RNA Sequencing Assays Research Articles

METRNL exerts cytoprotective effects on EPCs via regulation of the E2F1-TXNIP axis in obese limb ischemia

BackgroundObesity increases cardiovascular disease risk by impairing angiogenesis, primarily through dysfunction of endothelial progenitor cells (EPCs). METRNL, a recently identified secreted protein, exhibits diverse biological activities. However, its impact on EPC function and its role in obesity-related microvascular dysfunction remain unclear. This study aims to investigate the effects of METRNL on EPC function and its potential therapeutic mechanisms for promoting angiogenesis. MethodIn vitro, human EPCs derived from peripheral and umbilical cord blood were treated with recombinant METRNL protein (rMETRNL) and exposed to palmitic acid (PA). EPC proliferation, migration, and tube formation were assessed. Apoptosis and pyroptosis levels were evaluated using Western blotting, flow cytometry, scanning electron microscopy (SEM), immunofluorescence (IF), and enzyme-linked immunosorbent assay (ELISA). RNA sequencing, ChIP, and dual-luciferase assays were performed to investigate the regulatory mechanisms. In vivo, an obese mouse model with hind limb ischemia received local injections of METRNL-overexpressing EPCs in the ischemic muscle. Blood flow recovery was monitored using laser Doppler flowmetry and CD31 immunofluorescence. ResultsReplenishment of METNRL alleviated PA-induced apoptosis and pyroptosis of EPCs, while simultaneously enhancing their proliferation, migration, and tube formation. Mechanistically, RNA sequencing revealed that rMETRNL restoration downregulated E2F1 expression, and the protective effects of METRNL were partially reversed by E2F1 overexpression. Further, E2F1 was found to bind the TXNIP promoter region, promoting TXNIP transcription. Elevated TXNIP levels counteracted the beneficial effects of rMETRNL on EPC function in the presence of PA. In vivo, the transplantation of METRNL-overexpressing EPCs into the ischemic hind limbs of obese mice promoted angiogenesis, as evidenced by improved blood flow recovery and increased CD31 immunofluorescence in the ischemic tissues. ConclusionOur research emphasizes the potential of METRNL in reducing EPC cellular pyroptosis and promoting angiogenesis by inhibiting the E2F1-TXNIP signaling pathway. METRNL shows promise in treating obesity-related cardiovascular diseases through angiogenic therapy.

POU3F4 up-regulates Gli1 expression and promotes neuronal differentiation and synaptic development of hippocampal neural stem cells

BackgroundNeural stem cells (NSCs) are considered to be the most promising cell type for cell replacement therapy in neurodegenerative diseases. However, their low neuronal differentiation ratio impedes their application in such conditions. Elucidating the molecular mechanism of NSC differentiation may provide the necessary experimental basis for expanding their application. Previous studies have indicated that POU3F4 can induce neuronal differentiation of NSCs, this study aims to underly the possible exact mechanism of POU3F4 on the NSC differentiation and development.MethodsNSCs were isolated and cultured from the hippocampus of neonatal mice. The frozen hippocampal sections were prepared for immunohistochemical staining. Synaptic development was assessed using electron microscopy. High-throughput sequencing was employed to analyze the gene expression profile following the overexpression of Brn4. Gene expression levels were determined through Western blotting and qRT-PCR. Cell cycle and differentiation were evaluated using flow cytometry and immunofluorescent staining.ResultsIt was found that POU3F4 promoted the neuronal differentiation of hippocampal NSCs and synapse development, and inhibited NSC proliferation. POU3F4-deficient mice exhibited impairments in learning and memory. RNA sequencing and ChIP assays confirmed that Gli1 was downstream of POU3F4. Loss and gain function experiments indicated that Gli1 mediated POU3F4 promoting neuronal differentiation and synapse development. Forced expression of Gli1 in hippocampus improved learning and memory function of animal models.ConclusionsThe results suggest that POU3F4 and Gli1 promote neuronal differentiation and synaptic development of NSCs, and that Gli1 partially mediates the effects of POU3F4.Graphical abstract

Koala ocular disease grades are defined by chlamydial load changes and increases in Th2 immune responses.

This study employs bulk RNA sequencing, PCR, and ELISA assays to analyze the pathological factors affecting the outcomes of C. pecorum ocular infections in koalas. It investigates the immune responses and gene expression profiles associated with various stages of koala ocular chlamydiosis. A cohort of 114 koalas from Queensland, Australia were assessed, with 47% displaying clinical signs of ocular disease. Animals were classified into three cohorts: acute active disease (G1), chronic active disease (G2), and chronic inactive disease (G3), along with subclinical Chlamydia pecorum positive (H2) and healthy (H1) cohorts. Analysis of clinical, microbiological, humoral immune and cellular immune biomarkers revealed varying chlamydial loads and anti-chlamydial IgG levels across disease grades, with a negative correlation observed between ocular chlamydial load and anti-chlamydial IgG. Koala ocular mucosa gene expression analysis from 27 koalas identified shared expression pathways across disease cohorts, with a significant upregulation of IFNγ expression and tryptophan metabolism in all disease stages. These findings help elucidate immune response dynamics and molecular pathways underlying koala ocular chlamydiosis, providing insights crucial for disease management strategies.

TMIC-82. CHARACTERIZATION OF GENETIC MARKERS AND BIOLOGICAL PROCESSES UNDERLYING THE TRANSITION OF GLIOBLASTOMA CELLS FROM A DIFFERENTIATED TO A STEM-CELL-LIKE STATE

Abstract BACKGROUND The main drivers of Glioblastoma (GBM) tumor growth are elevated angiogenesis and heightened characteristics of stemness. These driving factors make GBM an extremely invasive and aggressive tumor. While the GBM tumor microenvironment can be classified into several molecular subtypes, one common characteristic is the atypical induction of various signal transduction pathways including the receptor tyrosine kinases (RTKs), pro-angiogenic, and stem-cell-determining transcription factors, which all play important roles in GBM tumor formation, growth, and progression. OBJECTIVE To investigate the regulations of RTKs, pro-angiogenic, and stem-cell–determining transcription factors in two different tumor environments - monolayer cultures that induce a more differentiated state and neurosphere cultures that select for stem-like cells. METHODS Neurosphere- and monolayer-forming cell samples were cultured from four primary GBM cell lines including HK-336, HK-374, U87, and GS-154. RNA sequencing was performed at the Technology Center for Genomics and Bioinformatics at the University of California, Los Angeles. The transcriptomic data findings were validated by qPCR and western blot assays. RESULTS Our transcriptomic data revealed the significant upregulation of EGFR, PDGFR-α, VEGFA, and SOX2 in the neurosphere-forming HK-336, HK-374, U87, and GS-154 primary GBM cells. Consistent with the transcriptomic data, western blot, and qPCR assays demonstrated significantly higher expressions of these genes in the neurosphere-forming compared to the monolayer-forming GBM cells. Neurosphere-forming GBM cells possess stem-cell-like characteristics with the ability to self-renew and differentiate via the induction of various genes and disease progression pathways. CONCLUSIONS Neurosphere-forming GBM cells demonstrate upregulation of SOX2, EGFR, PDGFR-α, and VEGFA in RNA sequencing, western blot, and qPCR assays. Multipotent drug therapies designed to target multiple gene regulation pathways involving RTKs, pro-angiogenic, and stem-cell-determining transcription factors may be necessary to effectively treat GBM. Understanding the underlying mechanisms driving these aberrant cellular pathways could provide valuable insights for developing targeted therapies against this aggressive brain cancer.

CSIG-19. IDENTIFICATION AND TARGETING OF TUMOR DRIVER SCHWANN(NF2LOSS) CELLS IN SPORADIC AND NF2-RELATED VESTIBULAR SCHWANNOMAS

Abstract Vestibular schwannomas (VS) arise from myelinating Schwann cells of CN VIII and are associated with severe morbidity due to local tumor growth. Sporadic and neurofibromatosis type 2 (NF2) associated VS are both characterized by NF2 (merlin) loss but the mechanisms remain unexplored. Using a multiomic approach, we dissected the role of NF2 loss in VS tumor formation and proliferation. We obtained surgical samples from 15 patients undergoing surgery for VS (sporadic, n=4; NF2, n=9), and performed single-cell or single-nucleus RNA sequencing (scRNAseq, n=4; snRNAseq, n=15), transposase-accessible chromatin (snATAC-seq, n=9), whole exome (n=12), and bulk DNA methylation assays (n=15). Transcription factor binding was assayed with ChIPseq. We validated our key findings with immunoblot, ELISA, RNAscope (n=8), and multiplex immunocytochemistry (mIHC; n=8). NF2fl/fl;Periostin-Cre+mice versus their Cre- control littermates treated with novel inhibitors of TEAD auto-palmitoylation (VTs). We mapped the VS transciptome and identified canonical Schwann cells, macrophages, T-cells and endothelial cells. Using the cells that had Chr22 loss (second hit deletions at the NF2 locus), we generated a NF2loss gene signature. We then identified Schwann(NF2loss) cells in all tumors, and found these enriched for YAP1/TAZ-TEAD, NRG1, and HIF-1α signaling pathways. Schwann(NF2loss) cells showed increased TEAD1 expression and chromatin accessibility for TEAD family transcription factor motifs. TEAD1 binding was observed at promoters of genes including VEGFA, EGFR, with strong enrichment for mitogenic pathways. We also found that VEFGA expression was restricted to Schwann(NF2loss) cells, and confirmed this with RNAscope and mIHC. Schwann(NF2loss) cells were key regulators of macrophages (M2-subtype, tissue resident) through M-CSF/IL-34 signaling. NF2fl/fl;Periostin-Cre+ mice showed increased VEGFA expression, and that was reversible by TEAD inhibition in-vivo with VTs. We report that Schwann(NF2loss) cells are key tumor drivers in VS. These cells are highly proliferative (YAP/TAZ-TEAD axis), drive angiogenesis (VEGFA expression), and promote tumor mass accretion (macrophage influx via M-CSF/IL-34 pathway) that can all be targeted via TEAD inhibition.

Preparation of Frozen Non-Human Primate Fetal Islets for Combined Single Nuclei RNA-Sequencing and ATAC-Sequencing, and Bulk Metabolomics.

One challenge in studies using tissue collected from multiple cohorts is avoiding batch effects when preparing for large-scale multi-omic experiments, such as combined single-cell RNA sequencing and metabolomics. The method in the current study utilizes flash-frozen pancreatic islets from fetal non-human primates collected over a span of two years for input into single-nucleus RNA sequencing and ATAC sequencing assays. The cytosolic fraction generated during nuclear extraction was retained for downstream capillary electrophoresis-mass spectrometry and subsequent metabolite quantification. This method allows for bulk analysis of metabolites that contribute to the changing transcriptomic and epigenomic landscapes within experimental conditions. It is applicable to many tissue types and maximizes the amount of information that can be extracted from samples that are not readily available. As the contribution of metabolism to the establishment of cellular identity via epigenetic modifications becomes more appreciated, techniques that allow for identifying the contribution of metabolites in specific cell types are timely and necessary.

Prospective study of the real impact of fusion centered genomic assays in patient management in a national collaborative group: the GETHI-XX-16 study.

Precision medicine represents a paradigm shift in oncology. Access to genetic testing and targeted therapies is frequently limited. Assays based on DNA sequencing can miss druggable alterations. We aimed to determine the impact of a free access program to RNA tests in patient management. We designed a multicenter prospective observational study within the Spanish National Group for Translational Oncology and Rare and Orphan Tumors (GETTHI). Eligible patients were adults with solid cancers that had progressed on standard therapies. Tumor samples were analyzed using two RNA sequencing assays (Trailblaze PharosTM and Archer FusionPlex Solid TumorTM). A central committee evaluated the actionability of genetic alterations and reported the findings to attending physicians, who made the final clinical management decisions. Between November 2016 and April 2019, 395 patients with 41 different tumors across 30 hospitals were included. Molecular analysis revealed actionable genetic alterations in 57 individuals (14.4%). Targeted therapies were advised for 23 and seven received a matched targeted therapy: two lung cancers (EML4-ALK and CD74-ROS1 fusion), three glioblastomas (EGFR point mutations), one oligodendroglioma (FGFR3-TACC3 fusion) and a prostate cancer (SND1-BRAF fusion). The outcomes included two tumor responses, one disease stabilization, one early withdrawal due to toxicity, one progression, and one unknown. Despite the growing knowledge of cancer biology and its translation to drug development, the overall impact of personalized treatments remains low. Access to comprehensive molecular tests covering properly all known actionable alterations and programs for a wide access to targeted therapies seem to be critical steps.

VNN2 regulates hepatic steroid synthesis in response to dietary changes

Peroxisome proliferator-activated receptor alpha (PPARα) plays a crucial role in regulating hepatic fat oxidation. Previous studies have identified VNN2 as a potential PPARα target gene in chicken liver. However, the specific function of VNN2 in hepatic lipid metabolism remains unclear. We utilized datasets GSM5764402, GSM5764403, GSE128340, GSE129840, and PRJEB44038 to investigate the expression pattern and potential function of VNN2 in chicken liver. Our analysis included RNA sequencing, qPCR, and triglyceride and total cholesterol assays for verification. Through analysis of single-cell RNA sequencing (scRNA-seq) data, we localized VNN2 expression at the cellular level and identified potential downstream targets of VNN2. We further examined these potential targets in VNN2 overexpressed and knockdown Leghorn male hepatoma (LMH) cells. Our findings revealed that VNN2 is highly expressed in hepatocytes with elevated lipid metabolism and steroid biosynthesis activity. This study confirms that VNN2 promotes steroid biosynthesis by upregulating MSMO1 and FDPS, providing new insights into its role in hepatic lipid metabolism.

Transcription factor TCF7L1 targeting HSPB6 is involved in EMT and PI3K/AKT/mTOR pathways in bladder cancer

Bladder cancer is notorious for its high recurrence and costly treatment burden, prompting a search for novel therapeutic targets. Our study focuses on HSPB6, a small heat shock protein whose reduced expression in bladder cancer suggests a role in tumor biology. Using an integrative approach of bioinformatics, RNA sequencing, and cell-based assays, we show that HSPB6 upregulation inhibits cancer cell proliferation and metastasis, while promoting apoptosis. Moreover, TCF7L1-mediated upregulation of HSPB6 leads to suppression of the PI3K/AKT/mTOR signaling pathway, a key driver of cancer progression. These results position HSPB6 as a compelling target for bladder cancer therapy, and its regulatory role in the PI3K/AKT/mTOR axis underscores its therapeutic potential. Our findings pave the way for future investigations into HSPB6-centered treatment strategies.

Translation profiling of stress-induced small proteins reveals a novel link among signaling systems.

Signaling networks allow adaptation to stressful environments by activating genes that counteract stressors. Small proteins (≤ 50 amino acids long) are a rising class of stress response regulators. Escherichia coli encodes over 150 small proteins, most of which lack phenotypes and their biological roles remain elusive. Using magnesium limitation as a stressor, we identify stress-induced small proteins using ribosome profiling, RNA sequencing, and transcriptional reporter assays. We uncover 17 small proteins with increased translation initiation, several of them transcriptionally upregulated by the PhoQ-PhoP two-component signaling system, crucial for magnesium homeostasis. Next, we describe small protein-specific deletion and overexpression phenotypes, underscoring their physiological significance in low magnesium stress. Most remarkably, we elucidate an unusual connection via a small membrane protein YoaI, between major signaling networks - PhoR-PhoB and EnvZ-OmpR in E. coli, advancing our understanding of small protein regulators in cellular signaling.

MIR194-2HG, a miRNA host gene activated by HNF4A, inhibits gastric cancer by regulating microRNA biogenesis

BackgroundMicroRNA host gene (MIRHG) lncRNA is a particular lncRNA subclass that can perform both typical and atypical lncRNA functions. The biological function of MIRHG lncRNA MIR194-2HG in cancer is poorly understood.MethodsLoss-of-function studies were performed in vivo and in vitro to reveal the biological function of MIR194-2HG in GC. MicroRNA PCR array, northern blotting, RNA sequencing, chromatin immunoprecipitation, and rescue assays were conducted to uncover the molecular mechanism of MIR194-2HG.ResultsIn this study, we reported an atypical lncRNA function of MIR194-2HG in GC. MIR194-2HG downregulation was clinically associated with malignant progression and poor prognosis in GC. Functional assays confirmed that MIR194-2HG knockdown significantly promoted GC proliferation and metastasis in vitro and in vivo. Mechanismically, MIR194-2HG was required for the biogenesis of miR-194 and miR-192, which were reported to be tumor-suppressor genes in GC. Moreover, hepatocyte nuclear factor HNF4A directly activated the transcription of MIR194-2HG and its derived miR-194 and miR-192. Meanwhile, BTF3L4 was proved to be a common target gene of miR-192 and miR-194. Rescue assay further confirmed that MIR194-2HG knockdown promotes GC progression through maintaining BTF3L4 overexpression in a miR-194/192-dependent manner.ConclusionThe dysregulated MIR194-2HG/BTF3L4 axis is responsible for GC progression. Targeting HNF4A to inhibit miR-192/194 expression may be a promising strategy for overcoming GC.

RNAs m6A modification facilitates UVB-induced photoaging

RNA N6-methylation (m6A) modification is common in eukaryotic mRNA and has been linked to various physiological disorders, including UVB-induced photoaging. To identify biological differences among photoaging. Three pairs of normal and photoaged skin tissues were collected for m6A RNA sequencing assay. Transcriptome profiles showed differential m6A methylation modifications in 1365 mRNAs in photoaging skin tissues. Pathway analysis revealed the involvement of cellular stress response and regulation of cell cycle G2/M phase transition in m6A-mRNAs. Further experiments validated the differential expression of m6A methyltransferases (METTL3 and METTL14) and hypermethylation modification in mRNAs (CENPE, PPM1B and TPM1). In vitro studies demonstrated that increased METTL3 and METTL14 levels promoted m6A methylation of CENPE, PPM1B and TPM1 in UVB-induced photoaging cells, and further experiments on mice showed that downregulation of METTL3 and METTL14 reduced m6A modifications in CENPE, PPM1B and TPM1, leading to the delayed appearance of photoaging phenotypes, suggesting that these genes could serve as potential therapeutic targets for treating photoaging. Our study characterized key transcriptome changes in photoaging and identified the role of METTL3 and METTL14 in mediating m6A modification, resulting in the upregulation of CENPE, PPM1B and TPM1 expression, which may be crucial in UVB-induced photoaging.

LGR6 protects against myocardial ischemia-reperfusion injury via suppressing necroptosis

Regulated necrosis (necroptosis) and apoptosis are important biological features of ischemia-reperfusion (I/R) injury. However, the molecular mechanisms underlying myocardial necroptosis remain elusive. Leucine rich repeat containing G protein-coupled receptor 6 (LGR6) has been reported to play important roles in various cardiovascular disease. In this study, we aimed to determine whether LGR6 suppresses I/R-induced myocardial necroptosis and the underlying molecular mechanisms. We generated LGR6 knockout mice and used ligation of left anterior descending coronary artery to produce an in vivo I/R model. The effects of LGR6 and its downstream molecules were subsequently identified using RNA sequencing and CHIP assays. We observed significantly downregulated LGR6 expression in hearts post myocardial I/R and cardiomyocytes post hypoxia and reoxygenation (HR). LGR6 deficiency promoted and LGR6 overexpression inhibited necroptosis and acute myocardial injury after I/R. Mechanistically, in vivo and in vitro experiments suggest that LGR6 regulates the expression of STAT2 and ZBP1 by activating the Wnt signaling pathway, thereby inhibiting cardiomyocyte necroptosis after HR. Inhibiting STAT2 and ZBP1 effectively alleviated the aggravating effect of LGR6 deficiency on myocardial necroptosis after I/R. Furthermore, activating LGR6 with RSPO3 also effectively protected mice from acute myocardial I/R injury. Our findings reveal that RSPO3-LGR6 axis downregulates the expression of STAT2 and ZBP1 through the Wnt signaling pathway, thereby inhibiting I/R-induced myocardial injury and necroptosis. Targeting the RSPO3-LGR6 axis may be a potential therapeutic strategy to treat myocardial I/R injury.

EPO modified MSCs protects SH-SY5Y cells against ischemia/hypoxia-induced apoptosis via REST-dependent epigenetic remodeling

Hypoxic-ischemic encephalopathy (HIE) is a diffuse brain tissue injury caused by acute ischemia and hypoxia, and it is most commonly found in newborn infants but can also occur in adults. Mesenchymal stem cell (MSC) therapies have showed improved outcomes for treating HIE-induced neuronal defects. However, many key issues associated with poor cell viability and tolerance of grafted MSCs after HIE remain to be resolved. Genetic engineering could endow MSCs with more robust regenerative capacities. Our research, along with that of other scientists, has found that the expression of intracellular erythropoietin (EPO) in human umbilical cord MSCs (hUC-MSCs) increases proportionally with the duration of hypoxia exposure. Furthermore, we observed that EPO, when introduced into the EPO gene-modified hUC-MSCs, can be secreted into the extracellular space. However, the underlying mechanisms that support the neuroprotective effects of EPO-MSCs remain unclear. EPO-MSCs, hUC-MSCs, and NC-MSCs were identified by flow cytometry, osteogenic, and adipogenic differentiation assays. The oxygen-glucose deprivation (OGD)-induced SH-SY5Y cell-line was established, and five groups were set up: control, 24-h ischemia-hypoxia, co-cultured with hUC-MSCs, NC-MSCs, and EPO-MSCs after hypoxia. LEGENDplex™ multi-factor flow cytometry was used to detect the secretion of inflammatory factors in cell supernatants and cerebrospinal fluid. Chromosome-targeted excision and tagging (CUT&Tag) sequencing was applied to detect genomic H3K4me2 modifications, and conjoint analysis with transcriptome sequencing (RNA-seq) was performed. Lentiviral vector infection was used to construct SH-SY5Y cells with stable knockdown of RE1-silencing transcription factor (REST), and flow cytometry was used to detect alterations in apoptosis. Finally, the molecular mechanism underlying the neuroprotective and anti-apoptotic effects of EPO-MSCs was investigated using RNA sequencing, qRT-PCR, and western blot assays. Our results suggest that EPO-MSCs are genetically engineered to secrete significantly more EPO. EPO-MSCs treatment has anti-apoptotic properties and offers neuronal protection during ischemic-hypoxic injury. Furthermore, RNA-seq results suggest that multiple inflammation-related genes were down-regulated after EPO-MSCs treatment. Application of RNA-seq and CUT&Tag combined analysis found that the expressions of REST were significantly up-regulated. Lentiviral vector infection to construct REST knockdown SH-SY5Y failed to rescue apoptosis after hypoxia and co-culture with EPO-MSCs, and SETD2-mediated H3K36me3 protein level expression was reduced. EPO-MSCs may promote neuronal survival by affecting H3K4me2 and thus activating the expression of REST and TET3. EPO-MSCs also upregulated the modification level of SETD2-mediated H3K36me3 and regulated the expression of inflammation-related genes such as PLCG2, as well as apoptosis genes BCL2A1. To investigate the neuroprotective effects of EPO-modified hUC-MSCs and the underlying epigenetic regulatory mechanisms, this study aims to provide a theoretical foundation for the potential application of EPO gene-modified hUC-MSCs in the treatment of HIE.

Excitatory neurons and oligodendrocyte precursor cells are vulnerable to focal cortical dysplasia type IIIa as suggested by single-nucleus multiomics.

Focal cortical dysplasia (FCD) is a heterogeneous group of cortical developmental malformations that constitute a common cause of medically intractable epilepsy. FCD type IIIa (FCD IIIa) refers to temporal neocortex alterations in architectural organisation or cytoarchitectural composition in the immediate vicinity of hippocampal sclerosis. Slight alterations in the temporal neocortex of FCD IIIa patients pose a challenge for the preoperative diagnosis and definition of the resection range. We have performed multimodal integration of single-nucleus RNA sequencing and single-nucleus assay for transposase-accessible chromatin sequencing in the epileptogenic cortex of four patients with FCD IIIa, and three relatively normal temporal neocortex were chosen as controls. Our study revealed that the most significant dysregulation occurred in excitatory neurons (ENs) and oligodendrocyte precursor cells (OPCs) in the epileptogenic cortex of FCD IIIa patients. In ENs, we constructed a transcription factor (TF)-hub gene regulatory network and found DAB1high ENs subpopulation mediates neuronal immunity characteristically in FCD IIIa. Western blotting and immunofluorescence were used to validate the changes in protein expression levels caused by some of the key genes. The OPCs were activated and exhibited aberrant phenotypes in FCD IIIa, and TFs regulating reconstructed pseudotime trajectory were identified. Finally, our results revealed aberrant intercellular communication between ENs and OPCs in FCD IIIa patients. Our study revealed significant and intricate alterations in the transcriptomes and epigenomes in ENs and OPCs of FCD IIIa patients, shedding light on their cell type-specific regulation and potential pathogenic involvement in this disorder. This work will help evaluate the pathogenesis of cortical dysplasia and epilepsy and explore potential therapeutic targets. Paired snRNA-seq and snATAC-seq data were intergrated and analysed to identify crucial subpopulations of ENs and OPCs in the epileptogenic cortex of FCD IIIa patients and explore their possible pathogenic role in the disease. A TF-hub gene regulatory network was constructed in ENs, and the DAB1high Ex-1 mediated neuronal immunity was characterstically in FCD IIIa patients. The OPCs were activated and exhibited aberrant phenotypes in FCD IIIa patients, and TFs regulating reconstructed pseudotime traectory were identified. Aberrant intercelluar communications between ENs and OPCs in FCD IIIa patients were identified.

Simultaneous mutations in ITPK4 and MRP5 genes result in a low phytic acid level without compromising salt tolerance in Arabidopsis.

Generation of crops with low phytic acid (myo-inositol-1,2,3,4,5,6-hexakisphosphate (InsP6)) is an important breeding direction, but such plants often display less desirable agronomic traits. In this study, through ethyl methanesulfonate-mediated mutagenesis, we found that inositol 1,3,4-trisphosphate 5/6-kinase 4 (ITPK4), which is essential for producing InsP6, is a critical regulator of salt tolerance in Arabidopsis. Loss of function of ITPK4 gene leads to reduced root elongation under salt stress, which is primarily because of decreased root meristem length and reduced meristematic cell number. The itpk4 mutation also results in increased root hair density and increased accumulation of reactive oxygen species during salt exposure. RNA sequencing assay reveals that several auxin-responsive genes are down-regulated in the itpk4-1 mutant compared to the wild-type. Consistently, the itpk4-1 mutant exhibits a reduced auxin level in the root tip and displays compromised gravity response, indicating that ITPK4 is involved in the regulation of the auxin signaling pathway. Through suppressor screening, it was found that mutation of Multidrug Resistance Protein 5 (MRP5)5 gene, which encodes an ATP-binding cassette (ABC) transporter required for transporting InsP6 from the cytoplasm into the vacuole, fully rescues the salt hypersensitivity of the itpk4-1 mutant, but in the itpk4-1 mrp5 double mutant, InsP6 remains at a very low level. These results imply that InsP6 homeostasis rather than its overall amount is beneficial for stress tolerance in plants. Collectively, this study uncovers a pair of gene mutations that confer low InsP6 content without impacting stress tolerance, which offers a new strategy for creating "low-phytate" crops.

A novel circRNA–miRNA–mRNA regulatory axis as a sex-specific biological variable in bronchopulmonary dysplasia

Abstract Babies born prematurely with gestational age <28 weeks usually develop a severe pulmonary complication called Bronchopulmonary Dysplasia (BPD) in response to hyperoxia. BPD is a sexually dimorphic pediatric disease with no curative options. Several micro RNAs (miRNAs) are implicated in BPD and are expressed differentially in males and females. Circular (circ) RNAs serve as sponges for their dedicated miRNAs to influence transcription and translation. We tested the dimorphism of these circular RNAs in BPD to assess their biological significance and unravel a circRNA–miRNA–mRNA regulatory axis in response to hyperoxia. Our RNA-Sequencing assay identified approximately 33 000 circRNAs at the alveolar stage of development with only a handful of them being expressed differentially between males and females in the control room air (RA) and hyperoxia-treated (BPD) groups. One circRNA, i.e circNfix was found to be associated with miR204-5p that targets the downstream mRNA target Ntrk2. To prove that circNfix regulates Ntrk2, we silenced circNfix using a GapmeR and found that Ntrk2 was also suppressed, leading to an improved alveolar phenotype in BPD male pups. From the results of our study, we can propose circNfix and Ntrk2 as novel key regulators in the pathogenesis and sexual dimorphism of BPD, while simultaneously proposing the use of circNfix GapmeR towards a potential therapeutic application.

A heterozygous SPRY4 variant identified in female infertility characterized by reduced oocyte potential and early embryonic arrest.

Can novel genetic factors contributing to early embryonic arrest in infertile patients be identified, along with the underlying mechanisms of the pathogenic variant? We identified a heterozygous variant in the SPRY4 (sprouty RTK signaling antagonist 4) in infertile patients and conducted in vitro and in vivo studies to investigate the effects of the variant/deletion, highlighting its critical role in female reproductive health. SPRY4 acts as a negative regulator of receptor tyrosine kinases (RTKs) and functions as a tumor suppressor. Its abnormal expression can lead to recurrent miscarriage by affecting trophoblast function. In mice, Spry4 knockout (KO) leads to craniofacial anomalies and growth defects. A human study links the SPRY4 variant to a male patient with isolated hypogonadotropic hypogonadism (IHH), hypothetically impacting gonadotropin-releasing hormone (GnRH) neurons, and causing reproductive dysfunctions. SPRY4 is thus potentially integral in regulating endocrine homeostasis and reproductive function. To date, no study has reported SPRY4 variants associated with female fertility, and a causal relationship has not been established with functional evidence. Whole-exome sequencing (WES) was performed in 392 infertile women who suffered from primary infertility of unknown reason, and the heterozygous SPRY4 variant were identified in one independent family. The infertile patients presenting were recruited from July 2017 to November 2023. Women diagnosed with primary infertility were recruited from the Reproduction Center of Zhongshan Hospital, Fudan University. Genomic DNA was extracted from peripheral blood for WES analysis. The SPRY4 variant were identified through WES, in silico analysis, and variant screening. All variants were confirmed by Sanger sequencing. The effects of the variants were investigated in human embryonic kidney (HEK) 293T (HEK293T) cells via western blotting, and in mouse oocytes and embryos through complementary RNA (cRNA) injection, RNA sequencing, fluorescence, absorbance, and RT-qPCR assays. Gene function was further examined in Spry4 KO mice via histology, western blotting, ELISA, and RT-qPCR assays. We identified a missense heterozygous pathogenic variant in SPRY4 (GRCh38, GenBank: NM_030964.5, c.157C>T p.(Arg53Trp), rs200531302) that reduces SPRY4 protein levels in HEK293T cells and disrupts the redox system and mitochondrial function in mouse oocyte, and perturbs developmental potential in mouse embryos. These phenotypes could be partially reversed by the exogenous addition of Nrf1 cRNA. Additionally, Spry4-/- mice exhibit ovarian oxidative stress and decreased ovarian function. Due to the limited WES data and population, we identified only one family with a SPRY4 mutation. The deeper mechanism and therapeutic strategy should be further investigated through mutant mice and recovery experiment. Our study has identified a pathogenic variant in SPRY4 associated with early embryonic arrest in humans. These findings enhance our understanding of the role of SPRY4 in early embryonic development and present a new genetic marker for female infertility. This work was supported by the National Natural Science Foundation of China (82071643 and 82171655) and Natural Science Foundation of Shanghai (22ZR1456200). None of the authors have any competing interests. N/A.

Whole genome regulatory effect of MoISW2 and consequences for the evolution of the rice plant pathogenic fungus Magnaporthe oryzae.

Isw2 proteins, ubiquitous across eukaryotes, exhibit a propensity for DNA binding and exert dynamic influences on local chromosome condensation in an ATP-dependent fashion, thereby modulating the accessibility of neighboring genes to transcriptional machinery. Here, we report the deletion of a putative MoISW2 gene, yielding substantial ramifications on plant pathogenicity. Subsequent gene complementation and chromatin immunoprecipitation sequencing (ChIP-seq) analyses were conducted to delineate binding sites. RNA sequencing (RNA-seq) assays revealed discernible impacts on global gene regulation along chromosomes in both mutant and wild-type strains, with comparative analyses against 55 external RNA-seq data sets corroborating these findings. Notably, MoIsw2-mediated binding and activities delineate genomic loci characterized by pronounced gene expression variability proximal to MoIsw2 binding sites, juxtaposed with comparatively stable expression in surrounding regions. The contingent genes influenced by MoIsw2 activity predominantly encompass niche-determinant genes, including those encoding secreted proteins, secondary metabolites, and stress-responsive elements, alongside avirulence genes. Furthermore, our investigations unveil a spatial correlation between MoIsw2 binding motifs and known transposable elements (TEs), suggesting a potential interplay wherein TE transposition at these loci could modulate the transcriptional landscape of Magnaporthe oryzae in a strain-specific manner. Collectively, these findings position MoIsw2 as a plausible master regulator orchestrating the delicate equilibrium between genes vital for biomass proliferation, akin to housekeeping genes, and niche-specific determinants crucial for ecological adaptability. Stress-induced TE transposition, in conjunction with MoIsw2 activity, emerges as a putative mechanism fostering enhanced mutagenesis and accelerated evolution of niche-determinant genes relative to housekeeping counterparts.IMPORTANCEIsw2 proteins are conserved in plants, fungi, animals, and other eukaryotes. We show that a fungal Isw2 protein in the rice pathogen Magnaporthe oryzae binds to retrotransposon (RT) DNA motifs and affects the epigenetic gene expression landscape of the fungal genome. Mainly ecological niche determinant genes close to the binding motifs are affected. RT elements occur frequently in DNA between genes in most organisms. They move place and multiply in the genome, especially under physiological stress. We further discuss the Isw2 and RT combined activities as a possible sought-after mechanism that can cause biased mutation rates and faster evolution of genes necessary for reacting to abiotic and biotic challenges. The most important biotic challenges for plant pathogens are the ones from the host plants' innate immunity. The overall result of these combined activities will be an adaptation-directed evolution of niche-determinant genes.

Schisandrin C inhibits AKT1-regulated cell proliferation in A549 cells

BackgroundLung cancer is the leading cause of cancer-related mortality. Cancer poses a significant challenge to human health and remains a persistent and pressing issue. Schisandrin C is one of the active ingredients of Schisandra chinensis and has various biological and pharmacological activities. This study aimed to investigate the effects of Schisandrin C on lung cancer and the underlying mechanism involved. MethodsA network pharmacology strategy was used to screen the target genes and pathways involved in the relationship between Schisandrin and lung cancer. Next, a single-cell RNA sequencing (scRNA-seq) assay revealed the expression of genes specifically expressed in lung cancer epithelial cells. A549 cells were subsequently treated with Schisandrin C for 24 h or 48 h, cell viability was assessed via MTT and EdU staining experiments, and target gene expression was measured via RT–qPCR and immunofluorescence assays. Moreover, lung cancer patient tissues were observed via multiplex immunofluroscence staining. ResultsAKT1, CA9, BRAF, EGFR, ERBB2 and PIK3CA were overlapping target genes for network pharmacology and the scRNA-seq strategy. In vitro, the RT–qPCR results indicated that Schisandrin C inhibited the mRNA expression of the AKT1, CA9, FASN, MMP1, EGFR and BRAF genes. In clinical samples from patients with lung cancer, the expression levels of CA9 and AKT1 were found to be significantly higher in lung tumor tissues than in the adjacent normal (TAN) tissues. Moreover, the administration of an AKT kinase inhibitor reversed the inhibitory effect of Schisandrin C on A549 cells proliferation, whereas the administration of a CA9 inhibitor failed to have a similar effect. ConclusionsSchisandrin C effectively suppressed the proliferation and viability of A549 cells. Its mechanism was related to the inhibition of the AKT1 signaling pathway.