Identification Of Novel Candidate Genes Research Articles

7644 Novel Candidate Genes for SRY-Negative 46,XX Differences of Sex Development with Testicular Differentiation

Abstract Disclosure: M.M. Ferrari: None. M.Y. Nishi: None. A.A. Jorge: None. A.F. Benedetti,: None. R.L. Batista: None. E.S. Silva: None. A. Martinez: None. V. Mericq: None. F.M. Carvalho: None. B.B. Mendonca: None. S. Domenice: None. Introduction: Gonadal development in mammals is a dynamic and complex process, which requires the interaction of multiple factors in a meticulous feedback control and self-regulation system. Defects in genes involved in this process may cause differences of sex development (DSD). In rare cases, the gonads of 46,XX individuals differentiate completely into testes (46,XX testicular DSD, 46,XX TDSD), or with the coexistence of testicular and ovarian tissues in the same individual (46,XX ovotesticular DSD, 46,XX OTDSD). Strategies of large-scale parallel sequencing have enabled the simultaneous analysis of known genes, as well as the identification of novel candidate genes contributing to molecular diagnosis of these conditions. Objective: To establish the molecular diagnosis of a cohort of SRY-negative 46,XX T/OTDSD patients using the whole exome sequencing (WES) technique. Patients and Methods: Twenty-three families (24 patients) were evaluated, 22 patients with sporadic disease, and one family with two affected siblings. Histological diagnosis of OTDSD was confirmed in all patients, except in two with the presumptive (non-histological) diagnosis of TDSD. WES was performed using the Illumina platform. The variants were classified according to ACMG criteria. Results: Six different candidate genes associated with the 46,XX DSD phenotype were identified in the 23 families (26%) studied; all in patients with OTDSD diagnosis. Two variants were classified as likely pathogenic in FLNB and SOX10 genes, and four as VUS in IMMP2L, SOX8, PRKACG, and CLASP1 genes. The unavailability of analysis of case-parent trio samples hampered the classification of some of the novel candidate allelic variants. All these candidate genes were selected as potential causes of OTDSD, based on evidence of direct or indirect interactions of these proteins with SOX9. In the two siblings with 46,XX OTDSD, the allelic variant c.397delT (p.Ser133Leufs*7) in IMMP2L was identified in a heterozygous state and was absent in the unaffected family members (mother and third XY sibling). A potential role of Immp2l had been previously associated with the etiology of XX female-to-male sex reversal in sheep lineage. Conclusion: Although establishing the genetic etiology of gonadal development abnormalities in individuals with 46,XX TDSD/OTDSD remains a challenge, the results of this study generated new information and perspectives on the mechanisms involved in gonadal development. Presentation: 6/3/2024

Considerations for reporting variants in novel candidate genes identified during clinical genomic testing

Since the first novel gene discovery for a Mendelian condition was made via exome sequencing, the rapid increase in the number of genes known to underlie Mendelian conditions coupled with the adoption of exome (and more recently, genome) sequencing by diagnostic testing labs has changed the landscape of genomic testing for rare diseases. Specifically, many individuals suspected to have a Mendelian condition are now routinely offered clinical ES. This commonly results in a precise genetic diagnosis but frequently overlooks the identification of novel candidate genes. Such candidates are also less likely to be identified in the absence of large-scale gene discovery research programs. Accordingly, clinical laboratories have both the opportunity, and some might argue a responsibility, to contribute to novel gene discovery, which should, in turn, increase the diagnostic yield for many conditions. However, clinical diagnostic laboratories must necessarily balance priorities for throughput, turnaround time, cost efficiency, clinician preferences, and regulatory constraints and often do not have the infrastructure or resources to effectively participate in either clinical translational or basic genome science research efforts. For these and other reasons, many laboratories have historically refrained from broadly sharing potentially pathogenic variants in novel genes via networks such as Matchmaker Exchange, much less reporting such results to ordering providers. Efforts to report such results are further complicated by a lack of guidelines for clinical reporting and interpretation of variants in novel candidate genes. Nevertheless, there are myriad benefits for many stakeholders, including patients/families, clinicians, and researchers, if clinical laboratories systematically and routinely identify, share, and report novel candidate genes. To facilitate this change in practice, we developed criteria for triaging, sharing, and reporting novel candidate genes that are most likely to be promptly validated as underlying a Mendelian condition and translated to use in clinical settings.

Considerations for reporting variants in novel candidate genes identified during clinical genomic testing.

Since the first novel gene discovery for a Mendelian condition was made via exome sequencing (ES), the rapid increase in the number of genes known to underlie Mendelian conditions coupled with the adoption of exome (and more recently, genome) sequencing by diagnostic testing labs has changed the landscape of genomic testing for rare disease. Specifically, many individuals suspected to have a Mendelian condition are now routinely offered clinical ES. This commonly results in a precise genetic diagnosis but frequently overlooks the identification of novel candidate genes. Such candidates are also less likely to be identified in the absence of large-scale gene discovery research programs. Accordingly, clinical laboratories have both the opportunity, and some might argue a responsibility, to contribute to novel gene discovery which should in turn increase the diagnostic yield for many conditions. However, clinical diagnostic laboratories must necessarily balance priorities for throughput, turnaround time, cost efficiency, clinician preferences, and regulatory constraints, and often do not have the infrastructure or resources to effectively participate in either clinical translational or basic genome science research efforts. For these and other reasons, many laboratories have historically refrained from broadly sharing potentially pathogenic variants in novel genes via networks like Matchmaker Exchange, much less reporting such results to ordering providers. Efforts to report such results are further complicated by a lack of guidelines for clinical reporting and interpretation of variants in novel candidate genes. Nevertheless, there are myriad benefits for many stakeholders, including patients/families, clinicians, researchers, if clinical laboratories systematically and routinely identify, share, and report novel candidate genes. To facilitate this change in practice, we developed criteria for triaging, sharing, and reporting novel candidate genes that are most likely to be promptly validated as underlying a Mendelian condition and translated to use in clinical settings.

Transcriptome analysis reveals the molecular mechanism of differences in growth between photoautotrophy and heterotrophy in Chlamydomonas reinhardtii.

The green alga Chlamydomonas reinhardtii can grow photoautotrophically utilizing light and CO2, and heterotrophically utilizing acetate. The physiological and biochemical responses of autotrophy and heterotrophy are different in C. reinhardtii. However, there is no complete understanding of the molecular physiology between autotrophy and heterotrophy. Therefore, we performed biochemical, molecular and transcriptome analysis of C. reinhardtii between autotrophy and heterotrophy. The cell growth characterization demonstrated that heterotrophic cell had enhanced growth rates, and autotrophic cell accumulated more chlorophyll. The transcriptome data showed that a total of 2,970 differentially expressed genes (DEGs) were identified from photoautotrophy 12h (P12h) to heterotrophy 12h (H12h). The DEGs were involved in photosynthesis, the tricarboxylic acid cycle (TCA), pyruvate and oxidative phosphorylation metabolisms. Moreover, the results of qRT-PCR revealed that the relative expression levels of malate dehydrogenase (MDH), succinate dehydrogenase (SDH), ATP synthase (ATPase), and starch synthase (SSS) were increased significantly from P12h and H12h. The protein activity of NAD-malate dehydrogenase (NAD-MDH) and succinate dehydrogenase (SDH) were significantly higher in the H12h group. The above results indicated that the high growth rate observed in heterotrophic cell may be the effects of environmental or genetic regulation of photosynthesis. Therefore, the identification of novel candidate genes in heterotrophy will contribute to the development of microalga strains with higher growth capacity and better performance for biomass production.

Molecular findings in patients for whole exome sequencing and mitochondrial genome assessment

ObjectiveWhole exome sequencing (WES) is becoming more widely used as a diagnostic tool in the field of medicine. In this article, we reported the diagnostic yield of WES and mitochondrial genome assessment in 2226 consecutive cases in a single clinical laboratory. Materials and methodsWe retrospectively analyzed consecutive WES reports from 2226 patients with various genetic disorders. WES-process was focused exclusively on the probands and aimed at a higher diagnostic capacity. We determined the diagnostic rate of WES overall and by phenotypic category, mode of inheritance, mitochondrial genome variant, and copy number variants (CNVs). ResultsAmong the 2226 patients who had diagnostic WES proband-only, the overall diagnostic yield of WES was 34.59% (770/2226). The highest diagnostic yield was observed in autosomal dominant disorders, at 45.58% (351/770), followed by autosomal recessive at 31.95%(246/770), X-linked disorder at 9.61%(74/770), and mitochondrial diseases at a notably lower 0.65%(5/770). The 12.21% (94/770) diagnoses were based on a total of 94 copy number variants reported from WES data. CNVs in children accounted for 67.02% of the total CNVs. While majority of the molecular diagnoses were related to nuclear genes, the inclusion of mitochondrial genome sequencing in the WES test contributed to five diagnoses. all mitochondrial diseases were identified in adults. ConclusionsThe proband-only WES provided a definitive molecular diagnosis for 34.59% of a large cohort of patients while analysis of WES simultaneously analyzed the SNVs, exons, mitochondrial genome, and CNVs, thereby improving the diagnostic yield significantly compared to the single-detection WES method; and facilitating the identification of novel candidate genes.

Whole exome sequencing of 491 individuals with inherited retinal diseases reveals a large spectrum of variants and identification of novel candidate genes

BackgroundInherited retinal diseases (IRDs) include a range of vision loss conditions caused by variants in different genes. The clinical and genetic heterogeneity make identification of the genetic cause challenging. Here,...

Identification of novel candidate genes associated with non-syndromic tooth agenesis in Mongolian families

ObjectivesThis study aimed to identify genetic variants associated with non-syndromic tooth agenesis (TA) in nine families from Mongolia using whole-exome sequencing (WES) and bioinformatics analysis.Material and methodsThe study enrolled 41 participants, including three inherited and six non-inherited families. WES analysis was performed on 14 saliva samples from individuals with non-syndromic TA. The potential candidate genes were identified through variant filtering and segregation analysis. The filtered variants were then analyzed in silico mutation impact analysis.ResultsWES analysis identified 21 variants associated with TA, and 5 of these variants met all filtering criteria. These variants were located in the exome region of MAST4, ITGA6, PITX2, CACNA1S, and CDON genes. The variant in PITX2 was found in eight participants from inherited and non-inherited families, while the MAST4 variant was identified in 6 participants from inherited families.ConclusionsThe study identified various genetic variant candidates associated with TA in different family groups, with PITX2 being the most commonly identified. Our findings suggest that MAST4 may also be a novel candidate gene for TA due to its association with the Wnt signaling pathway. Additionally, we found that five candidate genes related to focal adhesion and calcium channel complex were significant and essential in tooth development.Clinical relevanceIdentifying new pathogenic genes associated with TA can improve our understanding of the molecular mechanisms underlying the disease, leading to better diagnosis, prevention, and treatment. Early detection of TA based on biomarkers can improve dental management and facilitate orthodontic and prosthetic treatment.

Associative gene networks reveal novel candidates important for ADHD and dyslexia comorbidity

BackgroundAttention deficit hyperactivity disorder (ADHD) is commonly associated with developmental dyslexia (DD), which are both prevalent and complicated pediatric neurodevelopmental disorders that have a significant influence on children’s learning and development. Clinically, the comorbidity incidence of DD and ADHD is between 25 and 48%. Children with DD and ADHD may have more severe cognitive deficiencies, a poorer level of schooling, and a higher risk of social and emotional management disorders. Furthermore, patients with this comorbidity are frequently treated for a single condition in clinical settings, and the therapeutic outcome is poor. The development of effective treatment approaches against these diseases is complicated by their comorbidity features. This is often a major problem in diagnosis and treatment. In this study, we developed bioinformatical methodology for the analysis of the comorbidity of these two diseases. As such, the search for candidate genes related to the comorbid conditions of ADHD and DD can help in elucidating the molecular mechanisms underlying the comorbid condition, and can also be useful for genotyping and identifying new drug targets.ResultsUsing the ANDSystem tool, the reconstruction and analysis of gene networks associated with ADHD and dyslexia was carried out. The gene network of ADHD included 599 genes/proteins and 148,978 interactions, while that of dyslexia included 167 genes/proteins and 27,083 interactions. When the ANDSystem and GeneCards data were combined, a total of 213 genes/proteins for ADHD and dyslexia were found. An approach for ranking genes implicated in the comorbid condition of the two diseases was proposed. The approach is based on ten criteria for ranking genes by their importance, including relevance scores of association between disease and genes, standard methods of gene prioritization, as well as original criteria that take into account the characteristics of an associative gene network and the presence of known polymorphisms in the analyzed genes. Among the top 20 genes with the highest priority DRD2, DRD4, CNTNAP2 and GRIN2B are mentioned in the literature as directly linked with the comorbidity of ADHD and dyslexia. According to the proposed approach, the genes OPRM1, CHRNA4 and SNCA had the highest priority in the development of comorbidity of these two diseases. Additionally, it was revealed that the most relevant genes are involved in biological processes related to signal transduction, positive regulation of transcription from RNA polymerase II promoters, chemical synaptic transmission, response to drugs, ion transmembrane transport, nervous system development, cell adhesion, and neuron migration.ConclusionsThe application of methods of reconstruction and analysis of gene networks is a powerful tool for studying the molecular mechanisms of comorbid conditions. The method put forth to rank genes by their importance for the comorbid condition of ADHD and dyslexia was employed to predict genes that play key roles in the development of the comorbid condition. The results can be utilized to plan experiments for the identification of novel candidate genes and search for novel pharmacological targets.

P-696 Identification of novel candidate genes associated with meitotic aneuploidy in human embryos by whole-exome sequencing (WES)

Abstract Study question Can certain genetic variants in women cause a genetic predisposition to aneuploidy? Summary answer Our results suggest that the maternal variants identified in genes regulating meiotic processes could be useful genetic biomarkers for predicting a predisposition to embryonic aneuploidies. What is known already Errors in chromosome segregation during meiosis as chromosome synapsis, crossing-over and spindle building, occur frequently in human oocytes and cause aneuploidy in embryos. These errors increase dramatically in the oocytes of older women. However, the rate of producing aneuploidy oocytes varies among IVF patients for a given age. Recent publications have identified genetic variants that are crucial for producing healthy oocytes in female IVF patients. The association between maternal genetic variants and embryonic aneuploidy risk suggests the potential of using genomic data to predict embryonic aneuploidy risk. Our aim was to identify novel variants and candidate genes for embryonic aneuploidy. Study design, size, duration A prospective observational cohort study was done including 127 trophoectoderm biopsies from 29 couples who performed whole-exome sequencing (WES) and PGT-A between November 2019 and March 2022. Women were 35 years old or younger and normal karyotype for men and women. Patients were divided in two groups according to the embryo aneuploidy rate expected by their maternal age: ≤ 50% of aneuploid blastocysts as control group(n = 14), and ≥ 50% of aneuploid blastocysts as study group(n = 15). Participants/materials, setting, methods WES was performed using Trusight One Expanded Sequencing Panel (Illumina®). The following criteria were used for filtering and annotation of candidate variants: (1) minor allele frequency (MAF) <0.05 in the gnomAD and 1000 genomes, (2) variants in genes previously associated with chromosome segregation, chromatin cohesion, meiosis and cell division processes, (3) exonic/splicing boundaries variants, (4) variants having potentially strong/moderate functional effects on the protein evaluated using three in silico prediction algorithms (SIFT, PolyPhen-2 and MutationTaster). Main results and the role of chance Overall, the mean female and male age was 26.21 + 4.11y and 40.69 + 9.07y respectively. No differences were shown between groups for patient characteristics. Regarding PGT-A cycle no differences were seen between the number of oocytes and MII retrieved. However, the mean number of biopsied embryos per patient (5.36 + 2.50 vs 3.47 + 1.36; p < 0.05) as well as the percentage of embryos biopsied on day 5 (85.33 vs 32.69; p < 0.05) were higher in the control group. Finally, as expected, the percentage of aneuploidies was higher in the study group (18.64 vs 71.89; p < 0.05). 45 variants were identified in genes potentially associated to the mechanism related to the phenotype. After the variant filtering six probably pathogenic variants were identified. The variants found in the genes were: c.1397T>C (TLE6), c.169G>A (IKBKG), c.1227A>C (BUB1B), c.277G>A (TP73), c.190C>T (PLXNA3) and c.744C>G (AURKC). All variants were heterozygous and all of them were of maternal origin. The females carrying the candidate variants belonged to the study group, and two variants in different genes were identified in one patient. No potentially pathogenic variants were detected in patients from the control group. Therefore, the average detection rate of genetic variants with potential impact in embryo aneuploidy was 33.33% (5/15). Limitations, reasons for caution A notable strength of our study is the inclusion of both (male and female) genomic data. On the other hand, our study has certain limitations including the inherent challenges of any observational study, also, the pathogenicity of the identified variants should be validated in further functional studies. Wider implications of the findings We described new candidate genes that have never been associated to meiotic embryo aneuploidy and are involved in important biological processes (cell division and chromosome segregation). WES may be considered as an efficient tool to identify patients with higher risk of embryo aneuploidy allowing an individualized genetic counselling in advance. Trial registration number Not applicable

Identification of novel candidate genes leading to sex differentiation in primordial germ cells of Drosophila

Germline sex determination and differentiation are pivotal processes in reproduction. In Drosophila, sex determination of the germline occurs in primordial germ cells (PGCs), and the sex differentiation of these cells is initiated during embryogenesis. However, the molecular mechanism initiating sex differentiation remains elusive. To address this issue, we identified sex-biased genes using RNA-sequencing data of male and female PGCs. Our research revealed 497 genes that were differentially expressed more than twofold between sexes and expressed at high or moderate levels in either male or female PGCs. Among these genes, we used microarray data of PGCs and whole embryos to select 33 genes, which are predominantly expressed in PGCs compared to the soma, as candidate genes contributing to sex differentiation. Of 497 genes, 13 genes that were differentially expressed more than fourfold between sexes were also selected as candidates. Among the 46 (33 + 13) candidates, we confirmed the sex-biased expression of 15 genes by in situ hybridization and quantitative reverse transcription-polymerase chain reaction (qPCR) analysis. Six and nine genes were predominantly expressed in male and female PGCs, respectively. These results represent a first step toward elucidating the mechanisms that initiate sex differentiation in the germline.

Identification of novel candidate genes in East Asian COPD patients by the functional summary-based imputation and the unified test for molecular signatures: a transcriptome-wide association study

Identification of novel candidate genes in East Asian COPD patients by the functional summary-based imputation and the unified test for molecular signatures: a transcriptome-wide association study

Identification of Novel Candidate Genes for Familial Thyroid Cancer by Whole Exome Sequencing.

Thyroid carcinoma (TC) can be classified as medullary (MTC) and non-medullary (NMTC). While most TCs are sporadic, familial forms of MTC and NMTC also exist (less than 1% and 3-9% of all TC cases, respectively). Germline mutations in RET are found in more than 95% of familial MTC, whereas familial NMTC shows a high degree of genetic heterogeneity. Herein, we aimed to identify susceptibility genes for familial NMTC and non-RET MTC by whole exome sequencing in 58 individuals belonging to 18 Spanish families with these carcinomas. After data analysis, 53 rare candidate segregating variants were identified in 12 of the families, 7 of them located in previously TC-associated genes. Although no common mutated genes were detected, biological processes regulating functions such as cell proliferation, differentiation, survival and adhesion were enriched. The reported functions of the identified genes together with pathogenicity and structural predictions, reinforced the candidacy of 36 of them, suggesting new loci related to TC and novel genotype-phenotype correlations. Therefore, our strategy provides clues to possible molecular mechanisms underlying familial forms of MTC and NMTC. These new molecular findings and clinical data of patients may be helpful for the early detection, development of tailored therapies and optimizing patient management.

Co-expression networks regulating cotton fiber initiation generated by comparative transcriptome analysis between fiberless XZ142FLM and GhVIN1i

Cotton produces natural fiber as crucial raw material for textile industry and thus is economically one of the most important crops worldwide. Currently the mechanisms that control fiber initiation on ovules are still not well understood. In this study, we performed comparative transcriptome analysis between the natural fiberless mutant XZ142FLM and transgenic fiberless line GhVIN1i generated by RNAi silencing of GhVIN1 to identify molecular regulatory networks controlling fiber initiation. It was found that XZ142FLM and GhVIN1i shared many common differentially expressed genes (DEGs) in ovules during fiber initiation, and their respective DEGs were enriched in several identical pathways related to fiber initiation. Many reported fiber initiation or elongation related genes including GhMML3, GhVIN1, GhMYB25, GhHD-1, GhHOX3 exhibited similar expression patterns in XZ142FLM and GhVIN1i during fiber initiation, suggesting similar mechanisms of fiber initiation operating in the two fiberless lines, which was further verified by comparative temporal expression pattern analysis between TM-1/XZ142FLM and Coker 312/GhVIN1i. Co-expression regulatory networks for controlling fiber initiation were constructed for XZ142FLM and GhVIN1i, respectively, which centered on GhMML3 or GhVIN1 with many known fiber initiation/elongation related genes. Several transcription factors and hub genes were identified in the co-expression networks generated, which may facilitate future research in identification of novel candidate genes regulating fiber initiation and elongation. Overall, the results obtained in this study shed light on the regulatory networks mediated by GhMML3 and GhVIN1 for controlling fiber initiation in cotton.

Identification of novel candidate genes and predicted miRNAs in atopic dermatitis patients by bioinformatic methods

Atopic dermatitis (AD) is a common, chronic inflammatory dermatosis with relapsing eruptions. Our study used bioinformatics to find novel candidate differentially expressed genes (DEGs) and predicted miRNAs between AD patients and healthy controls. The Mesh term “atopic dermatitis” was retrieved to obtain DEGs in GEO datasets. DEGs between AD patients and healthy controls were analyzed using GEO2R. Overlapping DEGs between different datasets were obtained with use of Draw Venn software. GO and KEGG enrichment analyses were conducted by the use of DAVID. STRING and miRWalk were used to individually analyze PPI networks, interactions of candidate genes and predicted miRNAs. A total of 571 skin samples, as retrieved from 9 databases were assessed. There were 225 overlapping DEGs between lesioned skin samples of AD patients and that of healthy controls. Nineteen nodes and 160 edges were found in the largest PPI cluster, consisting of 17 up-regulated and 2 down-regulated nodes. Two KEGG pathways were identified, including the cell cycle (CCNB1, CHEK1, BUB1B, MCM5) and p53 (CCNB1, CHEK1, GTSE1) pathways. There were 56 nodes and 100 edges obtained in the miRNA-target gene network, with has-miR-17-5p targeted to 4 genes and has-miR-106b-5p targeted to 3 genes. While these findings will require further verification as achieved with experiments involving in vivo and in vitro modles, these results provided some initial insights into dysfunctional inflammatory and immune responses associated with AD. Such information offers the potential to develop novel therapeutic targets for use in preventing and treating AD.

Clinical genetics of spondylocostal dysostosis: A mini review.

Spondylocostal dysostosis is a genetic defect associated with severe rib and vertebrae malformations. In recent years, extensive clinical and molecular diagnosis advancements enabled us to identify disease-causing variants in different genes for such severe conditions. The identification of novel candidate genes enabled us to understand the developmental biology and molecular and cellular mechanisms involved in the etiology of these rare diseases. Here, we discuss the clinical and molecular targets associated with spondylocostal dysostosis, including clinical evaluation, genes, and pathways involved. This review might help us understand the basics of such a severe disorder, which might help in proper clinical characterization and help in future therapeutic strategies.

Novel homozygous stop-gain pathogenic variant of PPP1R13L gene leads to arrhythmogenic cardiomyopathy

BackgroundArrhythmogenic cardiomyopathy (ACM) is a heritable cardiac disease with two main features: electric instability and myocardial fibro-fatty replacement. There is no defined treatment except for preventing arrhythmias and sudden death. Detecting causative mutations helps identify the disease pathogenesis and family members at risk. We used whole-exome sequencing to determine a genetic explanation for an ACM-positive patient from a consanguineous family.MethodsAfter clinical analysis, cardiac magnetic resonance, and pathology, WES was performed on a two-year-old ACM proband. Variant confirmation and segregation of available pedigree members were performed by PCR and Sanger sequencing. The PPP1R13L gene was also analyzed for possible causative variants and their hitherto reported conditions.ResultsWe found a novel homozygous stop-gain pathogenic variant, c.580C > T: p.Gln194Ter, in the PPP1R13L gene, which was confirmed and segregated by PCR and Sanger sequencing. This variant was not reported in any databases.ConclusionsWES is valuable for the identification of novel candidate genes. To our knowledge, this research is the first report of the PPP1R13L c.580C > T variant. The PPP1R13L variant was associated with ACM as confirmed by cardiac magnetic resonance and pathology. Our findings indicate that PPP1R13L should be included in ACM genetic testing to improve the identification of at-risk family members and the diagnostic yield.

Supplemental Material from: Analysis of Bone Morphogenetic Protein 15 (BMP15)-induced transcriptome in human granulosa cells for the identification of novel candidate genes for Primary Ovarian Insufficiency

Supplemental Material from: Analysis of Bone Morphogenetic Protein 15 (BMP15)-induced transcriptome in human granulosa cells for the identification of novel candidate genes for Primary Ovarian Insufficiency

Identification of novel candidate genes and small molecule drugs in ovarian cancer by bioinformatics strategy.

BackgroundOvarian cancer (OC) is the most lethal type of malignancies in the female reproductive system. This study aimed to identify novel biomarkers and potential small molecule drugs in OC by integrating two expression profile datasets.MethodsGSE18520 and GSE14407 from the Gene Expression Omnibus (GEO) database were selected and the overlapped differentially expressed genes (DEGs) were detected. The Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genome (KEGG) pathway enrichment analysis were performed to establish the protein-protein interaction (PPI) network of DEGs and identified the hub genes. Gene Expression Profiling Interactive Analysis (GEPIA), Oncomine database and The Human Protein Atlas (HPA) were used to validate the expression of the identified hub genes. The prognostic value of these hub genes were evaluated by the Kaplan Meier plotter online tool. The expression of NCAPG was further explored by immunohistochemistry in our OC tissues. Moreover, CMap database was used to look for prospective small compounds with therapeutic efficacy based on OC RNA-seq.ResultsA total of 433 DEGs were identified. The DEGs were mainly enriched in negative regulation of transcription and pathways in cancer. A PPI network was constructed with 344 nodes and 1,596 interactions. The top ten module genes were chosen as hub genes. Among which, survival analysis showed that patients with high expression of CCNB1, TOP2A, NUSAP1, NCAPG, KIF20A and DLGAP5 had poorer survival results than those with low expression. These six genes were all overexpressed in OC tissue by means of bioinformatics analysis. In our clinical patients, the expression rate of NCAPG in OC tissues was significantly higher than that in benign serous ovarian cystadenoma and borderline serous ovarian cystadenoma tissues. Meanwhile, several small molecules with potential therapeutic efficacy against OC were identified in our study.ConclusionsBy means of bioinformatics analysis, we identified six real hub genes and indicated a group of candidate small molecule drugs as adjunctive agents for OC. They could be the potential novel biomarkers for the diagnosis and promising therapeutic targets of OC.

Identification of Novel Candidate Genes Involved in Apple Cuticle Integrity and Russeting-Associated Triterpene Synthesis Using Metabolomic, Proteomic, and Transcriptomic Data.

Apple russeting develops on the fruit surface when skin integrity has been lost. It induces a modification of fruit wax composition, including its triterpene profile. In the present work, we studied two closely related apple varieties, ‘Reinette grise du Canada’ and ‘Reinette blanche du Canada’, which display russeted and non-russeted skin phenotypes, respectively, during fruit development. To better understand the molecular events associated with russeting and the differential triterpene composition, metabolomics data were generated using liquid chromatography coupled to high-resolution mass spectrometry (LC-HRMS) and combined with proteomic and transcriptomic data. Our results indicated lower expression of genes linked to cuticle biosynthesis (cutin and wax) in russet apple throughout fruit development, along with an alteration of the specialized metabolism pathways, including triterpene and phenylpropanoid. We identified a lipid transfer protein (LTP3) as a novel player in cuticle formation, possibly involved in the transport of both cutin and wax components in apple skin. Metabolomic data highlighted for the first time a large diversity of triterpene-hydroxycinnamates in russeted tissues, accumulation of which was highly correlated with suberin-related genes, including some enzymes belonging to the BAHD (HXXXD-motif) acyltransferase family. Overall, this study increases our understanding about the crosstalk between triterpene and suberin pathways.

Genomic and physiological analyses of the zebrafish atrioventricular canal reveal molecular building blocks of the secondary pacemaker region

The atrioventricular canal (AVC) is the site where key structures responsible for functional division between heart regions are established, most importantly, the atrioventricular (AV) conduction system and cardiac valves. To elucidate the mechanism underlying AVC development and function, we utilized transgenic zebrafish line sqet31Et expressing EGFP in the AVC to isolate this cell population and profile its transcriptome at 48 and 72 hpf. The zebrafish AVC transcriptome exhibits hallmarks of mammalian AV node, including the expression of genes implicated in its development and those encoding connexins forming low conductance gap junctions. Transcriptome analysis uncovered protein-coding and noncoding transcripts enriched in AVC, which have not been previously associated with this structure, as well as dynamic expression of epithelial-to-mesenchymal transition markers and components of TGF-β, Notch, and Wnt signaling pathways likely reflecting ongoing AVC and valve development. Using transgenic line Tg(myl7:mermaid) encoding voltage-sensitive fluorescent protein, we show that abolishing the pacemaker-containing sinoatrial ring (SAR) through Isl1 loss of function resulted in spontaneous activation in the AVC region, suggesting that it possesses inherent automaticity although insufficient to replace the SAR. The SAR and AVC transcriptomes express partially overlapping species of ion channels and gap junction proteins, reflecting their distinct roles. Besides identifying conserved aspects between zebrafish and mammalian conduction systems, our results established molecular hallmarks of the developing AVC which underlies its role in structural and electrophysiological separation between heart chambers. This data constitutes a valuable resource for studying AVC development and function, and identification of novel candidate genes implicated in these processes.