Abstract: Retinoblastoma is a common intraocular malignant tumor in children. However, the molecular and genetic mechanisms of retinoblastoma remain unclear. The gene expression dataset GSE110811 was retrieved from Gene Expression Omnibus. After preprocessing, coexpression modules were constructed by weighted gene coexpression network analysis (WGCNA), and modules associated with clinical traits were identified. In addition, functional enrichment analysis was performed for genes in the indicated modules, and protein?protein interaction (PPI) networks and subnetworks were constructed based on these genes. Eight coexpression modules were constructed through WGCNA. Of these, the yellow module had the highest association with severity and age (r=0.82 and P=3e?07; r=0.72 and P=3e?05). The turquoise module had the highest association with months (r=?0.63 and P=5e?04). The genes in the two modules participate in multiple pathways of retinoblastoma, and by combining the PPI network and subnetworks; 10 hub genes were identified in the two modules. The present study identified coexpression modules and hub genes associated with clinical traits of retinoblastoma, providing novel insight into retinoblastoma progression.

Mao Y, Nie Q, Yang Y, Mao G. Identification of co?expression modules and hub genes of retinoblastoma via co?expression analysis and protein?protein interaction networks. Mol Med Rep. 2020;22(2):1155-1168.

Abstract: Translational regulation permeates neuronal function. Nociceptors are sensory neurons responsible for the detection of harmful stimuli. Changes in their activity, termed plasticity, are intimately linked to the persistence of pain. While inhibitors of protein synthesis robustly attenuate pain associated behavior, the underlying targets that support plasticity are largely unknown. Here, we examine the contribution of protein synthesis in regions of RNA annotated as non-coding. Based on analyses of previously reported ribosome profiling data, we provide evidence for widespread translation in non-coding transcripts and regulatory regions of mRNAs. We identify an increase in ribosome occupancy in the 5' untranslated regions of the calcitonin gene-related peptide(CGRP/Calca). We validate the existence of an upstream Open Reading Frame (uORF) using a series of reporter assays. Fusion of the uORF to a luciferase reporter revealed active translation in DRG neurons following nucleofection. Injection of the peptide corresponding to the CGRP encoded uORF resulted in pain associated behavioral responses in vivo and nociceptor sensitization in vitro. An inhibitor of heterotrimeric G protein signaling blocks both effects. Collectively, the data suggest pervasive translation in regions of the transcriptome annotated as non-coding in DRG neurons and identify a specific uORF encoded peptide that promotes pain sensitization through GPCR signaling.

Barragan-Iglesias P, Kunder N, Wanghzou A, et al. A peptide encoded within a 5’ untranslated region promotes pain sensitization in mice. Pain. 2021;Publish Ahead of Print.

Abstract: Hematopoietic cells are continuously replenished from progenitor cells that reside in the bone marrow. To evaluate molecular changes during this process, we analyzed the transcriptomes of freshly harvested human bone marrow progenitor (lineage-negative) and differentiated (lineage-positive) cells by single-molecule real-time (SMRT) full-length RNA-sequencing. This analysis revealed a ~5-fold higher number of transcript isoforms than previously detected and showed a distinct composition of individual transcript isoforms characteristic for bone marrow subpopulations. A detailed analysis of messenger RNA (mRNA) isoforms transcribed from the ANXA1 and EEF1A1 loci confirmed their distinct composition. The expression of proteins predicted from the transcriptome analysis was evaluated by mass spectrometry and validated previously unknown protein isoforms predicted e.g., for EEF1A1. These protein isoforms distinguished the lineage negative cell population from the lineage positive cell population. Finally, transcript isoforms expressed from paralogous gene loci (e.g., CFD, GATA2, HLA-A, B, and C) also distinguished cell subpopulations but were only detectable by full-length RNA sequencing. Thus, qualitatively distinct transcript isoforms from individual genomic loci separate bone marrow cell subpopulations indicating complex transcriptional regulation and protein isoform generation during hematopoiesis.

Deslattes Mays A, Schmidt M, Graham G, et al. Single-molecule real-time (Smrt) full-length rna-sequencing reveals novel and distinct mrna isoforms in human bone marrow cell subpopulations. Genes. 2019;10(4):253.

Abstract: The peptidergic system is the most abundant network of ligand-receptor-mediated signaling in humans. However, the physiological roles remain elusive for numerous peptides and more than 100 G protein-coupled receptors (GPCRs). Here we report the pairing of cognate peptides and receptors. Integrating comparative genomics across 313 species and bioinformatics on all protein sequences and structures of human class A GPCRs, we identify universal characteristics that uncover additional potential peptidergic signaling systems. Using three orthogonal biochemical assays, we pair 17 proposed endogenous ligands with five orphan GPCRs that are associated with diseases, including genetic, neoplastic, nervous and reproductive system disorders. We also identify additional peptides for nine receptors with recognized ligands and pathophysiological roles. This integrated computational and multifaceted experimental approach expands the peptide-GPCR network and opens the way for studies to elucidate the roles of these signaling systems in human physiology and disease.

Foster SR, Hauser AS, Vedel L, et al. Discovery of human signaling systems: pairing peptides to g protein-coupled receptors. Cell. 2019;179(4):895-908.e21.