A minimal set of internal control genes for gene expression studies in head and neck squamous cell carcinoma

Identification of crucial genes and pathways associated with prostate cancer in multiple databases

OBJECTIVE

Prostate cancer (PCa) is a malignant neoplasm of the urinary system. This study aimed to use bioinformatics to screen for core genes and biological pathways related to PCa.

METHODS

The GSE5957 gene expression profiles were obtained from the Gene Expression Omnibus (GEO) database to identify differentially expressed genes (DEGs). Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses of the DEGs were constructed by R language. Furthermore, protein-protein interaction (PPI) networks were generated to predict core genes. The expression levels of core genes were examined in the Tumor Immune Estimation Resource (TIMER) and Oncomine databases. The cBioPortal tool was used to study the co-expression and prognostic factors of the core genes. Finally, the core genes of signaling pathways were determined using gene set enrichment analysis (GSEA).

RESULTS

Overall, 874 DEGs were identified. Hierarchical clustering analysis revealed that these 24 core genes have significant association with carcinogenesis and development. LONRF1, CDK1, RPS18, GNB2L1 (RACK1), RPL30, and SEC61A1 directly related to the recurrence and prognosis of PCa.

CONCLUSIONS

This study identified the core genes and pathways in PCa and provides candidate targets for diagnosis, prognosis, and treatment.

K. S, T. S, Sachdeva K, Bathula C, K. V, K. S. N, Damodar S, Dhar SK, Das M. Relative quantification of BCL2 mRNA for diagnostic usage needs stable uncontrolled genes as reference

Dysregulation of BCL2 is a pathophysiology observed in haematological malignancies. For implementation of available treatment-options it is preferred to know the relative quantification of BCL2 mRNA with appropriate reference genes. For the choice of reference genes-(i) Reference Genes were selected by assessing variation of >60,000 genes from 4 RNA-seq datasets of haematological malignancies followed by filtering based on their GO biological process annotations and proximity of their chromosomal locations to known disease translocations. Selected genes were experimentally validated across various haematological malignancy samples followed by stability comparison using geNorm, NormFinder, BestKeeper and RefFinder. (ii) 43 commonly used Reference Genes were obtained from literature through extensive systematic review. Levels of BCL2 mRNA was assessed by qPCR normalized either by novel reference genes from this study or GAPDH, the most cited reference gene in literature and compared. The analysis showed PTCD2, PPP1R3B and FBXW9 to be the most unregulated genes across lymph-nodes, bone marrow and PBMC samples unlike the Reference Genes used in literature. BCL2 mRNA level shows a consistent higher expression in haematological malignancy patients when normalized by these novel Reference Genes as opposed to GAPDH, the most cited Reference Gene. These reference genes should also be applicable in qPCR platforms using Taqman probes and other model systems including cell lines and rodent models. Absence of sample from healthy-normal individual in diagnostic cases call for careful selection of Reference Genes for relative quantification of a biomarker by qPCR.BCL2 can be used as molecular diagnostics only if normalized with a set of reference genes with stable yet low levels of expression across different types of haematological malignancies.

Selecting reference genes in RT-qPCR based on equivalence tests: a network based approach

Because quantitative reverse transcription PCR (RT-qPCR) gene expression data are compositional, amounts of quantified RNAs must be normalized using reference genes. However, the two most used methods to select reference genes (NormFinder and geNorm) ignore the compositional nature of RT-qPCR data, and often lead to different results making reliable reference genes selection difficult. We propose a method, based on all pairwise equivalence tests on ratio of gene expressions, to select genes that are stable enough to be used as reference genes among a set a candidate genes. This statistical procedure controls the error of selecting an inappropriate gene. Application to 30 candidate reference genes commonly used in human studies, assessed by RT-qPCR in RNA samples from lymphoblastoid cell lines of 14 control subjects and 26 patients with bipolar disorder, allowed to select 7 reference genes. This selection was consistent with geNorm's ranking, less with NormFinder's ranking. Our results provide an important fundamental basis for reference genes identification using sound statistics taking into account the compositional nature of RT-qPCR data. The method, implemented in the SARP.compo package for R (available on the CRAN), can be used more generally to prove that a set of genes shares a common expression pattern.

Molecular Characterization, Phylogenetic, Expression, and Protective Immunity Analysis of OmpF, a Promising Candidate Immunogen Against Yersinia ruckeri Infection in Channel Catfish

Outer membrane porins, as the major components of Gram-negative bacterial membrane proteins, have been proven to be involved in interactions with the host immune system and potent protective antigen candidates against bacterial infection in fish. Outer membrane porin F (OmpF) is one of the major porins of Yersinia ruckeri (Y. ruckeri), the causative agent of enteric red mouth disease of salmonid and non-salmonid fish. In the present study, the molecular characterization and phylogenetic analysis of OmpF gene was studied, heterogenous expression, immunogenicity and protective immunity of OmpF were systemically evaluated as a subunit vaccine for channel catfish against Y. ruckeri infection. The results showed that OmpF gene was highly conserved among 15 known Yersinia species based on the analysis of conserved motifs, sequences alignment and phylogenetic tree, and was subjected to negative/purifying selection with global dN/dS ratios value of 0.649 throughout the evolution. Besides, OmpF was also identified to have immunogenicity by western blotting and was verified to be located on the surface of Y. ruckeri using cell surface staining and indirect immunofluorescence assays. Moreover, recombinant OmpF (rtOmpF) as a subunit vaccine was injected with commercial adjuvant ISA763, significantly enhanced the immune response by increasing serum antibody levels, lysozyme activity, complement C3 activity, total protein content, SOD activity, immune-related genes expression in the head kidney and spleen, and survival percent of channel catfish against Y. ruckeri infection. Thus, our present results not only enriched the information of molecular characterization and phylogenetics of OmpF, but also demonstrated that OmpF holds promise to be used as a potential antigen against Y. ruckeri infection in fish.