Chromatin interaction maps identify Wnt responsive cis-regulatory elements coordinating Paupar-Pax6 expression in neuronal cells

Hypothalamus Transcriptome Reveals Key lncRNAs and mRNAs Associated with Fecundity in Goats

The hypothalamus (hyp) serves as the regulatory hub of the neuroendocrine system, synthesizing and secreting reproductive hormones that modulate estrus, follicular maturation, and embryonic development in goats. This study employed RNA-seq analysis to examine gene expression in the hypothalamic tissue of Yunshang black goats during the luteal phase in goats with high fecundity (LP_HY), during the luteal phase in goats with low fecundity (LP_LY), during the follicular phase in goats with high fecundity (FP_HY), and during the follicular phase in goats with low fecundity (FP_LY). Differential long non-coding RNAs (DE lncRNAs) and differential mRNAs (DE mRNAs) were subjected to Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses and the construction of co-expression networks associated with reproduction. As a result, DE lncRNAs (390, 375, 405, and 394) and DE mRNAs (1836, 2047, 2003, and 1963) were identified in the four comparisons, namely FP_LY vs. FP_HY, LP_HY vs. FP_HY, LP_LY vs. FP_LY, and LP_LY vs. LP_HY, respectively. Functional annotations indicated significant enrichment of numerous DE lncRNAs and DE mRNAs in reproduction-related pathways such as the gonadotropin-releasing hormone pathway, the prolactin signaling pathway, the estrogen signaling pathway, the Wnt signaling pathway, oocyte meiosis, and progesterone-mediated oocyte maturation. The co-expression network of lncRNAs and target genes identified the interrelationships between reproduction-related genes such as IGF1, PORCN, PLCB2, MAPK8, PRLR, and CPEB2 with our newly discovered lncRNAs. This study expands the understanding of lncRNAs and mRNAs in goat hypothalamic tissue and provides new insights into molecular mechanisms related to goat reproduction.

Role of HNF4A-AS1/HNRNPC-mediated HNF4A ubiquitination protection against ritonavir-induced hepatotoxicity

Ritonavir (RTV) is an important drug for anti-human immunodeficiency virus treatment and is mainly metabolized by cytochrome P450 (CYP) 3A4. Clinically, the most common side effect of RTV treatment is hepatoxicity. We previously showed that the long noncoding RNA hepatocyte nuclear factor 4 alpha (HNF4A) antisense 1 (HNF4A-AS1) negatively regulated CYP3A4 expression and participated in RTV-induced hepatotoxicity in vitro, but the mechanism has not been well understood. In this study, similar results were observed in the mouse, where liver-specific knockdown of Hnf4aos (homolog of human HNF4A-AS1) led to increased serum aspartate (∼1.8-fold) and alanine transaminase (∼2.4-fold) levels and enlarged and degenerated hepatocytes 24 hours after RTV administration. Meanwhile, endoplasmic reticulum stress markers GRP78, PDI, and XBP-1 increased about 2.4-fold, 2.1-fold, and 2.7-fold, respectively. The aggravated liver injury correlated with Hnf4aos knockdown, attributable to heightened Cyp3a11 (homolog of human CYP3A4) expression (mRNA and protein levels were 1.8-fold and 2.5-fold, respectively). Importantly, in vitro studies revealed the underlying mechanism that HNF4A-AS1 mediated the interaction between heterogeneous nuclear ribonucleoprotein C and HNF4A, whereas heterogeneous nuclear ribonucleoprotein C promoted HNF4A degradation through the ubiquitination pathway, thereby decreasing CYP3A4 expression and alleviating RTV-induced liver injury. Overall, our findings unveil a novel mechanism by which HNF4A-AS1 regulates CYP3A4 expression to influence RTV-induced liver injury. SIGNIFICANCE STATEMENT: HNF4A-AS1 negatively regulates the expression of CYP3A4, whose overexpression is highly correlated with ritonavir (RTV)-induced liver injury. In this study, the role of Hnf4aos (homolog of human HNF4A-AS1) in RTV-induced hepatotoxicity was confirmed in mice. We found that HNF4A-AS1 and HNRNPC form a complex and facilitate the ubiquitination and degradation of HNF4A protein, thereby decreasing CYP3A4 expression and alleviating RTV hepatotoxicity.

The long noncoding RNA HNF1A-AS1 with dual functions in the regulation of cytochrome P450 3A4

Cytochrome P450 3A4 (CYP3A4) is the most important and abundant drug-metabolizing enzyme in the human liver. Inter-individual differences in the expression and activity of CYP3A4 affect clinical and precision medicine. Increasing evidence indicates that long noncoding RNAs (lncRNAs) play crucial roles in the regulation of CYP3A4 expression. Here, we showed that lncRNA hepatocyte nuclear factor 1 alpha-antisense 1 (HNF1A-AS1) exerted dual functions in regulating CYP3A4 expression in Huh7 and HepG2 cells. Mechanistically, HNF1A-AS1 served as an RNA scaffold to interact with both protein arginine methyltransferase 1 and pregnane X receptor (PXR), thereby facilitating their protein interactions and resulting in the transactivation of PXR and transcriptional alteration of CYP3A4 via histone modifications. Furthermore, HNF1A-AS1 bound to the HNF1A protein, a liver-specific transcription factor, thereby blocking its interaction with the E3 ubiquitin ligase tripartite motif containing 25, ultimately preventing HNF1A ubiquitination and protein degradation, further regulating the expression of CYP3A4. In summary, these results reveal the novel functions of HNF1A-AS1 as the transcriptional and post-translational regulator of CYP3A4; thus, HNF1A-AS1 may serve as a new indicator for establishing or predicting individual differences in CYP3A4 expression.

Roles of lncRNAs in brain development and pathogenesis: Emerging therapeutic opportunities

The human genome is pervasively transcribed, producing a majority of short and long noncoding RNAs (lncRNAs) that can influence cellular programs through a variety of transcriptional and post-transcriptional regulatory mechanisms. The brain houses the richest repertoire of long noncoding transcripts, which function at every stage during central nervous system development and homeostasis. An example of functionally relevant lncRNAs is species involved in spatiotemporal organization of gene expression in different brain regions, which play roles at the nuclear level and in transport, translation, and decay of other transcripts in specific neuronal sites. Research in the field has enabled identification of the contributions of specific lncRNAs to certain brain diseases, including Alzheimer's disease, Parkinson's disease, cancer, and neurodevelopmental disorders, resulting in notions of potential therapeutic strategies that target these RNAs to recover the normal phenotype. Here, we summarize the latest mechanistic findings associated with lncRNAs in the brain, focusing on their dysregulation in neurodevelopmental or neurodegenerative disorders, their use as biomarkers for central nervous system (CNS) diseases in vitro and in vivo, and their potential utility for therapeutic strategies.

Endogenous neural stem cells characterization using omics approaches: Current knowledge in health and disease

Neural stem cells (NSCs), an invaluable source of neuronal and glial progeny, have been widely interrogated in the last twenty years, mainly to understand their therapeutic potential. Most of the studies were performed with cells derived from pluripotent stem cells of either rodents or humans, and have mainly focused on their potential in regenerative medicine. High-throughput omics technologies, such as transcriptomics, epigenetics, proteomics, and metabolomics, which exploded in the past decade, represent a powerful tool to investigate the molecular mechanisms characterizing the heterogeneity of endogenous NSCs. The transition from bulk studies to single cell approaches brought significant insights by revealing complex system phenotypes, from the molecular to the organism level. Here, we will discuss the current literature that has been greatly enriched in the “omics era”, successfully exploring the nature and function of endogenous NSCs and the process of neurogenesis. Overall, the information obtained from omics studies of endogenous NSCs provides a sharper picture of NSCs function during neurodevelopment in healthy and in perturbed environments.

Ganglioglioma deep transcriptomics reveals primitive neuroectoderm neural precursor-like population

Gangliogliomas are brain tumors composed of neuron-like and macroglia-like components that occur in children and young adults. Gangliogliomas are often characterized by a rare population of immature astrocyte-appearing cells expressing CD34, a marker expressed in the neuroectoderm (neural precursor cells) during embryogenesis. New insights are needed to refine tumor classification and to identify therapeutic approaches. We evaluated five gangliogliomas with single nucleus RNA-seq, cellular indexing of transcriptomes and epitopes by sequencing, and/or spatially-resolved RNA-seq. We uncovered a population of CD34+ neoplastic cells with mixed neuroectodermal, immature astrocyte, and neuronal markers. Gene regulatory network interrogation in these neuroectoderm-like cells revealed control of transcriptional programming by TCF7L2/MEIS1-PAX6 and SOX2, similar to that found during neuroectodermal/neural development. Developmental trajectory analyses place neuroectoderm-like tumor cells as precursor cells that give rise to neuron-like and macroglia-like neoplastic cells. Spatially-resolved transcriptomics revealed a neuroectoderm-like tumor cell niche with relative lack of vascular and immune cells. We used these high resolution results to deconvolute clinically-annotated transcriptomic data, confirming that CD34+ cell-associated gene programs associate with gangliogliomas compared to other glial brain tumors. Together, these deep transcriptomic approaches characterized a ganglioglioma cellular hierarchy-confirming CD34+ neuroectoderm-like tumor precursor cells, controlling transcription programs, cell signaling, and associated immune cell states. These findings may guide tumor classification, diagnosis, prognostication, and therapeutic investigations.