sex differentiation in bipotential gonads and downstream cellular events governing fetal testis and ovary development in humans? The characterization of a dynamically regulated protein-coding and non-coding transcriptional landscape in developing human gonads of both sexes highlights a large number of potential key regulators that show an early sexually dimorphic expression pattern. Gonadal sex differentiation is orchestrated by a sexually dimorphic gene expression program in XX and XY developing fetal gonads. A comprehensive characterization of its non-coding counterpart offers promising perspectives for deciphering the molecular events underpinning gonad development and for a complete understanding of the etiology of disorders of sex development in humans. To further investigate the protein-coding and non-coding transcriptional landscape during gonad differentiation, we used RNA-sequencing (RNA-seq) and characterized the RNA content of human fetal testis (N = 24) and ovaries (N = 24) from 6 to 17 postconceptional week (PCW), a key period in sex determination and gonad development. First trimester fetuses (6-12 PCW) and second trimester fetuses (13-14 and 17 PCW) were obtained from legally induced normally progressing terminations of pregnancy. Total RNA was extracted from whole human fetal gonads and sequenced as paired-end 2 × 50 base reads. Resulting sequences were mapped to the human genome, allowing for the assembly and quantification of corresponding transcripts. This RNA-seq analysis of human fetal testes and ovaries at seven key developmental stages led to the reconstruction of 22 080 transcripts differentially expressed during testicular and/or ovarian development. In addition to 8935 transcripts displaying sex-independent differential expression during gonad development, the comparison of testes and ovaries enabled the discrimination of 13 145 transcripts that show a sexually dimorphic expression profile. The latter include 1479 transcripts differentially expressed as early as 6 PCW, including 39 transcription factors, 40 long non-coding RNAs and 20 novel genes. Despite the use of stringent filtration criteria (expression cut-off of at least 1 fragment per kilobase of exon model per million reads mapped, fold change of at least 2 and false discovery rate adjusted P values of less than <1%), the possibility of assembly artifacts and of false-positive differentially expressed transcripts cannot be fully ruled out. Raw data files (fastq) and a searchable table (.xlss) containing information on genomic features and expression data for all refined transcripts have been submitted to the NCBI GEO under accession number GSE116278. The intrinsic nature of this bulk analysis, i.e. the sequencing of transcripts from whole gonads, does not allow direct identification of the cellular origin(s) of the transcripts characterized. Potential cellular dilution effects (e.g. as a result of distinct proliferation rates in XX and XY gonads) may account for a few of the expression profiles identified as being sexually dimorphic. Finally, transcriptome alterations that would result from exposure to pre-abortive drugs cannot be completely excluded. Although we demonstrated the high quality of the sorted cell populations used for experimental validations using quantitative RT-PCR, it cannot be totally excluded that some germline expression may correspond to cell contamination by, for example, macrophages. For the first time, this study has led to the identification of 1000 protein-coding and non-coding candidate genes showing an early, sexually dimorphic, expression pattern that have not previously been associated with sex differentiation. Collectively, these results increase our understanding of gonad development in humans, and contribute significantly to the identification of new candidate genes involved in fetal gonad differentiation. The results also provide a unique resource that may improve our understanding of the fetal origin of testicular and ovarian dysgenesis syndromes, including cryptorchidism and testicular cancers. This work was supported by the French National Institute of Health and Medical Research (Inserm), the University of Rennes 1, the French School of Public Health (EHESP), the Swiss National Science Foundation [SNF n° CRS115_171007 to B.J.], the French National Research Agency [ANR n° 16-CE14-0017-02 and n° 18-CE14-0038-02 to F.C.], the Medical Research Council [MR/L010011/1 to P.A.F.] and the European Community's Seventh Framework Programme (FP7/2007-2013) [under grant agreement no 212885 to P.A.F.] and from the European Union's Horizon 2020 Research and Innovation Programme [under grant agreement no 825100 to P.A.F. and S.M.G.]. There are no competing interests related to this study.

Genome-Wide DNA Methylation Patterns in Suicide Victims: Identification of New Candidate Genes.

Suicide is a major global public health problem with significant impact on society. According to the World Health Organization, every year about 800.000 people commit suicide, while at the global level suicide accounts for 50% of all violent deaths among men and for 71% among women. Suicide is a complex phenomenon which cannot be attributed to a single causal factor, but to a combination of simultaneous effects of multiple factors which are expressed in the form of psychological, biological and sociological indicators. Analysis of epigenetic mechanisms (methylation of the DNA, modifications of histone proteins and (networks of) miRNA), which link the interaction between genes and the environment, could importantly contribute to better understanding of suicidal behaviour. Recent studies on suicidal behaviour and DNA methylation show differences in DNA methylation pattern, with numerous sites among suicide victims. Using next generation sequencing, genome-wide studies helped identify novel candidate genes while studies of already known candidate genes (such as glucocorticoid receptor and BDNF) gave us better insight into the interplay of genetics and epigenetics. Epigenetic studies importantly contribute to elucidation of new biomarkers for suicidal behaviour. However, present studies are very different in design and often performed on very small samples, and these limitations could be overcome with more careful study preparation.

Integrated Analysis of Germline and Tumor DNA Identifies New Candidate Genes Involved in Familial Colorectal Cancer.

Colorectal cancer (CRC) shows aggregation in some families but no alterations in the known hereditary CRC genes. We aimed to identify new candidate genes which are potentially involved in germline predisposition to familial CRC. An integrated analysis of germline and tumor whole-exome sequencing data was performed in 18 unrelated CRC families. Deleterious single nucleotide variants (SNV), short insertions and deletions (indels), copy number variants (CNVs) and loss of heterozygosity (LOH) were assessed as candidates for first germline or second somatic hits. Candidate tumor suppressor genes were selected when alterations were detected in both germline and somatic DNA, fulfilling Knudson’s two-hit hypothesis. Somatic mutational profiling and signature analysis were also performed. A series of germline-somatic variant pairs were detected. In all cases, the first hit was presented as a rare SNV/indel, whereas the second hit was either a different SNV (3 genes) or LOH affecting the same gene (141 genes). BRCA2, BLM, ERCC2, RECQL, REV3L and RIF1 were among the most promising candidate genes for germline CRC predisposition. The identification of new candidate genes involved in familial CRC could be achieved by our integrated analysis. Further functional studies and replication in additional cohorts are required to confirm the selected candidates.

Identification of New Candidate Genes in Patients With Mitochondrial Disease by High Resolution Chromosome Analysis on DNA Chip

Identification of New Candidate Genes in Patients With Mitochondrial Disease by High Resolution Chromosome Analysis on DNA Chip

Whole genome sequencing of breast cancer

Breast cancer was the first to take advantage of targeted therapy using endocrine therapy, and for up to 20% of all breast cancer patients a further significant improvement has been obtained by HER2‐targeted therapy. Greater insight in precision medicine is to some extent driven by technical and computational progress, with the first wave of a true technical advancement being the application of transcriptomic analysis. Molecular subtyping further improved our understanding of breast cancer biology and has through a new tumor classification enabled allocation of personalized treatment regimens. The next wave in technical progression must be next‐generation‐sequencing which is currently providing new and exciting results. Large‐scale sequencing data unravel novel somatic and potential targetable mutations as well as allowing the identification of new candidate genes predisposing for familial breast cancer. So far, around 15% of all breast cancer patients are genetically predisposed with most genes being factors in pathways implicated in genome maintenance. This review focuses on whole‐genome sequencing and the new possibilities that this technique, together with other high‐throughput analytic approaches, provides for a more individualized treatment course of breast cancer patients.

Proliferative Sickle Cell Retinopathy in SS and SC Hemoglobinopathies: Identification of New Candidate Genes

Retinopathy is one of the major clinical manifestations of sickle cell disease. Its clinical aspects vary depending on the presence or absence of vaso-proliferation, classifying this complication as non-proliferative and proliferative sickle cell retinopathy (PSCR). Endothelial cell activation, injury and dysfunction are importantly involved with pathophysiological mechanisms of sickle cell disease and its complications such as vascular disease. In this study we compared the gene expression profile of endothelial progenitor cells from patients with sickle cell disease and proliferative retinopathy versus without retinopathy. Endothelial Colony-Forming Cells (ECFC) were isolated and cultured from peripheral blood samples of three HbSS patients (Group I) and six HbSC patients (Group II) with proliferative retinopathy as well as from three HbSS patients (Group III) and four HbSC patients (Group IV) without retinopathy. Ophthalmologic evaluation: fundus biomicroscopy, retinal mapping and retinography was performed in all patients. The isolated ECFC were characterized by cobblestone morphology and flow cytometry. RNA was extracted from the cells and transcriptome analysis was performed by next-generation sequencing (RNA-seq). Differentially expressed genes were identified through DESeq2 package. Comparative transcriptome analysis between groups I and III has identified 16 differentially expressed transcripts, 10 negatively regulated and 5 positively regulated. Among these genes, we highlight the most upregulated genes, CDCP1 and NR5A2.The expression of CDCP1 (log2FoldChange = 3,712 and padj value = 0.007) and NR5A2 (log2FoldChange = 3,021 and padj value = 0.019) genes was higher in HbSS patients with PSCR than in patients without retinopathy.On the other side, comparative transcriptome analysis between groups II and IV has identified 34 differentially expressed transcripts, 24 negatively regulated and 10 positively regulated. Among these genes, we highlight the most upregulated genes, ROBO1 and SLC38A5. Importantly, the expression of ROBO1 (log2FoldChange = 4,325 and padj value = 1,35E-11)and SLC38A5 (log2FoldChange = 3,364 and padj value = 1,59E-07)genes was significantly higher in HbSC patients with PSCR than in patients without retinopathy. CDCP1 has been proposed to play a role in regulation of cell differentiation and proliferation through interactions with extracellular matrix.NR5A2 is a constitutively active orphan nuclear receptor. Some of the pathways regulated by nuclear receptors includeangiogenesis, inflammation, and lipid metabolic dysregulation, mechanisms also important in the initiation and development of several retinal diseases.The ROBO1-mediated pathway has been proposed as a target for the treatment of several ocular neovascular diseases. The SLC38A5 gene is the principal mediator of glutamine transport in retinal Müller cells. Since glutamine metabolism is crucial for vessel formation, the blockage of SLC38A5 transporter deserves further attention as an alternative strategy to the inhibition of pathological angiogenesis. Our data suggest that specific pathways can be involved in PSCR of SS and SC hemoglobinopathies. Treatment for PSCR remains palliative, so therapeutic strategies blocking these pathways may contribute to the future development of novel therapies. DisclosuresOzelo:BioMarin: Honoraria, Speakers Bureau; Grifols: Honoraria; Novo Nordisk: Honoraria, Research Funding, Speakers Bureau; Pfizer: Honoraria, Research Funding, Speakers Bureau; Shire: Honoraria, Research Funding, Speakers Bureau; Bioverativ: Honoraria, Research Funding.

Prioritization of Candidate Genes in QTL Regions for Physiological and Biochemical Traits Underlying Drought Response in Barley (Hordeum vulgare L.).

Drought is one of the most adverse abiotic factors limiting growth and productivity of crops. Among them is barley, ranked fourth cereal worldwide in terms of harvested acreage and production. Plants have evolved various mechanisms to cope with water deficit at different biological levels, but there is an enormous challenge to decipher genes responsible for particular complex phenotypic traits, in order to develop drought tolerant crops. This work presents a comprehensive approach for elucidation of molecular mechanisms of drought tolerance in barley at the seedling stage of development. The study includes mapping of QTLs for physiological and biochemical traits associated with drought tolerance on a high-density function map, projection of QTL confidence intervals on barley physical map, and the retrievement of positional candidate genes (CGs), followed by their prioritization based on Gene Ontology (GO) enrichment analysis. A total of 64 QTLs for 25 physiological and biochemical traits that describe plant water status, photosynthetic efficiency, osmoprotectant and hormone content, as well as antioxidant activity, were positioned on a consensus map, constructed using RIL populations developed from the crosses between European and Syrian genotypes. The map contained a total of 875 SNP, SSR and CGs, spanning 941.86 cM with resolution of 1.1 cM. For the first time, QTLs for ethylene, glucose, sucrose, maltose, raffinose, α-tocopherol, γ-tocotrienol content, and catalase activity, have been mapped in barley. Based on overlapping confidence intervals of QTLs, 11 hotspots were identified that enclosed more than 60% of mapped QTLs. Genetic and physical map integration allowed the identification of 1,101 positional CGs within the confidence intervals of drought response-specific QTLs. Prioritization resulted in the designation of 143 CGs, among them were genes encoding antioxidants, carboxylic acid biosynthesis enzymes, heat shock proteins, small auxin up-regulated RNAs, nitric oxide synthase, ATP sulfurylases, and proteins involved in regulation of flowering time. This global approach may be proposed for identification of new CGs that underlies QTLs responsible for complex traits.

Identification of new candidate genes for retinopathy in type 2 diabetics. Valencia Study on Diabetic Retinopathy (VSDR). Report number 3

Abstract Objective To identify genes involved in the pathogenic mechanisms of non-proliferative diabetic retinopathy (NPDR), among which include oxidative stress, extracellular matrix changes, and/or apoptosis, in order to evaluate the risk of developing this retinal disease in a type 2 diabetic (DM2) population. Material and methods A case–control study was carried out on 81 participants from the Valencia Study on Diabetic Retinopathy (VSDR) of both genders, with ages 25–85 years. They were classified into: (i) DM2 group (n = 49), with DR (+DR; n = 14) and without DR (−DR; n = 35), and (ii) control group (GC; n = 32). The protocols included a personal interview, standardized ophthalmological examination, and blood collection (to analyze the DNA for determining the gene expression (TP53, MMP9, and SLC23A2) in the study groups). Statistical analyses were performed using the SPSS v22.0 program. Results The TP53 and MMP9 genes showed a higher expression in the DM2 group compared to the GC, although the difference was only significant for the MMP9 gene (TP53: 10.40 ± 1.20 vs. 8.23 ± 1.36, p = 0.084; MMP9: 1.45 ± 0.16 vs. 0.95 ± 0.16, p = 0.036), and the SLC23A2 gene showed a significant lower expression in the DM2 vs. CG (5.58 ± 0.64 vs. 11.66 ± 1.90, p = 0.026). When sub-dividing the DM2 group according to the presence of retinopathy, the expression of the TP53, MMP9 and SLC23A2 genes showed significant differences between the DM2−RD, DM2+RD and GC groups (TP53: 9.95 ± 1.47 vs. 11.52 ± 2.05 vs. 8.23 ± 1.36, p = 0.038; MMP9: 1.47 ± 0.20 vs. 1.41 ± 0.27 vs. 0.95 ± 0.16, p = 0.021; SLC23A2: 5.61 ± 0.77 vs. 5.51 ± 1.21 vs. 11.66 ± 1.90, p = 0.018). Conclusions Genes involved in extracellular matrix integrity (MMP9) and/or apoptosis (TP53), could be considered potential markers of susceptibility to the development/progression of NPDR. Interestingly, the SLC232A2 gene (ascorbic acid transporter) can be considered a protector of the risk of the development/progression of the retinopathy.