Integrative Transcriptomic, Proteomic and Functional Analysis Reveals ATP1B3 as a Diagnostic and Potential Therapeutic Target in Hepatocellular Carcinoma

ATP1B3 may promote glioma proliferation and migration through MAPK/NF-KB signaling pathway

Objective

To investigate the function of ATPase Na+/K+ Transporting Subunit Beta 3 (ATP1B3) in gliomas and the molecular mechanisms associated with them in order to identify a novel target and approach for glioma clinical diagnosis and treatment.

Methods

The Cancer Genome Atlas (TCGA), a public tumor database, and the Chinese Glioma Genome Atlas (CGGA) were used to evaluate the differential expression of ATP1B3 in glioma cells of various grades. Its connection to patient survival and prognosis; The siRNA interference approach instantly reduced the amount of ATP1B3 expression in the glioma cell lines U87MG and U251MG. The knockdown efficiency was assessed by Western Blotting (WB) and RT-qPCR. Following ATP1B3 knockdown, the ability of glioma cells to proliferate, migrate, and invade was identified using the Transwell assay and CCK-8. The proteins that might interact with ATP1B3 were filtered out using the TCGA database and literature analysis. The WB assay was used to determine the expression level of Protein Phosphatase 1 Catalytic Subunit Alpha (PPP1CA) following ATP1B3 deletion, immunoprecipitation was used to determine the direct influence of the two proteins, and immunofluorescence was used to analyze the distribution of ATP1B3 and PPP1CA proteins in glioma cells. Cyclin D1 and vascular endothelial growth factor A(VEGFA) expression alterations following ATP1B3 deletion were identified using the WB assay. Following ATP1B3 knockdown, the WB assay was used to determine the expression levels of p-Raf1, p-MEK 1/2, p-ERK 1/2, p-IκBα, and p-P65 in the MAPK and NF-κB signaling pathway.

Results

Database analysis revealed a negative correlation between the patients' prognosis and the expression level of ATP1B3, and a positive correlation with the malignant degree of the glioma. The mRNA and protein expression levels of ATP1B3 were significantly decreased after knockout, and the proliferation, migration and invasion ability of cells in knockout group were significantly lower than those in control group, with statistical difference. The immunoprecipitation results were negative, and the knockdown group's PPP1CA expression was lower than the control group's. Following ATP1B3 knockdown, Cyclin D1 and VEGFA protein expression levels dropped, and the effects were statistically significant. There was a statistically significant drop in the expression levels of p-Raf1, p-MEK 1/2, p-ERK 1/2, p-IκBα, and p-P65 following ATP1B3 deletion.

Conclusion

In gliomas, ATP1B3 is highly expressed. Glioma cell motility, invasion, and proliferation all decline when ATP1B3 expression is lowered. The downstream protein PPP1CA is indirectly regulated by ATP1B3. By controlling the MAPK and NF-κB signaling pathways, ATP1B3 may have a role in the invasion, migration, and proliferation of glioma cells. As a result, the ATP1B3 gene might be a biological target for treatment and a possible neurotumor diagnostic.

TOMM40 Correlates with Cholesterol and is Predictive of a Favorable Prognosis in Endometrial Carcinoma

BACKGROUND

A link between cholesterol and endometrial cancer has been established, but current studies have been limited in their findings. We aimed to elucidate the causal relationship between cholesterol and endometrial cancer and to find prognostic genes for endometrial cancer.

METHODS

We first explored the causal relationship between total cholesterol and endometrial cancer using two-sample Mendelian randomization and then obtained differential genes to screen for prognosis-related genes in endometrial cancer. Then, we utilized pan-cancer analysis based on RNA sequencing data to evaluate the expression pattern and immunological role of the Translocase of Outer Mitochondrial Membrane 40 (TOMM40). Through multiple transcriptome datasets and multi-omics in-depth analysis, we comprehensively explore the relationship of TOMM40 expression with clinicopathologic characteristics, clinical outcomes and mutations in endometrial cancer. Lastly, we systematically associated the TOMM40 with different cancers from immunological properties from numerous perspectives, such as immune cell infiltration, immune checkpoint inhibitors, immunotherapy, gene mutation load and microsatellite instability.

RESULTS

We found a negative association between cholesterol and endometrial cancer. A total of 78 genes were enriched by relevant single nucleotide polymorphisms (SNPs), of which 12 upregulated genes and 5 downregulated genes in endometrial cancer. TOMM40 was found to be a prognostic gene associated with endometrial cancer by prognostic analysis. TOMM40 was found to be positively correlated with the infiltration of most immune cells and immunization checkpoints in a subsequent study. Meanwhile, TOMM40 also was an oncogene in many cancer types. High TOMM40 was associated with lower genome stability.

CONCLUSION

The findings of our study indicate that the maintenance of normal total cholesterol metabolism is associated with a decreased risk of developing endometrial cancer. Moreover, TOMM40 may have potential as a prognostic indicator for endometrial cancer.

Single-Cell Sequencing and Machine Learning Integration to Identify Candidate Biomarkers in Psoriasis: INSIG1

Background

Psoriasis represents a persistent, immune-driven inflammatory condition affecting the skin, characterized by a lack of well-established biologic treatments without adverse events. Consequently, the identification of novel targets and therapeutic agents remains a pressing priority in the field of psoriasis research.

Methods

We collected single-cell RNA sequencing (scRNA-seq) datasets and inferred T cell differentiation trajectories through pseudotime analysis. Bulk transcriptome and scRNA-seq data were integrated to identify differentially expressed genes (DEGs). Machine learning was employed to screen candidate genes. Correlation analysis was used to predict the interactions between cells expressing insulin-induced gene 1 (INSIG1) and other immune cells. Finally, drug docking was performed on INSIG1, and the expression levels of INSIG1 in psoriasis were verified through clinical and in vivo experiments, and further in vivo experiments established the efficacy of tetrandrine in the treatment of psoriasis.

Results

T cells were initially categorized into seven states, with differentially expressed genes in T cells (TDEGs) identified and their functions and signaling pathways. INSIG1 emerged as a characteristic gene for psoriasis and was found to be downregulated in psoriasis and potentially negatively associated with T cells, influencing psoriasis fatty acid metabolism, as inferred from enrichment and immunoinfiltration analyses. In the cellular communication network, cells expressing INSIG1 exhibited close interactions with other immune cells through multiple signaling channels. Furthermore, drug sensitivity showed that tetrandrine stably binds to INSIG1, could be a potential therapeutic agent for psoriasis.

Conclusion

INSIG1 emerges as a specific candidate gene potentially regulating the fatty acid metabolism of patients with psoriasis. In addition, tetrandrine shows promise as a potential treatment for the condition.

Establishment and validation of a novel CD8+ T cell-associated prognostic signature for predicting clinical outcomes and immunotherapy response in hepatocellular carcinoma via integrating single-cell RNA-seq and bulk RNA-seq

CD8+ T lymphocytes are critical in the immune response against neoplasms, yet the prognostic relevance of CD8+ T cell-associated genes in hepatocellular carcinoma (HCC) is not fully understood. We sourced single-cell RNA-sequencing (scRNA-seq) and bulk RNA-seq data for HCC from the GSE98638 dataset and The Cancer Genome Atlas (TCGA) repository. We utilized Weighted Gene Correlation Network Analysis (WGCNA) to identify CD8+ T cell-related genes. A clinical prognostic model for risk stratification was then constructed via Cox-Lasso regression analysis. The Immunophenotypic Score (IPS) was utilized to evaluate the potential of immunotherapeutic interventions in the categorized cohorts. Validation of the expression of CD8+ T cell-associated risk genes was performed using quantitative reverse transcription PCR (qRT-PCR). Integrating scRNA-seq with RNA-seq data, we identified five CD8+ T cell-related signature genes: IKBKE, ATP1B3, MSC, ADA, and BATF. Notably, HCC patients in the high-risk group had markedly decreased overall survival. Elevated infiltration levels of CD8+ T cells, B cells, and macrophages were observed in the high-risk group. Moreover, there was a positive correlation between the risk score and immune checkpoints (ICPs), including PDCD1, CD274, and CTLA4. Patients within the high-risk group subject to PD1 and CTLA4 blockade exhibited higher IPS levels. Additionally, the expression of the five risk genes was upregulated in HCC cell lines and tissues compared to normal cells and tissues. Our findings establish a prognostic signature based on CD8+ T cells, offering a potent predictive model for clinical outcomes and responsiveness to immunotherapy in HCC patients.

The platelet-related genes associated with the prognosis of HCC by regulating cycling T cell and prolif-TAMs

Accumulating evidence highlighted the important roles of platelets in the prognosis and progression of various tumors. Nevertheless, the role of platelet-related genes (PRGs) in HCC remains limited. In this work, 92 differentially expressed PRGs were described in HCC using TCGA and ICGC databases. Then, based on the different expressions of PRGs, we explored two subtypes and developed the PRGs prognostic signature in HCC. The PRGs signature was an independent prognosis factor associated with immune cell infiltration in HCC. Furthermore, two external validation sets verified the expression and prognosis of the PRGs signature gene in HCC. Finally, scRNA-seq analysis demonstrated that the signature genes (CENPE and KIF2C) were mainly expressed in cycling T cells and prolif-TAMs. Enrichment analysis showed that CENPE and KIF2C regulated the cell cycle and p53 pathways in these cells. In conclusion, this study builds the PRGs-related risk signature of HCC and reveals the potential mechanism by which these signature genes regulate the immune microenvironment in HCC.

ATP1A1 is a promising new target for melanoma treatment and can be inhibited by its physiological ligand bufalin to restore targeted therapy efficacy

Despite advancements in treating metastatic melanoma, many patients exhibit resistance to targeted therapies. Our study focuses on ATP1A1, a sodium pump subunit associated with cancer development. We aimed to assess ATP1A1 prognostic value in melanoma patients and examine the impact of its ligand, bufalin, on melanoma cell lines in vitro and in vivo. High ATP1A1 expression (IHC) correlated with reduced overall survival in melanoma patients. Resistance to BRAF inhibitor was linked to elevated ATP1A1 levels in patient biopsies (IHC, qPCR) and cell lines (Western blot, qPCR). Additionally, high ATP1A1 mRNA expression positively correlated with differentiation/pigmentation markers based on data from The Cancer Genome Atlas (TCGA) databases and Verfaillie proliferative gene signature analysis. Bufalin specifically targeted ATP1A1 in caveolae, (proximity ligation assay) and influenced Src phosphorylation (Western blot), thereby disrupting multiple signaling pathways (phosphokinase array). In vitro, bufalin induced apoptosis in melanoma cell lines by acting on ATP1A1 (siRNA experiments) and, in vivo, significantly impeded melanoma growth using a nude mouse xenograft model with continuous bufalin delivery via an osmotic pump. In conclusion, our study demonstrates that ATP1A1 could serve as a prognostic marker for patient survival and a predictive marker for response to BRAF inhibitor therapy. By targeting ATP1A1, bufalin inhibited cell proliferation, induced apoptosis in vitro, and effectively suppressed tumor development in mice. Thus, our findings strongly support ATP1A1 as a promising therapeutic target, with bufalin as a potential agent to disrupt its tumor-promoting activity.

Combining bulk and single-cell RNA-sequencing data to develop an NK cell-related prognostic signature for hepatocellular carcinoma based on an integrated machine learning framework

BACKGROUND

The application of molecular targeting therapy and immunotherapy has notably prolonged the survival of patients with hepatocellular carcinoma (HCC). However, multidrug resistance and high molecular heterogeneity of HCC still prevent the further improvement of clinical benefits. Dysfunction of tumor-infiltrating natural killer (NK) cells was strongly related to HCC progression and survival benefits of HCC patients. Hence, an NK cell-related prognostic signature was built up to predict HCC patients' prognosis and immunotherapeutic response.

METHODS

NK cell markers were selected from scRNA-Seq data obtained from GSE162616 data set. A consensus machine learning framework including a total of 77 algorithms was developed to establish the gene signature in TCGA-LIHC data set, GSE14520 data set, GSE76427 data set and ICGC-LIRI-JP data set. Moreover, the predictive efficacy on ICI response was externally validated by GSE91061 data set and PRJEB23709 data set.

RESULTS

With the highest C-index among 77 algorithms, a 11-gene signature was established by the combination of LASSO and CoxBoost algorithm, which classified patients into high- and low-risk group. The prognostic signature displayed a good predictive performance for overall survival rate, moderate to high predictive accuracy and was an independent risk factor for HCC patients' prognosis in TCGA, GEO and ICGC cohorts. Compared with high-risk group, low-risk patients showed higher IPS-PD1 blocker, IPS-CTLA4 blocker, common immune checkpoints expression but lower TIDE score, which indicated low-risk patients might be prone to benefiting from ICI treatment. Moreover, a real-world cohort, PRJEB23709, also revealed better immunotherapeutic response in low-risk group.

CONCLUSIONS

Overall, the present study developed a gene signature based on NK cell-related genes, which offered a novel platform for prognosis and immunotherapeutic response evaluation of HCC patients.

Unresectable hepatocellular carcinoma: transarterial chemoembolisation plus Huachansu - a single-center randomised controlled trial

OBJECTIVE

Huachansu, a Chinese medicine derived from the dried skin glands of toad venom, has been used in China since the 1970s to treat liver cancer. Transarterial chemoembolisation (TACE) is the standard of care for patients with unresectable hepatocellular carcinoma (HCC). This study evaluated the efficacy and safety of the combination of TACE and Huachansu in unresectable HCC.

METHODS

From September 2012 to September 2016, 120 patients diagnosed with unresectable HCC were prospectively enrolled. Patients were randomised at a 1:1 ratio into the combined treatment group (Huachansu-TACE) and the TACE treatment group. The primary endpoint was progression-free survival (PFS) and secondary endpoints were overall survival (OS) and safety. The exploration outcome serum Na+/K+-ATPase (NKA) α3 at baseline and 3-month follow-ups were compared for a prognostic role. All patients were subjected to 36-month follow-up.

RESULTS

A total of 112 patients who completed the study were included in the analysis. PFS and OS were significantly better in the Huachansu-TACE group than in the TACE group (p=0.029 and p=0.025, respectively), with a median PFS of 6.8 and 5.3; and a median OS of 14.8 months and 10.7 months, respectively. Although no prognostic significance was found between the baseline NKA-low and NKA-high groups in the patients' OS (p=0.48), its changes after 3-month follow-up showed significant prognostic values, of which, were 8.5 months and 23.8 months, respectively (p<0.001). Treatment-related adverse events were comparable between groups.

CONCLUSIONS

Huachansu-TACE is effective in prolonging the PFS and OS in patients with unresectable HCC.

TRIAL REGISTRATION NUMBER

NCT01715532.

Development and validation of an inflammatory response-related signature in triple negative breast cancer for predicting prognosis and immunotherapy

Background

Inflammation is one of the most important characteristics of tumor tissue. Signatures based on inflammatory response-related genes (IRGs) can predict prognosis and treatment response in a variety of tumors. However, the clear function of IRGs in the triple negative breast cancer (TNBC) still needs to be explored.

Methods

IRGs clusters were discovered via consensus clustering, and the prognostic differentially expressed genes (DEGs) across clusters were utilized to develop a signature using a least absolute shrinkage and selection operator (LASSO). Verification analyses were conducted to show the robustness of the signature. The expression of risk genes was identified by RT-qPCR. Lastly, we formulated a nomogram to improve the clinical efficacy of our predictive tool.

Results

The IRGs signature, comprised of four genes, was developed and was shown to be highly correlated with the prognoses of TNBC patients. In contrast with the performance of the other individual predictors, we discovered that the IRGs signature was remarkably superior. Also, the ImmuneScores were elevated in the low-risk group. The immune cell infiltration showed significant difference between the two groups, as did the expression of immune checkpoints.

Conclusion

The IRGs signature could act as a biomarker and provide a momentous reference for individual therapy of TNBC.

Bioactive C21 Steroidal Glycosides from Euphorbia kansui Promoted HepG2 Cell Apoptosis via the Degradation of ATP1A1 and Inhibited Macrophage Polarization under Co-Cultivation

Euphorbia kansui is clinically used for the treatment of esophageal cancer, lung cancer, cancerous melanoma, asthma, pleural disorders, ascites, and pertussis, among other conditions. In this study, 12 steroids were obtained and identified from E. kansui, and cynsaccatol L (5), which showed the best effects in terms of inhibiting the proliferation of HepG2 cells and the immune regulation of macrophages. Furthermore, 5 induced typical apoptotic characteristics in HepG2 cells, such as morphological changes and the caspase cascade, as well as inducing autophagy-dependent apoptosis via mitochondrial dysfunction and reactive oxygen species (ROS) accumulation. The antitumor mechanism of 5 might be related to promoting the endocytosis and degradation of ATP1A1 protein and then down-regulating the downstream AKT and ERK signaling pathways. Furthermore, the antiproliferation effect of 5 in co-cultivation with macrophages was investigated, which showed that 5 promoted the apoptosis of HepG2 cells by modulating the release of inflammatory cytokines, such as TNF-α and IFN-γ; regulating the M2-subtype polarization of macrophages; promoting the phagocytosis of macrophages. In conclusion, 5 exerted anti-proliferative effects by promoting the degradation of ATP1A1 and inhibiting the ATP1A1-AKT/ERK signaling pathway in HepG2. Furthermore, it regulated macrophage function in co-cultivation, thereby further exerting adjuvant anti-HepG2 activity.

Single-cell transcriptome profiling of the stepwise progression of head and neck cancer

Head and neck squamous cell carcinoma (HNSCC) undergoes stepwise progression from normal tissues to precancerous leukoplakia, primary HNSCC, and metastasized tumors. To delineate the heterogeneity of tumor cells and their interactions during the progression of HNSCC, we employ single-cell RNA-seq profiling for normal to metastasized tumors. We can identify the carcinoma in situ cells in leukoplakia lesions that are not detected by pathological examination. In addition, we identify the cell type subsets of the Galectin 7B (LGALS7B)-expressing malignant cells and CXCL8-expressing fibroblasts, demonstrating that their abundance in tumor tissue is associated with unfavorable prognostic outcomes. We also demonstrate the interdependent ligand-receptor interaction of COL1A1 and CD44 between fibroblasts and malignant cells, facilitating HNSCC progression. Furthermore, we report that the regulatory T cells in leukoplakia and HNSCC tissues express LAIR2, providing a favorable environment for tumor growth. Taken together, our results update the pathobiological insights into cell-cell interactions during the stepwise progression of HNSCCs.

Trimethylamine-N-oxide (TMAO) mediates the crosstalk between the gut microbiota and hepatic vascular niche to alleviate liver fibrosis in nonalcoholic steatohepatitis

Liver fibrosis is one main histological characteristic of nonalcoholic steatohepatitis (NASH), a disease paralleling a worldwide surge in metabolic syndromes with no approved therapies. The role of the gut microbiota in NASH pathogenesis has not been thoroughly illustrated, especially how the gut microbiota derives metabolites to influence the distal liver in NASH. Here, we performed 16S rDNA amplicon sequencing analysis of feces from a mouse NASH model induced by a Western diet and CCl4 injury and found genera under Streptococcaceae, Alcaligenaceae, Oscillibacter, and Pseudochrobactrum, which are related metabolites of TMAO. Injection of the gut microbial metabolite TMAO reduced the progression of liver fibrosis in the mouse NASH model. Further analysis revealed that the anti-fibrotic TMAO normalized gut microbiota diversity and preserved liver sinusoidal endothelial cell integrity by inhibiting endothelial beta 1-subunit of Na (+), K (+)-ATPase (ATP1B1) expression. Collectively, our findings suggest TMAO-mediated crosstalk between microbiota metabolites and hepatic vasculature, and perturbation of this crosstalk disrupts sinusoidal vasculature to promote liver fibrosis in NASH.

Genomic Analyses for Selective Signatures and Genes Involved in Hot Adaptation Among Indigenous Chickens From Different Tropical Climate Regions

Climate change, especially weather extremes like extreme cold or extreme hot, is a major challenge for global livestock. One of the animal breeding goals for sustainable livestock production should be to breed animals with excellent climate adaptability. Indigenous livestock and poultry are well adapted to the local climate, and they are good resources to study the genetic footprints and mechanism of the resilience to weather extremes. In order to identify selection signatures and genes that might be involved in hot adaptation in indigenous chickens from different tropical climates, we conducted a genomic analysis of 65 indigenous chickens that inhabit different climates. Several important unique positively selected genes (PSGs) were identified for each local chicken group by the cross-population extended haplotype homozygosity (XP-EHH). These PSGs, verified by composite likelihood ratio, genetic differentiation index, nucleotide diversity, Tajima’s D, and decorrelated composite of multiple signals, are related to nerve regulation, vascular function, immune function, lipid metabolism, kidney development, and function, which are involved in thermoregulation and hot adaptation. However, one common PSG was detected for all three tropical groups of chickens via XP-EHH but was not confirmed by other five types of selective sweep analyses. These results suggest that the hot adaptability of indigenous chickens from different tropical climate regions has evolved in parallel by taking different pathways with different sets of genes. The results from our study have provided reasonable explanations and insights for the rapid adaptation of chickens to diverse tropical climates and provide practical values for poultry breeding.

Na+/K+ ATPase α1 and β3 subunits are localized to the basolateral membrane of trophectoderm cells in human blastocysts

STUDY QUESTION

Is there a relation between specific Na+/K+ ATPase isoform expression and localization in human blastocysts and the developmental behavior of the embryo?

SUMMARY ANSWER

Na+/K+ ATPase α1, β1 and β3 are the main isoforms expressed in human blastocysts and no association was found between the expression level of their respective mRNAs and the rate of blastocyst expansion.

WHAT IS KNOWN ALREADY

In mouse embryos, Na+/K+ ATPase α1 and β1 are expressed in the basolateral membrane of trophectoderm (TE) cells and are believed to be involved in blastocoel formation (cavitation).

STUDY DESIGN, SIZE, DURATION

A total of 20 surplus embryos from 11 patients who underwent IVF and embryo transfer at a university hospital between 2009 and 2018 were analyzed.

PARTICIPANTS/MATERIALS, SETTING, METHODS

After freezing and thawing Day 5 human blastocysts, their developmental behavior was observed for 24 h using time-lapse imaging, and the expression of Na+/K+ ATPase isoforms was examined using quantitative RT-PCR (RT-qPCR). The expressed isoforms were then localized in blastocysts using fluorescent immunostaining.

MAIN RESULTS AND THE ROLE OF CHANCE

RT-qPCR results demonstrated the expression of Na+/K+ ATPase α1, β1 and β3 isoforms in human blastocysts. Isoforms α1 and β3 were localized to the basolateral membrane of TE cells, and β1 was localized between TE cells. A high level of β3 mRNA expression correlated with easier hatching (P = 0.0261).

LARGE SCALE DATA

N/A.

LIMITATIONS, REASONS FOR CAUTION

The expression of mRNA and the localization of proteins of interest were verified, but we have not been able to perform functional analysis.

WIDER IMPLICATIONS OF THE FINDINGS

Of the various Na+/K+ ATPase isoforms, expression levels of the α1, β1 and β3 mRNAs were clearly higher than other isoforms in human blastocysts. Since α1 and β3 were localized to the basolateral membrane via fluorescent immunostaining, we believe that these subunits contribute to the dilation of the blastocoel. The β1 isoform is localized between TE cells and may be involved in tight junction formation, as previously reported in mouse embryos.

STUDY FUNDING/COMPETING INTEREST(S)

This work was supported by the JSPS KAKENHI (https://www.jsps.go.jp/english/index.html), grant number 17K11215. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. The authors have no conflicts of interest.

Regulatory effect of insulin on the structure, function and metabolism of Na+/K+-ATPase (Review)

Na+/K+-ATPase is an ancient enzyme, the role of which is to maintain Na+ and K+ gradients across cell membranes, thus preserving intracellular ion homeostasis. The regulation of Na+/K+-ATPase is affected by several regulatory factors through a number of pathways, with hormones serving important short-term and long-term regulatory functions. Na+/K+-ATPase can also be degraded through activation of the ubiquitin proteasome and autophagy-lysosomal pathways, thereby affecting its abundance and enzymatic activity. As regards the regulatory effect of insulin, it has been found to upregulate the relative abundance of Na+/K+-ATPase and restore the transport efficiency in multiple in vitro and in vivo experiments. Therefore, elucidating the role of insulin in the regulation Na+/K+-ATPase may help uncover new drug targets for the treatment of related diseases. The aim of the present study was to review the structure and function of Na+/K+-ATPase and to discuss the possible mechanisms through which it may be regulated by insulin, in order to investigate the possibility of designing new therapies for related diseases.