scholarly journals A comparative genomic approach using mouse and fruit fly data to discover genes involved in testis function in hymenopterans with a focus on Nasonia vitripennis

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Charlotte Lécureuil ◽  
Sophie Fouchécourt ◽  
Rémi Eliautout ◽  
Vanessa Guérin ◽  
Kevin Hidalgo ◽  
...  
Keyword(s):  
Gene Expression ◽  
Male Fertility ◽  
Expression Profiles ◽  
Comparative Method ◽  
Gene Expression Profiles ◽  
Fruit Fly ◽  
Comparative Genomic ◽  
Nasonia Vitripennis ◽  
Phenotypic Data ◽  
Hymenopteran Species

Abstract Background Spermatogenesis appears to be a relatively well-conserved process even among distantly related animal taxa such as invertebrates and vertebrates. Although Hymenopterans share many characteristics with other organisms, their complex haplodiploid reproduction system is still relatively unknown. However, they serve as a complementary insect model to Drosophila for studying functional male fertility. In this study, we used a comparative method combining taxonomic, phenotypic data and gene expression to identify candidate genes that could play a significant role in spermatogenesis in hymenopterans. Results Of the 546 mouse genes predominantly or exclusively expressed in the mouse testes, 36% had at least one ortholog in the fruit fly. Of these genes, 68% had at least one ortholog in one of the six hymenopteran species we examined. Based on their gene expression profiles in fruit fly testes, 71 of these genes were hypothesized to play a marked role in testis function. Forty-three of these 71 genes had an ortholog in at least one of the six hymenopteran species examined, and their enriched GO terms were related to the G2/M transition or to cilium organization, assembly, or movement. Second, of the 379 genes putatively involved in male fertility in Drosophila, 224 had at least one ortholog in each of the six Hymenoptera species. Finally, we showed that 199 of these genes were expressed in early pupal testis in Nasonia vitripennis; 86 exhibited a high level of expression, and 54 displayed modulated expression during meiosis. Conclusions In this study combining phylogenetic and experimental approaches, we highlighted genes that may have a major role in gametogenesis in hymenopterans; an essential prerequisite for further research on functional importance of these genes.

scholarly journals Artificial Neural Network to Predict Varicocele Impact on Male Fertility through Testicular Endocannabinoid Gene Expression Profiles

2018 ◽  
Vol 2018 ◽  
pp. 1-15
Author(s):  
Davide Perruzza ◽  
Nicola Bernabò ◽  
Cinzia Rapino ◽  
Luca Valbonetti ◽  
Ilaria Falanga ◽  
...  
Keyword(s):  
Neural Network ◽  
Gene Expression ◽  
Artificial Neural Network ◽  
Male Fertility ◽  
Cannabinoid Receptors ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Gene Expression Profiles ◽  
Artificial Neural ◽  
The Relationship

The relationship between varicocele and fertility has always been a matter of debate because of the absence of predictive clinical indicators or molecular markers able to define the severity of this disease. Even though accumulated evidence demonstrated that the endocannabinoid system (ECS) plays a central role in male reproductive biology, particularly in the testicular compartment, to date no data point to a role for ECS in the etiopathogenesis of varicocele. Therefore, the present research has been designed to investigate the relationship between testicular ECS gene expression and fertility, using a validated animal model of experimental varicocele (VAR), taking advantage of traditional statistical approaches and artificial neural network (ANN). Experimental induction of VAR led to a clear reduction of spermatogenesis in left testes ranging from a mild (Johnsen score 7: 21%) to a severe (Johnsen score 4: 58%) damage of the germinal epithelium. However, the mean number of new-borns recorded after two sequential matings was quite variable and independent of the Johnsen score. While the gene expression of biosynthetic and degrading enzymes of AEA (NAPE-PLD and FAAH, respectively) and of 2-AG (DAGLα and MAGL, respectively), as well as their binding cannabinoid receptors (CB1 and CB2), did not change between testes and among groups, a significant downregulation of vanilloid (TRPV1) expression was recorded in left testes of VAR rats and positively correlated with animal fertility. Interestingly, an ANN trained by inserting the left and right testicular ECS gene expression profiles (inputs) was able to predict varicocele impact on male fertility in terms of mean number of new-borns delivered (outputs), with a very high accuracy (average prediction error of 1%). The present study provides unprecedented information on testicular ECS gene expression patterns during varicocele, by developing a freely available predictive ANN model that may open new perspectives in the diagnosis of varicocele-associated infertility.

Genomic Complexity and Recurrent Aberration in Multiple Myeloma: Analysis of a Compendium of aCGH and Gene Expression Profiles.

Blood ◽  
2008 ◽  
Vol 112 (11) ◽  
pp. 1682-1682
Author(s):  
Wee-Joo Chng ◽  
Ian Lee ◽  
Victor Jimenez-zepeda ◽  
Esteban Braggio ◽  
Jonathan Keats ◽  
...  
Keyword(s):  
Gene Expression ◽  
Multiple Myeloma ◽  
Proportional Hazards ◽  
Expression Profiles ◽  
Clinical Status ◽  
Gene Expression Profiles ◽  
Cox Proportional Hazards ◽  
Comparative Genomic ◽  
Initial Attempt ◽  
Genomic Complexity

Abstract Multiple Myeloma (MM) is the second most prevalent haematological disorder in the US with great recent progress propelled by various technological and therapeutic advances. Nevertheless, the complexity of MM genomes remains inadequately characterized. We have combined high-resolution (44K Agilent) array comparative genomic hybridization (aCGH) and gene expression data with clinical outcomes in an initial attempt at indexing genomic complexity in MM and its clinical implication in 100 MM patients. We enumerated the Number of Aberrations per Tumor (NAPT) as defined by the ADM-1 algorithm available within CGH Analytics. There appear to be no difference in degree of genetic complexity between hyperdiploid and non-hyperdiploid myeloma. Generally, t(11;14) have low NAPT whereas D2 tumors have high NAPT. Amongst the high-risk genetic subtypes, tumors with maf translocations have relatively low NAPT whereas t(4;14) have high NAPT. Whilst a Multivariate Cox Proportional Hazards regression of survival outcome showed little statistical support for popular indicators such as ploidy and TC classification, results for NAPT were considerably more encouraging (p~ 0.07, median survival of 40 months in low complexity vs 18 months in high). Log-rank tests further supported prognosis based on NAPT independent of clinical status and ploidy. To characterize complexity, we clustered aCGH profiles by clinical status, ploidy and TC classification. Clear patterns of aggregation and recurrent aberration were observed suggesting that they were possibly instrument to aberrant gene expression. Indeed, expression of a large proportion of genes approximately 2Mb of the recurrent breakpoints varied significantly between patients carrying aberrations vis-a-viz others that did not. Comparison against known gene sets showed an enrichment for cell-cycle and apoptosis genes. We are presently characterizing several such breakpoint-associated genes for their functional significance.

Follicular Lymphomas with and without Translocation t(14;18) Differ in Gene Expression Profiles and Genetic Alterations.

Blood ◽  
2007 ◽  
Vol 110 (11) ◽  
pp. 360-360
Author(s):  
Ellen Leich ◽  
Itziar Salaverria ◽  
Silvia Bea ◽  
Andreas Zettl ◽  
Randy D. Gascoyne ◽  
...  
Keyword(s):  
Gene Expression ◽  
Protein Level ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Gene Expression Signature ◽  
Genetic Alterations ◽  
Gene Set Enrichment Analysis ◽  
Comparative Genomic ◽  
Survival Times ◽  
Bcl2 Expression

Abstract Follicular lymphoma (FL) is a B-cell non-Hodgkin lymphoma that is characterized in approximately 85% of cases by the chromosomal translocation t(14;18) involving BCL2. While FL3b generally lack the t(14;18), this translocation is also absent in 15% of FL grades 1, 2 and 3a. The current study was designed to identify the frequency of t(14;18)-negative FL in a series of 166 cases of FL1, 2 and 3a in which global gene expression profiles had been established previously (Dave et al., NEJM351:2159–69, 2004). Furthermore, we sought to compare genetic alterations and gene expression profiles between FL with and without the t(14;18). Combined polymerase chain reaction (PCR) and tissue microarray-based fluorescence in situ hybridization (FISH) identified 17 t(14;18)-negative FL cases in this series (9%). Virtually all FL cases carrying the t(14;18) showed BCL2 expression by immunohistochemistry (Dako, clone 124), whereas 11 of the FL cases without a t(14;18) were BCL2-negative at the protein level. Clinically, there was no difference between the t(14;18)-negative and -positive FL subgroups regarding age and gender distribution as well as in median survival times. Comparative genomic hybridization (CGH) in the 166 FL cases revealed a characteristic pattern of chromosomal gains and losses, as previously described. However, significant differences were observed between the t(14;18)-negative and -positive FL subgroups. Specifically, the t(14;18)-positive FL subgroup showed gains of chromosomes 18q (18%), 8q (12%) and X (13%), as well as losses of 13q (16%) and 10q (16%), whereas none of these aberrations were observed in the t(14;18)-negative FL cases. To compare gene expression between the two groups, we used gene set enrichment analysis (GSEA), BRB array tools and a two-sided t-test. Cell cycle-associated genes were found to be enriched in the t(14;18)-negative FL subset. These differences were even more pronounced in FL cases that lacked both the t(14;18) and BCL2 expression at the protein level. Importantly, genes expressed in non-malignant bystander cells appeared also differentially enriched and a cytotoxic gene expression signature was found to be more prominent in t(14;18)-negative FL. These findings point to a different composition of the non-neoplastic cells in t(14;18)-positive and -negative FL and could indicate subtle differences in the immunological microenvironment of t(14;18)-negative FL.

Molecular Heterogeneity of Multiple Myeloma: Pathogenesis, Prognosis, and Therapeutic Implications

2011 ◽  
Vol 29 (14) ◽  
pp. 1893-1897 ◽  
Author(s):  
Avet-Loiseau Hervé ◽  
Magrangeas Florence ◽  
Moreau Philippe ◽  
Attal Michel ◽  
Facon Thierry ◽  
...  
Keyword(s):  
Gene Expression ◽  
Multiple Myeloma ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Chromosome 17 ◽  
Comparative Genomic ◽  
Specific Gene ◽  
Molecular Heterogeneity ◽  
Significant Heterogeneity ◽  
Hodgkin's Lymphomas

Multiple myeloma (MM) is characterized by a significant heterogeneity at the molecular level. The first level is the chromosomal one. Although cytogenetics is difficult to assess in MM, patients can be divided into two categories: hyperdiploidy and non-hyperdiploidy (about half in each group). Using molecular cytogenetic techniques, several subgroups of patients are identified, particularly on the basis of 14q32 translocations. This chromosomal heterogeneity is confirmed by genomic techniques (gene expression profiling or single nucleotide polymorphism/comparative genomic hybridization arrays). Unsupervised analyses of gene expression profiles identified several subgroups of patients, essentially on the basis of chromosomal abnormalities such as hyperdiploidy or 14q32 translocations. However, these analyses failed to separate MM into subentities, which could lead to specific therapeutic approaches, as is the case for non-Hodgkin's lymphomas. Nevertheless, these chromosomal/genomic data can be used for prognostication of patients. Specific chromosomal changes, such as loss of the short arm of chromosome 17, or specific gene expression profiles clearly identify patients with short survival. No molecular change so far has been associated with long survival or even cure, probably because of the short follow-up observed in all studies. So far, it is unclear how to use this massive amount of data to treat patients. Because of the complex and heterogeneous picture of the molecular profiles, it is unexpected that targeted therapies might play a role in MM. The only recognized indication is to propose bortezomib-based approaches for the treatment of patients displaying the translocation t(4;14).

scholarly journals Follicular lymphomas with and without translocation t(14;18) differ in gene expression profiles and genetic alterations

Blood ◽  
2009 ◽  
Vol 114 (4) ◽  
pp. 826-834 ◽  
Author(s):  
Ellen Leich ◽  
Itziar Salaverria ◽  
Silvia Bea ◽  
Andreas Zettl ◽  
George Wright ◽  
...  
Keyword(s):  
Gene Expression ◽  
B Cell ◽  
Expression Profiles ◽  
Snp Array ◽  
Gene Expression Profiles ◽  
Chromosomal Translocation ◽  
Genetic Alterations ◽  
Comparative Genomic ◽  
Molecular Features ◽  
Cd10 Expression

Abstract Follicular lymphoma (FL) is genetically characterized by the presence of the t(14;18)(q32;q21) chromosomal translocation in approximately 90% of cases. In contrast to FL carrying the t(14;18), their t(14;18)-negative counterparts are less well studied about their immunohistochemical, genetic, molecular, and clinical features. Within a previously published series of 184 FLs grades 1 to 3A with available gene expression data, we identified 17 FLs lacking the t(14;18). Comparative genomic hybridization and high-resolution single nucleotide polymorphism (SNP) array profiling showed that gains/amplifications of the BCL2 gene locus in 18q were restricted to the t(14;18)-positive FL subgroup. A comparison of gene expression profiles showed an enrichment of germinal center B cell–associated signatures in t(14;18)-positive FL, whereas activated B cell–like, NFκB, proliferation, and bystander cell signatures were enriched in t(14;18)-negative FL. These findings were confirmed by immunohistochemistry in an independent validation series of 84 FLs, in which 32% of t(14;18)-negative FLs showed weak or absent CD10 expression and 91% an increased Ki67 proliferation rate. Although overall survival did not differ between FL with and without t(14;18), our findings suggest distinct molecular features of t(14;18)-negative FL.

scholarly journals TraitCorr – correlating gene expression measurements with phenotypic data

2019 ◽  
Author(s):  
Thomas Nussbaumer ◽  
Christian Wagner ◽  
Parviz Heidari
Keyword(s):  
Gene Expression ◽  
User Interface ◽  
System Biology ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Rna Seq ◽  
Phenotypic Data ◽  
Descriptive Information ◽  
Phenotype Data

AbstractToday, transcriptomes and microarrays can be generated and analysed in high quantity. In addition, experiments often include descriptive information about each sample which needs to be compared to the gene expression profiles. The understanding of the relationships between gene expression and phenotype is introduced as new challenge in system biology. Combining expression (RNA-seq and microarray) and phenotype data could reveal the role or effects of each gene on traits. To address all these needs, the user-interface TraitCorr was developed which allows to determine genes that are significantly correlating with a selected trait. Furthermore, it allows to determine significantly correlated genes among different traits and provides visualisation and analysis possibilities.

1327: Gene Expression Profiles in Benign Prostatic Hyperplasia

2004 ◽  
Vol 171 (4S) ◽  
pp. 349-350
Author(s):  
Gaelle Fromont ◽  
Michel Vidaud ◽  
Alain Latil ◽  
Guy Vallancien ◽  
Pierre Validire ◽  
...  
Keyword(s):  
Gene Expression ◽  
Benign Prostatic Hyperplasia ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Prostatic Hyperplasia
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