Transcriptional Expression Profiles Research Articles

Abstract TMP120: Transcriptomic Analysis Reveals Common Age Independent Immunomodulatory Proteins As A Mode Of Neuroprotection In P2X4R KO Mice After Ischemic Stroke

Background and Purpose: Identification of a new potential drug target protein and their plausible mechanism for stroke treatment is critically needed. We earlier showed that genetic deletion as well as short term pharmacological inhibition of P2X4R, a purinergic receptor for adenosine triphosphate ATP, provides acute neuroprotection and thus can be potential drug targets to treat ischemic stroke. However, potential mechanisms remain unknown. Therefore, in this study, we employed RNA-seq technology to identify the gene expression profiles, pathways analysis and qPCR validation of differentially expressed genes (DEGs). This analysis will identify role of those DEGs in certain biological processes responsible for P2X4R dependent neuroprotection after stroke. Methods: We subjected young (8-12 weeks-old n= 4/group), and aged (12-18-month-old; n=8/group) male and female Global P2X4 KO and littermate WT mice to right middle cerebral artery occlusion MCAo for 60 min followed by 3 day of reperfusion. After 3 days, mice were sacrificed and prefrontal cortex tissue was isolated to extract total RNA using Trizol and used for RNA-seq sample preparations as well as for validation by Nanostring mediated qPCR technique. DESeq2 and Gene Ontology (GO) and /or Ingenuity Pathway Analysis (IPA) were used to identify mRNA transcript expression profiles and biological pathway. qPCR was analyzed with nSolver Data Analysis Support system. Results: We found 2246 DEGs in P2X4R KO vs WT tissue after stroke. Out of these DEGs 1920 gene were downregulated and 325 genes were upregulated in KO. GO/IPA analysis of top 300 DEGs suggests an enrichment of ion channel transport system, inflammation and extracellular matrix component genes. QPCR validation of top 30 DEGs revealed down regulation of two common age independent genes: Lnterleukin-6 ( IL-6) , an inflammatory cytokine and Cytotoxic T Lymphocyte-Associated Protein 2 alpha ( Ctla2a ), an immunosuppressive factor KO group. Conclusion: This data suggests P2X4R mediated neuroprotection after stroke is brought by attenuation of immune modulatory pathways in both young and aged mice of both sexes. Future studies will delineate the detailed role of IL-6 and Ctla2a in P2X4R mediated neuroprotection mechanisms after stroke.

PIMREG is a prognostic biomarker involved in immune microenvironment of clear cell renal cell carcinoma and associated with the transition from G1 phase to S phase.

Clear cell renal cell carcinoma (ccRCC) is one of the most common tumors in the world and affects human health seriously. PIMREG is a mitotic regulator which is essential to the metaphase-to-anaphase transition in cell cycle. Although PIMREG plays a crucial role in the malignant progression of tumors, there are few reports on its role in ccRCC. The transcriptional expression profile and clinical data of PIMREG were downloaded from TCGA database and verified by qRT-PCR. Kaplan-Meier plotter was used to analyze the effect of PIMREG on overall survival (OS), disease specific survival (DSS) and progression-free interval (PFI) of patients with ccRCC. Univariable and multivariable Cox regression analysis were used to determine the independent prognostic factors of ccRCC. The effects of PIMREG on cell migration and invasion were detected by wound healing assay and transwell invasion assay, and CCK-8 assay, colony formation assay and cell cycle assay were used to detect the effect of PIMREG on cell proliferation. In addition, the changes in cell cycle related proteins were detected by western blot. PIMREG was highly expressed in human ccRCC and was positively correlated with pathologic stage, TNM stage and histologic grade. In addition, patients with high expression of PIMREG had a poor prognosis. Univariable and multivariable Cox regression analysis identified that PIMREG was an independent prognostic factor of ccRCC. Additionally, PIMREG was also closely related to immune cell infiltration. Experiments in vitro identified that the knockdown of PIMREG could significantly inhibit the proliferation, migration and invasion abilities of ccRCC. The expression of cyclin D1, CDK4 and CDK6 was also significantly reduced after PIMREG knockdown. PIMREG plays a vital role in the development of ccRCC and may become a potential therapeutic target in the future.

Increased expression of TBC1D10B as a potential prognostic and immunotherapy relevant biomarker in liver hepatocellular carcinoma

The TBC1 domain family member 10B (EPI64B/TBC1D10B), a member of the RabGAP EPI64 subfamily, contains a TBC domain that confers GTPase-activating protein activity. Even though overexpression of TBC1D10B has been reported to promote tumor invasion and metastasis in gastric adenocarcinoma, the prognostic value of TBC1D10B and its correlation with DNA methylation and immune infiltration in hepatocellular carcinoma are still not known. Transcriptional expression profiles of TBC1D10B between hepatocellular carcinoma tissues and normal tissues were downloaded from The Cancer Genome Atlas and Gene Expression Omnibus. The Clinical Proteomic Tumor Analysis Consortium and the Human Protein Atlas were used to assess the TBC1D10B protein expression. The biological functions of TBC1D10B were evaluated by the Metascape database and by Gene Set Enrichment Analysis (GSEA). Receiver operating characteristic (ROC) curve analysis was used to distinguish hepatocellular carcinoma from adjacent normal tissues. The effect of TBC1D10B on survival was estimated using the Kaplan–Meier method. DNA methylation in the TBC1D10B gene was assessed using the online MEXPRESS and MethSurv tools. The association between TBC1D10B mRNA expression and immune cell infiltration was investigated by the TIMER2 web server, tumor immune estimation resource and single-sample GSEA. This study found that TBC1D10B is highly expressed in hepatocellular carcinoma and that increased TBC1D10B mRNA expression is associated with female sex, lower Body Mass Index, high level of alpha fetal protein, and worse clinical stages. The mRNA and protein levels of TBC1D10B were verified in cells. Functional annotation indicated enrichment with negative regulation of the cell cycle, extracellular matrix, and corresponding pathways in the high-TBC1D10B phenotype. The ROC curve analysis showed that, with a cutoff level of 2.912, the accuracy, sensitive, and specificity in differentiate TBC1D10B hepatocellular carcinoma from adjacent controls were 0.931, 0.920, and 0.802, respectively. Kaplan–Meier survival analysis showed that hepatocellular carcinoma patients with high TBC1D10B had a worse prognosis than those with low TBC1D10B, especially in patients with a weight below 70 kg, height above 170 cm, and histological G2 and G3. We also found that the methylation of TBC1D10B was associated with the prognosis in patients with hepatocellular carcinoma. Moreover, correlation analysis indicated that TBC1D10B mRNA expression was positively correlated with infiltration levels of most immune cells, but negatively correlated with Th17 and cytotoxic cells infiltration. Our study indicates that increased TBC1D10B expression in hepatocellular carcinoma may play a role in tumorigenesis by regulating the cell cycle and extracellular matrix. TBC1D10B may be a novel prognostic and predictive marker and immune therapeutic target in hepatocellular carcinoma patients.

Cloning, homology modelling and expression analysis of Oryza sativa WNK gene family

With No Lysine kinases (WNKs) represents a gene family that encodes Ser/Thr kinases, with anomalous disposition of catalytic lysine residue in subdomain I. In plants, WNKs had been linked to circadian rhythm, photoperiodic response and abiotic stress tolerance with mechanism yet undeciphered. In the present study, full-length CDS sequences of rice WNKs (OsWNK1 to 8) were cloned from indica cultivar IR64. A total of six highly conserved kinase subdomains were identified. Comparative analysis of protein sequences from six different species of rice showed varying magnitudes of substitution (76.2 %), deletion (15.4 %), and addition (8.4 %) events. ConSurf analysis coupled with CASTp results identified functional residues that were clustered together in modelled 3-D structures. Among post-translational modifications (PTMs) studied, 87.7 % of phosphorylation sites were predicted. Mined protein-protein interactions (PPIs) depicted OsWNKs to interact notably with other OsWNK members and with key proteins like PRR95 involved in photoperiodic response and protein phosphatase like PP2C involved in ABA signalling. Gene duplication analysis revealed two paralogous duplicated gene pairs: WNK6-WNK9 and WNK7-WNK8. Oryza sativa showed maximum syntenic relationship with Sorghum bicolor among the compared species. OsWNKs showed differential transcript expression profiles on treatment with plant growth regulators indicating its versatile role in plant growth and development.

Transcription factor TOX maintains the expression of Mst1 in controlling the early mouse NK cell development.

Rationale: TOX is a DNA-binding factor required for the development of multiple immune cells and the formation of lymph nodes. However, the temporal regulation mode of TOX on NK cell development and function needs to be further explored. Methods: To investigate the role of TOX in NK cells at distinct developmental phases, we deleted TOX at the hematopoietic stem cell stage (Vav-Cre), NK cell precursor (CD122-Cre) stage and late NK cell developmental stage (Ncr1-Cre), respectively. Flow cytometry was used to detect the development and functional changes of NK cell when deletion of TOX. RNA-seq was used to assess the differences in transcriptional expression profile of WT and TOX-deficient NK cells. Published Chip-seq data was exploited to search for the proteins directly interact with TOX in NK cells. Results: The deficiency of TOX at the hematopoietic stem cell stage severely retarded NK cell development. To a less extent, TOX also played an essential role in the physiological process of NKp cells differentiation into mature NK cells. Furthermore, the deletion of TOX at NKp stage severely impaired the immune surveillance function of NK cells, accompanied by down-regulation of IFN-γ and CD107a expression. However, TOX is dispensable for mature NK cell development and function. Mechanistically, by combining RNA-seq data with published TOX ChIP-seq data, we found that the inactivation of TOX at NKp stage directly repressed the expression of Mst1, an important intermediate kinase in Hippo signaling pathway. Mst1 deficient at NKp stage gained the similar phenotype with Toxfl/flCD122Cre mice. Conclusion: In our study, we conclude that TOX coordinates the early mouse NK cell development at NKp stage by maintaining the expression of Mst1. Moreover, we clarify the different dependence of the transcription factor TOX in NK cells biology.

The STAT1/HMGB1/NF-κB pathway in chronic inflammation and kidney injury after cisplatin exposure.

Rationale: Cisplatin, a potent chemotherapeutic drug, induces side effects in normal tissues including the kidney. To reduce the side effects, repeated low-dose cisplatin (RLDC) is commonly used in clinical setting. While RLDC reduces acute nephrotoxicity to certain extents, a significant portion of patients later develop chronic kidney problems, underscoring the need for novel therapeutics to alleviate the long-term sequelae of RLDC therapy. Methods: In vivo, the role of HMGB1 was examined by testing HMGB1 neutralizing antibodies in RLDC mice. In vitro, the effects of HMGB1 knockdown on RLDC-induced nuclear factor-κB (NF-κB) activation and fibrotic phenotype changes were tested in proximal tubular cells. To study signal transducer and activator of transcription 1 (STAT1), siRNA knockdown and its pharmacological inhibitor Fludarabine were used. We also searched the Gene Expression Omnibus (GEO) database for transcriptional expression profiles and evaluated kidney biopsy samples from CKD patients to verify the STAT1/HMGB1/NF-κB signaling axis. Results: We found that RLDC induced kidney tubule damage, interstitial inflammation, and fibrosis in mice, accompanied by up-regulation of HMGB1. Blockage of HMGB1with neutralizing antibodies and Glycyrrhizin suppressed NF-κB activation and associated production of pro-inflammatory cytokines, reduced tubular injury and renal fibrosis, and improved renal function after RLDC treatment. Consistently, knockdown of HMGB1 decreased NF-κB activation and prevented the fibrotic phenotype in RLDC-treated renal tubular cells. At the upstream, knockdown of STAT1 suppressed HMGB1 transcription and cytoplasmic accumulation in renal tubular cells, suggesting a critical role of STAT1 in HMGB1 activation. Upregulation of STAT1/HMGB1/NF-κB along with inflammatory cytokines was also verified in kidney tissues of CKD patients. Conclusion: These results unravel the STAT1/HMGB1/NF-κB pathway that contributes to persistent inflammation and chronic kidney problems after cisplatin nephrotoxicity, suggesting new therapeutic targets for kidney protection in cancer patients receiving cisplatin chemotherapy.

Genome-Wide Characterization and In-silico Transcriptional Expression Analysis of PEBP Family in Solanum lycopersicum L.

Phosphatidylethanolamine-binding proteins (PEBPs) are an important gene family with highly conserved protein sequences represented in three taxonomic divisions. In plants, PEBP genes are an important actors in the regulation of flowering time, plant architecture and seed dormancy. Despite this, PEBP genes have not been genome-wide identified and systematically analyzed in tomato. In this study, the PEBP gene family in tomato, one of the economically important Solanum species, was comprehensively identified genome-wide and characterized by bioinformatics tools. Here, 12 PEBP genes were identified, which were classified into four clades based on their phylogenetic relationships and the presence of the structurally conserved domain/motif. In addition, the gene structure, conserved protein structure, promoter regions, and digital expression levels of these PEBP genes were determined. Digital expression profiling of SlPEBP transcripts revealed their expression in most developmental and anatomical tissues. These results will provide the further functional and evolutionary characterization of PEBP genes in tomato.

Phylogenetic, Structural and Functional Evolution of the LHC Gene Family in Plant Species.

Light-harvesting chlorophyll a/b-binding (LHC) superfamily proteins play a vital role in photosynthesis. Although the physiological and biochemical functions of LHC genes have been well-characterized, the structural evolution and functional differentiation of the products need to be further studied. In this paper, we report the genome-wide identification and phylogenetic analysis of LHC genes in photosynthetic organisms. A total of 1222 non-redundant members of the LHC family were identified from 42 species. According to the phylogenetic clustering of their homologues with Arabidopsis thaliana, they can be divided into four subfamilies. In the subsequent evolution of land plants, a whole-genome replication (WGD) event was the driving force for the evolution and expansion of the LHC superfamily, with its copy numbers rapidly increasing in angiosperms. The selection pressure of photosystem II sub-unit S (PsbS) and ferrochelatase (FCII) families were higher than other subfamilies. In addition, the transcriptional expression profiles of LHC gene family members in different tissues and their expression patterns under exogenous abiotic stress conditions significantly differed, and the LHC genes are highly expressed in mature leaves, which is consistent with the conclusion that LHC is mainly involved in the capture and transmission of light energy in photosynthesis. According to the expression pattern and copy number of LHC genes in land plants, we propose different evolutionary trajectories in this gene family. This study provides a basis for understanding the molecular evolutionary characteristics and evolution patterns of plant LHCs.

The ecdysis triggering hormone system is essential for reproductive success in Mythimna separata (Walker).

Ecdysis triggering hormone (ETH) was originally discovered as a key hormone that regulates insect moulting via binding to its receptor, ETH receptor (ETHR). However, the precise role of ETH in moth reproduction remains to be explored in detail. ETH function was verified in vivo using Mythimna separata (Walker), an important cereal crop pest. RT-qPCR analysis revealed that transcriptional expression profiles of MsepETH showed evident sexual dimorphism in the adult stage. MsepETH expression increased in the females on day 3 and persisted thereafter till day 7, consistent with female ovarian maturation, and was merely detectable in males. Meanwhile, MsepETH expression levels were significantly higher in the trachea than in other tissues. MsepETHR-A and MsepETHR-B were expressed in both sexes and were significantly higher in the antennae than in other tissues. MsepETH and MsepETHR knockdown in females by RNA interference significantly reduced the expression of MsepETH, MsepETHR-A, MsepETHR-B, MsepJHAMT, and MsepVG, which delayed egg-laying and significantly reduced egg production. RNAi 20-hydroxyecdysone (20E) receptor (EcR) decreased MsepETH expression whereas injecting 20E restored egg production that had been disrupted by MsepETH interference. Meanwhile, RNAi juvenile hormone (JH) methoprene tolerant protein (Met) also decreased MsepETH expression and smearing JH analog methoprene (Meth) restored egg production. In conclusion, the reproduction roles of ETH, JH, and 20E were investigated in M. separata. These findings will lay the foundation for future research to develop an antagonist that reduces female reproduction and control strategies for pest insects.

Relative infectivity of the SARS-CoV-2 Omicron variant in human alveolar cells.

With the continuous emergence of highly transmissible SARS-CoV-2 variants, the comparison of their infectivity has become a critical issue for public health. However, a direct assessment of the viral characteristic has been challenging because of the lack of appropriate experimental models and efficient methods. Here, we integrated human alveolar organoids and single-cell transcriptome sequencing to facilitate the evaluation. In a proof-of-concept study with four highly transmissible SARS-CoV-2 variants, including GR (B.1.1.119), Alpha (B.1.1.7), Delta (B.1.617.2), and Omicron (BA.1), a rapid evaluation of the relative infectivity was possible. Our system demonstrates that the Omicron variant is 5- to 7-fold more infectious to human alveolar cells than the other SARS-CoV-2 variants at the initial stage of infection. To our knowledge, for the first time, this study measures the relative infectivity of the Omicron variant under multiple virus co-infection and provides new experimental procedures that can be applied to monitor emerging viral variants.

Decoding Gene Expression Signatures Underlying Vegetative to Inflorescence Meristem Transition in the Common Bean

The tropical common bean (Phaseolus vulgaris L.) is an obligatory short-day plant that requires relaxation of the photoperiod to induce flowering. Similar to other crops, photoperiod-induced floral initiation depends on the differentiation and maintenance of meristems. In this study, the global changes in transcript expression profiles were analyzed in two meristematic tissues corresponding to the vegetative and inflorescence meristems of two genotypes with different sensitivities to photoperiods. A total of 3396 differentially expressed genes (DEGs) were identified, and 1271 and 1533 were found to be up-regulated and down-regulated, respectively, whereas 592 genes showed discordant expression patterns between both genotypes. Arabidopsis homologues of DEGs were identified, and most of them were not previously involved in Arabidopsis floral transition, suggesting an evolutionary divergence of the transcriptional regulatory networks of the flowering process of both species. However, some genes belonging to the photoperiod and flower development pathways with evolutionarily conserved transcriptional profiles have been found. In addition, the flower meristem identity genes APETALA1 and LEAFY, as well as CONSTANS-LIKE 5, were identified as markers to distinguish between the vegetative and reproductive stages. Our data also indicated that the down-regulation of the photoperiodic genes seems to be directly associated with promoting floral transition under inductive short-day lengths. These findings provide valuable insight into the molecular factors that underlie meristematic development and contribute to understanding the photoperiod adaptation in the common bean.

Comprehensive Genomic Analysis for Identifying FZD6 as a Novel Diagnostic Biomarker for Acute Myeloid Leukemia.

As a family of G protein-coupled receptors (GPCRs) with a seven-span transmembrane structure, frizzled class receptors (FZDs) play crucial roles in regulating multiple biological functions. However, their transcriptional expression profile and prognostic significance in acute myeloid leukemia (AML) are unclear. In AML, the role of FZDs was explored by performing the comprehensive analysis on the relationship between clinical characteristics and mRNA expression profiles from public databases including cBioPortal for Cancer Genomics, Gene Expression Profile Interactive Analysis (GEPIA), and Cancer Cell Line Encyclopedia (CCLE). We identified that in the majority of 27 AML cell lines, frizzled class receptor 6 (FZD6) was high-expressed. A significantly higher expression of FZD6 in AML patients was observed when compared to normal controls (P < 0.01). Compared with intermediate and poor/adverse risk group patients, FZD6 expressed much lower in cytogenetic favorable risk group patients (P < 0.0001). Patients with higher-expressed FZD6 were associated with shorter overall survival (OS) (P = 0.0089) rather than progression-free survival (PFS). However, the predictive effect of FZD6 on OS could be reversed by hematopoietic stem cell transplantation (HSCT). The data of gene set enrichment analysis (GSEA) demonstrated that 4 gene sets, including MYC targets, HEME metabolism, E2F targets, and UV response, were differentially enriched in the high-expression FZD6 group. To conclude, the study suggested that high expression of FZD6 might be a novel poor prognostic biomarker for AML treatment.

Gene Expression in Bronchial Epithelial Cell Responses to Vanadium Exposure.

Vanadium exposure has the adverse effect on lung function in human, whereas the detailed mechanisms of vanadium exposure-induced pulmonary toxicity are limited. Hence, the present study aimed to investigate the hub genes and signaling pathways related to sodium metavanadate (SMV)-induced pulmonary toxicity. The transcript expression profile GSE36684 downloaded from Gene Expression Omnibus contained eight human bronchial epithelial cell (HBEC) samples including five SMV-treated and three control HBEC samples. Totally 455 differentially expressed genes (DEGs) were screened, especially 201 and 254 genes were up- and down-regulated in the HBECs treated with SMV. Gene ontology analysis suggested that the DEGs were mainly involved in signal transduction, the response to drug, cell proliferation, adhesion, and migration. Pathway analysis demonstrated that the DEGs were primarily participated in NF-κB, Wnt, MAPK, and PI3K-Akt signaling pathways. Moreover, the hub genes, including ITGA5, ITGB3, ITGA2, LAMC2, MMP2, and ITGA4, might contribute to SMV-induced pulmonary toxicity. Our study improves the understanding of the molecular mechanisms by which SMV induced the pulmonary toxicity.

Comprehensive analysis of chemokines family and related regulatory ceRNA network in lung adenocarcinoma

Lung adenocarcinoma (LUAD) is one of the world's commonest malignancies with a high fatality rate. Chemokines not only regulate immune response but also participate in tumor development and metastasis and yet the mechanism of chemokines in LUAD remains unclear. In this study, transcriptional expression profiles, mutation data, and copy number variation data were downloaded from The Cancer Genome Atlas (TCGA). Risk gene protein expression was assessed by the Clinical Proteomic Tumor Analysis Consortium (CPTAC) and the Human Protein Atlas (HPA). Gene Expression Omnibus (GEO) data was used to validate the prognostic model. We summarized the genetic mutation variation landscape of chemokines. The risk prognosis model was developed based on differentially expressed chemokines, and patients in the high-risk score (RS) group had lower survival rates. Gene Set Enrichment Analysis (GSEA) revealed that high-RS patients were associated with metabolic transformation pathways, while low-RS patients were associated with immune-related pathways. Compared with the high-RS group, the low-RS group had higher immune/stromal/estimate scores calculated by the ESTIMATE package. The proportion of immune cells obtained using the CIBERSORT package was significantly different between the two groups. Most of the immune checkpoints were highly expressed in low-RS samples. Finally, we discovered that the lncRNA MIR17HG/AC009299.3/miR-21–5p/CCL20 regulatory network might be crucial in the pathogenesis of LUAD. In conclusion, we developed a risk signature and chemokine-related competing endogenous RNA (ceRNA) network.

307P Differential expression profiling of transcripts in stage IIIA non-small cell lung cancer (NSCLC) of smokers and non-smokers cases of north India: A geneto-environmental study

Several epidemiological and experimental studies suggest that the etiology of many chronic illnesses is caused by the joint effect between genetics and the environment. Smoking tobacco is the major hazard feature for lung cancer in Indian subcontinent especially men, compare to woman where, other important risk factors i.e., exposure to agents and level of pollutions are responsible. So, the aim of the study is to compare the expression level of transcript-based biomarkers IDH1, CEA, Cyfra21-1, and TPA in NSCLC fifty tumor tissue stage IIIa patients compared to control benign tissues of smokers and non-smokers cases living in areas with air quality categorized as poor (AQI 201–300) or moderate (AQI 101–200).

Identification of Differentially Expressed Intronic Transcripts in Osteosarcoma.

Over the past decade; the discovery and characterization of long noncoding RNAs (lncRNAs) have revealed that they play a major role in the development of various diseases; including cancer. Intronic transcripts are one of the most fascinating lncRNAs that are located within intron regions of protein-coding genes, which have the advantage of encoding micropeptides. There have been several studies looking at intronic transcript expression profiles in cancer; but almost none in osteosarcoma. To overcome this problem; we have investigated differentially expressed intronic transcripts between osteosarcoma and normal bone tissues. The results highlighted that NRG1-IT1; FGF14-IT1; and HAO2-IT1 were downregulated; whereas ER3-IT1; SND1-IT1; ANKRD44-IT1; AGAP1-IT1; DIP2A-IT1; LMO7DN-IT1; SLIT2-IT1; RNF216-IT1; and TCF7L1-IT1 were upregulated in osteosarcoma tissues compared to normal bone tissues. Furthermore, we identified if the transcripts encode micropeptides and the transcripts' locations in a cell.

BCL6 deletion in CD4 T cells does not affect Th2 effector mediated immunity in the skin.

Recent studies propose that T follicular helper (Tfh) cells possess a high degree of functional plasticity in addition to their well-defined roles in mediating interleukin-4-dependent switching of germinal center B cells to the production of immunoglobulin (Ig)G1 and IgE antibodies. In particular Tfh cells have been proposed to be an essential stage in Th2 effector cell development that are able to contribute to innate type 2 responses. We used CD4-cre targeted deletion of BCL6 to identify the contribution Tfh cells make to tissue Th2 effector responses in models of atopic skin disease and lung immunity to parasites. Ablation of Tfh cells did not impair the development or recruitment of Th2 effector subsets to the skin and did not alter the transcriptional expression profile or functional activities of the resulting tissue resident Th2 effector cells. However, the accumulation of Th2 effector cells in lung Th2 responses was partially affected by BCL6 deficiency. These data indicate that the development of Th2 effector cells does not require a BCL6 dependent step, implying Tfh and Th2 effector populations follow separate developmental trajectories and Tfh cells do not contribute to type 2 responses in the skin.

Differential transcript expression profiles of susceptible and resistant pigeonpea cultivars at an early time point during Fusarium udum infection.

Differential transcript expression profiles of susceptible and resistant pigeonpea cultivars at an early time point during Fusarium udum infection.

Transcriptional Modification and Potential Intracellular Signaling Mechanisms in Human Macrophages Primed by Interferon-γ

To explore the transcriptional gene expression profile up-regulated in human macrophages stimulated by interferon-γ (IFN-γ) and the underlying intracellular signaling mechanisms. RNA-seq was used to sequence and compare the differential gene expression profiles of human macrophage cell line U937 before and after IFN-γ stimulation, and the significantly up-regulated genes were screened out, which were verified by fluorescence-based real-time quantitative polymerase chain reaction (qPCR) in U937 and THP1 cell lines, respectively. JAK/STAT, MAPK/ERK and PI3K/AKT pathway inhibitors were added to simultaneously to the cultured U937 cells upon IFN-γ priming to detect their effects on the expressions of the up-regulated genes to explore the key regulatory mechanisms. RNA-seq and qPCR results showed that, the well-recognized chemokines CXCL9, CXCL10 and CXCL11, the APOL family including APOL1, APOL2, APOL3, APOL4, APOL6 and GBP family GBP1, GBP2, GBP3, GBP4 and GBP5 as well were significantly up-regulated in IFN-γ-stimulated U937 cells. JAK/STAT3 pathway inhibitor inhibited the upregulation of APOL1, APOL4, GBP1, GBP4 and GBP5 genes induced by IFN-γ, while MAPK/ERK pathway inhibitor inhibited the upregulation of CXCL10 gene. PI3K/AKT pathway inhibitor inhibited the upregulation of APOL1,APOL4, APOL6, GBP1 and GBP5 genes induced by IFN-γ, all three signal pathway inhibitors could inhibit the upregulation of CXCL9 gene, and none of them could inhibit the upregulation of APOL3 gene. Upon IFN-γ stimulation, some family molecules of APOL and GBP in macrophages are significantly up-regulated, and PI3K/AKT, JAK/STAT3 and MAPK/ERK pathways have positive regulation on their expressions, respectively.

TEx-MST: tissue expression profiles of MANE select transcripts.

Recently, a new reference transcript dataset [Matched Annotation from the NCBI and EMBL-EBI (MANE) select] was released by NCBI and EMBL-EBI to make available a new unified representative transcript for human protein-coding genes. While the main purpose of MANE project is to provide a harmonized gene and transcript information standard, there is no explicit tissue expression information about these MANE select transcripts. In this report, we tried to provide useful expression profiles of MANE select transcripts in various normal human tissues to allow further interrogation of their molecular modulations and functional significance. We obtained the new V9 transcript expression dataset from the Genotype-Tissue Expression (GTEx) web portal. This new GTEx dataset, based on a long-read sequencing platform, affords better assessment of the expression of alternative spliced transcripts. This tissue expression profiles of MANE select transcripts (TEx-MST) database not only provides the basic information of MANE select transcripts but also tissue expression profiles on alternative transcripts in protein-coding genes. Users can initiate the interrogation by gene symbol searches or by browsing the MANE genes with various criteria (such as genome locations or expression rankings). We further utilized the GENCODE biotype feature to identify the top-ranked protein-coding transcripts by choosing the most expressed protein-coding transcripts from GTEx datasets (both V8 and V9 datasets). In summary, there are 18 083 genes matched between MANE and GTEx. Among them, 13 245 MANE select transcripts matched with the top-ranked protein-coding transcripts in GTEx V9 dataset, which underlined the dominate expression of MANE select transcripts. This TEx-MST web bioinformatic database provides a visualized user interface for the normal tissue expression patterns of MANE select transcripts using the newly released GTEx dataset. Database URL: TEx-MST is available at https://texmst.ibms.sinica.edu.tw/