bioRxiv Science⌕ Search
Home/Archive/bioRxiv

bioRxiv · 10.1101/2020.12.21.423732

Identification of potential and novel target genes in pituitary prolactinoma by bioinformatics analysis

Ghatnatti, V. B.·Vastrad, B. M.·Patil, S.·Vastrad, C. M.·Kotturshetti, I. B.
View original source ↗Export metadata ↓

Abstract

Pituitary prolactinoma is one of the most complicated and fatally pathogenic pituitary adenomas. Therefore, there is an urgent need to improve our understanding of the underlying molecular mechanism that drives the initiation, progression, and metastasis of pituitary prolactinoma. The aim of the present study was to identify the key genes and signaling pathways associated with pituitary prolactinoma using bioinformatics analysis. Transcriptome microarray dataset GSE119063 was acquired from Gene Expression Omnibus datasets, which included 5 pituitary prolactinoma samples and 4 normal pituitaries samples. We screened differentially expressed genes (DEGs) with limma and investigated their biological function by pathway and Gene Ontology (GO) enrichment analysis. A protein-protein interaction (PPI) network of the up and down DEGs were constructed and analyzed by HIPPIE and Cytoscape software. Module analyses were performed. In addition, a target gene - miRNA network and target gene - TF network of the up and down DEGs were constructed by NetworkAnalyst and Cytoscape software. The set of DEGs exhibited an intersection consisting of 989 genes (461 up-regulated and 528 down-regulated), which may be associated with pituitary prolactinoma. Pathway enrichment analysis showed that the 989 DEGs were significantly enriched in the retinoate biosynthesis II, signaling pathways regulating pluripotency of stem cells, ALK2 signaling events, vitamin D3 biosynthesis, cell cycle and aurora B signaling. Gene Ontology (GO) enrichment analysis also showed that sensory organ morphogenesis, extracellular matrix, hormone activity, nuclear division, condensed chromosome and microtubule binding. In the PPI network and modules, SOX2, PRSS45, CLTC, PLK1, B4GALT6, RUNX1 and GTSE1 were considered as hub genes. In the target gene miRNA network and target gene - TF network, LINC00598, SOX4, IRX1 and UNC13A were considered as hub genes. Using integrated bioinformatics analysis, we identified candidate genes in pituitary prolactinoma, which may improve our understanding of the mechanisms of the pathogenesis and integration; genes may be therapeutic targets and prognostic markers for pituitary prolactinoma.

Explore related subjects

genomicsPreprint

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Ghatnatti, V. B., Vastrad, B. M., Patil, S., Vastrad, C. M., Kotturshetti, I. B.. 2020-12-22. Identification of potential and novel target genes in pituitary prolactinoma by bioinformatics analysis. https://doi.org/10.1101/2020.12.21.423732

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

Contig-Resolved Genetic Context of Antimicrobial Resistome in Sediments of Two Contrasting Wastewater-Impacted Rivers

River sediments harbor diverse antimicrobial resistance (AMR) determinants; however, gene abundance alone provides limited insight into their genomic context, mobility potential, and associated bacterial hosts. This study employed an assembly- and read-mapping metagenomic framework to surface-sediment metagenomes (40.78 Gb clean data) from two contrasting wastewater-impacted Indian rivers, Adyar (Chennai) and Musi (Hyderabad), retaining sample-, contig- and open reading frame level provenance. ARG-carrying contigs (ACCs; n = 2,402) were annotated for mobile genetic elements (MGEs), biocide/metal resistance genes (BMRGs), virulence factor genes (VFGs), nitrogen-cycling genes (NCycGs), and putative host taxonomy. The resistomes exhibited substantial diversity (264 ARG subtypes) and spatial heterogeneity, with subtype richness in the Adyar (up to 171 subtypes) than in the Musi, where richness progressively declined downstream. Rank IV determinants dominated ARG abundance (77.82%), whereas Rank I determinants accounted for only 9.89%. MGEs were detected on just 3.12% (75/2,402) of ACCs, predominantly comprising plasmid-like contigs and proximal ARG-MGE associations. Co-occurrence with BMRGs was observed on 386 ACCs, whereas VFGs were uncommon (26 ACCs) and primarily represented dual-annotated efflux and envelope-integrity determinants rather than independent virulence loci. NCyc annotations were sparse (12 ACCs), with no evidence of complete nitrification or denitrification pathways. Taxonomic classification resolved 217 ACCs to the species level, with no matches to curated human pathogenic bacteria. Only two Acinetobacter-assigned ACCs exhibited both genus-level pathogenicity and mobility evidence. These findings highlight the importance of integrating mobility and host-taxonomic information to distinguish baseline environmental resistance from potential priorities for AMR surveillance.

genomics↗
bioRxiv2026

Time-resolved single-cell screening reveals the dynamic regulatory architecture of human cardiogenesis

Congenital heart disease (CHD) originates during early embryogenesis, yet when disease genes act cannot be determined from existing data. Human fetal heart atlases lack critical time points, and perturbation screens that systematically assess gene function currently profile at most a few time points. Here we combined single-cell CRISPR screening of 400 disease-relevant genes in cardioids, sampled daily over seven developmental days (~975,000 cells), with a matched multiome atlas. Perturbation phenotypes were strongly dependent on developmental stage. Perturbations that reshaped cell-fate allocation or gene expression were enriched for CHD-linked genes, and most acted already during progenitor stages. Timing was largely independent of the target gene's own expression, marking instead when a cell state became functionally dependent on it, and some effects persisted after expression declined. Consensus gene regulatory networks integrating perturbation and multiome data recovered stage-specific regulators and nominated HOXB2 and HOXB3 as candidate cardiac regulators. Many perturbations converged on shared downstream programmes, which were reorganised through differentiation. Effects correlated in progenitors were maintained in differentiated cells, split into distinct programmes, converged with other perturbations or disappeared entirely, indicating that gene function is highly context dependent. Beyond advancing our understanding of the developmental regulatory logic underlying CHD, our work provides a resource for developing context-dependent models for in silico prediction of perturbation effects.

genomics↗
bioRxiv2026

A Y-specific translocated gsdf copy is a candidate master sex-determining gene in common dab (Limanda limanda)

Sex-determining systems in flatfishes are highly diverse, and even closely related species can differ in both sex-determining loci and heterogametic systems. In common dab (Limanda limanda), the genetic basis of sex determination has not yet been established. Here, we investigated sex determination using pooled whole-genome sequencing combined with long-read genome sequencing of females and males from Iceland and Norway. Genome-wide allele-frequency analyses identified sex-associated regions consistent with male heterogamety (XX/XY), with the strongest signal on chromosome 16. Comparison of the existing reference assembly, which represents an X haplotype at this locus, with a haplotype-resolved male PacBio HiFi assembly revealed a [~]21.5 kb Y-specific insertion on chromosome 16. The insertion showed complete coverage in male pools but little or no coverage in female pools from either population. It contained a translocated genomic segment including a copy of gonadal soma-derived factor (gsdf) and a predicted gene of unknown function. Comparative genomic analyses were consistent with this segment originating from an autosomal gsdf-containing region on chromosome 1. Given the recurrent recruitment of gsdf as a sex-determining factor in teleosts, we designate the Y-linked copy gsdfY and identify it as the strongest candidate for the master sex-determining gene in common dab. Additional broad sex-associated differentiation on chromosome 19 was restricted to the Icelandic samples and may reflect population-specific expansion of the sex-linked region, although its structural basis remains unresolved. Together, these findings provide the first genomic characterization of sex determination in common dab and demonstrate how gene duplication and translocation can contribute to the evolution of novel sex-determining systems in flatfishes.

genomics↗