Integrated Transcriptome Analysis Research Articles

Integrative analysis of DNA methylome and transcriptome reveals epigenetic regulation of bisphenols-induced cardiomyocyte hypertrophy

Cardiac hypertrophy, a kind of cardiomyopathic abnormality, might trigger heart contractile and diastolic dysfunction, and even heart failure. Currently, bisphenols (BPs) including bisphenol A (BPA), and its alternatives bisphenol AF (BPAF), bisphenol F (BPF) and bisphenol S (BPS) are ubiquitously applied in various products and potentially possess high cardiovascular risks for humans. However, the substantial experimental evidences of BPs on heart function, and their structure-related effects on cardiomyocyte hypertrophy are still urgently needed. DNA methylation, a typical epigenetics, play key roles in BPs-induced transcription dysregulation, thereby affecting human health including cardiovascular system. Thus, in this study, we performed RNA-seq and reduced representation bisulfite sequencing (RRBS) to profile the landscapes of BPs-induced cardiotoxicity and to determine the key roles of DNA methylation in the transcription. Further, the capabilities of three BPA analogues, together with BPA, in impacting heart function and changing DNA methylation and transcription were compared. We concluded that similar to BPA, BPAF, BPF and BPS exposure deteriorated heart function in a mouse model, and induced cardiomyocyte hypertrophy in a H9c2 cell line. BPAF, BPF and BPS all played BPA-like roles in both transcriptive and methylated hierarchies. Moreover, we validated the expression levels of four cardiomyocyte hypertrophy related candidate genes, Psmc1, Piptnm2, Maz and Dusp18, which were all upregulated and with DNA hypomethylation. The findings on the induction of BPA analogues on cardiomyocyte hypertrophy and DNA methylation revealed their potential detrimental risks in heart function of humans.

Multi-omics approaches revealed the therapeutic mechanisms of Suo-Quan-Wan for treating overactive bladder in spontaneously hypertensive rats

Ethnopharmacological relevanceSuo-Quan-Wan (SQW), a traditional Chinese prescription, has been used for hundreds of years to alleviate overactive bladder (OAB) symptoms such as frequent and nocturnal urination. However, limited modern research on OAB therapeutic targets has hindered the use and development of SQW. Aim of the studyThis study aimed to investigate the biological mechanisms and key targets of SQW on OAB in spontaneously hypertensive rats (SHR) using an integrated analysis of network pharmacology, transcriptome and metabolome. MethodsRats were divided into five groups: model group (SHR), control group (WKY), darifenacin group, high dose (SQWH) and low dose (SQWL) group. Urodynamic parameters and histological examination were detected. Network pharmacology, transcriptome, and metabolome were used to screen for disease gene targets, differential mRNA, and differential metabolites, respectively. The biological targets and mechanisms of SQW for OAB were analyzed. Western blotting was performed to verify the proteins of key differential targets. ResultsUrodynamics revealed a significant decrease in storage parameters in SHR. After SQW treatment, the inter-contraction interval, voided volume and bladder capacity increased by 2–3 times, as well as bladder compliance. Additionally, SQW improved the pathological changes in the urinary tract epithelium and the detrusor layer of the bladder in SHR. Metabolomic results showed an increase in arachidonic acid (AA) and cyclic adenosine monophosphate (cAMP) in plasma, suggesting the involvement of arachidonic acid metabolism and purine metabolism in SQW treatment. The downregulation of cytochrome P450 1B1 (CYP1B1), thromboxane-A synthase (TBXAS1), polyunsaturated fatty acid 5-lipoxygenase (ALOX5), and cAMP-specific 3′,5′-cyclic phosphodiesterase 4B (PDE4B) were confirmed through topological analysis and Venn analysis of omics data and network pharmacology. These proteins affected the metabolism of AA and cAMP, respectively, and consequently affected downstream proteins, such as transient receptor potential (TRP) cation channel proteins (e.g. TRPV1, TRPA1, and TRPM8), myosin light chain kinase (MLCK), and the phosphorylation of myosin regulatory light chain (p-MLC). ConclusionThis study initially elucidated the importance of AA and cAMP in the treatment of SQW, indicating the AA-CYP1B1/TBXAS1/ALOX5-TRPA1/TRPV1/TRPM8 and cAMP-PDE4B-MLCK-p-MLC pathways as the important pathways in SQW-treated SHR bladder in vivo.

Integrated analysis of transcriptome and proteome for exploring mechanism of promoting proliferation of equine satellite cells associated with leucine

The proliferation and differentiation of skeletal muscle satellite cells (SCs) are necessary for the development of mature skeletal muscle. Leucine (Leu) is both an essential amino acid (EAA) and a branched-chain amino acid (BCAA), which has attracted worldwide attention due to its ability to repair and become new fibers. We separated the equine SCs into the control group (CON) and the Leu-supplemented group (LEU), which the cells were cultured in Leu-deprived and Leu-supplemented media respectively. We combined the transcriptome (RNA-Seq) and quantitative proteome (TMT) profiling analyses on proliferation of equine SCs associated with Leu. 1839 up-regulated and 631 down-regulated genes made up the 2470 differentially expressed genes (DEGs), and the 253 differentially abundant proteins (DEPs) included 118 up-regulated and 135 down-regulated proteins. 110 overlapping genes were verified based on the mRNA and protein translation relationship. Moreover, by comparing overlapped pathways through enrichment analysis, we found 13 genes not only appeared among 110 key DEGs/DEPs but also enriched in the KEGG overlapping signaling pathway, including CCL26, STAT2, PCK2, ASNS, GPT2, SHMT2, PHGDH, PGAM2, PSAT1, FTL, HMOX1, STEAP1 and STEAP2. To our knowledge, this is the first report in the world to systematically show how Leu regulated the growth of equine SCs. Leu deficiency inhibits the proliferation of equine SCs and development of fresh muscle fibers was proved in this paper. The main genes in charge of the Leu-induced proliferation of horse SCs have been found. These genes will make it easier to understand the mechanism at work and offer new information for enhancing the performance of sport horses and alleviating the equine muscle damage during exercise in the future.

Unraveling dynamic interactions between tumor-associated macrophages and consensus molecular subtypes in colorectal cancer: An integrative analysis of single-cell and bulk RNA transcriptome

BackgroundAccumulating research substantiated that tumor-associated macrophages (TAMs) have a significant impact on the tumorigenesis, progression, and distant metastasis, representing a novel target for various cancers. However, the underlying dynamic changes and interactions between TAMs and tumor cells remain largely elusive in colorectal cancer (CRC). MethodsWe depicted the dynamic changes of macrophages using sing-cell RNA-seq data and extracted TAM differentiation-related genes. Next, we utilized the weighted gene co-expression network analysis (WGCNA) to acquire CMS-related modular genes using bulk RNA-seq data. Finally, we utilized univariate Cox and Lasso Cox regression analyses to identify TAM differentiation-related biomarkers and established a novel risk signature model. We employed quantitative real-time polymerase chain reaction (qRT-PCR) on CRC tissue samples and used immunohistochemistry (IHC) data frome the HPA database to validate the mRNA and protein expression of prognostic genes. The interaction of TAMs and each consensus molecular subtype (CMS) subpopulation was analyzed at the cellular level. ResultsA total of 47,285 cells from single-cell dataset and 1197 CRC patients from bulk dataset were obtained. Among those, 6400 myeloid cells were re-clustered and annotated. RNASE1, F13A1, DAPK1, CLEC10A, RPN2, REG4 and RGS19 were identified as prognostic genes and the risk signature model was established based on the above genes. The qRT-PCR analysis indicated that the expression of RNASE1 and DAPK1 were significantly up-regulated in CRC tumor tissues. The cell-cell communication analysis demonstrated complex interactions between TAMs and CMS malignant cell subpopulations. ConclusionThis study presents an in-depth dissection of the dynamic features of TAMs in the tumor microenvironment and provides promising therapeutic targets for CRC.

Identification of molecular signatures in acute myocardial infarction based on integrative analysis of proteomics and transcriptomics

BackgroundMyocardial infarction (MI) is one of the most serious cardiovascular diseases, characterized by a rapid and irreversible decline in myocardial function. Early detection of patients with MI and prolonging the optimal therapeutic window of acute myocardial infarction (AMI) are particularly important. This study aimed to identify the diagnostic biomarkers and novel therapeutic targets for acute myocardial infarction. MethodWe generated the AMI mouse models by ligating the proximal left anterior descending coronary artery. Six time points—Sham, AMI 10-min, 1-h, 6-h, 24-h, and 72-h—were chosen to examine the molecular changes that occur during the AMI process. RNA-seq and DIA-MS were performed on the infarcted left ventricular tissues of AMI mice at each time point. Co-expression pattern genes were screened from myocardial infarction samples at different time points by time-series analysis. Gene Ontology (GO) function and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were used to examine these genes. Using the Interactive Gene/Protein Retrieval Tool (STRING) database, the protein-protein interaction network (PPI) was constructed and the hub genes were identified. In order to evaluate the diagnostic value of hub genes, a receiver operating characteristic (ROC) curve was constructed. An independent data set, GSE163772, confirmed the diagnostic value of hub genes further. ResultWe obtained the expression profiles at different time points after the occurrence of heart failure through high-throughput sequencing, and found 167 genes with similar expression patterns through time series analysis. The immune response and immune-related pathways had the greatest enrichment of these genes. Among them, Itgb2 Syk, Tlr4, Tlr2, Itgax, and Lcp2 may play key roles as hub genes. Combined with the results of proteomic analysis, it was found that the expression of Coro1a in both omics increased with time. The results of external validation showed that TLR2, ITGAX, and LCP2 had good predictive ability for AMI diagnosis. ConclusionItgb2, Syk, Tlr4, Tlr2, Itgax, Lcp2 and Coro1a are considered to be the seven key genes significantly associated with AMI. Our results may provide potential targets for the prevention of adverse ventricular remodeling and the treatment of AMI.

Integrative analysis of metabolome and transcriptome reveals the different metabolite biosynthesis profiles related to palatability in winter and spring shoot in moso bamboo

Moso bamboo winter shoot has good taste and rich nutritional value. To reveal the causes and regulatory mechanism of palatability deterioration from winter to spring shoot, a conjoint analysis of metabolome and transcriptome was conducted on winter and spring shoots of moso bamboo. Totally 909 metabolites were characterized for the first time. The significant increase of hydrolyzed tannin content intensified the bitterness of spring shoot, which was positively regulated by key metabolite (gallic acid) and genes (DAHPS, DHQS, DHQ, SDH) in the biosynthesis pathway of hydrolyzed tannin. The accumulation of lignified components enhanced the roughness of spring shoot, which was closely connected with the significant changes of important metabolites (cinnamic acid, ferulic acid, UDP-glucose and UDP-xylose) and up-regulation of most enzyme genes involved in the biosynthesis pathways of lignin, cellulose and hemicellulose. The present study provides theoretical support for understanding palatability transition and directional improvement of edible quality of moso bamboo shoots.

Integrative transcriptome and metabolome analysis reveals the mechanisms of light-induced pigmentation in purple waxy maize.

Waxy maize, mainly consumed at the immature stage, is a staple and vegetable food in Asia. The pigmentation in the kernel of purple waxy maize enhances its nutritional and market values. Light, a critical environmental factor, affects anthocyanin biosynthesis and results in pigmentation in different parts of plants, including in the kernel. SWL502 is a light-sensitive waxy maize inbred line with purple kernel color, but the regulatory mechanism of pigmentation in the kernel resulting in purple color is still unknown. In this study, cyanidin, peonidin, and pelargonidin were identified as the main anthocyanin components in SWL502, evaluated by the ultra-performance liquid chromatography (UPLC) method. Investigation of pigment accumulation in the kernel of SWL502 was performed at 12, 17, and 22 days after pollination (DAP) under both dark and light treatment conditions via transcriptome and metabolome analyses. Dark treatment affected genes and metabolites associated with metabolic pathways of amino acid, carbohydrate, lipid, and galactose, biosynthesis of phenylpropanoid and terpenoid backbone, and ABC transporters. The expression of anthocyanin biosynthesis genes, such as 4CL2, CHS, F3H, and UGT, was reduced under dark treatment. Dynamic changes were identified in genes and metabolites by time-series analysis. The genes and metabolites involved in photosynthesis and purine metabolism were altered in light treatment, and the expression of genes and metabolites associated with carotenoid biosynthesis, sphingolipid metabolism, MAPK signaling pathway, and plant hormone signal transduction pathway were induced by dark treatment. Light treatment increased the expression level of major transcription factors such as LRL1, myc7, bHLH125, PIF1, BH093, PIL5, MYBS1, and BH074 in purple waxy maize kernels, while dark treatment greatly promoted the expression level of transcription factors RVE6, MYB4, MY1R1, and MYB145. This study is the first report to investigate the effects of light on waxy maize kernel pigmentation and the underlying mechanism at both transcriptome and metabolome levels, and the results from this study are valuable for future research to better understand the effects of light on the regulation of plant growth.

BCL3 rearrangements in B-cell lymphoid neoplasms occur in two breakpoint clusters associated with different diseases.

The t(14;19)(q32;q13) often juxtaposes BCL3 with immunoglobulin heavy chain (IGH) resulting in overexpression of the gene. In contrast to other oncogenic translocations, BCL3 rearrangement (BCL3-R) has been associated with a broad spectrum of lymphoid neoplasms. Here we report an integrative whole-genome sequence, transcriptomic, and DNA methylation analysis of 13 lymphoid neoplasms with BCL3-R. The resolution of the breakpoints at single base-pair revealed that they occur in two clusters at 5' (n=9) and 3' (n=4) regions of BCL3 associated with two different biological and clinical entities. Both breakpoints were mediated by aberrant class switch recombination of the IGH locus. However, the 5' breakpoints (upstream) juxtaposed BCL3 next to an IGH enhancer leading to overexpression of the gene whereas the 3' breakpoints (downstream) positioned BCL3 outside the influence of the IGH and were not associated with its expression. Upstream BCL3-R tumors had unmutated IGHV, trisomy 12, and mutated genes frequently seen in chronic lymphocytic leukemia (CLL) but had an atypical CLL morphology, immunophenotype, DNA methylome, and expression profile that differ from conventional CLL. In contrast, downstream BCL3-R neoplasms were atypical splenic or nodal marginal zone lymphomas (MZL) with mutated IGHV, complex karyotypes and mutated genes typical of MZL. Two of the latter four tumors transformed to a large B-cell lymphoma. We designed a novel fluorescence in situ hybridization assay that recognizes the two different breakpoints and validated these findings in 17 independent tumors. Overall, upstream or downstream breakpoints of BCL3-R are mainly associated with two subtypes of lymphoid neoplasms with different (epi)genomic, expression, and clinicopathological features resembling atypical CLL and MZL, respectively.

Integrated transcriptomic and metabolomic analysis reveals the response of pearl oyster (Pinctada fucata martensii) to long-term hypoxia

The frequency at which organisms are exposed to hypoxic conditions in aquatic environments is increasing due to coastal eutrophication and global warming. To reveal the effects of long-term hypoxic stress on metabolic changes of pearl oyster, commonly known as Pinctada (Pinctada fucata martensii), the present study performed the integrated analysis of transcriptomics and metabolomics to investigate the global changes of genes and metabolites following 25 days hypoxia challenge. Transcriptome analysis detected 1108 differentially expressed genes (DEGs) between the control group and the hypoxia group. The gene ontology (GO) analysis of DEGs revealed that they are significantly enriched in functions such as “microtubule−based process”, “histone (H3–K4, H3–K27, and H4–K20) trimethylation”, “histone H4 acetylation”, “kinesin complex”, and “ATPase activity”, and KEGG pathway functions, such as “DNA replication”, “Apoptosis”, and “MAPK signaling pathways”. Metabolome analysis identified 68 significantly different metabolites from all identified metabolites, and associated with 25 metabolic pathways between the control and hypoxia groups. These pathways included aminoacyl−tRNA biosynthesis, arginine and proline metabolism, and phenylalanine metabolism. Our integrated analysis suggested that pearl oysters were subject to oxidative stress, apoptosis, immune inhibition, and neuronal excitability reduction under long-term hypoxic conditions. We also found a remarkable depression in a variety of biological functions under long-term hypoxia, including metabolic rates, biomineralization activities, and the repression of reorganization of the cytoskeleton and cell metabolism. These findings provide a basis for elucidating the mechanisms used by marine bivalves to cope with long-term hypoxic stress.

Integrative Transcriptomic Analysis Reveals Upregulated Apoptotic Signaling in Wound-Healing Pathway in Rat Liver Fibrosis Models.

Liver fibrosis, defined by the aberrant accumulation of extracellular matrix proteins in liver tissue due to chronic inflammation, represents a pressing global health issue. In this study, we investigated the transcriptomic signatures of three independent liver fibrosis models induced by bile duct ligation, carbon tetrachloride, and dimethylnitrosamine (DMN) to unravel the pathological mechanisms underlying hepatic fibrosis. We observed significant changes in gene expression linked to key characteristics of liver fibrosis, with a distinctive correlation to the burn-wound-healing pathway. Building on these transcriptomic insights, we further probed the p53 signaling pathways within the DMN-induced rat liver fibrosis model, utilizing western blot analysis. We observed a pronounced elevation in p53 protein levels and heightened ratios of BAX/BCL2, cleaved/pro-CASPASE-3, and cleaved/full length-PARP in the livers of DMN-exposed rats. Furthermore, we discovered that orally administering oligonol-a polyphenol, derived from lychee, with anti-oxidative properties-effectively countered the overexpressions of pivotal apoptotic genes within these fibrotic models. In conclusion, our findings offer an in-depth understanding of the molecular alterations contributing to liver fibrosis, spotlighting the essential role of the apoptosis pathway tied to the burn-wound-healing process. Most importantly, our research proposes that regulating this pathway, specifically the balance of apoptosis, could serve as a potential therapeutic approach for treating liver fibrosis.

Classification of IDH wild-type glioblastoma tumorspheres into low- and high-invasion groups based on their transcriptional program

BackgroundGlioblastoma (GBM), one of the most lethal tumors, exhibits a highly infiltrative phenotype. Here, we identified transcription factors (TFs) that collectively modulate invasion-related genes in GBM.MethodsThe invasiveness of tumorspheres (TSs) were quantified using collagen-based 3D invasion assays. TF activities were quantified by enrichment analysis using GBM transcriptome, and confirmed by cell-magnified analysis of proteome imaging. Invasion-associated TFs were knocked down using siRNA or shRNA, and TSs were orthotopically implanted into mice.ResultsAfter classifying 23 patient-derived GBM TSs into low- and high-invasion groups, we identified active TFs in each group—PCBP1 for low invasion, and STAT3 and SRF for high invasion. Knockdown of these TFs reversed the phenotype and invasion-associated-marker expression of GBM TSs. Notably, MRI revealed consistent patterns of invasiveness between TSs and the originating tumors, with an association between high invasiveness and poor prognosis. Compared to controls, mice implanted with STAT3- or SRF-downregulated GBM TSs showed reduced normal tissue infiltration and tumor growth, and prolonged survival, indicating a therapeutic response.ConclusionsOur integrative transcriptome analysis revealed three invasion-associated TFs in GBM. Based on the relationship among the transcriptional program, invasive phenotype, and prognosis, we suggest these TFs as potential targets for GBM therapy.

Integrated analysis of transcriptome, metabolome and physiology revealed the molecular mechanisms for elevated pH-mediated-mitigation of aluminum-toxicity in Citrus sinensis leaves

The contribution of aluminum (Al)-pH-interaction-responsive metabolites and genes to Al-tolerance in Citrus leaves is still poorly understood. Seedlings of ‘Xuegan’ (Citrus sinensis) were supplied with nutrient solution at a pH of 4.0 or 3.0 and an Al concentration of 1 or 0 mM for 18 weeks. Thereafter, we investigated the impacts of Al-pH interactions on plant growth; Al concentrations in leaves and roots; and metabolome, transcriptome, and related physiological indices in leaves. Elevated pH ameliorated Al-toxicity-induced reduction of seedling (leaf) growth. Here, we screened 867 upregulated and 1041 downregulated genes, and 43 [eight primary metabolites (PMs) + 35 secondary metabolites (SMs)] and 28 downregulated (23 PMs + five SMs) in pH 3.0 + 1 mM Al-treated leaves (P3AL) vs. pH 3.0 + 0 mM Al-treated leaves (P3L); and 410 upregulated and 149 downregulated genes, and 75 upregulated (20 PMs + 55 SMs) and 32 downregulated (25 PMs + seven SMs) metabolites in pH 4.0 + 1 mM Al-treated leaves (P4AL) vs. pH 4.0 + 0 mM Al-treated leaves (P4L), implying that elevated pH ameliorated Al-toxic impacts on gene expression, but it enhanced the adaptability of metabolites to Al-stress. Further analysis suggested that raised pH-mediated-amelioration of leaf Al-stress involved the several aspects, including: (a) decreased accumulation of callose and low methylesterified pectin, increased accumulation of high methylesterified pectin, and enhanced cell wall stability; (b) less alterations of lipid metabolism and downregulation of PMs; (c) increased biosynthesis and accumulation of SMs; and (d) enhanced ability to maintain energy, phosphate and cell redox homeostasis, and less oxidative injury due to higher ability to maintain the balance between reactive oxygen species and aldehyde generation and detoxification. Some metabolic pathways such as glycolysis / gluconeogenesis and phenylpropanoid pathway; metabolites such as callose and phenolic compounds; and genes such as xyloglucan endotransglucosylase/hydrolases, purple acid phosphatases, phytochelatin synthase 3, and cysteine synthase, might involve in raised pH-induced amelioration of leaf Al-stress. Also, some similarities and differences existed between leaves and roots in Al-pH-interaction-responsive metabolites and genes.

Orchestration of a blood-derived and ADARB1-centred network in Alzheimer's and Parkinson's disease

The peripheral immune system is thought to influence the pathogenesis of the central nervous system in Alzheimer's disease (AD) and Parkinson's disease (PD). This study aimed to investigate the characteristics of peripheral leukocytes in AD and PD by comprehensively analyzing the transcriptomic and metabolic features in the blood (NCONTROL = 15; NAD = 11; NPD = 13). The study found an ADARB1-centered module that was associated with diagnosis, phenethylamine, and glutamate. The module consisted of ADARB1, a vital RNA-editing enzyme, LINC02960, and 109 miRNAs. The study also predicted that the ADARB1 and involved regulators were targeted by miRNAs in the ADARB1 module. The integrated analysis of transcriptome and metabolic panel revealed a central role of ADARB1, miR-199b-5p, miR-26a, miR-450b-5p, miR-34c-5p, glutamate and phenethylamine in the regulatory relationships. The study highlights a set of synergetic non-coding RNA related to ADARB1 in the blood ecosystem of AD and PD with dynamic glutamate and phenethylamine, providing new insights into the pathogenesis of these diseases.

Integrated Transcriptome Analysis Identified Key Expansin Genes Associated with Wheat Cell Wall, Grain Weight and Yield.

This research elucidates the dynamic expression of expansin genes during the wheat grain (Triticum aestivum L.) development process using comprehensive meta-analysis and experimental validation. We leveraged RNA-seq data from multiple public databases, applying stringent criteria for selection, and identified 60,852 differentially expressed genes across developmental stages. From this pool, 28,558 DEGs were found to exhibit significant temporal regulation in at least two different datasets and were enriched for processes integral to grain development such as carbohydrate metabolism and cell wall organization. Notably, 30% of the 241 known expansin genes showed differential expression during grain growth. Hierarchical clustering and expression level analysis revealed temporal regulation and distinct contributions of expansin subfamilies during the early stages of grain development. Further analysis using co-expression networks underscored the significance of expansin genes, revealing their substantial co-expression with genes involved in cell wall modification. Finally, qPCR validation and grain morphological analysis under field conditions indicated a significant negative correlation between the expression of select expansin genes, and grain size and weight. This study illuminates the potential role of expansin genes in wheat grain development and provides new avenues for targeted genetic improvements in wheat.

Secreted Peptide SpPIP1 Modulates Disease Resistance and Salt Tolerance in Tomato.

Tomato is a globally important horticultural and economic crop, but its productivity is severely affected by various stresses. Plant small secretory peptides have been identified as crucial mediators in plant resistance. Here, we conducted a comparative transcriptome analysis and identified the prePIP1 gene from Solanum pimpinellifolium (SpprePIP1), as an ortholog of Arabidopsis prePIP1 encoding the precursor protein of PAMP-induced SSP 1. The expression level of SpprePIP1 is transcriptionally induced in tomato upon infection with Phytophthora infestans (P. infestans), the pathogen responsible for late blight. Overexpression of SpprePIP1 resulted in enhanced tomato resistance to P. infestans. In addition, exogenous application of SpPIP1, whether through spraying or irrigation, improved tomato resistance by enhancing the transcript accumulations of pathogenesis-related proteins, as well as reactive oxygen species and the jasmonic acid (JA) levels. Integrated analysis of transcriptomics and metabolomics revealed the potential contributions of JA and phenylpropanoid biosynthesis to SpPIP1-induced tomato immunity. Additionally, SpPIP1 may strengthen tomato resistance to salt stress through the ABA signaling pathway. Overall, our findings demonstrate that SpPIP1 positively regulates tomato tolerance to P. infestans and salt stress, making it a potential plant elicitor for crop protection in an environmentally friendly way.

The lysosome-phagosome pathway mediates immune regulatory mechanisms in Mesocentrotus nudus against Vibrio coralliilyticus infection.

Sea urchins are a popular model species for studying invertebrate diseases. The immune regulatory mechanisms of the sea urchin Mesocentrotus nudus during pathogenic infection are currently unknown. This study aimed to reveal the potential molecular mechanisms of M. nudus during resistance to Vibrio coralliilyticus infection by integrative transcriptomic and proteomic analyses. Here, we identified a total of 135,868 unigenes and 4,351 proteins in the four infection periods of 0h, 20h, 60h and 100h in M. nudus. In the I20, I60 and I100 infection comparison groups, 10,861, 15,201 and 8,809 differentially expressed genes (DEGs) and 2,188, 2,386 and 2,516 differentially expressed proteins (DEPs) were identified, respectively. We performed an integrated comparative analysis of the transcriptome and proteome throughout the infection phase and found very a low correlation between transcriptome and proteome changes. KEGG pathway analysis revealed that most upregulated DEGs and DEPs were involved in immune strategies. Notably, "lysosome" and "phagosome" activated throughout the infection process, could be considered the two most important enrichment pathways at the mRNA and protein levels. The significant increase in phagocytosis of infected M. nudus coelomocytes further demonstrated that the lysosome-phagosome pathway played an important immunological role in M. nudus resistance to pathogenic infection. Key gene expression profiles and protein‒protein interaction analysis revealed that cathepsin family and V-ATPase family genes might be key bridges in the lysosome-phagosome pathway. In addition, the expression patterns of key immune genes were verified using qRT‒PCR, and the different expression trends of candidate genes reflected, to some extent, the regulatory mechanism of immune homeostasis mediated by the lysosome-phagosome pathway in M. nudus against pathogenic infection. This work will provide new insights into the immune regulatory mechanisms of sea urchins under pathogenic stress and help identify key potential genes/proteins for sea urchin immune responses.

Integrative single-cell analysis of cardiac and pulmonary sarcoidosis using publicly available cardiac and bronchoalveolar lavage fluid sequencing datasets.

Cardiac presentation of autoimmune sarcoidosis, known as cardiac sarcoidosis (CS), is a poorly understood disease with high mortality and low diagnosis rate. While CS is an immunological syndrome, little is known about how cardiac parenchymal and stromal cells mediate its pathogenesis. Moreover, while most current sarcoidosis research is based on research in pulmonary sarcoidosis (PS), it remains unclear how much both presentations of sarcoidosis overlap. To tackle these concerns, we leveraged publicly available sarcoidosis transcriptomic datasets. Two publicly available bronchoalveolar lavage single-cell RNA sequencing datasets were integrated to analyze PS relative to control. Additionally, two publicly available cardiac single-nucleus RNA sequencing datasets were integrated to analyze CS relative to control. Following integration, we ran cell-cell communication, transcription factor, and differential expression analyses on parenchymal, stromal, and immune subsets identified in our analysis. Our analysis revealed that there was an expansion of stromal and immune cells in PS and CS. We also observed upregulation of Th17.1 and attenuated activation transcriptional profiles in the immune cells of CS and PS relative to control. Additionally, we found upregulation of pro-inflammatory and pro-fibrotic transcriptional profiles in the cardiac stromal cells of CS relative to control. We also found that cardiomyocytes exhibited upregulated cardiac stress and proliferation transcriptional profiles in CS relative to control. Our integrative transcriptomic analysis shows that despite tissue-specific differences, there are shared transcriptional trends between CS and PS. It also shows that stromal and parenchymal populations exhibit transcriptional trends that could explain their pathogenic role in CS.

Deep immunophenotyping reveals clinically distinct cellular states and ecosystems in large-scale colorectal cancer

Determining the diverse cell types in the tumor microenvironment (TME) and their organization into cellular communities, is critical for understanding the biological heterogeneity and therapy of cancer. Here, we deeply immunophenotype the colorectal cancer (CRC) by integrative analysis of large-scale bulk and single cell transcriptome of 2350 patients and 53,137 cells. A rich landscape of 42 cellular states and 7 ecosystems in TMEs is uncovered and extend the previous immune classifications of CRC. Functional pathways and potential transcriptional regulators analysis of cellular states and ecosystems reveal cancer hallmark-related pathways and several critical transcription factors in CRC. High-resolution characterization of the TMEs, we discover the potential utility of cellular states (i.e., Monocytes/Macrophages and CD8 T cell) and ecosystems for prognosis and clinical therapy selection of CRC. Together, our results expand our understanding of cellular organization in TMEs of CRC, with potential implications for the development of biomarkers and precision therapies.

Lipid-correlated alterations in the transcriptome are enriched in several specific pathways in the postmortem prefrontal cortex of Japanese patients with schizophrenia.

Schizophrenia is a chronic relapsing psychiatric disorder that is characterized by many symptoms and has a high heritability. There were studies showing that the phospholipid abnormalities in subjects with schizophrenia (Front Biosci, S3, 2011, 153; Schizophr Bull, 48, 2022, 1125; Sci Rep, 7, 2017, 6; Anal Bioanal Chem, 400, 2011, 1933). Disturbances in prefrontal cortex phospholipid and fatty acid composition have been reported in subjects with schizophrenia (Sci Rep, 7, 2017, 6; Anal Bioanal Chem, 400, 2011, 1933; Schizophr Res, 215, 2020, 493; J Psychiatr Res, 47, 2013, 636; Int J Mol Sci, 22, 2021). For exploring the signaling pathways contributing to the lipid changes in previous study (Sci Rep, 7, 2017, 6), we performed two types of transcriptome analyses in subjects with schizophrenia: an unbiased transcriptome analysis solely based on RNA-seq data and a correlation analysis between levels of gene expression and lipids. RNA-Seq analysis was performed in the postmortem prefrontal cortex from 10 subjects with schizophrenia and 5 controls. Correlation analysis between the transcriptome and lipidome from 9 subjects, which are the same samples in the previous lipidomics study (Sci Rep, 7, 2017, 6). Extraction of differentially expressed genes (DEGs) and further sequence and functional group analysis revealed changes in gene expression levels in phosphoinositide 3-kinase (PI3K)-Akt signaling and the complement system. In addition, a correlation analysis clarified alterations in ether lipid metabolism pathway, which is not found as DEGs in transcriptome analysis alone. This study provided results of the integrated analysis of the schizophrenia-associated transcriptome and lipidome within the PFC and revealed that lipid-correlated alterations in the transcriptome are enriched in specific pathways including ether lipid metabolism pathway.

Exploring Transcriptional Regulation of Hyperaccumulation in Sedum plumbizincicola through Integrated Transcriptome Analysis and CRISPR/Cas9 Technology.

The cadmium hyperaccumulator Sedum plumbizincicola has remarkable abilities for cadmium (Cd) transport, accumulation and detoxification, but the transcriptional regulation mechanisms responsible for its Cd hyperaccumulation remain unknown. To address this knowledge gap, we conducted a comparative transcriptome study between S. plumbizincicola and the non-hyperaccumulating ecotype (NHE) of Sedum alfredii with or without Cd treatment. Our results revealed many differentially expressed genes involved in heavy metal transport and detoxification that were abundantly expressed in S. plumbizincicola. Additionally, we identified a large number of differentially expressed transcription factor genes, highlighting the complexity of transcriptional regulatory networks. We further screened four transcription factor genes that were highly expressed in the roots of S. plumbizincicola as candidate genes for creating CRISPR/Cas9 knockout mutations. Among these, the SpARR11 and SpMYB84 mutant lines exhibited decreased Cd accumulation in their aboveground parts, suggesting that these two transcription factors may play a role in the regulation of the Cd hyperaccumulation in S. plumbizincicola. Although further research will be required to determine the precise targeted genes of these transcription factors, combined transcriptome analysis and CRISPR/Cas9 technology provides unprecedented opportunities for identifying transcription factors related to Cd hyperaccumulation and contributes to the understanding of the transcriptional regulation mechanism of hyperaccumulation in S. plumbizincicola.