A first complete catalog of highly expressed genes in eight chicken tissues reveals uncharacterized gene families specific for the chicken testis

Based on next-generation sequencing, we established a repertoire of differentially overexpressed genes (DoEG) in eight adult chicken tissues: testis, brain, lung, liver, kidney, muscle, heart, and intestine. With 4499 DoEG, the testis had the highest number and proportion of DoEG compared with the seven somatic tissues. The testis DoEG set included the highest proportion of long noncoding RNAs (lncRNAs; 1851, representing 32% of the lncRNA genes in the whole genome) and the highest proportion of protein-coding genes (2648, representing 14.7% of the protein-coding genes in the whole genome). The main significantly enriched Gene Ontology terms related to the protein-coding genes are "reproductive process," "tubulin binding," "microtubule cytoskeleton." By using real-time quantitative reverse transcription polymerase chain reaction, we confirmed the overexpression of genes that encode proteins already described in chicken sperm (such as CABYR, SPAT18 and CDK5RAP2) but whose testis origin had not been confirmed previously. Moreover, we demonstrated the overexpression of vertebrate orthologs of testis genes not yet described in the adult chicken testis (such as NEK2, AK7 and CCNE2). Using clustering according to primary sequence homology, we found that 67% (1737) of the 2648 testis protein-coding genes were unique genes. This proportion was significantly higher than the somatic tissues except muscle. We clustered the other 911 testis protein-coding genes into 495 families, from which 47 had all paralogs overexpressed in the testis. Among these 47 testis-specific families, eight contain uncharacterized members without orthologs in other metazoans except birds: these families are then specific for chickens (probably more broadly birds).

Identification of Overexpressed Genes in Malignant Pleural Mesothelioma

Malignant pleural mesothelioma (MPM) is a fatal tumor lacking effective therapies. The characterization of overexpressed genes could constitute a strategy for identifying drivers of tumor progression as targets for novel therapies. Thus, we performed an integrated gene-expression analysis on RNAseq data of 85 MPM patients from TCGA dataset and reference samples from the GEO. The gene list was further refined by using published studies, a functional enrichment analysis, and the correlation between expression and patients' overall survival. Three molecular signatures defined by 15 genes were detected. Seven genes were involved in cell adhesion and extracellular matrix organization, with the others in control of the mitotic cell division or apoptosis inhibition. Using Western blot analyses, we found that ADAMTS1, PODXL, CIT, KIF23, MAD2L1, TNNT1, and TRAF2 were overexpressed in a limited number of cell lines. On the other hand, interestingly, CTHRC1, E-selectin, SPARC, UHRF1, PRSS23, BAG2, and MDK were abundantly expressed in over 50% of the six MPM cell lines analyzed. Thus, these proteins are candidates as drivers for sustaining the tumorigenic process. More studies with small-molecule inhibitors or silencing RNAs are fully justified and need to be undertaken to better evaluate the cancer-driving role of the targets herewith identified.