The emerging role of XBP1 in cancer

Integrated analysis of single‑cell and bulk RNA sequencing data to construct a risk assessment model based on plasma cell immune‑related genes for predicting patient prognosis and therapeutic response in lung adenocarcinoma

Plasma cells serve a crucial role in the human immune system and are important in tumor progression. However, the specific role of plasma cell immune-related genes (PCIGs) in tumor progression remains unclear. Therefore, the present study aimed to establish a risk assessment model for patients with lung adenocarcinoma (LUAD) based on PCIGs. The data used in the present study were obtained from The Cancer Genome Atlas and the Gene Expression Omnibus databases. After identifying nine PCIGs, a risk assessment model was constructed and a nomogram was developed for predicting patient prognosis. To explore the molecular mechanism and clinical significance, gene set enrichment analysis (GSEA), tumor mutational burden (TMB) analysis, tumor microenvironment (TME) analysis and drug sensitivity prediction were performed. Furthermore, the accuracy of the model was validated using reverse transcription-quantitative PCR (RT-qPCR). The present study constructed a risk assessment model consisting of nine PCIGs. Kaplan-Meier survival curves indicated a worse prognosis in the high-risk subgroup (risk score ≥0.982) compared with that in the low-risk subgroup. The nomogram exhibited predictive value for survival prediction (area under the curve=0.727). GSEA enrichment analysis revealed enrichment of the focal adhesion and extracellular matrix-receptor interaction pathways in the high-risk group. Moreover, the high-risk group exhibited a higher TMB, as demonstrated by the TME analysis showing lower ESTIMATE scores. Drug sensitivity prediction facilitated potential drug selection. Subsequently, differential gene expression was validated in multiple LUAD cell lines using RT-qPCR. In conclusion, the risk assessment model based on nine PCIGs may be used to predict the prognosis and drug selection in patients with LUAD.

GOReverseLookup: A gene ontology reverse lookup tool

BACKGROUND AND OBJECTIVE

The Gene Ontology (GO) project has been pivotal in providing a structured framework for characterizing genes and annotating them to specific biological concepts. While traditional gene annotation primarily focuses on mapping genes to GO terms, descriptors of biological concepts, there is a growing need for tools facilitating reverse querying. This paper introduces GOReverseLookup, a novel tool designed to identify over- or underrepresented genes in researcher-defined states of interest (phenotypes), described by sets of GO terms. GOReverseLookup supplements the existing power of Gene Ontology by the possibility of orthologous gene querying across several databases, such as Ensembl and UniProtKB. This combination allows for a more nuanced identification of significant genes across a range of cross-species research contexts.

METHODS

GOReverseLookup queries genes associated with input GO terms. Bundles of GO terms encapsulate user-defined states of interest, e.g., angiogenesis. In the second stage of the analysis, all GO terms associated with each gene are fetched, and finally, the statistical relevance of the genes being involved in one (or all) of the defined states of interests is computed.

RESULTS

The two presented use cases illustrate its utility in discovering genes related to rheumatoid arthritis and genes linked with chronic inflammation and tumorigenesis. In both cases, GOReverseLookup discovered a substantial number of genes significantly associated with the aforementioned states of interest.

CONCLUSIONS

GOReverseLookup proves to be a valuable resource for unraveling the genetic basis of phenotypes, with diverse practical potentials in functional genomics, systems biology, and drug discovery. We anticipate that GOReverseLookup will significantly aid in identifying potential gene targets during the initial research phases.

Endoplasmic reticulum stress and unfolded protein response: Roles in skeletal muscle atrophy

Skeletal muscle atrophy is commonly present in various pathological states, posing a huge burden on society and patients. Increased protein hydrolysis, decreased protein synthesis, inflammatory response, oxidative stress, mitochondrial dysfunction, endoplasmic reticulum stress (ERS) and unfolded protein response (UPR) are all important molecular mechanisms involved in the occurrence and development of skeletal muscle atrophy. The potential mechanisms of ERS and UPR in skeletal muscle atrophy are extremely complex and have not yet been fully elucidated. This article elucidates the molecular mechanisms of ERS and UPR, and discusses their effects on different types of muscle atrophy (muscle atrophy caused by disuse, cachexia, chronic kidney disease (CKD), diabetes mellitus (DM), amyotrophic lateral sclerosis (ALS), spinal muscular atrophy (SMA), spinal and bulbar muscular atrophy (SBMA), aging, sarcopenia, obesity, and starvation), and explores the preventive and therapeutic strategies targeting ERS and UPR in skeletal muscle atrophy, including inhibitor therapy and drug therapy. This review aims to emphasize the importance of endoplasmic reticulum (ER) in maintaining skeletal muscle homeostasis, which helps us further understand the molecular mechanisms of skeletal muscle atrophy and provides new ideas and insights for the development of effective therapeutic drugs and preventive measures for skeletal muscle atrophy.

Single-cell sequencing reveals the role of aggrephagy-related patterns in tumor microenvironment, prognosis and immunotherapy in endometrial cancer

Background

As a type of autophagy, aggrephagy degrades the aggregation of misfolded protein in cells and plays an important role in key genetic events for various cancers. However, aggrephagy functions within the tumor microenvironment (TME) in endometrial cancer (EC) remain to be elucidated.

Methods

A total of 36,227 single cells from single-cell RNA-seq data derived from five EC tumor samples were comprehensively analyzed using a nonnegative matrix factorization (NMF) algorithm for 44 aggrephagy-related genes. Bulk RNA-seq cohorts from public repositories were utilized to assess the prognostic value of aggrephagy-related TME clusters and predict immune checkpoint blockade immunotherapeutic response in EC.

Results

Fibroblasts, macrophages, CD8+T cells, and lymphatic endothelial cells were categorized into two to five aggrephagy-related subclusters, respectively. CellChat analysis showed that the aggrephagy-related subtypes of TME cells exhibited extensive interactions with tumor epithelial cells, particularly for macrophages. Moreover, aggrephagy regulators may be significantly associated with the pseudotime trajectories of major TME cell types as well as the clinical and biological features of EC. Bulk-seq analysis showed that these aggrephagy-related subclusters had significant predictive value for the survival and immune checkpoint blockade response in EC patients. Notably, immunohistochemical staining results manifested that the TUBA1A+ macrophage subtype was linked to less lymph node metastasis and longer survival, which were consistent with the bioinformatics analysis findings.

Conclusions

This study provided a novel view of aggrephagy signaling in the EC tumor microenvironment, and intervention of aggrephagy was expected to improve the survival rate of EC patients.

Tumor Cell-Expressed Herpesvirus Entry Mediator Regulates Proliferation and Adaptive Immunity in Ovarian Cancer

BACKGROUND

Ovarian cancer (OvCa) is a prevalent gynecological malignancy with an increasing incidence and high mortality rate. Although the role of the herpesvirus entry mediator (HVEM), encoded by the TNFRSF14 gene, is currently considered pivotal in various types of cancer, the regulation of tumor cell-expressed HVEM in OvCa remains inadequately understood.

METHODS

Specimens were used to detect HVEM expression via quantitative RT-PCR and flow cytometry. The proliferation of the murine OvCa cell line ID8 was determined using the Cell Counting Kit-8, colony formation, and EdU staining assays. The immune constituents within the ascites fluid and spleen of tumor-bearing mice were analyzed by flow cytometry. Bioinformatics analysis was performed to explore cytokines, chemokines, and signaling pathways regulated by HVEM, and differential expression levels were confirmed via quantitative RT-PCR and western blot analysis.

RESULTS

Herein, we identified a significant upregulation of HVEM in OvCa tissues compared with that in benign tissues and observed dominant expression of HVEM in CD45⁻EpCAM⁺ subsets in OvCa specimens. Tumor cell-expressed HVEM was found to promote OvCa cell proliferation by partly activating spliced X-box-binding protein 1 (XBP1s)-c-Myc signaling. In mouse models, knockdown of Tnfrsf14 in ID8 cells alleviated OvCa progression and specifically affected the frequency and function of T cells in the ascites fluid and spleen. In addition, tumor cell-expressed HVEM altered chemokine expression (CXCL1/9/10/11 and CCL2/4/5) and STAT signal activation (STAT5 and STAT6) in ID8 cells.

CONCLUSION

This study investigated the effects of HVEM on OvCa and validated its potential as a therapeutic marker for treating OvCa.

A probabilistic modeling framework for genomic networks incorporating sample heterogeneity

Probabilistic graphical models are powerful tools to quantify, visualize, and interpret network dependencies in complex biological systems such as high-throughput -omics. However, many graphical models assume sample homogeneity, limiting their effectiveness. We propose a flexible Bayesian approach called graphical regression (GraphR), which (1) incorporates sample heterogeneity at different scales through a regression-based formulation, (2) enables sparse sample-specific network estimation, (3) identifies and quantifies potential effects of heterogeneity on network structures, and (4) achieves computational efficiency via variational Bayes algorithms. We illustrate the comparative efficiency of GraphR against existing state-of-the-art methods in terms of network structure recovery and computational cost across multiple settings. We use GraphR to analyze three multi-omic and spatial transcriptomic datasets to investigate inter- and intra-sample molecular networks and delineate biological discoveries that otherwise cannot be revealed by existing approaches. We have developed a GraphR R package along with an accompanying Shiny App that provides comprehensive analysis and dynamic visualization functions.

Cellular EMT-status governs contact guidance in an electrospun TACS-mimicking in vitro model

In this study, an advanced nanofiber breast cancer in vitro model was developed and systematically characterized including physico-chemical, cell-biological and biophysical parameters. Using electrospinning, the architecture of tumor-associated collagen signatures (TACS5 and TACS6) was mimicked. By employing a rotating cylinder or static plate collector set-up, aligned fibers (TACS5-like structures) and randomly orientated fibers (TACS6-like structures) fibers were produced, respectively. The biocompatibility of these fibers was enhanced by collagen coating, ensuring minimal toxicity and improved cell attachment. Various breast cancer cell lines (MCF7, HCC1954, MDA-MB-468, and MDA-MB-231) were cultured on these fibers to assess epithelial-to-mesenchymal transition (EMT) markers, cellular morphology, and migration. Aligned fibers (TACS5) significantly influenced EMT-related changes, promoting cellular alignment, spindle-shaped morphology and a highly migratory phenotype in mesenchymal and hybrid EMT cells (MDA-MB-468, MDA-MB-231). Conversely, epithelial cells (MCF7, HCC1954) showed limited response, but - under growth factor treatment - started to infiltrate the fibrous scaffold and underwent EMT-like changes, particularly on TACS5-mimicks, emphasizing the interplay of topographical cues and EMT induction. The biophysical analysis revealed a clear correlation between cellular EMT status and cell mechanics, with increased EMT correlating to decreased total cellular stiffness. Cancer cell mechanics, however, were found to be dynamic during biochemical and topographical EMT-induction, exceeding initial stiffness by up to 2-fold. These findings highlight the potential of TACS5-like nanofiber scaffolds in modeling the tumor microenvironment and studying cancer cell behavior and mechanics.

Direct inhibition of tumor hypoxia response with synthetic transcriptional repressors

Many oncogenic transcription factors (TFs) are considered to be undruggable because of their reliance on large protein-protein and protein-DNA interfaces. TFs such as hypoxia-inducible factors (HIFs) and X-box-binding protein 1 (XBP1) are induced by hypoxia and other stressors in solid tumors and bind to unfolded protein response element (UPRE) and hypoxia-induced response element (HRE) motifs to control oncogenic gene programs. Here, we report a strategy to create synthetic transcriptional repressors (STRs) that mimic the basic leucine zipper domain of XBP1 and recognize UPRE and HRE motifs. A lead molecule, STR22, binds UPRE and HRE DNA sequences with high fidelity and competes with both TFs in cells. Under hypoxia, STR22 globally suppresses HIF1α binding to HRE-containing promoters and enhancers, inhibits hypoxia-induced gene expression and blocks protumorigenic phenotypes in triple-negative breast cancer (TNBC) cells. In vivo, intratumoral and systemic STR22 treatment inhibited hypoxia-dependent gene expression, primary tumor growth and metastasis of TNBC tumors. These data validate a novel strategy to target the tumor hypoxia response through coordinated inhibition of TF-DNA binding.

Yes-associated protein plays oncogenic roles in human sporadic colorectal adenomas

The role of Hippo-Yes-associated protein (YAP) in human colorectal cancer (CRC) presents contradictory results. We examined the function of YAP in the early stages of CRC by quantitatively measuring the expression of phospho-YAPS127 (p-YAP) and five APC-related proteins in 145 sporadic adenomas from the Tennessee Colorectal Polyp Study, conducting APC sequencing for 114 adenomas, and analyzing YAP-correlated cancer pathways using gene expression data from 326 adenomas obtained from Gene Expression Omnibus. The p-YAP expression was significantly correlated with YAP expression (r = 0.53, P < .0001) and nuclear β-catenin (r = 0.26, P = .0018) in adenoma tissues. Both p-YAP and nuclear β-catenin were associated with APC mutations (P = .05). A strong association was observed between p-YAP overexpression and advanced adenoma odds (OR = 12.62, 95% CI = 4.57-34.86, P trend < .001), which persisted after adjusting for covariates and biomarkers (OR = 12.31, 95% CI = 3.78-40.10, P trend < .0001). P-YAP exhibited a sensitivity of 77.4% and specificity of 78.2% in defining advanced versus nonadvanced adenomas. Additionally, synergistic interaction was noted between p-YAP positivity and nuclear β-catenin on advanced adenomas (OR = 16.82, 95% CI = 4.41-64.08, P < .0001). YAP-correlated genes were significantly enriched in autophagy, unfolded protein response, and sirtuin pathways showing predominantly pro-tumorigenic alterations. Collectively, YAP plays an oncogenic role in interacting with Wnt as well as other cancer pathways within human sporadic adenomas. P-YAP could be a potential biomarker for human high-risk sporadic adenomas.

The Dual Role of Survival Genes in Neurons and Cancer Cells: a Strategic Clinical Application of DX2 in Neurodegenerative Diseases and Cancer

In cancer cells, survival genes contribute to uncontrolled growth and the survival of malignant cells, leading to tumor progression. Neurons are post-mitotic cells, fully differentiated and non-dividing after neurogenesis and survival genes are essential for cellular longevity and proper functioning of the nervous system. This review explores recent research findings regarding the role of survival genes, particularly DX2, in degenerative neuronal tissue cells and cancer cells. Survival gene DX2, an exon 2-deleted splice variant of AIMP2 (aminoacyl-tRNA synthetase-interacting multi-functional protein 2), was found to be overexpressed in various cancer types. The potential of DX2 inhibitors as an anti-cancer drug arises from its unique ability to interact with various oncoproteins, such as KRAS and HSP70. Meanwhile, AIMP2 has been reported as a multifunctional cell death-inducing gene, and survival gene DX2 directly and indirectly inhibits AIMP2-induced cell death. DX2 plays multifaceted survival roles in degenerating neurons via various signaling pathways, including PARP 1, TRAF2, and p53 pathways. It is noteworthy that genes that were previously classified as oncogenes, such as AKT and XBP1, are now being considered as curative transgenes for targeting neurodegenerative diseases. A strategic direction for clinical application of survival genes in neurodegenerative disease and in cancer is justified.

ALKBH5-Mediated m6A Modification of XBP1 Facilitates NSCLC Progression Through the IL-6-JAK-STAT3 Pathway

The X-box-binding protein 1 (XBP1) is an important transcription factor during endoplasmic reticulum stress response, which was reported as an oncogene in non-small cell lung cancer (NSCLC) tumorigenesis and development. However, the regulatory mechanism of XBP1 expression in NSCLC progression was less reported. N6-methyladenosine (m6A) RNA modification is an emerging epigenetic regulatory mechanism for gene expression. This study aimed to investigate the regulatory role of the m6A modification in XBP1 expression in NSCLC. We identified XBP1 as a downstream target of ALKBH5-mediated m6A modification in A549 and PC9 cells. Knockdown of ALKBH5 increased the m6A modification and the stability of XBP1 mRNA, while overexpression of ALKBH5 had the opposite effect. Furthermore, IGF2BP3 was confirmed to be a reader of XBP1 m6A methylation and to enhance the stability of XBP1 mRNA. Additionally, IGF2BP3 knockdown significantly reversed the increase in XBP1 stability mediated by ALKBH5 depletion. In vivo and in vitro experiments demonstrated that ALKBH5/IGF2BP3 promotes the proliferation, migration, and invasion of NSCLC cells by upregulating XBP1 expression. In addition, we also showed that XBP1 promoted NSCLC cell proliferation, migration, and invasion by activating IL-6-JAK-STAT3 signaling. Our research suggested that ALKBH5-mediated m6A modification of XBP1 facilitates NSCLC progression through the IL-6-JAK-STAT3 pathway.

Roles of X-box binding protein 1 in liver pathogenesis

The prevalence of drug-induced liver injury (DILI) and viral liver infections presents significant challenges in modern healthcare and contributes to considerable morbidity and mortality worldwide. Concurrently, metabolic dysfunctionassociated steatotic liver disease (MASLD) has emerged as a major public health concern, reflecting the increasing rates of obesity and leading to more severe complications such as fibrosis and hepatocellular carcinoma. X-box binding protein 1 (XBP1) is a distinct transcription factor with a basic-region leucine zipper structure, whose activity is regulated by alternative splicing in response to disruptions in endoplasmic reticulum (ER) homeostasis and the unfolded protein response (UPR) activation. XBP1 interacts with a key signaling component of the highly conserved UPR and is critical in determining cell fate when responding to ER stress in liver diseases. This review aims to elucidate the emerging roles and molecular mechanisms of XBP1 in liver pathogenesis, focusing on its involvement in DILI, viral liver infections, MASLD, fibrosis/cirrhosis, and liver cancer. Understanding the multifaceted functions of XBP1 in these liver diseases offers insights into potential therapeutic strategies to restore ER homeostasis and mitigate liver damage.

Expression quantitative trait loci influence DNA damage-induced apoptosis in cancer

BACKGROUND

Genomic instability and evading apoptosis are two fundamental hallmarks of cancer and closely linked to DNA damage response (DDR). By analyzing expression quantitative trait loci (eQTL) upon cell stimulation (called exposure eQTL (e2QTL)) it is possible to identify context specific gene regulatory variants and connect them to oncological diseases based on genome-wide association studies (GWAS).

RESULTS

We isolate CD8+ T cells from 461 healthy donors and stimulate them with high doses of 5 different carcinogens to identify regulatory mechanisms of DNA damage-induced apoptosis. Across all stimuli, we find 5,373 genes to be differentially expressed, with 85% to 99% of these genes being suppressed. While upregulated genes are specific to distinct stimuli, downregulated genes are shared across conditions but exhibit enrichment in biological processes depending on the DNA damage type. Analysis of eQTL reveals 654 regulated genes across conditions. Among them, 47 genes are significant e2QTL, representing a fraction of 4% to 5% per stimulus. To unveil disease relevant genetic variants, we compare eQTL and e2QTL with GWAS risk variants. We identify gene regulatory variants for KLF2, PIP4K2A, GPR160, RPS18, ARL17B and XBP1 that represent risk variants for oncological diseases.

CONCLUSION

Our study highlights the relevance of gene regulatory variants influencing DNA damage-induced apoptosis in cancer. The results provide new insights in cellular mechanisms and corresponding genes contributing to inter-individual effects in cancer development.

Integrative pan-cancer analysis reveals a common architecture of dysregulated transcriptional networks characterized by loss of enhancer methylation

Aberrant DNA methylation contributes to gene expression deregulation in cancer. However, these alterations' precise regulatory role and clinical implications are still not fully understood. In this study, we performed expression-methylation Quantitative Trait Loci (emQTL) analysis to identify deregulated cancer-driving transcriptional networks linked to CpG demethylation pan-cancer. By analyzing 33 cancer types from The Cancer Genome Atlas, we identified and confirmed significant correlations between CpG methylation and gene expression (emQTL) in cis and trans, both across and within cancer types. Bipartite network analysis of the emQTL revealed groups of CpGs and genes related to important biological processes involved in carcinogenesis including proliferation, metabolism and hormone-signaling. These bipartite communities were characterized by loss of enhancer methylation in specific transcription factor binding regions (TFBRs) and the CpGs were topologically linked to upregulated genes through chromatin loops. Penalized Cox regression analysis showed a significant prognostic impact of the pan-cancer emQTL in many cancer types. Taken together, our integrative pan-cancer analysis reveals a common architecture where hallmark cancer-driving functions are affected by the loss of enhancer methylation and may be epigenetically regulated.

Origins and molecular effects of hypoxia in cancer

Hypoxia (insufficient O2) is a pivotal factor in cancer progression, triggering genetic, transcriptional, translational and epigenetic adaptations associated to therapy resistance, metastasis and patient mortality. In this review, we outline the microenvironmental origins and molecular mechanisms responsible for hypoxic cancer cell adaptations in situ and in vitro, whilst outlining current approaches to stratify, quantify and therapeutically target hypoxia in the context of precision oncology.

Elucidation of the role of XBP1 in the progression of complete hydatidiform mole to invasive mole through RNA-seq

OBJECTIVE

A complete hydatidiform mole (CHM) is a common disease and is known to develop post-molar gestational trophoblast neoplasia (GTN). However, the molecular mechanisms underlying the progression of CHM to post-molar GTN remain largely unknown. In this study, we investigated the molecular factors associated with the progression using RNA-seq.

METHODS

We included 13 patients with CHM and performed RNA-seq using freshly frozen samples. We identified differentially expressed genes between patients who developed GTN (GTN group) and those who achieved spontaneous remission after uterine evacuation (SR group), and performed pathway analysis. Then, functional analyses were performed on choriocarcinoma (JAR and JEG-3) and CHM (Hmol1-3B and Hmol1-2C) cells. Moreover, we evaluated the in vivo tumorigenicity of XBP1-overexpressed Hmol1-3B cells.

RESULTS

The gene expression profiles were separated into two groups, and an upstream regulator analysis was performed using 281 differentially expressed genes. We focused on transcription factors and identified that 33 transcription factors were activated in the GTN group. Then, excluding those with low expression levels in clinical samples and cell lines, XBP1 was selected for further analysis. Additionally, XBP1 downregulation significantly decreased the migration and invasive abilities of choriocarcinoma cells, whereas XBP1 overexpression significantly increased the migration and invasive abilities of CHM cells. Furthermore, animal experiments showed that tumor weight and blood human chorionic gonadotropin (hCG) levels were significantly higher in the XBP1-overexpressing Hmol1-3B-bearing mice than those in the control mice.

CONCLUSION

RNA-seq identified XBP1 as a key factor in post-molar GTN, suggesting it contributes to the development of post-molar GTN.

The genetic architecture of protein interaction affinity and specificity

The encoding and evolution of specificity and affinity in protein-protein interactions is poorly understood. Here, we address this question by quantifying how all mutations in one protein, JUN, alter binding to all other members of a protein family, the 54 human basic leucine zipper transcription factors. We fit a global thermodynamic model to the data to reveal that most affinity changing mutations equally affect JUN's affinity to all its interaction partners. Mutations that alter binding specificity are relatively rare but distributed throughout the interaction interface. Specificity is determined both by features that promote on-target interactions and by those that prevent off-target interactions. Approximately half of the specificity-defining residues in JUN contribute both to promoting on-target binding and preventing off-target binding. Nearly all specificity-altering mutations in the interaction interface are pleiotropic, also altering affinity to all partners. In contrast, mutations outside the interface can tune global affinity without affecting specificity. Our results reveal the distributed encoding of specificity and affinity in an interaction interface and how coiled-coils provide an elegant solution to the challenge of optimizing both specificity and affinity in a large protein family.

Multiple cell-death patterns predict the prognosis and drug sensitivity of melanoma patients

Background

Melanoma, a malignant tumor of the skin, presents challenges in its treatment process involving modalities such as surgery, chemotherapy, and targeted therapy. However, there is a need for an ideal model to assess prognosis and drug sensitivity. Programmed cell death (PCD) modes play a crucial role in tumor progression and has the potential to serve as prognostic and drug sensitivity indicators for melanoma.

Methods

We analyzed 13 PCD modes including apoptosis, necroptosis, ferroptosis, pyroptosis, netotic cell death, entotic cell death, lysosome-dependent cell death, parthanatos, autophagy-dependent cell death, oxeiptosis, disulfidptosis, and alkaliptosis. These modes were used to construct a model that incorporated genes related to these 13 PCD modes to establish a cell death index (CDI) to conduct prognosis analysis. Transcriptomic, genomic, and clinical data were collected from cohorts including TCGA-SKCM, GSE19234, and GSE65904 to validate this model.

Results

A CDI consisting of ten gene signatures was established using machine learning algorithms and divided into two groups based on CDI values. The high CDI group exhibited relatively lower numbers of immune-infiltrating cells and showed resistance to commonly used drugs such as docetaxel and axitinib. Our validation results demonstrated good discrimination in PCA analysis between CDI groups, and melanoma patients with higher CDI values had worse postoperative prognoses (all p < 0.01).

Conclusion

The CDI model, incorporating multiple PCD modes, accurately predicts the clinical prognosis and drug sensitivity of melanoma patients.

XBP1 Facilitating NF-κB-p65 Nuclear Translocation Promotes Macrophage-Originated Sterile Inflammation Via Regulating MT2 Transcription in the Ischemia/Reperfusion Liver

BACKGROUND & AIMS

XBP1, most conserved transcription factor of endoplasmic reticulum stress, plays important roles in physiological and pathologic settings and has profound effects on disease progression and prognosis, so it is necessary to investigate XBP1 in macrophage-originated sterile inflammation during liver ischemia/reperfusion injury (IRI). Macrophage XBP1 expression and liver injury are analyzed in patients undergoing ischemia-related hepatectomy.

METHODS

A myeloid-specific male XBP1-knockout (XBP1M-KO) strain is created for function and mechanism of XBP1 on macrophage-derived sterile inflammation in murine liver IRI with in vitro parallel research. Macrophages cocultured with hypoxia-treated hepatocytes are applied to investigate impact of XBP1 in vitro, with analysis of RNA sequencing and databases.

RESULTS

Clinically, macrophage XBP1 expression significantly increases in ischemic liver tissues and positively correlates with liver injury after hepatectomy. Less hepatocellular damage is presented in XBP1M-KO mice than in XBP1-proficient (XBP1FL/FL) control animals. In vitro, XBP1 deficiency inhibits sterile inflammation and migration in macrophages cocultured with hypoxia-treated hepatocytes. Analysis of RNA sequencing and databases determines Metallothionein 2 (MT2) as XBP1 target gene, negatively regulated by binding with its promoter. XBP1 deficiency increases MT2 and IKBα expression, but inhibits nuclear factor-κB-p65 phosphorylation, markedly neutralizing XBP1M-KO-related benefits by promoting sterile inflammation during liver IRI.

CONCLUSIONS

XBP1 promotes macrophage-originated sterile inflammation, increases liver IRI by binding to MT2 promoter, and regulates MT2/nuclear factor-κB pathway, potentially therapeutic for clinical liver IRI.

Targeting the Ferroptosis and Endoplasmic Reticulum Stress Signaling Pathways by CBX7 in Myocardial Ischemia/reperfusion Injury

Ferroptosis and endoplasmic reticulum stress (ERS) are common events in the process of myocardial ischemia/reperfusion injury (IRI). The suppression of chromobox7 (CBX7) has been reported to protect against ischemia/reperfusion injury, This research is purposed to expose the impacts and mechanism of CBX7 in myocardial IRI. CBX7 expression was detected using RT-qPCR and western blotting analysis. CCK-8 assay detected cell viability. Inflammatory response and oxidative stress were detected by ELISA, DCFH-DA probe and related assay kits. Flow cytometry analysis and caspase3 activity assay were used to detect cell apoptosis. C11-BODIPY 581/591 staining and ferro-orange staining were used to detect lipid reactive oxygen species (ROS) and Fe2+ level, respectively. Western blotting was used to detect the expression of proteins associated with apoptosis, ferroptosis and ERS. In the hypoxia/reoxygenation (H/R) model of rat cardiomyocytes H9c2, CBX7 was highly expressed. CBX7 interference significantly protected against inflammatory response, oxidative stress, apoptosis, ferroptosis and ERS induced by H/R in H9c2 cells. Moreover, after the pretreatment with ferroptosis activator erastin or ERS agonist Tunicamycin (TM), the protective effects of CBX7 knockdown on the inflammation, oxidative stress and apoptosis in H/R-induced H9c2 cells was partially abolished. To summarize, CBX7 down-regulation may exert anti-ferroptosis and anti-ERS activities to alleviate H/R-stimulated myocardial injury.

Longitudinal multiomics analysis of aggressive pituitary neuroendocrine tumors: comparing primary and recurrent tumors from the same patient, reveals genomic stability and heterogeneous transcriptomic profiles with alterations in metabolic pathways

Pituitary neuroendocrine tumors (PitNET) represent the vast majority of sellar masses. Some behave aggressively, growing rapidly and invading surrounding tissues, with high rates of recurrence and resistance to therapy. Our aim was to establish patterns of genomic, transcriptomic and methylomic evolution throughout time in primary and recurrent tumors from the same patient. Therefore, we performed transcriptome- and exome-sequencing and methylome microarrays of aggressive, primary, and recurrent PitNET from the same patient. Primary and recurrent tumors showed a similar exome profile, potentially indicating a stable genome over time. In contrast, the transcriptome of primary and recurrent PitNET was dissimilar. Gonadotroph, silent corticotroph, as well as metastatic corticotroph and a somatotroph PitNET expressed genes related to fatty acid biosynthesis and metabolism, phosphatidylinositol signaling, glycerophospholipid and phospholipase D signaling, respectively. Diacylglycerol kinase gamma (DGKG), a key enzyme in glycerophospholipid metabolism and phosphatidylinositol signaling pathways, was differentially expressed between primary and recurrent PitNET. These alterations did not seem to be regulated by DNA methylation, but rather by several transcription factors. Molecular docking showed that dasatinib, a small molecule tyrosine kinase inhibitor used in the treatment of chronic lymphocytic and acute lymphoblastic leukemia, could target DGKG. Dasatinib induced apoptosis and decreased proliferation in GH3 cells. Our data indicate that pituitary tumorigenesis could be driven by transcriptomically heterogeneous clones, and we describe alternative pharmacological therapies for aggressive and recurrent PitNET.

Comprehensive mendelian randomization reveals atrial fibrillation-breast cancer relationship and explores common druggable targets

Background

Atrial fibrillation (AF) and breast cancer pose significant risks to human health. The reasons behind the concurrent occurrence of AF and breast cancer remain unclear, leading to complex treatment approaches. Mendelian Randomization (MR) analyses aim to offer genetic evidence supporting the causation of AF and breast cancer and to investigate common druggable genes associated with both conditions.

Methods

We used two-samples of MR to sequentially explore the causal relationship between atrial fibrillation and breast cancer, and between atrial fibrillation and breast cancer therapeutic drugs, and verified the stability of the results through colocalization analysis. We utilized the Connectivity map database to infer the direction of drug effects on disease. Finally, we explored druggable genes that play a role in AF and breast cancer and performed a Phenome-wide MR analysis to analyze the potential side effects of drug targets.

Results

We found 15 breast cancer therapeutic drugs that significantly support a causal association between AF and breast cancer through expression in blood and/or atrial appendage tissue. Among these, activation of ANXA5 by Docetaxel, inhibition of EIF5A by Fulvestrant, and inhibition of GNA12 by Tamoxifen increased the risk of AF, while inhibition of ANXA5 by Gemcitabine and Vinorebine and inhibition of PCGF6 by Paclitaxel reduced the risk of AF. Inhibition of MSH6 and SF3B1 by Cyclophosphamide, as well as inhibition of SMAD4 and PSMD2 and activation of ASAH1 and MLST8 by Doxorubicin can have bidirectional effects on AF occurrence. XBP1 can be used as a common druggable gene for AF and breast cancer, and there are no potential side effects of treatment against this target.

Conclusion

This study did not find a direct disease causality between AF and breast cancer but identified 40 target genes for 15 breast cancer therapeutic drugs associated with AF, clarified the direction of action of 8 breast cancer therapeutic drugs on AF, and finally identified one common druggable target for AF and breast cancer.

Oxidative stress-mediated epigenetic remodeling, metastatic progression and cell signaling in cancer

Cancer is a serious public health issue and cases are rising at a high rate around the world. Altered production of reactive oxygen species (ROS) causes oxidative stress (OS) which plays a vital role in cancer development by disrupting signaling pathways and genomic integrity in the cellular microenvironment. In this study, we reviewed the regulation of noncoding RNAs, histone modifications, and DNA methylation which OS is involved in. These mechanisms promote cancer growth, metastasis, and resistance to chemotherapeutic agents. There is significant potential to improve patient outcomes through the development of customized medications and interventions that precisely address the role of OS in the onset and progression of cancer. Redox-modulating drugs, antioxidant-based therapies, and measures to restore regular cellular activity and OS-modulated signaling pathways are some examples of these strategies. One other hypothesis rationalizes the cancer-suppressing effect of OS, which acts as a two-edged condition that warns against the use of antioxidants for cancer treatment and management. The present study was executed to review the impact of OS on epigenetic machinery, the evolution of metastatic cancer, and how OS mediates cellular signaling. Along with, insights into the potential of targeting OS-mediated mechanisms for cancer therapy.

Unraveling the dual role of ADAM10: Bridging the gap between cancer and Alzheimer's disease

An inverse association between Alzheimer's disease (AD) and cancer has been proposed. Patients with a cancer history have a decreased risk of developing AD, and AD patients have a reduced cancer incidence, which is not seen in vascular dementia patients. Given this association, common molecular and biological mechanisms that could explain this inverse relationship have been proposed before, such as Peptidylprolyl Cis/Trans Isomerase, NIMA-Interacting 1 (Pin1), Wingless and Int-1 (Wnt), and transformation-related protein 53 (p53)-mediated pathways, along with inflammation and oxidative stress-related proteins. A Disintegrin And Metalloprotease 10 (ADAM10) is a protease responsible for the cleavage of key AD- and cancer-related substrates, and it has inverse roles in those diseases: neuroprotective and disease-promoting, respectively. Thus, herein, we review the relevant literature linking AD and cancer and propose how ADAM10 activity might modulate the inverse association between the diseases. Understanding how this protease mediates those two conditions might raise some considerations in the ADAM10 pharmacological modulation for treating AD and cancer.

Endoplasmic reticulum stress responses and epigenetic alterations in arsenic carcinogenesis

Arsenic is a well-known human carcinogen whose environmental exposure via drinking water, food, and air impacts millions of people across the globe. Various mechanisms of arsenic carcinogenesis have been identified, ranging from damage caused by excessive production of free radicals and epigenetic alterations to the generation of cancer stem cells. A growing body of evidence supports the critical involvement of the endoplasmic stress-activated unfolded protein response (UPR) in promoting as well as suppressing cancer development/progression. Various in vitro and in vivo models have also demonstrated that arsenic induces the UPR via activation of the PERK, IRE1α, and ATF6 proteins. In this review, we discuss the mechanisms of arsenic-induced endoplasmic reticulum stress and the role of each UPR pathway in the various cancer types with a focus on the epigenetic regulation and function of the ATF6 protein. The importance of UPR in arsenic carcinogenesis and cancer stem cells is a relatively new area of research that requires additional investigations via various omics-based and computational tools. These approaches will provide interesting insights into the mechanisms of arsenic-induced cancers for prospective target identification and development of novel anti-cancer therapies.

Impact of Obesity-Related Endoplasmic Reticulum Stress on Cancer and Associated Molecular Targets

Obesity, characterized by excessive body fat, is closely linked to endoplasmic reticulum (ER) stress, leading to insulin resistance and type 2 diabetes. Inflammatory pathways like c-Jun N-terminal kinase (JNK) worsen insulin resistance, impacting insulin signaling. Moreover, ER stress plays a substantial role in cancer, influencing tumor cell survival and growth by releasing factors like vascular endothelial growth factor (VEGF). The unfolded protein response (UPR) is pivotal in this process, offering both pro-survival and apoptotic pathways. This review offers an extensive exploration of the sophisticated connection between ER stress provoked by obesity and its role in both the onset and advancement of cancer. It delves into the intricate interplay between oncogenic signaling and the pathways associated with ER stress in individuals who are obese. Furthermore, this review sheds light on potential therapeutic strategies aimed at managing ER stress induced by obesity, with a focus on addressing cancer initiation and progression. The potential to alleviate ER stress through therapeutic interventions, which may encompass the use of small molecules, FDA-approved medications, and gene therapy, holds great promise. A more in-depth examination of pathways such as UPR, ER-associated protein degradation (ERAD), autophagy, and epigenetic regulation has the potential to uncover innovative therapeutic approaches and the identification of predictive biomarkers.

Single-cell analysis reveals landscape of endometrial cancer response to estrogen and identification of early diagnostic markers

BACKGROUND

The development of endometrial cancer (EC) is closely related to the abnormal activation of the estrogen signaling pathway. Effective diagnostic markers are important for the early detection and treatment of EC.

METHOD

We downloaded single-cell RNA sequencing (scRNA-seq) and spatial transcriptome (ST) data of EC from public databases. Enrichment scores were calculated for EC cell subpopulations using the "AddModuleScore" function and the AUCell package, respectively. Six predictive models were constructed, including logistic regression (LR), Gaussian naive Bayes (GaussianNB), k-nearest neighbor (KNN), support vector machine (SVM), extreme gradient boosting (XGB), and neural network (NK). Subsequently, receiver-operating characteristics with areas under the curves (AUCs) were used to assess the robustness of the predictive model.

RESULT

We classified EC cell coaggregation into six cell clusters, of which the epithelial, fibroblast and endothelial cell clusters had higher estrogen signaling pathway activity. We founded the epithelial cell subtype Epi cluster1, the fibroblast cell subtype Fib cluster3, and the endothelial cell subtype Endo cluster3 all showed early activation levels of estrogen response. Based on EC cell subtypes, estrogen-responsive early genes, and genes encoding Stage I and para-cancer differentially expressed proteins in EC patients, a total of 24 early diagnostic markers were identified. The AUCs values of all six classifiers were higher than 0.95, which indicates that the early diagnostic markers we screened have superior robustness across different classification algorithms.

CONCLUSION

Our study elucidates the potential biological mechanism of EC response to estrogen at single-cell resolution, which provides a new direction for early diagnosis of EC.

Population pharmacokinetic model for oral ORIN1001 in Chinese patients with advanced solid tumors

Background: ORIN1001, a first-in-class oral IRE1-α endoribonuclease inhibitor to block the activation of XBP1, is currently in clinical development for inhibiting tumor growth and enhancing the effect of chemical or targeted therapy. Early establishment of a population pharmacokinetic (PopPK) model could characterize the pharmacokinetics (PK) of ORIN1001 and evaluate the effects of individual-specific factors on PK, which will facilitate the future development of this investigational drug. Methods: Non-linear mixed effect model was constructed by Phoenix NLME software, utilizing the information from Chinese patients with advanced solid tumors in a phase I clinical trial (Register No. NCT05154201). Statistically significant PK covariates were screened out by a stepwise process. The final model, after validating by the goodness-of-fit plots, non-parametric bootstrap, visual predictive check and test of normalized prediction distribution errors, was further applied to simulate and evaluate the impact of covariates on ORIN1001 exposure at steady state up to 900 mg per day as a single agent. Results: A two-compartment model with first-order absorption (with lag-time)/elimination was selected as the best structural model. Total bilirubin (TBIL) and lean body weight (LBW) were considered as the statistically significant covariates on clearance (CL/F) of ORIN1001. They were also confirmed to exert clinically significant effects on ORIN1001 steady-state exposure after model simulation. The necessity of dose adjustments based on these two covariates remains to be validated in a larger population. Conclusion: The first PopPK model of ORIN1001 was successfully constructed, which may provide some important references for future research.

Use of Oleuropein and Hydroxytyrosol for Cancer Prevention and Treatment: Considerations about How Bioavailability and Metabolism Impact Their Adoption in Clinical Routine

The fact that the Mediterranean diet could represent a source of natural compounds with cancer-preventive and therapeutic activity has been the object of great interest, especially with regard to the mechanisms of action of polyphenols found in olive oil and olive leaves. Secoiridoid oleuropein (OLE) and its derivative hydroxytyrosol (3,4-dihydroxyphenylethanol, HT) have demonstrated anti-proliferative properties against a variety of tumors and hematological malignancies both in vivo and in vitro, with measurable effects on cellular redox status, metabolism, and transcriptional activity. With this review, we aim to summarize the most up-to-date information on the potential use of OLE and HT for cancer treatment, making important considerations about OLE and HT bioavailability, OLE- and HT-mediated effects on drug metabolism, and OLE and HT dual activity as both pro- and antioxidants, likely hampering their use in clinical routine. Also, we focus on the details available on the effects of nutritionally relevant concentrations of OLE and HT on cell viability, redox homeostasis, and inflammation in order to evaluate if both compounds could be considered cancer-preventive agents or new potential chemotherapy drugs whenever their only source is represented by diet.

Modulating endoplasmic reticulum stress attenuates mast cell degranulation

OBJECTIVES

Degranulation of mast cells leads to direct allergic symptoms. The underlying mechanism needs to be explored further. Endoplasmic reticulum (ER) stress is involved in the pathogenesis of allergic conditions. The objective of this study is to gain a better understanding of the mechanism of mast cell degranulation.

METHODS

Bone marrow derived mast cells and mast cells isolated from the airway tissues were prepared. The role of ER stress in mediating the release of mast cells was tested. RNA sequencing (RNAseq) was used to investigate the genetic activities of mast cells.

RESULTS

Our observation showed that sensitization increased ER stress in mast cells. X-box-1 binding protein (XBP1) activity was linked to mast cell degranulation. Modulation of ER stress or XBP1 expression regulates the release of the mast cell mediator. XBP1 promoted the mediator release of mast cells by activating spleen tyrosine kinase (Syk). Activation of eukaryotic initiation factor 2a (eIF2a) inhibited XBP1 in mast cells. Semaphorin 3A was effective in preventing experimental allergic rhinitis (AR) due to its ability to suppress the release of mast cell mediators.

CONCLUSIONS

ER stress is associated with the mast cell degranulation. By inhibiting XBP1, the crucial molecule of ER stress, mast cell degranulation can be suppressed and experimental AR can be mitigated.

Expression and Clinical Significance of IRE1-XBP1s, p62, and Caspase-3 in Colorectal Cancer Patients

Background

Three main cell signaling pathways including the endoplasmic reticulum stress (ERS) response, autophagy, and apoptosis play critical roles in both cell survival and death. They were found to crosstalk with one another during tumorigenesis and cancer progression. This study aimed to investigate the expression of the spliced form of X-box binding protein 1 (XBP1s), p62, and caspase-3, as the essential biomarkers of ERS, autophagy, and apoptosis in patients with colorectal cancer (CRC), as well as the correlation between their expression and clinicopathological data.

Methods

This retrospective study was conducted on formalin-fixed paraffin-embedded (FFPE) blocks, which were collected from patients and their tumor margins, from the tumor bank of Imam Khomeini Hospital (Tehran, Iran) from 2017 to 2019. Tissue microarray (TMA) was used to measure the XBP1s, p62, and caspase-3 biomarkers. Data were analyzed using SPSS software version 20, and P≤0.05 was considered statistically significant.

Results

Evaluating the total of 91 patients, a significant relationship was found between XBP1s expression and TNM stage (P=0.003), primary tumor (pT) (P=0.054), and the degree of differentiation (P=0.006); and between caspase-3 with pT (P=0.004), and lymphovascular invasion (P=0.02). However, no significant correlation was found between p62 and clinicopathological data. Furthermore, a positive relationship between XBP1s and p62 was confirmed (correlation coefficient: 22.2% and P=0.05).

Conclusion

Our findings indicated that XBP1s could be considered as a target for therapy in personalized medicine.

FT895 Impairs Mitochondrial Function in Malignant Peripheral Nerve Sheath Tumor Cells

Neurofibromatosis type 1 (NF1) stands as a prevalent neurocutaneous disorder. Approximately a quarter of NF1 patients experience the development of plexiform neurofibromas, potentially progressing into malignant peripheral nerve sheath tumors (MPNST). FT895, an HDAC11 inhibitor, exhibits potent anti-tumor effects on MPNST cells and enhances the cytotoxicity of cordycepin against MPNST. The study aims to investigate the molecular mechanism underlying FT895's efficacy against MPNST cells. Initially, our study unveiled that FT895 disrupts mitochondrial biogenesis and function. Post-FT895 treatment, reactive oxygen species (ROS) in MPNST notably increased, while mitochondrial DNA copy numbers decreased significantly. Seahorse analysis indicated a considerable decrease in basal, maximal, and ATP-production-coupled respiration following FT895 treatment. Immunostaining highlighted FT895's role in promoting mitochondrial aggregation without triggering mitophagy, possibly due to reduced levels of XBP1, Parkin, and PINK1 proteins. Moreover, the study using CHIP-qPCR analysis revealed a significant reduction in the copy numbers of promoters of the MPV17L2, POLG, TFAM, PINK1, and Parkin genes. The RNA-seq analysis underscored the prominent role of the HIF-1α signaling pathway post-FT895 treatment, aligning with the observed impairment in mitochondrial respiration. In summary, the study pioneers the revelation that FT895 induces mitochondrial respiratory damage in MPNST cells.

MicroRNA-495: a therapeutic and diagnostic tumor marker

Therapeutic and diagnostic progresses have significantly reduced the mortality rate among cancer patients during the last decade. However, there is still a high rate of mortality among cancer patients. One of the important reasons involved in the high mortality rate is the late diagnosis in advanced tumor stages that causes the failure of therapeutic strategies in these patients. Therefore, investigating the molecular mechanisms involved in tumor progression has an important role in introducing the efficient early detection markers. MicroRNAs (miRNAs) as stable factors in body fluids are always considered as non-invasive diagnostic and prognostic markers. In the present review, we investigated the role of miR-495 in tumor progression. It has been reported that miR-495 has mainly a tumor suppressor function through the regulation of transcription factors and tyrosine kinases as well as cellular processes such as multidrug resistance, chromatin remodeling, and signaling pathways. This review can be an effective step towards introducing the miR-495 as a non-invasive diagnostic/prognostic marker as well as a suitable target in tumor therapy.

Unlocking Dendritic Cell-Based Vaccine Efficacy through Genetic Modulation-How Soon Is Now?

The dendritic cell (DC) vaccine anti-cancer strategy involves tumour-associated antigen loading and maturation of autologous ex vivo cultured DCs, followed by infusion into the cancer patient. This strategy stemmed from the idea that to induce a robust anti-tumour immune response, it was necessary to bypass the fundamental immunosuppressive mechanisms of the tumour microenvironment that dampen down endogenous innate immune cell activation and enable tumours to evade immune attack. Even though the feasibility and safety of DC vaccines have long been confirmed, clinical response rates remain disappointing. Hence, the full potential of DC vaccines has yet to be reached. Whether this cellular-based vaccination approach will fully realise its position in the immunotherapy arsenal is yet to be determined. Attempts to increase DC vaccine immunogenicity will depend on increasing our understanding of DC biology and the signalling pathways involved in antigen uptake, maturation, migration, and T lymphocyte priming to identify amenable molecular targets to improve DC vaccine performance. This review evaluates various genetic engineering strategies that have been employed to optimise and boost the efficacy of DC vaccines.

STF-083010 an inhibitor of IRE1α endonuclease activity affects mitochondrial respiration and generation of mitochondrial membrane potential

STF-083010 is an inhibitor of endonuclease activity of inositol requiring-enzyme 1α (IRE1α) that is involved in activation of IRE1α-XBP1 axis of the unfolded protein response after ER stress. STF-083010 was tested as a possible antitumor agent in some previous studies exhibiting the ability either to induce death of tumour cells or to increase sensitivity of tumours cells to other neoplastic agents. STF-083010 exhibits also hepatoprotective effects in different models of liver injury and hepatic steatohepatitis. We have shown that STF-083010 has significant impact on mitochondrial functions that is not dependent on the way of STF-083010 application. We have observed that STF-083010 decrease of both maximal respiration (representing maximal electron transfer capacity of mitochondrial respiratory chain) and spare respiratory capacity after either incubation of the SH-SY5Y cells with STF-083010 or direct addition of STF-083010 to the respiration medium. In addition, we have documented impact of STF-083010 on generation of mitochondrial membrane potential (ΔΨm) that could be a result of decreased mitochondrial substrate level phosphorylation. Finally, increased sensitivity of ΔΨm to uncoupler in the presence of STF-083010 was documented. Our results indicate that STF-083010 has important impact on mitochondrial functions independently of its ability to inhibit endonuclease activity of IRE1α that is involved in activation of IRE1α-XBP1 axis of the unfolded protein response after ER stress. The impact of STF-083010 on mitochondrial functions could be associated with its possible off-target effect.

The Role of XBP1 in bone metabolism

Bone is a dynamic organ that, once formed, undergoes a constant remodeling process that includes bone resorption and synthesis. Osteoclasts and osteoblasts are primarily responsible for controlling this process. X-box binding protein 1 (XBP1), a transcription factor, affects the metabolism of bones in various ways. In recent years, numerous studies have revealed that XBP1 plays a vital role in bone metabolism, including osteoclast and osteoblast development, as well as in regulating immune cell differentiation that affects the immune microenvironment of bone remodeling. In this review, we highlight the regulatory mechanisms of XBP1 on osteoclasts and osteoblasts, how XBP1 affects the immune microenvironment of bone remodeling by influencing the differentiation of immune cells, and predict the possible future research directions of XBP1 to provide new insights for the treatment of bone-related metabolic diseases.

The expression of lncRNAs CASC2, NEAT1, LINC00299 in breast cancer tissues and their relationship with the XBP1 splicing rate in Iranian patients during 2014-2019: A cross-sectional study

Background and Aims

Breast cancer is a leading cause of incidence and mortality in women globally. Identifying new molecular markers can aid in cancer diagnosis, targeted therapy, and treatment monitoring. This study aimed to measure the expression of the X-box binding protein 1 (XBP1) gene, an index of the unfolded protein response (UPR), and long noncoding RNAs (lncRNAs), including Nuclear Enriched Abundant Transcript 1 (NEAT1), Cancer Susceptibility Candidate 2 (CASC2), and Long Intergenic Nonprotein Coding RNA 299 (LINC00299), as possible regulators of the UPR pathway.

Methods

Total RNA was extracted from 40 samples of breast tumor tissues and their respective controls. The expression level of lncRNAs CASC2, NEAT1, and LINC00299 was quantified using reverse transcription-polymerase chain reaction (RT-PCR). The ratio of the spliced form of XBP1 to its unspliced form (XBP1u) was determined by PCR and electrophoresis.

Results

The results showed a 2.8-fold increase in the ratio of XBP1s/u in breast cancer tissues compared to adjacent nonmalignant samples (p < 0.05). Additionally, the level of lncRNAs NEAT1, CASC2, and LINC00299 in breast tumor tissues increased significantly by twofold, 1.5-fold, and 2.3-fold, respectively, compared to adjacent nonmalignant samples (p < 0.05).

Conclusions

Based on the association between the expression of lncRNAs CASC2, LINC00299, and NEAT1 and the XBP1s/u ratio, these lncRNAs could be potential regulators of the UPR pathway. Also, CASC2 and NEAT1 genes could be suggested as suitable biomarkers to distinguish cancerous tissue from noncancerous breast tissue due to their significant increase in expression in cancerous samples compared to adjacent noncancerous.

XBP1 as a novel molecular target to attenuate drug resistance in hepatocellular carcinoma

INTRODUCTION

Despite improvements in clinical management of hepatocellular carcinoma (HCC), prognosis remains poor with a 5-year survival rate less than 40%. Drug resistance in HCC makes it challenging to treat; therefore, it is imperative to develop new therapeutic strategies. Higher expression of X-box binding protein 1 (XBP1) in tumor cells is highly correlated with poor prognosis. In tumor cells, XBP1 modulates the unfolded protein response (UPR) to restore homeostasis in endoplasmic reticulum. Targeting XBP1 could be a promising therapeutic strategy to overcome HCC resistance and improve the survival rate of patients.

AREAS COVERED

This review provides the recent evidence that indicates XBP1 is involved in HCC drug resistance via DNA damage response, drug inactivation, and inhibition of apoptosis. In addition, the potential roles of XBP1 in inducing resistance in HCC cells were highlighted, and we showed how its inhibition could sensitize tumor cells to controlled cell death.

EXPERT OPINION

Due to the diversity in molecular mechanism of multidrug-resistance, targeting one specific pathway is inadequate. XBP1 inhibition could be a potential therapeutic target to overcome verity of resistance mechanisms. The main function of this transcription factor in HCC treatment response is an attractive area for further studies and should be discussed more.

ER Stress, the Unfolded Protein Response and Osteoclastogenesis: A Review

Endoplasmic reticulum (ER) stress and its adaptive mechanism, the unfolded protein response (UPR), are triggered by the accumulation of unfolded and misfolded proteins. During osteoclastogenesis, a large number of active proteins are synthesized. When an imbalance in the protein folding process occurs, it causes osteoclasts to trigger the UPR. This close association has led to the role of the UPR in osteoclastogenesis being increasingly explored. In recent years, several studies have reported the role of ER stress and UPR in osteoclastogenesis and bone resorption. Here, we reviewed the relevant literature and discussed the UPR signaling cascade response, osteoclastogenesis-related signaling pathways, and the role of UPR in osteoclastogenesis and bone resorption in detail. It was found that the UPR signal (PERK, CHOP, and IRE1-XBP1) promoted the expression of the receptor activator of the nuclear factor-kappa B ligand (RANKL) in osteoblasts and indirectly enhanced osteoclastogenesis. IRE1 promoted osteoclastogenesis via promoting NF-κB, MAPK signaling, or the release of pro-inflammatory factors (IL-6, IL-1β, and TNFα). CREBH promoted osteoclast differentiation by promoting NFATc1 expression. The PERK signaling pathway also promoted osteoclastogenesis through NF-κB and MAPK signaling pathways, autophagy, and RANKL secretion from osteoblasts. However, salubrinal (an inhibitor of eIF2α dephosphorylation that upregulated p-eIF2α expression) directly inhibited osteoclastogenesis by suppressing NFATc1 expression and indirectly promoted osteoclastogenesis by promoting RANKL secretion from osteoblasts. Therefore, the specific effects and mechanisms of p-PERK and its downstream signaling on osteoclastogenesis still need further experiments to confirm. In addition, the exact role of ATF6 and BiP in osteoclastogenesis also required further exploration. In conclusion, our detailed and systematic review provides some references for the next step to fully elucidate the relationship between UPR and osteoclastogenesis, intending to provide new insights for the treatment of diseases caused by osteoclast over-differentiation, such as osteoporosis.

Identification of a Novel Protein-Based Prognostic Model in Gastric Cancers

Gastric cancer (GC) is the third leading cause of cancer-related deaths worldwide. However, there are still no reliable biomarkers for the prognosis of this disease. This study aims to construct a robust protein-based prognostic prediction model for GC patients. The protein expression data and clinical information of GC patients were downloaded from the TCPA and TCGA databases, and the expressions of 218 proteins in 352 GC patients were analyzed using bioinformatics methods. Additionally, Kaplan-Meier (KM) survival analysis and univariate and multivariate Cox regression analysis were applied to screen the prognosis-related proteins for establishing the prognostic prediction risk model. Finally, five proteins, including NDRG1_pT346, SYK, P90RSK, TIGAR, and XBP1, were related to the risk prognosis of gastric cancer and were selected for model construction. Furthermore, a significant trend toward worse survival was found in the high-risk group (p = 1.495 × 10-7). The time-dependent ROC analysis indicated that the model had better specificity and sensitivity compared to the clinical features at 1, 2, and 3 years (AUC = 0.685, 0.673, and 0.665, respectively). Notably, the independent prognostic analysis results revealed that the model was an independent prognostic factor for GC patients. In conclusion, the robust protein-based model based on five proteins was established, and its potential benefits in the prognostic prediction of GC patients were demonstrated.

Prognostic subtypes of thyroid cancer was constructed based on single cell and bulk-RNA sequencing data and verified its authenticity

There has been an increase in the mortality rate of thyroid cancer (THCA), which is the most common endocrine malignancy. We identified six distinct cell types in the THAC microenvironment by analyzing single-cell RNA sequencing (Sc-RNAseq) data from 23 THCA tumor samples, indicating high intratumoral heterogeneity. Through re-dimensional clustering of immune subset cells, myeloid cells, cancer-associated fibroblasts, and thyroid cell subsets, we deeply reveal differences in the tumor microenvironment of thyroid cancer. Through an in-depth analysis of thyroid cell subsets, we identified the process of thyroid cell deterioration (normal, intermediate, malignant cells). Through cell-to-cell communication analysis, we found a strong link between thyroid cells and fibroblasts and B cells in the MIF signaling pathway. In addition, we found a strong correlation between thyroid cells and B cells, TampNK cells, and bone marrow cells. Finally, we developed a prognostic model based on differentially expressed genes in thyroid cells from single-cell analysis. Both in the training set and the testing set, it can effectively predict the survival of thyroid patients. In addition, we identified significant differences in the composition of immune cell subsets between high-risk and low-risk patients, which may be responsible for their different prognosis. Through in vitro experiments, we identify that knockdown of NPC2 can significantly promote thyroid cancer cell apoptosis, and NPC2 may be a potential therapeutic target for thyroid cancer. In this study, we developed a well-performing prognostic model based on Sc-RNAseq data, revealing the cellular microenvironment and tumor heterogeneity of thyroid cancer. This will help to provide more accurate personalized treatment for patients in clinical diagnosis.

The role of unfolded protein response-associated miRNAs in immunogenic cell death amplification: A literature review and bioinformatics analysis

Immunogenic cell death (ICD) is a type of cellular death that is elicited in response to the specific types of anti-cancer therapies and enhances the anti-tumor immune responses by the combination of antigenicity and adjuvanticity of dying tumor cells. There is a well-established interlink between endoplasmic reticulum stress (ERS) and ICD elicited by anti-cancer therapies. Most recent evidences support that unfolded protein response (UPR)-associated miRNAs can be key players in the ERS-induced ICD. Hence, in the present study, we conducted a literature review on the role of these miRNAs and associated molecular pathways that may regulate ICD. We first collected UPR-associated miRNAs that promote ERS-induced apoptosis and then focused on microRNAs (miRNAs) that promote ERS-induced apoptosis via PERK/eIF2α/ATF4/CHOP pathway activation, as the main core for ICD and release of damage-associated molecular patterns. To better identify PERK/eIF2α/ATF4/CHOP pathway-inducing miRNAs that can be used as potential therapeutic targets for improving ICD in cancer treatment, we did a comprehensive bioinformatics analysis and network construction. Our results showed that "pathways in cancer", "MAPK signaling pathway", "PI3K-Akt signaling pathway", and "Cellular senescence", which correlate with UPR components and ERS induction, were among the significant signaling pathways related to the target genes of these miRNAs. Furthermore, a protein-protein interaction (PPI) network was constructed, which revealed the involvement of the PPI-extracted hub genes in the regulation of proliferation and apoptosis. In conclusion, we propose that these types of miRNAs can be considered as the potential cancer therapy options for better induction of ICD in combination with other ICD inducers.

New class of fused [3,2-b][1,2,4]triazolothiazoles for targeting glioma in vitro

Glioma is aggressive malignant tumor with limited therapeutic interventions. Herein we report the synthesis of fused bicyclic 1,2,4-triazolothiazoles by a one-pot multi-component approach and their activity against C6 rat and LN18 human glioma cell lines. The target compounds 2-(6-phenylthiazolo[3,2-b][1,2,4]triazol-2-yl) isoindoline-1,3-diones and (E)-1-phenyl-N-(6-phenylthiazolo[3,2-b][1,2,4]triazol-2-yl) methanimines were obtained by the reaction of 5-amino-4H-1,2,4-triazole-3-thiol with substituted phenacyl bromide, phthalic anhydride, and different aromatic aldehydes in EtOH/HCl under reflux conditions. In C6 rat glioma cell lines, compounds 4g and 6i showed good cytotoxic activity with IC₅₀ values of 8.09 and 8.74 μM, respectively, resulting in G1 and G2-M phase arrest of the cell cycle and activation of apoptosis by modulating phosphorylation of ERK and AKT pathway.

Exosomal miR-205-5p derived from periodontal ligament stem cells attenuates the inflammation of chronic periodontitis via targeting XBP1

INTRODUCTION

Chronic periodontitis (CP) is an inflammatory periodontal disease with high incidence and complex pathology. This research is aimed to investigate the function of exosomal miR-205-5p (Exo-miR-205-5p) in CP and the underlying molecular mechanisms.

METHOD

Exo-miR-205-5p was isolated from miR-205-5p mimics-transfected periodontal ligament stem cells (PDLSCs), and subsequently cocultured with lipopolysaccharide (LPS)-induced cells or injected into LPS-treated rats. The mRNA expression of inflammatory factors and Th17/Treg-related factors were measured by quantitative real-time PCR. The contents of inflammatory factors and the percentages of Th17/Treg cells were measured by enzyme-linked immunosorbent assay and flow cytometry, respectively. Besides, the target relation between miR-205-5p and X-box binding protein 1 (XBP1) was explored.

RESULTS

MiR-205-5p was downregulated in LPS-induced PDLSCs and corresponding exosomes. Exo-miR-205-5p inhibited inflammatory cell infiltration, decreased the production of TNF-α, IL-1β, and IL-6, and decreased the percentage of Th17 cells in LPS-treated rats. In addition, XBP1 was a target of miR-205-5p. Overexpression of XBP1 weakened the effects of Exo-miR-205-5p on inhibiting inflammation and regulating Treg/Th17 balance in LPS-induced cells.

CONCLUSIONS

Exo-miR-205-5p derived from PDLSCs relieves the inflammation and balances the Th17/Treg cells in CP through targeting XBP1.

Mechanism and Role of Endoplasmic Reticulum Stress in Osteosarcoma

Osteosarcoma is the most common malignant bone tumor, often occurring in children and adolescents. The etiology of most patients is unclear, and the current conventional treatment methods are chemotherapy, radiotherapy, and surgical resection. However, the sensitivity of osteosarcoma to radiotherapy and chemotherapy is low, and the prognosis is poor. The development of new and useful treatment strategies for improving patient survival is an urgent need. It has been found that endoplasmic reticulum (ER) stress (ERS) affects tumor angiogenesis, invasion, etc. By summarizing the literature related to osteosarcoma and ERS, we found that the unfolded protein response (UPR) pathway activated by ERS has a regulatory role in osteosarcoma proliferation, apoptosis, and chemoresistance. In osteosarcoma, the UPR pathway plays an important role by crosstalk with autophagy, oxidative stress, and other pathways. Overall, this article focuses on the relationship between ERS and osteosarcoma and reviews the potential of drugs or gene targets associated with ERS for the treatment of osteosarcoma.

Molecular Mechanism Underlying Role of the XBP1s in Cardiovascular Diseases

Spliced X-box binding protein-1 (XBP1s) is a protein that belongs to the cAMP-response element-binding (CREB)/activating transcription factor (ATF) b-ZIP family with a basic-region leucine zipper (bZIP). There is mounting evidence to suggest that XBP1s performs a critical function in a range of different cardiovascular diseases (CVDs), indicating that it is necessary to gain a comprehensive knowledge of the processes involved in XBP1s in various disorders to make progress in research and clinical therapy. In this research, we provide a summary of the functions that XBP1s performs in the onset and advancement of CVDs such as atherosclerosis, hypertension, cardiac hypertrophy, and heart failure. Furthermore, we discuss XBP1s as a novel therapeutic target for CVDs.

GeneFriends: gene co-expression databases and tools for humans and model organisms

Gene co-expression analysis has emerged as a powerful method to provide insights into gene function and regulation. The rapid growth of publicly available RNA-sequencing (RNA-seq) data has created opportunities for researchers to employ this abundant data to help decipher the complexity and biology of genomes. Co-expression networks have proven effective for inferring the relationship between the genes, for gene prioritization and for assigning function to poorly annotated genes based on their co-expressed partners. To facilitate such analyses we created previously an online co-expression tool for humans and mice entitled GeneFriends. To continue providing a valuable tool to the scientific community, we have now updated the GeneFriends database and website. Here, we present the new version of GeneFriends, which includes gene and transcript co-expression networks based on RNA-seq data from 46 475 human and 34 322 mouse samples. The new database also encompasses tissue-specific gene co-expression networks for 20 human and 21 mouse tissues, dataset-specific gene co-expression maps based on TCGA and GTEx projects and gene co-expression networks for additional seven model organisms (fruit fly, zebrafish, worm, rat, yeast, cow and chicken). GeneFriends is freely available at http://www.genefriends.org/.

Comprehensive analysis of potential cellular communication networks in advanced osteosarcoma using single-cell RNA sequencing data

Osteosarcoma (OS) is a common bone cancer in children and adolescents, and metastasis and recurrence are the major causes of poor treatment outcomes. A better understanding of the tumor microenvironment is required to develop an effective treatment for OS. In this paper, a single-cell RNA sequencing dataset was taken to a systematic genetic analysis, and potential signaling pathways linked with osteosarcoma development were explored. Our findings revealed 25 clusters across 11 osteosarcoma tissues, with 11 cell types including “Chondroblastic cells”, “Osteoblastic cells”, “Myeloid cells”, “Pericytes”, “Fibroblasts”, “Proliferating osteoblastic cells”, “Osteoclasts”, “TILs”, “Endothelial cells”, “Mesenchymal stem cells”, and “Myoblasts”. The results of Cell communication analysis showed 17 potential cellular communication networks including “COLLAGEN signaling pathway network”, “CD99 signaling pathway network”, “PTN signaling pathway network”, “MIF signaling pathway network”, “SPP1 signaling pathway network”, “FN1 signaling pathway network”, “LAMININ signaling pathway network”, “FGF signaling pathway network”, “VEGF signaling pathway network”, “GALECTIN signaling pathway network”, “PERIOSTIN signaling pathway network”, “VISFATIN signaling pathway network”, “ITGB2 signaling pathway network”, “NOTCH signaling pathway network”, “IGF signaling pathway network”, “VWF signaling pathway network”, “PDGF signaling pathway network”. This research may provide novel insights into the pathophysiology of OS’s molecular processes.

Circular RNA circ_0079593 facilitates glioma development via modulating miR-324-5p/XBP1 axis

Glioma is a common brain tumor with high mortality. Circular RNAs (circRNAs) play crucial roles in tumor occurrence and development. However, the function and molecular basis of circ_0079593 in glioma remain unknown. Quantitative real-time PCR (qPCR) and Western blot were used for expression determination of circ_0079593, microRNA-324-5p (miR-324-5p) and X-box binding protein 1 (XBP1). Cell Counting Kit-8 (CCK-8), colony formation, flow cytometry, transwell assays, and tube formation assay were employed to evaluate cell functions. Glycolysis was determined via detecting glucose consumption, lactate production and ATP level. The binding relationship between miR-324-5p and circ_0079593 or XBP1 was validated by dual-luciferase reporter assay and RNA Immunoprecipitation (RIP) assay. Besides, xenograft assay was applied to test tumor growth in vivo. Circ_0079593 and XBP1 levels were elevated, while miR-324-5p level was declined in glioma. Silencing of circ_0079593 restrained proliferation, mobility, angiogenesis and glycolysis and induced apoptosis in glioma cells. Circ_0079593 accelerated glioma progression via sequestering miR-324-5p, one of the targets of circ_0079593. XBP1 was a target gene of miR-324-5p, and miR-324-5p alleviated the malignant growth of glioma by repressing XBP1. Furthermore, silence of circ_0079593 hindered tumor growth in vivo. Circ_0079593 contributed to the malignant evolution of glioma via modulating miR-324-5p and downstream XBP1 gene, suggesting that circ_0079593 might be a promising therapeutic target for glioma. Circ_0079593 was boosted in glioma. Circ_0079593 depletion restrained glioma progression. Circ_0079593 triggered glioma development via miR-324-5p/XBP1 axis. Circ_0079593 silence suppressed glioma tumorigenesis in vivo.