Analysis Of Sequence Data Research Articles

Screening of the key genes and signaling pathways for schizophrenia using bioinformatics and next generation sequencing data analysis

Schizophrenia is thought to be the most prevalent chronic psychiatric disorder. Researchers have identified numerous proteins associated with the occurrence and development of schizophrenia. This study aimed to identify potential core genes and pathways involved in schizophrenia through exhaustive bioinformatics and next generation sequencing (NGS) data analyses using GSE106589 NGS data of neural progenitor cells and neurons obtained from healthy controls and patients with schizophrenia. The NGS data were downloaded from the Gene Expression Omnibus database. NGS data was processed by the DESeq2 package in R software, and the differentially expressed genes (DEGs) were identified. Gene ontology (GO) enrichment analysis and REACTOME pathway enrichment analysis were carried out to identify potential biological functions and pathways of the DEGs. Protein-protein interaction network, module, micro-RNA (miRNA)-hub gene regulatory network, transcription factor (TF)-hub gene regulatory network, and drug-hub gene interaction network analysis were performed to identify the hub genes, miRNA, TFs, and drug molecules. Potential hub genes were analyzed using receiver operating characteristic curves in the R package. In this investigation, an overall 955 DEGs were identified: 478 genes were remarkably upregulated and 477 genes were distinctly downregulated. These genes were enriched for GO terms and pathways mainly involved in the multicellular organismal process, G protein-coupled receptor ligand binding, regulation of cellular processes, and amine ligand-binding receptors. MYC, FN1, CDKN2A, EEF1G, CAV1, ONECUT1, SYK, MAPK13, TFAP2A, and BTK were considered the potential hub genes. The MiRNA-hub gene regulatory network, TF-hub gene regulatory network, and drug-hub gene interaction network were constructed successfully and predicted key miRNAs, TFs, and drug molecules for schizophrenia diagnosis and treatment. On the whole, the findings of this investigation enhance our understanding of the potential molecular mechanisms of schizophrenia and provide potential targets for further investigation.

Biophysical model for joint analysis of chromatin and RNA sequencing data

Biophysical model for joint analysis of chromatin and RNA sequencing data

Vamsapriya yadongensis sp. nov. (Vamsapriyaceae, Xylariales) from Southwestern China

During an investigation of microfungi in the Xizang Autonomous Region (Tibet), China, a specimen was collected from unidentified terrestrial dead wood. Based on morphological and phylogenetic analyses, the specimen is described as a new species, Vamsapriya yadongensis. Phylogenetic analyses of combined ITS, LSU, rpb2, and tub2 sequence data indicate that Vamsapriya yadongensis is a sister to V. uniseptata. However, it differs from Vamsapriya uniseptata by its comparatively larger conidia, synnemata and higher number of conidial septa. Detailed morphological descriptions, illustrations, a synopsis table, phylogenetic affinities and key to the genus are provided.

CXCR1+ neutrophil infiltration orchestrates response to third-generation EGFR-TKI in EGFR mutant non-small-cell lung cancer

Although third-generation Epidermal growth factor receptor—tyrosine kinase inhibitors (EGFR-TKI) is standard of care for patients with EGFR-mutant Non-small cell lung cancer (NSCLC), little is known about the predictors of response or resistance. Here, we integrated single-cell RNA (scRNA) sequencing, bulk RNA sequencing, multiplexed immunofluorescence and flow cytometry data from pretreatment and post-resistant tumor samples of EGFR-mutant NSCLC patients received third-generation EGFR-TKIs. We show that resistant samples had a markedly enriched CXCR1+ neutrophils infiltration (P < 0.01) than pretreatment samples, which were distinguished from other subtypes of neutrophils and displayed immunosupressive characteristics. Spatial analysis showed that increased CXCR1+ neutrophils predominantly infiltrated into the tumor core in resistant samples and the average distance of neutrophils to tumor cells markedly reduced from 33 to 19 μm. Deep analysis of scRNA and bulk RNA sequencing data revealed the increased interactions between CXCR1+ neutrophils and tumor cells and activated TNF-α/NF-κB signaling pathway in tumor cells of resistant samples. In vitro and in vivo experiments validated that CXCR1+ neutrophils resulted in resistance to third-generation EGFR-TKI via activating TNF-α/NF-κB signaling pathway in tumor cells. Importantly, patients with low pretreatment CXCR1+ neutrophil infiltration abundance had a dramatically longer progression-free survival (11.8 vs. 7.5 months; P = 0.019) and overall survival (33.0 vs. 23.5 months; P = 0.029) than those with high infiltration abundance. Collectively, these findings suggest that CXCR1+ neutrophils infiltration was associated with the efficacy of third-generation EGFR-TKI in patients with EGFR-mutant NSCLC.

Effects of supplemental feeding of Chinese herbal mixtures to perinatal sows on reproductive performance, immunity, and breast milk quality of sows

The aim of this study was to investigate the impact of supplementary feeding with Chinese herbal mixtures on perinatal sows, focusing on their reproductive performance, immunity and breast milk quality. Sixty healthy pregnant sows (Large white, 4 parities) were randomly allocated into five treatment groups (n = 12 per group): the control group received a basal diet, the TRT1 group received a basal diet supplemented with 2 kg/t Bazhen powder (BZP), while the TRT2, TRT3, and TRT4 groups received a basal diet supplemented with 1 kg/t, 2 kg/t, and 3 kg/t Qi-Zhu-Gui-Shao soothing liver and replenishing blood powder (QZGSP), respectively. The trial lasted for a duration of 5 weeks, commencing from day 100 of gestation and concluding on day 21 postpartum. The results showed that supplemental feeding of 2 kg/t and 3 kg/t QZGSP to periparturient sows significantly improved reproductive performance to different degrees, as evidenced by the shortened farrowing intervals and increased average daily feed intake and milk yield. Supplemental feeding of 2 kg/t and/or 3 kg/t QZGSP significantly elevated levels of IL-4, IL-10, IgG, and IgA in sow serum while reduced levels of TNF-α and IL-1β in sow serum. In addition, supplemental feeding of 2 kg/t and 3 kg/t QZGSP to perinatal sows significantly increased the protein and fat content in colostrum and milk. Analysis of 16S rRNA gene amplicon sequencing data in colostrum and milk microbiota revealed that supplemental feeding of QZGSP to perinatal sows is influenced the composition of colostrum and milk composition in sows. Specifically, at the genus level, a decrease in the relative abundance of Escherichia-Shigella, Staphylococcus and Streptococcus was observed in the TRT3 and/or TRT4 groups on day 0 of lactation. The findings from this study indicate that supplemental feeding of 2 kg/t and 3 kg/t QZGSP significantly improved the reproductive performance, immunity and milk quality in sows. Therefore, QZGSP is a beneficial feed additive for perinatal sows.

Acid ceramidase controls proteasome inhibitor resistance and is a novel therapeutic target for the treatment of relapsed / refractory multiple myeloma.

Multiple myeloma (MM) patients are often refractory to targeted therapies including proteasome inhibitors (PIs). Here, analysis of RNA sequencing data derived from 672 patients with newly diagnosed or relapsed/refractory disease identified the acid ceramidase, ASAH1, as a key regulator of PI resistance. Genetic or pharmacological blockade of ASAH1 remarkably restored PI sensitivity and protected mice from resistant MM progression in vivo. Mechanistically, ASAH1 depletion of ceramide promoted SET inhibition of PP2A phosphatase activity thus facilitating the increased expression and activity of the pro-survival proteins, MCL-1, and BCL-2. We corroborated these findings in human MM datasets, and in ex vivo patient MM cells. These preclinical studies suggest that ASAH1 may be a potential therapeutic target for the treatment of relapsed/refractory MM (RRMM).

OCTN2 expression and function in the Sertoli cells of testes from patients with non-obstructive azoospermia.

Among couples, male factors account for approximately 50% of infertility cases, with nonobstructive azoospermia (NOA) representing one of the most clinically common and severe categories of male infertility, affecting approximately 10-15% of patients. Currently, L-carnitine is clinically used to improve spermatogenesis by regulating Sertoli cell function. Multiple clinical trials have described the efficacy of L-carnitine in treating NOA. Notably, Sertoli cells rely on organic carnitine transporter 2 (OCTN2) for carnitine transport. However, it remains unknown whether OCTN2 expression is involved in the pathological process of NOA. To investigate the expression and function of OCTN2 in Sertoli cells from patients with NOA. Ten testicular tissue samples were collected, including five from a healthy group and five from a group of patients with NOA. Immunohistochemistry and immunofluorescence were used to detect the expression of OCTN2 in testicular tissue. Additionally, an Octn2-KO TM4 cell line (a mouse testicular Sertoli cell line) was constructed to explore the function of OCTN2 expression in Sertoli cells through transcriptomic sequencing, cell proliferation experiments, metabolomic analysis, and Western blot analysis. Compared with those of the healthy group, the immunohistochemistry results revealed a significant decrease in OCTN2 expression in the Sertoli cells of the NOA group. Further investigation through cell proliferation experiments revealed a reduction in the proliferative capacity of the Octn2-KO TM4 cell line. Transcriptomic sequencing and metabolomic data analysis revealed a decrease in autophagy in the Octn2-KO TM4 cell line. Western blot analysis subsequently verified the expression levels of autophagy-related proteins. In the Sertoli cells of NOA patients, decreased OCTN2 protein expression leads to decreased cell proliferation and autophagy abnormalities, which may play a crucial role in the spermatogenic dysfunction observed in NOA patients.

Four new free-living marine nematode species (Plectida: Ceramonematidae) and two new species records (Desmodorida: Desmodorinae) from Rangitāhua / Kermadec Islands, Aotearoa / New Zealand

Kermadec Islands is a remote subtropical island arc in the Southwest Pacific Ocean located 800–1000 km northeast of New Zealand’s North Island. Until now, no data was available on the nematode fauna living in the seafloor environments surrounding these islands. A single sample of subtidal coarse sediments from the Raoul Island coast yielded four new ceramonematid species: Ceramonema taikoraha sp. nov., C. taiora sp. nov., Metadasynemoides taihua sp. nov. and Pselionema huakita sp. nov. This new discovery is the first addition to the family since 2008 and brings the total number of valid ceramonematid species globally to 67 species. Dichotomous identification keys are provided for valid species of Ceramonema, Metadasynemoides and Pselionema. The desmodorid species Acanthopharynx dormitata and Desmodora bilacinia, were also recorded from Raoul Island some 1350 km away from their type locality in Wellington Harbour (New Zealand’s North Island). These species may have a relatively widespread distribution but testing this hypothesis will require further morphological comparisons and analyses of molecular sequence data to confirm the status of the Kermadec specimens.

OSCC-derived EVs educate fibroblasts and remodel collagen landscape

Cancer-associated myofibroblasts (mCAFs) represent a significant component of the tumor microenvironment due to their contributions to extracellular matrix (ECM) remodeling. The pro-tumor mechanisms of extracellular vesicles (EVs) by regulating mCAFs and related collagens remain poorly understood in oral squamous cell carcinoma (OSCC). In this study, through analysis of single-cell sequencing data and immunofluorescence staining, we confirmed the increased presence of mCAFs and enrichment of specific collagen types in OSCC tissues. Furthermore, we demonstrated that OSCC-derived EVs promote the transformation of fibroblasts into mCAFs, leading to tumor invasion. Proteomic analysis identified the presence of TGF-β1 in EVs and revealed its role in inducing mCAFs via the TGF-β1/Smad3 signaling pathway. Experiments in vivo confirmed that EVs, particularly those carrying TGF-β1, trigger COL18high COL5high matrix deposition, thereby forming the pro-tumor ECM in OSCC. In summary, our investigation unveils the significant involvement of OSCC-derived EVs in orchestrating the differentiation of fibroblasts into mCAFs and modulating specific collagen types within the ECM. Therefore, this study provides a theoretical basis for targeting the EV-mediated TGF-β1 signaling pathway as a potential therapeutic strategy for OSCC.

Missense variants in the TRPMr7 α-kinase domain are associated with recurrent pediatric acute liver failure

Background: Pediatric acute liver failure (PALF) is a rare and life-threatening condition. In up to 50% of PALF cases, the underlying etiology remains unknown during routine clinical testing. This lack of knowledge complicates clinical management and liver transplantation decisions. Recently, whole-exome sequencing has identified genetic disorders in a large number of cases without specific laboratory biomarkers or metabolic fingerprints. Methods: We describe how further analysis of whole-exome sequencing data combined with proteomic analyses in 5 previously unsolved PALF patients, where no pathogenic variants in genes previously associated with acute liver failure were identified, revealed rare biallelic variants in transient receptor potential cation channel subfamily M member 7 (TRPM7). Results: We establishe TRPM7 as a novel disease gene for PALF. Yet, the cation channel kinase TRPM7 has not been associated with any Mendelian disorder. No homozygous loss-of-function variants were found in in-house exomes or publicly available databases. Rare biallelic TRPM7-variants were significantly enriched in the PALF cohort compared with a pediatric control cohort. Viral infections preceded the majority of PALF episodes. Recurrent PALF episodes characterized the disease course with rapid progression, leading to early death in 3 cases. Proteomic analyses of patient fibroblasts unveiled significantly reduced TRPM7 protein levels, indicative of functional impairment. Severely reduced Mg2+ levels in one individual with a mutation in the channel domain suggests a potential interaction between disturbed Mg2+ homeostasis and PALF. The consistent presence of mutations in the TRPM7 protein-kinase-domain across all patients suggests its specific relevance in PALF. Conclusions: Our data extend the genetic spectrum of recurrent PALF and prompt consideration of TRPM7 in children with unexplained liver failure.

Journey to the West: migration patterns of the riparian montane genus Myricaria

Myricaria Desv. (Tamaricaceae) is a genus of riparian plants found in montane regions throughout Eurasia. We present molecular phylogenies covering the entire Eurasian range of the genus using the chloroplast interspacer region psbA-trnH, the chloroplast region trnL-trnF, and the nuclear ribosomal Internal Transcribed Spacer (ITS). Biogeographical analyses of the DNA sequencing data based on Takhtajan's Floristic Provinces using a Bayesian Binary Markov Chain Monte Carlo reconstruction show that the origin of Myricaria is the Tibetan Floristic Province, specifically in the Qinghai-Tibetan Plateau. A molecular clock analysis was also performed. We estimate that the crown age of Myricaria is around 22.8 Ma and that the common ancestor of all European Myricaria occurred around 8.8 Ma ago. By covering the entire native range of the genus, our analyses confirm previous hypotheses on the origin and migration patterns of Myricaria, namely a central Asian centre of origin, followed by a westward migration to Europe via the central Asian mountain ranges, the Caucasus, and Eastern Europe. The divergence times and migration routes of Myricaria are remarkably similar to that of the genus Hippophae L.

M6A RNA Methylation Modulates Autophagy by Targeting Map1lc3b in Bisphenol A Induced Leydig Cell Dysfunction

Bisphenol A (BPA) exposure can affect testicular Leydig cells (LCs), potentially causing male infertility. Research suggests that RNA epigenetic response to environmental exposure may impact LCs function and testosterone production, but the role of N6-methyladenosine (m6A) RNA methylation in mediating BPA exposure and its regulatory mechanisms remain unknown. Here, we demonstrate that BPA exposure significantly reduces testosterone biosynthesis and upregulates m6A modification in LCs using both in vivo and in vitro models. The involvement of the m6A "writer" METTL3 and the "eraser" ALKBH5 in regulating LCs m6A levels during BPA exposure was discovered, highlighting their central role. Manipulating these factors to reduce m6A methylation levels demonstrated potential for alleviating BPA-induced damage to LCs. Furthermore, integrated analysis of transcriptomic and MeRIP sequencing data reveals that the upregulation of m6A levels induced by BPA specifically targets the Map1lc3b mRNA, a pivotal regulator of autophagy, thereby exerting suppressive effects on autophagic processes. In conclusion, our findings suggest that targeting m6A RNA methylation could be a potential therapeutic approach to mitigate BPA-induced reproductive toxicity, offering novel insights into the epigenetic regulation of male reproductive health.

Elucidating the molecular and immune interplay between head and neck squamous cell carcinoma and diffuse large B-cell lymphoma through bioinformatics and machine learning.

Head and neck squamous cell carcinoma (HNSCC) contributes significantly to global health challenges, presenting primarily in the oral cavity, pharynx, nasopharynx, and larynx. HNSCC has a high propensity for lymphatic metastasis. Diffuse large B-cell lymphoma (DLBCL), the most common subtype of non-Hodgkin lymphoma, exhibits significant heterogeneity and aggressive behavior, leading to high mortality rates. Epstein-Barr virus (EBV) is notably associated with DLBCL and certain types of HNSCC. The purpose of this study is to elucidate the molecular and immune interplay between HNSCC and DLBCL using bioinformatics and machine learning (ML) to identify shared biomarkers and potential therapeutic targets. Differentially expressed genes (DEGs) were identified using the "limma" package in R from the HNSCC dataset in The Cancer Genome Atlas (TCGA) database, and relevant modules were selected through weighted gene co-expression network analysis (WGCNA) from a DLBCL dataset in the Gene Expression Omnibus (GEO) database. Based on their intersection genes, functional enrichment analyses were conducted using Gene Ontology (GO), Disease Ontology, and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. Protein-protein interaction (PPI) networks and ML algorithms were employed to screen for biomarkers. The prognostic value of these biomarkers was evaluated using Kaplan-Meier (K-M) survival analysis and receiver operating characteristic (ROC) curve analyses. The Human Protein Atlas (HPA) database facilitated the examination of messenger RNA (mRNA) and protein expressions. Further analyses of mutations, immune infiltration, drug predictions, and pan-cancer impacts were performed. Additionally, single-cell RNA sequencing (scRNA-seq) data analysis at the cell type level was conducted to provide deeper insights into the tumor microenvironment. From 2,040 DEGs and 1,983 module-related genes, 85 shared genes were identified. PPI analysis with six algorithms proposed 21 prospective genes, followed ML examination yielded 16 candidates. Survival and ROC analyses pinpointed four hub genes-ACACB, MMP8, PAX5, and TNFAIP6-as significantly associated with patient outcomes, demonstrating high predictive capabilities. Evaluations of mutations and immune infiltration, coupled with drug prediction and a comprehensive cancer analysis, highlighted these biomarkers' roles in tumor immune response and treatment efficacy. The scRNA-seq data analysis revealed an increased abundance of fibroblasts, epithelial cells and mononuclear phagocyte system (MPs) in HNSCC tissues compared to lymphoid tissues. MMP8 showed higher expression in five cell types in HNSCC tissues, while TNFAIP6 and PAX5 exhibited higher expression in specific cell types. Leveraging bioinformatics and ML, this study identified four pivotal genes with significant diagnostic capabilities for DLBCL and HNSCC. The survival analysis corroborates their diagnostic accuracy, supporting the development of a diagnostic nomogram to assist in clinical decision-making.

Multimodal analysis of RNA sequencing data powers discovery of complex trait genetics

RNA sequencing has the potential to reveal many modalities of transcriptional regulation, such as various splicing phenotypes, but studies on gene regulation are often limited to gene expression due to the complexity of extracting and analyzing multiple RNA phenotypes. Here, we present Pantry, a framework to efficiently generate diverse RNA phenotypes from RNA sequencing data and perform downstream integrative analyses with genetic data. Pantry generates phenotypes from six modalities of transcriptional regulation (gene expression, isoform ratios, splice junction usage, alternative TSS/polyA usage, and RNA stability) and integrates them with genetic data via QTL mapping, TWAS, and colocalization testing. We apply Pantry to Geuvadis and GTEx data, finding that 4768 of the genes with no identified eQTL in Geuvadis have QTL in at least one other transcriptional modality, resulting in a 66% increase in genes over eQTL mapping. We further found that the QTL exhibit modality-specific functional properties that are further reinforced by joint analysis of different RNA modalities. We also show that generalizing TWAS to multiple RNA modalities approximately doubles the discovery of unique gene-trait associations, and enhances identification of regulatory mechanisms underlying GWAS signal in 42% of previously associated gene-trait pairs.

New direction: identification of immunoinflammatory subtypes and potential therapeutic targets for cholangiocarcinoma

BackgroundCholangiocarcinoma (CHOL) is a rare cancer with low survival rates. Despite advances in precision medicine targeting molecular subtypes, the immune subtypes of CHOL remain poorly understood. This study aimed to identify immune subtypes of CHOL and investigate their implications in the metabolic regulation of macrophage functions in inflammation.MethodsWe conducted a comprehensive analysis of transcriptome and single-cell sequencing data from multiple databases to classify the immune subtypes of CHOL. Immune cell infiltration within the tumor microenvironment (TME) and the metabolic pathways involved in macrophage activation and polarization were also analyzed.ResultsTwo distinct immune subtypes, immune-infiltrated CS1 and immune-depleted CS2, were identified in CHOL. CS1 exhibited a highly active TME with substantial immune cell infiltration, including macrophages, and activation of immune-related signaling pathways, such as inflammatory and interferon pathways. In contrast, CS2 was characterized by a deficiency in immune components and poorer prognosis. Metabolic regulation of macrophages, particularly the downregulation of oxidative phosphorylation in CS1, suggested a shift towards glycolysis as an energy source for activated macrophages, contributing to the immune-responsive phenotype observed in CS1. Additionally, the oncogenic role of DLX5 in CHOL was revealed, with potential impacts on macrophage functions in inflammation.ConclusionThis study provides insights into immune subtype classification, novel biomarker identification, and the metabolic regulation of macrophage functions in CHOL. Understanding macrophage metabolic reprogramming within immune subtypes may contribute to the development of targeted immunotherapies for CHOL.

The identification of key genes and pathways in polycystic ovary syndrome by bioinformatics analysis of next-generation sequencing data

BackgroundPolycystic ovary syndrome (PCOS) is a reproductive endocrine disorder. The specific molecular mechanism of PCOS remains unclear. The aim of this study was to apply a bioinformatics approach to reveal related pathways or genes involved in the development of PCOS.MethodsThe next-generation sequencing (NGS) dataset GSE199225 was downloaded from the gene expression omnibus (GEO) database and NGS dataset analyzed is obtained from in vitro culture of PCOS patients’ muscle cells and muscle cells of healthy lean control women. Differentially expressed gene (DEG) analysis was performed using DESeq2. The g:Profiler was utilized to analyze the gene ontology (GO) and REACTOME pathways of the differentially expressed genes. A protein–protein interaction (PPI) network was constructed and module analysis was performed using HiPPIE and cytoscape. The miRNA-hub gene regulatory network and TF-hub gene regulatory network were constructed. The hub genes were validated by using receiver operating characteristic (ROC) curve analysis.ResultsWe have identified 957 DEG in total, including 478 upregulated genes and 479 downregulated gene. GO terms and REACTOME pathways illustrated that DEG were significantly enriched in regulation of molecular function, developmental process, interferon signaling and platelet activation, signaling, and aggregation. The top 5 upregulated hub genes including HSPA5, PLK1, RIN3, DBN1, and CCDC85B and top 5 downregulated hub genes including DISC1, AR, MTUS2, LYN, and TCF4 might be associated with PCOS. The hub gens of HSPA5 and KMT2A, together with corresponding predicted miRNAs (e.g., hsa-mir-34b-5p and hsa-mir-378a-5p), and HSPA5 and TCF4 together with corresponding predicted TF (e.g., RCOR3 and TEAD4) were found to be significantly correlated with PCOS.ConclusionsThese study uses of bioinformatics analysis of NGS data to obtain hub genes and key signaling pathways related to PCOS and its associated complications. Also provides novel ideas for finding biomarkers and treatment methods for PCOS and its associated complications.

A rare genetic variant in APEX1 is associated with familial amyotrophic lateral sclerosis with slow progression.

Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disorder characterized by loss of motor neurons and progressive muscle weakness. We aimed to identify the pathogenic genetic variants in familial ALS (fALS) pedigrees and to elucidate their impact on the disease phenotype. Through the analysis of whole-genome sequencing data of 34 fALS probands that screened negative for mutations in the most common ALS-causing genes, we identified a rare missense variant in APEX1 (NM_001641.4: c.22G > A, p.Gly8Arg) associated with ALS in one pedigree. Fluorescence microscopy images using green fluorescent protein (GFP)-fusion proteins suggested that this amino acid substitution could cause an impairment in nuclear localization of the protein. We described the clinical characteristics of this cohort analyzed and found that patients carrying this variant exhibit lower motor neuron onset and prolonged survival. The relation between APEX1 and ALS occurrence has been elusive despite evidence of a neuroprotective role for the gene. This study provides evidence linking an APEX1 variant with fALS and information on the distinct clinical manifestation. This study contributes to the understanding of the genetic basis of ALS, as well as a potential mechanism leading to loss of neurons, highlighting possible opportunities of targeted treatment harnessing the DNA repair process or ameliorating the oxidative stress.

Integrated analyses of multi-omic data derived from paired primary lung cancer and brain metastasis reveal the metabolic vulnerability as a novel therapeutic target

BackgroundLung cancer brain metastases (LC-BrMs) are frequently associated with dismal mortality rates in patients with lung cancer; however, standard of care therapies for LC-BrMs are still limited in their efficacy. A deep understanding of molecular mechanisms and tumor microenvironment of LC-BrMs will provide us with new insights into developing novel therapeutics for treating patients with LC-BrMs.MethodsHere, we performed integrated analyses of genomic, transcriptomic, proteomic, metabolomic, and single-cell RNA sequencing data which were derived from a total number of 154 patients with paired and unpaired primary lung cancer and LC-BrM, spanning four published and two newly generated patient cohorts on both bulk and single cell levels.ResultsWe uncovered that LC-BrMs exhibited a significantly greater intra-tumor heterogeneity. We also observed that mutations in a subset of genes were almost always shared by both primary lung cancers and LC-BrM lesions, including TTN, TP53, MUC16, LRP1B, RYR2, and EGFR. In addition, the genome-wide landscape of somatic copy number alterations was similar between primary lung cancers and LC-BrM lesions. Nevertheless, several regions of focal amplification were significantly enriched in LC-BrMs, including 5p15.33 and 20q13.33. Intriguingly, integrated analyses of transcriptomic, proteomic, and metabolomic data revealed mitochondrial-specific metabolism was activated but tumor immune microenvironment was suppressed in LC-BrMs. Subsequently, we validated our results by conducting real-time quantitative reverse transcription PCR experiments, immunohistochemistry, and multiplexed immunofluorescence staining of patients’ paired tumor specimens. Therapeutically, targeting oxidative phosphorylation with gamitrinib in patient-derived organoids of LC-BrMs induced apoptosis and inhibited cell proliferation. The combination of gamitrinib plus anti-PD-1 immunotherapy significantly improved survival of mice bearing LC-BrMs. Patients with a higher expression of mitochondrial metabolism genes but a lower expression of immune genes in their LC-BrM lesions tended to have a worse survival outcome.ConclusionsIn conclusion, our findings not only provide comprehensive and integrated perspectives of molecular underpinnings of LC-BrMs but also contribute to the development of a potential, rationale-based combinatorial therapeutic strategy with the goal of translating it into clinical trials for patients with LC-BrMs.

Single-cell RNA sequencing reveals key regulators and differentiation trajectory of iPSC-derived cardiomyocytes

Cardiac differentiation of human pluripotent stem cells is not only a new strategy of regenerative therapy for cardiovascular disease treatment but also provides unique opportunities for the study of in vitro disease models and human heart development. To elucidate the dynamic gene regulatory networks and pivotal regulators involved in the cardiomyocyte differentiation process, we conducted an analysis of single-cell RNA sequencing data obtained from the reprogramming of two human induced pluripotent stem cell (iPSC) lines into cardiomyocytes. The data were collected from 32,365 cells at 4 stages of this process. We successfully identified cardiomyocyte clusters and several other cell clusters with different molecular characteristics derived from iPSC and described the differentiation trajectory of cardiomyocytes during differentiation in vitro. Through differential gene analysis and SCENIC analysis, we identified several candidate genes including CREG and NR2F2 that play an important regulatory role in cardiomyocyte lineage commitment. This study provides the key differentiation trajectory of heart differentiation in vitro at single-cell resolution and reveals the molecular basis of heart development and differentiation of iPSC-derived cardiomyocytes.

Molecular diagnoses and candidate gene identification in the congenital heart disease cohorts of the 100,000 genomes project.

Congenital heart disease (CHD) describes a structural cardiac defect present from birth. A cohort of participants recruited to the 100,000 Genomes Project (100 kGP) with syndromic CHD (286 probands) and familial CHD (262 probands) were identified. "Tiering" following genome sequencing data analysis prioritised variants in gene panels linked to participant phenotype. To improve diagnostic rates in the CHD cohorts, we implemented an agnostic de novo Gene Discovery Pipeline (GDP). We assessed de novo variants (DNV) for unsolved CHD participants following filtering to select variants of interest in OMIM-morbid genes, as well as novel candidate genes. The 100kGP CHD cohorts had low rates of pathogenic diagnoses reported (combined CHD "solved" 5.11% (n = 28/548)). Our GDP provided diagnostic uplift of nearly one third (1.28% uplift; 5.11% vs. 6.39%), with a new or potential diagnosis for 9 additional participants with CHD. When a filtered DNV occurred within a non-morbid gene, our GDP prioritised biologically-plausible candidate CHD genes (n = 79). Candidate variants occurred in both genes linked to cardiac development (e.g. AKAP13 and BCAR1) and those currently without a known role (e.g. TFAP2C and SETDB1). Sanger sequencing of a cohort of patients with CHD did not identify a second de novo variant in the candidate dataset. However, literature review identified rare variants in HMCN1, previously reported as causative for pulmonary atresia, confirming the approach utility. As well as diagnostic uplift for unsolved participants of the 100 kGP, our GDP created a dataset of candidate CHD genes, which forms an important resource for further evaluation.