Cell Surface Receptor Signaling Pathway Research Articles

Integrating ATAC-Seq and RNA-Seq Reveals the Signal Regulation Involved in the Artemia Embryonic Reactivation Process.

Embryonic diapause is a common evolutionary adaptation observed across a wide range of organisms. Artemia is one of the classic animal models for diapause research. The current studies of Artemia diapause mainly focus on the induction and maintenance of the embryonic diapause, with little research on the molecular regulatory mechanism of Artemia embryonic reactivation. The first 5 h after embryonic diapause breaking has been proved to be most important for embryonic reactivation in Artemia. In this work, two high-throughput sequencing methods, ATAC-seq and RNA-seq, were integrated to study the signal regulation process in embryonic reactivation of Artemia at 5 h after diapause breaking. Through the GO and KEGG enrichment analysis of the high-throughput datasets, it was showed that after 5 h of diapause breaking, the metabolism and regulation of Artemia cyst were quite active. Several signal transduction pathways were identified in the embryonic reactivation process, such as G-protein-coupled receptor (GPCR) signaling pathway, cell surface receptor signaling pathway, hormone-mediated signaling pathway, Wnt, Notch, mTOR signaling pathways, etc. It indicates that embryonic reactivation is a complex process regulated by multiple signaling pathways. With the further protein structure analysis and RT-qPCR verification, 11 GPCR genes were identified, in which 5 genes function in the embryonic reactivation stage and the other 6 genes contribute to the diapause stage. The results of this work reveal the signal transduction pathways and GPCRs involved in the embryonic reactivation process of Artemia cysts. These findings offer significant clues for in-depth research on the signal regulatory mechanisms of the embryonic reactivation process and valuable insights into the mechanism of animal embryonic diapause.

P-787 Gestational diabetes in mice induces embryonic fibro-adipogenic progenitors memory that impedes the recovery of injured skeletal muscle in adult offspring

Abstract Study question Whether and how intrauterine hyperglycemia induced by Gestational diabetes steadily influences the function and fate of mesenchymal stem cells, specifically fibro-adipogenic progenitors. Summary answer Gestational diabetes in mice caused declines in self-renewal and paracrine in fibro-adipogenic progenitors, prompted adipogenesis and fibrosis, destroyed recovery after muscular injury in adult offspring. What is known already Gestational diabetes contributed to the increased susceptibility to metabolic disorders, cardiovascular diseases and atherosclerosis. Intrauterine hyperglycemia promoted placental inflammation and endowed the hematopoietic stem and progenitor cells. As an important mesenchymal stem cell, fibro-adipogenic progenitors (FAPs) play a key role in the process of “replace, repair, regeneration, restore and regress”. When acute injury happens to skeletal muscle, the fibro-adipogenic progenitors cluster start to renew itself and differentiate into functional cells like fibroblasts or adipocytes, secrete cytokines to nearby myoblasts, inducing myotube formation and muscle regeneration by cell-cell communication. Study design, size, duration Pregnant mice were randomly divided into control (CTR) and gestational diabetes (GDM) groups, GDM group was intraperitoneally injected with 100 mg/kg streptozotocin on gestational days (GDs) 6.5 and 12.5, while CTR group was treated with vehicle buffer. Only when random blood glucose level was higher than 16.8 mmol/L beginning on GD13.5 were regarded as the GDM group. At 8 weeks of offspring, we intramuscular injected cardiotoxin (CTX) to induce acute tibialis anterior muscle injury. Participants/materials, setting, methods 7 days after CTX intramuscular injection (CTX-D7) in offspring, mice were sacrificed and tiabialis anterior muscle was selected. Perilipin immunochemical and immunofluorescent staining, MASSON and Sirius Red staining were used to evaluate the recovery extent between CTR and GDM groups. Then we used fluorescence-activated cell sorting to evaluate the self proliferation of fibro-adipogenic cells at CTX-D3. We also collected FAPs to perform induced differentiation in vitro, co-culture with myoblast and SMART-sequence to explore underlying mechanism. Main results and the role of chance 7 days after cardiotoxin injection (CTX-D7), we used WGA to mark injured myofibers, eMHC to mark regenerated myofibers. Immunofluorescence and hematoxylin-eosin staining showed the muscle fibers in GDM male were still severe damaged and inadequate recovered when compared to CTR group. Perilipin immunochemical staining demonstrated more lipids deposition in GDM male muscle. MASSON and Sirius Red staining also revealed increased accumulation of collagen fibers in GDM group. Fluorescence-activated cell sorting firstly displayed depletion in numbers of Lineage-VCAM-Sca-1+ fibro-adipogeneic progenitors (FAPs) compartment in GDM group at CTX-D3 compared to CTR group. Using α-SMA to mark collagen fibers, perilipin to mark adiposity cells, we also observed activation of the FAPs into fibrosis or adipogenesis by in vitro induced differentiation. Myotubes formation experiment showed that myotubes were thinner and fusion extent was worse in myoblasts co-cultured with GDM FAPs rather than CTR FAPs. Finally, we performed SMART-sequence of FAPs between groups. Regarding p < 0.05 and the absolute of log2 foldchange >1 as significance, we totally found 1572 down-regulated genes, 1527 up-regulated genes in GDM FAPs. And the GO term analysis showed us that WNT signaling pathway, cell surface receptor signaling pathway were most highly affected. Limitations, reasons for caution We haven’t found out the key molecule in WNT signaling pathway, and how intrauterine hyperglycemia steadily affected FAP’s function remains to be explored. Also, whether other mesenchymal stem cells are influenced by short-term intrauterine hyperglycemia needs to be clarified. Wider implications of the findings Fibro-adipogenic progenitors is an important part of mesenchymal stem cells. These results demonstrated GDM in mice might induce mesenchymal memory that affects the long-term health of the offspring, which reminds us the stemness of GDM progenitors or stem cells might be destroyed and its cell-cell function may be also damaged. Trial registration number ZJU20210047

Signaling Transduction Pathways and G-Protein-Coupled Receptors in Different Stages of the Embryonic Diapause Termination Process in Artemia.

Artemia is a widely distributed small aquatic crustacean, renowned for its ability to enter a state of embryonic diapause. The embryonic diapause termination (EDT) is closely linked to environmental cues, but the precise underlying mechanisms remain elusive. In this study, ATAC-seq and RNA-seq sequencing techniques were employed to explore the gene expression profiles in Artemia cysts 30 min after EDT. These profiles were compared with those during diapause and 5 h after EDT. The regulatory mechanisms governing the EDT process were analyzed through Gene Ontology (GO) enrichment analysis of differentially expressed genes. Furthermore, the active G-protein-coupled receptors (GPCRs) were identified through structural analysis. The results unveiled that the signaling transduction during EDT primarily hinges on GPCRs and the cell surface receptor signaling pathway, but distinct genes are involved across different stages. Hormone-mediated signaling pathways and the tachykinin receptor signaling pathway exhibited heightened activity in the '0-30 min' group, whereas the Wnt signaling pathway manifested its function solely in the '30 min-5 h' group. These results imply a complete divergence in the mechanisms of signal regulation during these two stages. Moreover, through structural analysis, five GPCRs operating at different stages of EDT were identified. These findings provide valuable insights into the signal regulation mechanisms governing Artemia diapause.

Single-cell profiling of response to neoadjuvant chemo-immunotherapy in surgically resectable esophageal squamous cell carcinoma

BackgroundThe efficacy of neoadjuvant chemo-immunotherapy (NAT) in esophageal squamous cell carcinoma (ESCC) is challenged by the intricate interplay within the tumor microenvironment (TME). Unveiling the immune landscape of ESCC in the context of NAT could shed light on heterogeneity and optimize therapeutic strategies for patients.MethodsWe analyzed single cells from 22 baseline and 24 post-NAT treatment samples of stage II/III ESCC patients to explore the association between the immune landscape and pathological response to neoadjuvant anti-PD-1 combination therapy, including pathological complete response (pCR), major pathological response (MPR), and incomplete pathological response (IPR).ResultsSingle-cell profiling identified 14 major cell subsets of cancer, immune, and stromal cells. Trajectory analysis unveiled an interesting link between cancer cell differentiation and pathological response to NAT. ESCC tumors enriched with less differentiated cancer cells exhibited a potentially favorable pathological response to NAT, while tumors enriched with clusters of more differentiated cancer cells may resist treatment. Deconvolution of transcriptomes in pre-treatment tumors identified gene signatures in response to NAT contributed by specific immune cell populations. Upregulated genes associated with better pathological responses in CD8 + effector T cells primarily involved interferon-gamma (IFNγ) signaling, neutrophil degranulation, and negative regulation of the T cell apoptotic process, whereas downregulated genes were dominated by those in the immune response-activating cell surface receptor signaling pathway. Natural killer cells in pre-treatment tumors from pCR patients showed a similar upregulation of gene expression in response to IFNγ but a downregulation of genes in the neutrophil-mediated immunity pathways. A decreased cellular contexture of regulatory T cells in ESCC TME indicated a potentially favorable pathological response to NAT. Cell–cell communication analysis revealed extensive interactions between CCL5 and its receptor CCR5 in various immune cells of baseline pCR tumors. Immune checkpoint interaction pairs, including CTLA4-CD86, TIGIT-PVR, LGALS9-HAVCR2, and TNFSF4-TNFRSF4, might serve as additional therapeutic targets for ICI therapy in ESCC.ConclusionsThis pioneering study unveiled an intriguing association between cancer cell differentiation and pathological response in esophageal cancer patients, revealing distinct subgroups of tumors for which neoadjuvant chemo-immunotherapy might be effective. We also delineated the immune landscape of ESCC tumors in the context of clinical response to NAT, which provides clinical insights for better understanding how patients respond to the treatment and further identifying novel therapeutic targets for ESCC patients in the future.

Molecular Mechanisms Underlying Abnormal Activation of T Cells in Idiopathic Aplastic Anemia and Hypoplastic Myelodysplastic Neoplasms

Idiopathic aplastic anemia (AA) and hypoplastic myelodysplastic neoplasms (MDS-h) are severe hematopoietic disorders characterized by pancytopenia and hypoplastic bone marrow. There is compelling evidence that these distinct clinical entities share a common pathophysiology based on the damage of hematopoietic stem and progenitor cells (HSPCs) by cytotoxic T cells. Expanded T cells overproduce proinflammatory cytokines, resulting in decreased proliferation and increased apoptosis of HSPCs. To uncover the molecular mechanisms underlying this abnormal immune response, we used RNA-Seq for the transcriptome analysis of T cells from patients with idiopathic AA and MDS-h. CD3+ cells were isolated from peripheral blood of 15 patients with AA or MDS-h at diagnosis and 6 healthy blood donors. The RNA-Seq library was constructed by NEB Next Ultra II Directional RNA Library Prep Kit and the data were analysed by R software 4.0.2. Functional annotation of differently expressed genes was performed using DAVID database and Gene Set Enrichment Analysis (GSEA). Principal component analysis-based clustering of RNA-Seq data defined the three major components for AA and MDS-h patients, and healthy individuals (Fig. 1A). As expected, the control samples formed a distinct group, meanwhile patient samples partially clustered together. The same results were obtained using unsupervised hierarchical clustering. The differential expression analysis (DEA) identified 256 significantly upregulated and 96 downregulated genes (ІlogFCІ>1, FDR<0.05) in patients compared to controls. Notably, the DEA detected many long noncoding RNAs (lncRNAs) including upregulated lncRNAs associated with immunological disturbances (e.g. CDC42-IT1 and NEAT1), and oncogenesis (e.g. ACAP2-IT1, and FAM238A). Particularly, NEAT1 positively regulates differentiation of CD4+ T cells into Th17 cells through STAT3 protein. Autoreactive T cells may be further stimulated by increased expression of S100A8/A9 detected in the patient cells. Gene Ontology (GO) analysis annotated the upregulated genes in AA/MDS-h to biological processes associated with oxygen transport, B cell receptor signaling pathway, innate immune response, positive regulation of inflammatory response, and apoptotic process, etc. (adjusted p<0.05) (Fig. 1B). The downregulated genes were significantly enriched in processes related to adaptive immune response, cell surface receptor signaling pathway, mitochondrial ATP synthesis coupled proton transport, etc. (adjusted p<0.05) (Fig.1B). B cell receptor signaling pathway was enriched by upregulated genes such as BANK1, MEF2C, and SYK whose deregulation is associated with autoimmune disorders. Herein, the activation of apoptosis is likely driven via AP-1 positive modulators that showed increased expressions in the patients. These modulators are essential for T cell activation and regulatory T cell differentiation. Pathway enrichment analysis determined the following signaling pathways (adjusted p<0.05): B cell receptor signaling pathway, osteoclast differentiation, oxidative phosphorylation, chemical carcinogenesis - reactive oxygen species, and cytokine-cytokine receptor interaction. The GSEA using the Hallmark gene sets showed that DNA Repair and Oxidative Phosphorylation were significantly negatively correlated with patient phenotype (Fig. 1C). Both GSEA and pathway analysis revealed that oxidative phosphorylation was supressed in patient-derived T cells. This is consistent with previous metabolic findings demonstrating that a transition from oxidative phosphorylation to glycolysis is a sign of T cell activation and it is critical for support of rapid cell growth. In conclusion, our study suggests the possible mechanisms of aberrant T cellular-immunity in idiopathic AA and MDS-h. Consistent with abnormal biological features of T cells, a large number of deregulated genes in the patients was involved in immune and inflammatory responses. Furthermore, our analyses revealed novel pathways, such as oxidative phosphorylation, as well as candidates ( TLR2, and CDC42-IT1) for functional studies. The deregulation of multiple lncRNAs in the patients indicates their implication in the molecular pathogenesis and thus their roles in bone marrow failure need to be explored. Supported by AZV (NU21-03-00565), and MH CZ-DRO (UHKT, 00023736).

C-type lectin-like receptor-2 (CLEC-2) is a key regulator of kappa-carrageenan-induced tail thrombosis model in mice

Kappa-carrageenan (KCG), which is used to induce thrombosis in laboratory animals for antithrombotic drug screening, can trigger platelet aggregation. However, the cell-surface receptor and related signaling pathways remain unclear. In this study, we investigated the molecular basis of KCG-induced platelet activation using light-transmittance aggregometry, flow cytometry, western blotting, and surface plasmon resonance assays using platelets from platelet receptor-deficient mice and recombinant proteins. KCG-induced tail thrombosis was also evaluated in mice lacking the platelet receptor. We found that KCG induces platelet aggregation with α-granule secretion, activated integrin αIIbβ3, and phosphatidylserine exposure. As this aggregation was significantly inhibited by the Src family kinase inhibitor and spleen tyrosine kinase (Syk) inhibitor, a tyrosine kinase-dependent pathway is required. Platelets exposed to KCG exhibited intracellular tyrosine phosphorylation of Syk, linker activated T cells, and phospholipase C gamma 2. KCG-induced platelet aggregation was abolished in platelets from C-type lectin-like receptor-2 (CLEC-2)-deficient mice, but not in platelets pre-treated with glycoprotein VI-blocking antibody, JAQ1. Surface plasmon resonance assays showed a direct association between murine/human recombinant CLEC-2 and KCG. KCG-induced thrombosis and thrombocytopenia were significantly inhibited in CLEC-2-deficient mice. Our findings show that KCG induces platelet activation via CLEC-2.

Protein-based bandpass filters for controlling cellular signaling with chemical inputs

Biological signal processing is vital for cellular function. Similar to electronic circuits, cells process signals via integrated mechanisms. In electronics, bandpass filters transmit frequencies with defined ranges, but protein-based counterparts for controlled responses are lacking in engineered biological systems. Here, we rationally design protein-based, chemically responsive bandpass filters (CBPs) showing OFF-ON-OFF patterns that respond to chemical concentrations within a specific range and reject concentrations outside that range. Employing structure-based strategies, we designed a heterodimeric construct that dimerizes in response to low concentrations of a small molecule (ON), and dissociates at high concentrations of the same molecule (OFF). The CBPs have a multidomain architecture in which we used known drug receptors, a computationally designed protein binder and small-molecule inhibitors. This modular system allows fine-tuning for optimal performance in terms of bandwidth, response, cutoff and fold changes. The CBPs were used to regulate cell surface receptor signaling pathways to control cellular activities in engineered cells.

Proteome Analysis for Inflammation Related to Acute and Convalescent Infection

Infectious diseases are a significant burden in global healthcare. Pathogens engage with different host defense mechanisms. However, it is currently unknown if there are disease-specific immune signatures and/or if different pathogens elicit common immune-associated molecular entities to common therapeutic interventions. We studied patients enrolled through the Human Immunology Project Consortium (HIPC), which focuses on immune responses to various infections. Blood samples were collected and analyzed from patients during infection and follow-up time points at the convalescent stage. The study included samples from patients with Lyme disease (LD), tuberculosis (TB), malaria (MLA), dengue virus (DENV), and West Nile virus (WNV), as well as kidney transplant patients with cytomegalovirus (CMV) and polyomavirus (BKV) infections. Using an antibody-based assay, we quantified ~ 350 cell surface markers, cytokines, and chemokines involved in inflammation and immunity. Unique protein signatures were identified specific to the acute phase of infection irrespective of the pathogen type, with significant changes during convalescence. In addition, tumor necrosis factor receptor superfamily member 6 (TNR6), C–C Motif Chemokine Receptor 7 (CCR7), and C–C motif chemokine ligand-1 (CCL1) were increased in the acute and convalescent phases across all viral, bacterial, and protozoan compared to blood from healthy donors. Furthermore, despite the differences between pathogens, proteins were enriched in common biological pathways such as cell surface receptor signaling pathway and response to external stimulus. In conclusion, we demonstrated that irrespective of the pathogen type, there are common immunoregulatory and proinflammatory signals.

Role of the membrane-spanning 4A gene family in lung adenocarcinoma.

Lung adenocarcinoma, which is the second most prevalent cancer in the world, has a poor prognosis and a low 5-year survival rate. The MS4A protein family is crucial to disease development and progression, particularly for cancers, allergies, metabolic disorders, autoimmune diseases, infections, and neurodegenerative disorders. However, its involvement in lung adenocarcinoma remains unclear. In this study, we found that 11 MS4A family genes were upregulated or downregulated in lung adenocarcinoma. Furthermore, we described the genetic variation landscape of the MS4A family in lung adenocarcinoma. Notably, through functional enrichment analysis, we discovered that the MS4A family is involved in the immune response regulatory signaling pathway and the immune response regulatory cell surface receptor signaling pathway. According to the Kaplan-Meier curve, patients with lung adenocarcinoma having poor expression of MS4A2, MS4A7, MS4A14, and MS4A15 had a low overall survival rate. These four prognostic genes are substantially associated with immune-infiltrating cells, and a prognosis model incorporating them may more accurately predict the overall survival rate of patients with lung adenocarcinoma than current models. The findings of this study may offer creative suggestions and recommendations for the identification and management of lung adenocarcinoma.

Overexpression of POLA2 in hepatocellular carcinoma is involved in immune infiltration and predicts a poor prognosis

BackgroundHepatocellular carcinoma (HCC) is the second malignancy worldwide. POLA2 initiates DNA replication, regulates cell cycle and gene repair that promote tumorigenesis and disease progression. However, the prognostic and biological function roles of POLA2 in HCC had not been conclusively determined.MethodsThe expression levels and prognosis role of POLA1 and POLA2 in HCC were analyzed based on TCGA-LIHC database and recruited 24 HCC patients. Gene mutations were analyzed using “maftools” package. POLA2 and immune cells correlations were analyzed by TIMER. POLA2 co-expressed genes functional enrichment were evaluated using Metascape. The mRNA and protein level of POLA2 was detected in HCC cells and tissues. Cell migration, invasion, proliferation, cell cycle and HCC cell lines derived xenograft model were performed to investigate POLA2 biological function.ResultsPOLA2 was significantly high expressed in HCC than in normal liver tissue in both TCGA-LIHC and our collected HCC samples. In validation cohort, POLA2 significantly related to tumor differentiation, tumor size and Ki-67 (p < 0.05). In TCGA-LIHC cohort, overexpression of POLA2 predicted a low OS and associated with different clinical stages. Multivariate Cox regression showed overexpression of POLA2 effectively distinguished the prognosis at different T, N, M, stages and grades of HCC. POLA2 expression correlated with mutation burden, immune cells infiltration and immune-associated genes expression of HCC. Functional enrichment revealed that POLA2 co-expressed genes were linked to cellular activity, plasma membrane protein complex and leukocyte activity, immune response-regulated cell surface receptor signaling pathway, and immune response-regulated signaling pathway. Moreover, POLA2 was also positively co-expressed with some immune checkpoints (CD274, CTL-4, HAVCR2, PDCD1, PDCD1LG2, TIGIT, and LAG3) (p < 0.001). Gene knockdown revealed that POLA2 promoted proliferation, migration, invasion, and cell cycle of SMMC-7721 and HepG2. The HCC xenograft tumor model also demonstrated remarkably tumor size inhibition, tumor proliferation inhibtion and tumor necrosis promotion when POLA2 knockdown.ConclusionsPOLA2 influenced immune microenvironment and tumor progression of HCC indicated that it might be a potential molecular marker for prognostic evaluation or a therapeutic target for HCC.

Identification of High Tolerance to Jujube Witches' Broom in Indian Jujube (Ziziphus mauritiana Lam.) and Mining Differentially Expressed Genes Related to the Tolerance through Transcriptome Analysis.

The jujube witches' broom (JWB) disease is a severe threat to jujube trees, with only a few cultivars being genuinely tolerant or resistant to phytoplasma. The defense mechanism of jujube trees against phytoplasma is still unclear. In this study, we aimed to investigate the tolerance mechanism of Indian jujube 'Cuimi' to JWB and identify the key genes that contribute to JWB high tolerance. Based on the symptoms and phytoplasma concentrations after infection, we confirmed the high tolerance of 'Cuimi' to JWB. Comparative transcriptome analysis was subsequently performed between 'Cuimi' and 'Huping', a susceptible cultivar of Chinese jujube. Unique gene ontology (GO) terms were identified in 'Cuimi', such as protein ubiquitination, cell wall biogenesis, cell surface receptor signaling pathway, oxylipin biosynthetic process, and transcription factor activity. These terms may relate to the normal development and growth of 'Cuimi' under phytoplasma infection. We identified 194 differential expressed genes related to JWB high tolerance, involved in various processes, such as reactive oxygen species (ROS), Ca2+ sensors, protein kinases, transcription factors (TFs), lignin, and hormones. Calmodulin-like (CML) genes were significantly down-regulated in infected 'Cuimi'. We speculated that the CML gene may act as a negative regulatory factor related to JWB high tolerance. Additionally, the cinnamoyl-CoA reductase-like SNL6 gene was significantly up-regulated in infected 'Cuimi', which may cause lignin deposition, limit the growth of phytoplasma, and mediate immune response of 'Cuimi' to phytoplasma. Overall, this study provides insights into the contribution of key genes to the high tolerance of JWB in Indian jujube 'Cuimi'.

Oligomerization of a plant helper NLR requires cell-surface and intracellular immune receptor activation

Plant disease resistance involves both detection of microbial molecular patterns by cell-surface pattern recognition receptors and detection of pathogen effectors by intracellular NLR immune receptors. NLRs are classified as sensor NLRs, involved in effector detection, or helper NLRs required for sensor NLR signaling. TIR-domain-containing sensor NLRs (TNLs) require helper NLRs NRG1 and ADR1 for resistance, and helper NLR activation of defense requires the lipase-domain proteins EDS1, SAG101, and PAD4. Previously, we found that NRG1 associates with EDS1 and SAG101 in a TNL activation-dependent manner [X. Sun et al., Nat. Commun. 12, 3335 (2021)]. We report here how the helper NLR NRG1 associates with itself and with EDS1 and SAG101 during TNL-initiated immunity. Full immunity requires coactivation and mutual potentiation of cell-surface and intracellular immune receptor-initiated signaling [B. P. M. Ngou, H.-K. Ahn, P. Ding, J. D. G. Jones, Nature 592, 110-115 (2021), M. Yuanet al.,Nature 592, 105-109 (2021)]. We find that while activation of TNLs is sufficient to promote NRG1-EDS1-SAG101 interaction, the formation of an oligomeric NRG1-EDS1-SAG101 resistosome requires the additional coactivation of cell-surface receptor-initiated defense. These data suggest that NRG1-EDS1-SAG101 resistosome formation invivo is part of the mechanism that links intracellular and cell-surface receptor signaling pathways.

ABI3BP is a prognosis biomarker related with clinicopathological features and immunity infiltration of lung tumor.

Background: The primary factor of cancer mortality is lung tumor. ABI3BP gene encodes an extracellular matrix bind protein associated to multiplication and derivation. However, the prognosis score of ABI3BP for lung tumor and its relation with immunity cellular infiltration for lung tumor have not been reported. Methods: Public repository systems (Timer, GEPIA, TCGA, HPA) were utilized to explore expression of ABI3BP for lung tumor, and explored the relation of ABI3BP and clinicopathological parameters. TCGA information set was utilized for cox analysis for data with one or more variables of ABI3BP for lung tumor. STRING was utilized to explore ABI3BP regulatory networks. GO/KEGG enrichment analysis as well as enrichment analysis of gene sets were carried out for ABI3BP co-expression via R package. And finally we explored the relation of expression of ABI3BP and lung tumor immunity invasion, exploring the influence of ABI3BP level of expression on immunotreatment and whether immunity invasion would affect the prognosis of patients with lung tumor. Results: ABI3BP is downregulated in LUAD and LUSC, and associated to lung tumor phase and prognosis. Univariate and multivariate cox regression showed that ABI3BP was an independent prognostic factor in patients with lung tumors. The extracellular matrix protein-coding gene and the ABI3BP-related gene were intersected to obtain 10 hub genes. On the basis of GO/KEGG enrichment analysis, hub genes are closely associated to immunity-associated pathways including T cell receptor signaling pathway, immune response-activating cell surface receptor signaling pathway. Finally, the expression of ABI3BP is closely related to immune cell infiltration and immune cell marker set, and the expression of ABI3BP can help predict the therapeutic effect of immune checkpoint inhibitors and improve the prognosis of patients. Conclusion: ABI3BP could be a new target for lung tumor that could be utilized as a diagnostic and therapeutic tool.

Susceptibility identification for seasonal influenza A/H3N2 based on baseline blood transcriptome.

Influenza susceptibility difference is a widely existing trait that has great practical significance for the accurate prevention and control of influenza. Here, we focused on the human susceptibility to the seasonal influenza A/H3N2 of healthy adults at baseline level. Whole blood expression data for influenza A/H3N2 susceptibility from GEO were collected firstly (30 symptomatic and 19 asymptomatic). Then to explore the differences at baseline, a suite of systems biology approaches - the differential expression analysis, co-expression network analysis, and immune cell frequencies analysis were utilized. We found the baseline condition, especially immune condition between symptomatic and asymptomatic, was different. Co-expression module that is positively related to asymptomatic is also related to immune cell type of naïve B cell. Function enrichment analysis showed significantly correlation with "B cell receptor signaling pathway", "immune response-activating cell surface receptor signaling pathway" and so on. Also, modules that are positively related to symptomatic are also correlated to immune cell type of neutrophils, with function enrichment analysis showing significantly correlations with "response to bacterium", "inflammatory response", "cAMP-dependent protein kinase complex" and so on. Responses of symptomatic and asymptomatic hosts after virus exposure show differences on resisting the virus, with more effective frontline defense for asymptomatic hosts. A prediction model was also built based on only baseline transcription information to differentiate symptomatic and asymptomatic population with accuracy of 0.79. The results not only improve our understanding of the immune system and influenza susceptibility, but also provide a new direction for precise and targeted prevention and therapy of influenza.

Severe Burn Injury Significantly Alters the Gene Expression and m6A Methylation Tagging of mRNAs and lncRNAs in Human Skin.

N6-methyladenosine (m6A) modulates RNA metabolism and functions in cell differentiation, tissue development, and immune response. After acute burns, skin wounds are highly susceptible to infection and poor healing. However, our understanding of the effect of burn injuries on m6A methylation and their potential mechanism is still limited. Human m6A-mRNA&lncRNA Epitranscriptomic microarray was used to obtain comprehensive mRNA and lncRNA transcriptome m6A profiling and gene expression patterns after burn injuries in human skin tissue. Bioinformatic and functional analyses were conducted to find molecular functions. Microarray profiling showed that 65 mRNAs and 39 lncRNAs were significantly hypermethylated; 5492 mRNAs and 754 lncRNAs were significantly hypomethylated. Notably, 3989 hypomethylated mRNAs were down-expressed and inhibited many wound healing biological processes and pathways including in the protein catabolic process and supramolecular fiber organization pathway; 39 hypermethylated mRNAs were up-expressed and influenced the cell surface receptor signaling pathway and inflammatory response. Moreover, we validated that m6A regulators (METTL14, METTL16, ALKBH5, FMR1, and HNRNPC) were significantly downregulated after burn injury which may be responsible for the alteration of m6A modification and gene expression. In summary, we found that homeostasis in the skin was disrupted and m6A modification may be a potential mechanism affecting trauma infection and wound healing.

A pan-cancer analysis of the biological function and clinical value of BTLA in tumors

B and T-lymphocyte attenuator (BTLA) plays an immunosuppressive role by inhibiting T- and B-cell functions. BTLA is associated with a variety of diseases, especially cancer immunity. However, the function of BTLA in various cancers and its clinical prognostic value have still not been comprehensively analyzed. This study aimed to identify the relationship between BTLA and cancer from the perspectives of differences in BTLA expression, its clinical value, immune infiltration, and the correlation with immune-related genes in various cancers. Data regarding mRNA expression, miRNA expression, lncRNA expression, and clinical data of patients of 33 existing cancers were collected from the TCGA database. Target miRNA of BTLA and the lncRNA that interacts with the target miRNA were obtained from the StarBase database. Based on bioinformatics analysis methods, the relationship between various types of cancers and BTLA was thoroughly investigated, and a competing endogenous RNA network of BTLA, target miRNA, and interacting lncRNA was constructed. The Kaplan-Meier (KM) prognostic analysis of BTLA and target miRNA (has-miR-137) in various types of cancers was completed using the KM plotter. BTLA expression varied in different cancers, with statistical significance in nine cancer types. KM plotter to analyze the overall survival (OS) and regression-free survival prognosis of cancer patients revealed that the BTLA expression was statistically different in the OS of 11 types of cancers out of 21 types of cancers; the OS of 8 type of cancers was also statistically different. Correlation analysis of tumor immune genes revealed a positive correlation of BTLA expression with immunosuppressive gene (CTLA4 and PDCD1) expression. Gene Set Enrichment Analysis showed that BTLA and its co-expressed genes mainly act through biological processes and pathways, including immune response regulation, cell surface receptor signaling pathway, antigen binding, antigen receptor-mediated signaling pathway, and leukocyte migration. BTLA has the potential as a prognostic marker for CLL, COAD, NSCLC, and OV and a diagnostic marker for CLL, COAD, and KIRC. BTLA has a close and complex relationship with the occurrence and development of tumors, and cancer immunotherapy for BTLA is worthy of further analysis.

Elucidating breed-specific variants of native pigs in Korea: insights into pig breeds’ genomic characteristics

ABSTRACT Although conserving native pig breeds is important in Korea, research on the genomic aspects to identify breed-specific variations in native pig breeds is uncommon. Single nucleotide polymorphisms (SNPs) can be a powerful source for identifying breed-specific variants. We used whole genome sequencing data, including Jeju Native Pig (JNP), Korean Native Pig (KNP), Korean Wild Boar (KWB), and other western commercial pig breeds to determine native pig breed-specific SNPs. Furthermore, the goal was not only to determine the genomic specificity of native pig breeds but also to identify SNPs that carry breed-specific information (breed-informative SNPs) that can be related to breed characteristics. The representative characteristics of native pigs are their unique meat quality and disease resistance. We surveyed the gene ontology (GO) of native pigs with breed-specific SNPs. Examining the genes associated with GO may contribute to revealing the reasons for the unique characteristics of native pig breeds. The enriched GOs terms were neuron projection development, cell surface receptor signaling pathway, ion homeostasis in JNP, cell adhesion and wound healing in KNP, and DNA repair and reproduction in KWB. We expect that this study of breed-specific SNPs will enable us to gain a deeper understanding of native pigs in Korea.

Comprehensive Genome-Wide Analysis of Wnt Gene Family and Expression Profiling during Limb Regeneration in Portunus trituberculatus

Wnt genes encode a family of secretory glycoproteins that are involved in various stages of organ development through regulation of cell proliferation, differentiation, and growth. Recently, Wnt genes have been shown to play an important role in regeneration processes. However, there have been no previous genome-wide analyses of the Wnt gene family members in crab species. In this study, a total of 13 Wnt family genes were identified from the genome of the swimming crab Portunus trituberculatus and classified into three main groups based on the conserved domain, protein sequence, and motifs. Chromosome location analysis showed that tandem duplication may have resulted in the expansion of the PtWnt gene family. RNA-seq results indicated that most PtWnt genes had a higher Fragments Per Kilobase of transcript sequences per Million base pairs (FPKM) value in the regenerating limb bud muscle than in the normal limb muscle, and the genes were enriched in a number of pathways that had biological functions underlying limb regeneration such as the cell surface receptor signaling pathway, the hippo signaling pathway, receptor binding, and basal cell carcinoma. Moreover, quantitative real-time PCR (RT-qPCR) analysis confirmed that the expression levels of nine PtWnts except for PtWnt1, PtWnt2, and PtWnt6 had a consistently increasing trend during limb regeneration. PtWnt1, PtWnt2, and PtWnt6 exhibited significantly up- or down-regulated expression at different limb regeneration stages. These results provide valuable information for further evolutionary and functional characterization of PtWnt genes and indicate the complexity and specialized mechanism of the Wnt signaling pathway regulating regeneration in crustaceans.

Gene Network Analysis of the Transcriptome Impact of SARS-CoV-2 Interacting MicroRNAs in COVID-19 Disease.

According to the World Health Organization (WHO), as of June 2022, over 536 million confirmed COVID-19 disease cases and over 6.3 million deaths had been globally reported. COVID-19 is a multiorgan disease involving multiple intricated pathological mechanisms translated into clinical, biochemical, and molecular changes, including microRNAs. MicroRNAs are essential post-transcriptional regulators of gene expression, being involved in the modulation of most biological processes. In this study, we characterized the biological impact of SARS-CoV-2 interacting microRNAs differentially expressed in COVID-19 disease by analyzing their impact on five distinct tissue transcriptomes. To this end, we identified the microRNAs’ predicted targets within the list of differentially expressed genes (DEGs) in tissues affected by high loads of SARS-CoV-2 virus. Next, we submitted the tissue-specific lists of the predicted microRNA-targeted DEGs to gene network functional enrichment analysis. Our data show that the upregulated microRNAs control processes such as mitochondrial respiration and cytokine and cell surface receptor signaling pathways in the heart, lymph node, and kidneys. In contrast, downregulated microRNAs are primarily involved in processes related to the mitotic cell cycle in the heart, lung, and kidneys. Our study provides the first exploratory, systematic look into the biological impact of the microRNAs associated with COVID-19, providing a new perspective for understanding its multiorgan physiopathology.

Mechanism of Liangfu Pills in treatment of functional dyspepsia: based on network pharmacology and experimental verification

This study aims to explore the potential mechanism of Liangfu Pills in the treatment of functional dyspepsia(FD) based on network pharmacology and molecular docking, and verify the mechanism by animal experiment. The active components of Liangfu Pills were screened from Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform(TCMSP), and the targets of Liangfu Pills were predicted by SwissTargetPrediction. The targets of FD were retrieved from GeneCards. On this basis, the common targets of the disease and the pills were yielded and the protein interaction was retrieved based on STRING. The core targets were screened out, followed by Gene Oncology(GO) term enrichment and Kyoto Encyclopedia of Genes and Genomes(KEGG) pathway enrichment analysis with DAVID. Finally, molecular docking was carried out with the help of AutoDock Tools to predict the binding degree between the effective components of Liangfu Pills and core targets. A total of 19 active components of Liangfu Pills and 591 FD-related targets were screened out by network pharmacology, of which 253 were common targets of the disease and the prescription. Liangfu Pills was mainly involved in the biological processes of response to drug, negative regulation of transcription, positive regulation of apoptotic process, and cell surface receptor signaling pathway, and the KEGG pathways of hypoxia-inducible factor-1(HIF-1) signaling pathway, serotonergic synapse, tumor necrosis factor(TNF) signaling pathway, cyclic adenosine monophosphate(cAMP) signaling pathway, calcium signal pathway, and inflammatory mediator regulation of transient receptor potential(TRP) channels. The results of molecular docking showed that the key active components of Liangfu Pills had certain binding activity to the targets mitogen-activated protein kinase 1(MAPK1), protein kinase B(AKT1), transient receptor potential cation channel subfamily V member 1(TRPV1), 5-hydroxytryptamine receptor 1 A(HTR1 A), and 5-hydroxytryptamine receptor 2 A(HTR2 A). FD was induced in rats, and then Liangfu Pills was given to FD rats for 7 days. The results showed that Liangfu Pills could significantly relieve the symptoms of FD rats, significantly increase the expression of 5-hydroxytryptamine(5-HT), and down-regulate the expression of TRPV1. Through network pharmacology, molecular docking, and experimental verification, this study proved that Liangfu Pills improved FD through multiple components and multiple targets. The result lays a basis for further research on the mechanism and clinical application of Liangfu Pills in the treatment of FD.