A necroptosis related prognostic model of pancreatic cancer based on single cell sequencing analysis and transcriptome analysis

The HNRNPC/CELF2 signaling pathway drives glycolytic reprogramming and mitochondrial dysfunction in drug-resistant acute myeloid leukemia

BACKGROUND

Acute myeloid leukemia (AML) is an aggressive cancer with high treatment resistance, often leading to poor patient outcomes. Metabolic reprogramming plays a critical role in AML progression, influencing drug resistance (DR) and tumor survival. This study investigates the HNRNPC/CELF2 signaling pathway and its impact on AML cell metabolism and DR.

RESULTS

The study identified that HNRNPC regulates the expression of CELF2 through m6 A modification. In drug-resistant AML cells, increased HNRNPC expression and decreased CELF2 expression were associated with upregulated glycolysis, enhanced glucose consumption, lactate production, and mitochondrial dysfunction. Knockdown of HNRNPC reduced glycolysis and cell invasion, while CELF2 knockdown reversed these effects. Conversely, HNRNPC overexpression enhanced glycolysis and cell migration, which were counteracted by CELF2 overexpression.

CONCLUSIONS

The HNRNPC/CELF2 axis plays a pivotal role in metabolic reprogramming, driving AML progression and chemotherapy resistance. Targeting this pathway may offer new therapeutic strategies to overcome resistance and improve treatment outcomes in AML patients.

Development of a hypoxia-responsive macrophage prognostic model using single-cell and bulk RNA sequencing in pancreatic cancer

OBJECTIVE

Pancreatic ductal adenocarcinoma (PDAC) is characterized by a low survival rate and limited responsiveness to current therapies. The role of hypoxia in the tumor microenvironment is critical, influencing tumor progression and therapy resistance. The aim of this study was to implement the complex dynamics of the hypoxic tumor microenvironment in PDAC in a hypoxia-related prognosis model.

METHODS

We utilized single-cell RNA sequencing (scRNA-seq) data and integrated it with TCGA-PAAD database to identify hypoxia-responsive macrophage subsets and related genes. Kaplan-Meier survival analysis, Cox regression, and Lasso regression methods were employed to construct and validate a hypoxia-related prognostic model. The model's effectiveness was evaluated through its predictive capabilities regarding chemotherapy sensitivity and overall survival.

RESULTS

Our research integrated data from scRNA-seq and the TCGA-PAAD database to construct a hypoxia-related prognostic model that encompassed 13 critical genes. This hypoxia model independently predicted chemotherapy response and poor outcomes, outperforming traditional clinicopathologic features. Additionally, a pan-cancer analysis affirmed the relevance of our hypoxia-related genes across multiple malignancies, particularly highlighting KRTCAP2 as a pivotal biomarker associated with worse prognosis and reduced immune infiltration.

CONCLUSION

Our findings underscored the prognostic potential of hypoxia-related model and offered a novel avenue for therapeutic targeting, aiming to ameliorate outcomes in pancreatic cancer.

Exploring the impact of the liver-intestine-brain axis on brain function in non-alcoholic fatty liver disease

This study investigates the molecular complexities of non-alcoholic fatty liver disease (NAFLD)-induced brain dysfunction, with a focus on the liver-intestine-brain axis and potential therapeutic interventions. The main objectives include understanding critical microbiota shifts in NAFLD, exploring altered metabolites, and identifying key regulatory molecules influencing brain function. The methods employed encompassed 16S ribosomal RNA (rRNA) sequencing to scrutinize stool microbiota in NAFLD patients and healthy individuals, non-targeted metabolomics using LC-MS to uncover elevated levels of deoxycholic acid (DCA) in NAFLD mice, and single-cell RNA sequencing (scRNA-seq) to pinpoint the pivotal gene Hpgd in microglial cells and its downstream Janus kinase 2/signal transducer and activator of transcription 3 (JAK2/STAT3) signaling pathway. Behavioral changes and brain function were assessed in NAFLD mice with and without Fecal microbiota transplantation (FMT) treatment, utilizing various assays and analyses. The results revealed significant differences in microbiota composition, with increased levels of Bacteroides in NAFLD patients. Additionally, elevated DCA levels were observed in NAFLD mice, and FMT treatment demonstrated efficacy in ameliorating liver function and brain dysfunction. Hpgd inhibition by DCA activated the JAK2/STAT3 pathway in microglial cells, leading to inflammatory activation, inhibition of mitochondrial autophagy, induction of neuronal apoptosis, and reduction in neuronal action potentials. This study elucidates the intricate molecular mechanisms underlying the liver-gut-brain axis in NAFLD, and the identification of increased DCA and the impact of JAK2/STAT3 signaling on microglial cells highlight potential therapeutic targets for addressing NAFLD-induced brain dysfunction.

HNF4α-Mediated LINC02560 Promotes Papillary Thyroid Carcinoma Progression by Targeting the miR-505-5p/PDE4C Axis

Papillary thyroid carcinoma (PTC) is the most common subtype of thyroid malignancy, and its progression is closely associated with patient outcomes. This study investigated the role of the long non-coding RNA LINC02560 in the pathogenesis and aggressiveness of PTC through cell culture, transfection, RT-qPCR, Western blot analysis, and various functional assays, such as MTT, EdU, colony formation, wound healing, and Transwell migration assays. Our results revealed a significant upregulation of LINC02560 in PTC tissues, correlating with poor prognosis in affected patients. Functional analyses demonstrated that silencing of LINC02560 markedly inhibited the proliferation, migration, and invasion of the PTC cell lines, KTC-1, and BCPAP, whereas overexpression promoted these aggressive traits. Mechanistically, LINC02560 acted as a competitive endogenous RNA, sponging miR-505-5p and alleviating its suppression on PDE4C degradation, thereby activating the P-AKT and epithelial-mesenchymal transition (EMT) signaling pathways. Additionally, HNF4α was identified as a transcription factor capable of enhancing the expression of LINC02560. In conclusion, our findings elucidate the critical HNF4α/LINC02560/miR-505-5p/PDE4C axis in PTC pathology, presenting this regulatory network as a promising biomarker combination and potential therapeutic target to improve patient outcomes and survival rates, warranting further clinical investigation to validate these insights and support the development of targeted therapies in PTC management.

Silver Nanoparticles Prepared Using Magnolia officinalis Are an Effective Antimicrobial Agent on Candida albicans, Escherichia coli, and Staphylococcus aureus

Silver nanoparticles (AgNPs) prepared by plants are simple, eco-friendly, and economical. In this study, Magnolia officinalis (MO) extract was applied to synthesize MO@AgNPs. Ultraviolet-visible (UV-vis) spectrum analysis indicated a peak at 440 nm. Most of the particles were spherical with sizes from 1 to approximately 60 nm based on transmission electron microscopy (TEM). X-ray diffraction (XRD) patterns showed a face-centered cubic crystal structure. The zeta value of MO@AgNPs was - 36.5 ± 0.6 mV, which was stable at 25 °C and 4 °C. Growth kinetic studies and the Kirby-Bauer diffusion method showed significant inhibitory activity on Candida albicans (ATCC 10231), Escherichia coli (ATCC BAA-2340), and Staphylococcus aureus (ATCC 25923); the minimum inhibitory concentrations (MIC) were 3, 9, and 9 μg/mL, and corresponding minimum bactericidal concentrations (MBC) were 5, 11, and 9 μg/mL, respectively. MO@AgNPs exhibited better antifungal activity compared to AgNPs prepared using sodium citrate. Further research revealed that MO@AgNPs increased the permeability of bacterial cell membranes. Moreover, the effect of MO@AgNPs on Candida albicans was significantly enhanced by blocking autophagy. The reactive oxygen species (ROS) induced by MO@AgNPs in Candida albicans was limited and may be related to its good antioxidant activity. Finally, MO@AgNPs have no significant cytotoxicity to the human liver LO2 cell line under 20 μg/mL.

The multifaceted role of phosphodiesterase 4 in tumor: from tumorigenesis to immunotherapy

Phosphodiesterase 4 (PDE4) is an enzyme that specifically hydrolyzes the second messenger cAMP and has a critical role in the regulation of a variety of cellular functions. In recent years, PDE4 has attracted great interest in cancer research, and its role in tumorigenesis and development has been gradually elucidated. Research indicates that abnormal expression or heightened activity of PDE4 is associated with the initiation and progression of multiple cancers, including lung, colorectal, and hematological cancers, by facilitating cell proliferation, migration, invasion, and anti-apoptosis. Moreover, PDE4 also influences the tumor immune microenvironment, significantly immune evasion by suppressing anti-tumor immune responses, reducing T-cell activation, and promoting the polarization of tumor-associated macrophages toward a pro-tumorigenic phenotype. However, the PDE4 family may have both oncogenic and tumor-suppressive effects, which could depend on the specific type and grade of the tumor. PDE4 inhibitors have garnered substantial interest as potential anti-cancer therapeutics, directly inhibiting tumor cell growth and restoring immune surveillance capabilities to enhance the clearance of tumor cells. Several PDE4 inhibitors are currently under investigation with the aim of exploring their potential in cancer therapy, particularly in combination strategies with immune checkpoint inhibitors, to improve therapeutic efficacy and mitigate the side effects of conventional chemotherapy. This review provides an overview of PDE4 in tumorigenesis, drug resistance, immunotherapy, and the anti-tumor actions of its inhibitors, intending to guide the exploration of PDE4 as a new target in tumor therapy.

Enhancing cardiac repair post-myocardial infarction: a study on GATM/Gel hydrogel therapeutics

BACKGROUND AND PURPOSE

Significant advancements in therapeutic approaches are imperative to address the prevalent impact of myocardial infarction (MI) on morbidity and mortality rates worldwide. This study explores the therapeutic potential of GATM/Gel hydrogel, focusing on its ability to enhance cardiac repair and functionality after MI through modulation of inflammatory and repair pathways.

EXPERIMENTAL APPROACH

The effects of GATM/Gel hydrogel on cardiac recovery were studied in a murine MI model. HA-CHO and gelatin solutions were mixed in situ using a dual syringe with a static mixing needle, and the resulting hydrogel was applied directly to the epicardium during MI modeling, followed by repositioning of the heart and closure of the thorax. Comprehensive in vivo assessments-including echocardiography, electrocardiography, and histopathological analysis-were combined with molecular techniques such as RT-qPCR, Western blotting, and immunofluorescence to elucidate the underlying mechanisms. Key cellular and molecular changes were tracked, focusing on macrophage polarization, angiogenesis, and modulation of the TNF/TNFR2 signaling pathway.

KEY RESULTS

Employing the GATM/Gel hydrogel led to a substantial improvement in heart function, shown through enhanced ejection fraction and fractional shortening, and reduced infarction size compared to control groups. Mechanistically, the hydrogel promoted the polarization of anti-inflammatory M2 macrophages and stimulated angiogenesis. Moreover, treatment with GATM/Gel hydrogel altered the TNF/TNFR2 pathway, pivotal in mediating inflammatory responses and facilitating myocardial repair. The discoveries highlight the possibility of GATM/Gel hydrogels as an innovative remedy for MI, providing a twofold role in regulating inflammation and fostering recovery.

Exploring the Effects of Metformin on the Body via the Urine Proteome

Metformin is the first-line medication for treating type 2 diabetes mellitus, with more than 200 million patients taking it daily. Its effects are extensive and play a positive role in multiple areas. Can its effects and potential mechanisms be explored through the urine proteome? In this study, 166 differential proteins were identified following the administration of 150 mg/(kg·d) of metformin to rats for five consecutive days. These included complement component C6, pyruvate kinase, coagulation factor X, growth differentiation factor 15, carboxypeptidase A4, chymotrypsin-like elastase family member 1, and L-lactate dehydrogenase C chain. Several of these proteins have been reported to be directly affected by metformin or associated with its effects. Multiple biological pathways enriched by these differential proteins, or proteins containing differentially modified peptides, have been reported to be associated with metformin, such as the glutathione metabolic process, negative regulation of gluconeogenesis, and the renin-angiotensin system. Additionally, some significantly changed proteins and enriched biological pathways, not yet reported to be associated with metformin's effects, may provide clues for exploring its potential mechanisms. In conclusion, the application of the urine proteome offers a comprehensive and systematic approach to exploring the effects of drugs, providing a new perspective on the study of metformin's mechanisms.

Exploratory analysis of a Novel RACK1 mutation and its potential role in epileptic seizures via Microglia activation

Seizures is a prevalent neurological disorder with a largely elusive pathogenesis. In this study, we identified the key gene RACK1 and its novel mutation RACK1-p.L206P as being associated with seizures through single-cell transcriptome sequencing (scRNA-seq) and whole exome sequencing (WES) techniques. Our findings reveal that the RACK1-p.L206P mutation significantly enhances proliferation, migration, phagocytic ability, and inflammatory activation in human microglia, which in turn affects neuronal excitability and synaptic function, culminating in typical seizure symptoms in the seizures. These effects were further validated in a mouse model using CRISPR/Cas9 gene editing technology. Mutant microglia exhibited increased activation and induced apoptosis in hippocampal neurons, leading to higher action potential frequency and excitatory synaptic marker expression. In vivo experiments demonstrated that RACK1-p.L206P mutant mice displayed classic seizure symptoms, with increased neuronal excitability and a tendency for action potential bursts during initial depolarization, along with more frequent spike discharges. Additionally, excitatory synapse density and size in the hippocampal CA1 region of mutant mice were significantly elevated, accompanied by increased expression of VGLUT1 and PSD95 within microglia. This study offers novel insights into the molecular mechanisms underlying seizures in the seizures and presents valuable clues for the development of future therapeutic strategies.

Integrative multi-omics analysis reveals the role of toll-like receptor signaling in pancreatic cancer

As one of the most destructive and invasive cancers, pancreatic cancer exhibits complex tumor heterogeneity, which has been a major challenge for clinicians in terms of patient treatment and prognosis. The toll-like receptor (TLR) pathway is closely related to the immune microenvironment within various cancer tissues. To explore the development pattern of pancreatic cancer and find an ideal biomarker, our research has explored the mechanism of the TLR pathway in pancreatic cancer. We collected single-cell expression data from 57,024 cells and transcriptomic data from 945 pancreatic cancer patients, and conducted a series of analyses at both the single-cell and transcriptomic levels. By calculating the TLR pathway score, we clustered pancreatic cancer patients and conducted a series of analyses including metabolic pathways, immune microenvironment, drug sensitivity and so on. In the process of building prognostic models, we screened 33 core genes related to the prognosis of pancreatic cancer, and combined a series of machine learning algorithms to build the prognosis model of pancreatic cancer. We used single cell sequencing to clarify the complex intrinsic relationship between TLR pathway and pancreatic cancer. The strongest TLR signals were observed in macrophages and endothelial cells. With the occurrence of pancreatic cancer, the TLR signal of various cell types gradually increased, but with the increase of the malignant degree of ductal epithelial cells, the TLR signal gradually weakened. Cluster analysis showed that patients with the most active TLR pathway had severe dysregulation of immune microenvironment and the worst prognosis. Finally, we combined a series of machine learning algorithms to build a pancreatic cancer prognosis model that includes four genes (NT5E, TGFBI, ANLN, and FAM83A). The model showed strong performance in predicting the survival state of pancreatic cancer samples. We explored the important role of TLR pathway in pancreatic cancer and established and validated a new prognosis model for pancreatic cancer based on TLR-related genes.

Oncogenic mechanisms of COL10A1 in cancer and clinical challenges (Review)

Collagen type X α1 chain (COL10A1), a gene encoding the α‑1 chain of type X collagen, serves a key role in conferring tensile strength and structural integrity to tissues. Upregulation of COL10A1 expression has been observed in different malignancies, including lung, gastric and pancreatic cancer, and is associated with poor prognosis. The present review provides an updated synthesis of the evolving biological understanding of COL10A1, with a particular focus on its mechanisms of action and regulatory functions within the context of tumorigenesis. For example, it has been established that increased COL10A1 expression promotes cancer progression by activating multiple signaling pathways, including the TGF‑β1/Smad, MEK/ERK and focal adhesion kinase signaling pathways, thereby inducing proliferation, invasion and migration. Additionally, COL10A1 has been demonstrated to induce epithelial‑mesenchymal transition and reshapes the extracellular matrix within tumor tissues. Furthermore, on the basis of methyltransferase‑like 3‑mediated N6‑methyladenosine methylation, COL10A1 intricately regulates the epitranscriptomic machinery, thereby augmenting its oncogenic role. However, although COL10A1 serves a pivotal role in gene transcription and the orchestration of tumor growth, the question of whether COL10A1 would serve as a viable therapeutic target remains a subject of scientific hypothesis requiring rigorous examination. Variables such as distinct tumor microenvironments and treatment associations necessitate further experimental validation. Therefore, a comprehensive assessment and understanding of the functional and mechanistic roles of COL10A1 in cancer may pave the way for the development of innovative cancer treatment strategies.

Identification and Validation of Senescence-Related Signature by Combining Single Cell and Bulk Transcriptome Data Analysis to Predict the Prognosis and Identify the Key Gene CAV1 in Pancreatic Cancer

Background

The role of cellular senescence in the tumor microenvironment of pancreatic cancer (PC) remains unclear, particularly regarding its impact on prognosis and immunotherapy outcomes.

Methods

We utilized single-cell sequencing datasets (GSE155698 and GSE154778) for pancreatic cancer from the Gene Expression Omnibus (GEO) database and bulk RNA-seq data from the University of California, Santa Cruz (UCSC) and International Cancer Genome Consortium (ICGC) repositories, creating three patient cohorts: The Cancer Genome Atlas (TCGA) cohort, PAAD-AU cohort, and PAAD-CA cohort. Dimensionality reduction cluster analysis processed the single-cell data, while weighted gene co-expression network analysis (WGCNA) and differential expression gene analysis were applied to bulk RNA-seq data. Prognostic models were developed using Cox proportional hazards (COX) and least absolute shrinkage and selection operator (LASSO) regression, with validation through survival analysis, decision curve analysis, and principal component analysis (PCA). Tumor mutation data were analyzed using the "maftools" package, and the immune microenvironment was assessed with TIMER2 data.

Results

We developed a senescence-related (SENR) six-gene prognostic signature for PC, which stratifies patients by risk, with high-risk groups showing poorer prognoses. This model also offers predictive insights into tumor mutations and immune microenvironment characteristics. Caveolin-1 (CAV1) emerged as a significant prognostic biomarker, with functional validation showing its role in promoting cancer cell proliferation and migration, highlighting its potential as a therapeutic target.

Conclusion

This study provides a novel senescence-related prognostic tool for PC, enhancing patient stratification for prognosis and immunotherapy, and identifies CAV1 as a key gene with clinical significance for targeted interventions.

Matrine alkaloids modulating DNA damage repair in chemoresistant non-small cell lung cancer cells

BACKGROUND

Non-small cell lung cancer (NSCLC) presents a significant challenge in the medical field due to its high incidence and resistance to chemotherapy. Chemoresistance in NSCLC diminishes treatment efficacy and contributes to poor patient outcomes. Matrine alkaloids have shown promise in reversing chemotherapy resistance in NSCLC by targeting DNA repair mechanisms.

METHODS

Utilizing molecular dynamics simulations, we explored the interactions between Matrine alkaloids and DNA repair-related proteins to elucidate their impact on NSCLC cells. In vitro experiments involved treating A549/DDP cells with Matrine alkaloids to evaluate their sensitizing effects on lung cancer cells. Additionally, animal model experiments were conducted to validate the therapeutic potential of Matrine alkaloids in NSCLC treatment.

RESULTS

Our findings demonstrate that Matrine alkaloids disrupt DNA damage repair processes in NSCLC cells, leading to increased sensitivity to chemotherapy. Molecular docking studies revealed the intricate mechanisms by which Matrine alkaloids interact with DNA repair proteins, impacting cell survival and proliferation. Both cell experiments and animal models confirmed the chemosensitizing effects of Matrine alkaloids in NSCLC treatment.

CONCLUSION

Matrine alkaloids offer a promising avenue for overcoming chemotherapy resistance in NSCLC by interfering with DNA repair pathways. This study lays a solid foundation for future clinical investigations into the potential of Matrine alkaloids as effective therapeutic agents for enhancing NSCLC treatment outcomes.

Long non-coding RNAs in ferroptosis, pyroptosis and necroptosis: from functions to clinical implications in cancer therapy

As global population ageing accelerates, cancer emerges as a predominant cause of mortality. Long non-coding RNAs (lncRNAs) play crucial roles in cancer cell growth and death, given their involvement in regulating downstream gene expression levels and numerous cellular processes. Cell death, especially non-apoptotic regulated cell death (RCD), such as ferroptosis, pyroptosis and necroptosis, significantly impacts cancer proliferation, invasion and metastasis. Understanding the interplay between lncRNAs and the diverse forms of cell death in cancer is imperative. Modulating lncRNA expression can regulate cancer onset and progression, offering promising therapeutic avenues. This review discusses the mechanisms by which lncRNAs modulate non-apoptotic RCDs in cancer, highlighting their potential as biomarkers for various cancer types. Elucidating the role of lncRNAs in cell death pathways provides valuable insights for personalised cancer interventions.

Identification of prostate cancer bone metastasis related genes and potential therapy targets by bioinformatics and in vitro experiments

The aetiology of bone metastasis in prostate cancer (PCa) remains unclear. This study aims to identify hub genes involved in this process. We utilized machine learning, GO, KEGG, GSEA, Single-cell analysis, ROC methods to identify hub genes for bone metastasis in PCa using the TCGA and GEO databases. Potential drugs targeting these genes were identified. We validated these results using 16 specimens from patients with PCa and analysed the relationship between the hub genes and clinical features. The impact of APOC1 on PCa was assessed through in vitro experiments. Seven hub genes with AUC values of 0.727-0.926 were identified. APOC1, CFH, NUSAP1 and LGALS1 were highly expressed in bone metastasis tissues, while NR4A2, ADRB2 and ZNF331 exhibited an opposite trend. Immunohistochemistry further confirmed these results. The oxidative phosphorylation pathway was significantly enriched by the identified genes. Aflatoxin B1, benzo(a)pyrene, cyclosporine were identified as potential drugs. APOC1 expression was correlated with clinical features of PCa metastasis. Silencing APOC1 significantly inhibited PCa cell proliferation, clonality, and migration in vitro. This study identified 7 hub genes that potentially facilitate bone metastasis in PCa through mitochondrial metabolic reprogramming. APOC1 emerged as a promising therapeutic target and prognostic marker for PCa with bone metastasis.

Identification and Comprehensive Analysis of circRNA-miRNA-mRNA Regulatory Networks in A2780 Cells Treated with Resveratrol

Ovarian cancer (OC) is one of the most commonplace gynecological malignancies. This study explored the effects of resveratrol (RES) on OC cell proliferation and apoptosis. Proliferation activity was measured for A2780 cells treated with RES for 24 h and 48 h at concentrations of 0, 10, 25, 50, 75, 100, 150, 200, and 300 μM. RNA sequencing (RNA-seq) was performed to analyze the circular RNA (circRNA), microRNA (miRNA), and messenger RNA (mRNA) expression spectrum. The differentially expressed genes included 460 circRNAs, 1988 miRNAs, and 1671 mRNAs, and they were subjected to analyses including Gene Ontology, the Kyoto Encyclopedia of Genes and Genomes (KEGG), and Reactome enrichment. We selected signaling pathways enriched in the cell processes by mRNA KEGG, comprehensively analyzed the circRNA-miRNA-mRNA regulatory network, and verified several miRNAs expressed in the regulatory network diagram using the quantitative real-time polymerase chain reaction. The data showed that the cell proliferation of A2780 cells treated with RES for 24 h or 48 h decreased with increasing concentrations of RES. The circRNA-miRNA-mRNA regulatory network that we constructed provides new insights into the ability of RES to inhibit cell proliferation and promote apoptosis in A2780 cells.

Combining single-cell and bulk RNA sequencing, NK cell marker genes reveal a prognostic and immune status in pancreatic ductal adenocarcinoma

The NK cell is an important component of the tumor microenvironment of pancreatic ductal adenocarcinoma (PDAC), also plays a significant role in PDAC development. This study aimed to explore the relationship between NK cell marker genes and prognosis, immune response of PDAC patients. By scRNA-seq data, we found the proportion of NK cells were significantly downregulated in PDAC and 373 NK cell marker genes were screened out. By TCGA database, we enrolled 7 NK cell marker genes to construct the signature for predicting prognosis in PDAC patients. Cox analysis identified the signature as an independent factor for pancreatic cancer. Subsequently, the predictive power of signature was validated by 6 GEO datasets and had an excellent evaluation. Our analysis of relationship between the signature and patients' immune status revealed that the signature has a strong correlation with immunocyte infiltration, inflammatory reaction, immune checkpoint inhibitors (ICIs) response. The NK cell marker genes are closely related to the prognosis and immune capacity of PDAC patients, and they have potential value as a therapeutic target.

Single-Cell RNA Sequencing Analysis Reveals Metabolic Changes in Epithelial Glycosphingolipids and Establishes a Prognostic Risk Model for Pancreatic Cancer

OBJECTIVE

Metabolic reprogramming serves as a distinctive feature of cancer, impacting proliferation and metastasis, with aberrant glycosphingolipid expression playing a crucial role in malignancy. Nevertheless, limited research has investigated the connection between glycosphingolipid metabolism and pancreatic cancer.

METHODS

This study utilized a single-cell sequencing dataset to analyze the cell composition in pancreatic cancer tissues and quantified single-cell metabolism using a newly developed computational pipeline called scMetabolism. A gene signature developed from the differential expressed genes (DEGs), related to epithelial cell glycosphingolipid metabolism, was established to forecast patient survival, immune response, mutation status, and reaction to chemotherapy with pancreatic adenocarcinoma (PAAD).

RESULTS

The single-cell sequencing analysis revealed a significant increase in epithelial cell proportions in PAAD, with high glycosphingolipid metabolism occurring in the cancerous tissue. A six-gene signature prognostic model based on abnormal epithelial glycosphingolipid metabolism was created and confirmed using publicly available databases. Patients with PAAD were divided into high- and low-risk categories according to the median risk score, with those in the high-risk group demonstrating a more unfavorable survival outcome in all three cohorts, with higher rates of gene mutations (e.g., KRAS, CDKN2A), increased levels of immunosuppressive cells (macrophages, Th2 cells, regulatory T cells), and heightened sensitivity to Acetalax and Selumetinlb.

CONCLUSIONS

Abnormal metabolism of glycosphingolipids in epithelial cells may promote the development of PAAD. A model utilizing a gene signature associated with epithelial glycosphingolipids metabolism has been established, serving as a valuable indicator for the prognostic stratification of patients with PAAD.

The application of proteomics and phosphoproteomics to reveal the molecular mechanism of salidroside in ameliorating myocardial hypoxia

Salidroside (SAL), belonging to a kind of the main active ingredient of Rhodiola rosea, is extensively utilized for anti-hypoxia and prevention of altitude sickness in the plateau region of China. However, the research on the systemic changes induced by SAL at intracellular protein level is still limited, especially at protein phosphorylation level. These limitations hinder a comprehensive understanding of the regulatory mechanisms of SAL. This study aimed to investigate the potential molecular mechanism of SAL in ameliorating the acute myocardial hypoxia induced by cobalt chloride using integrated proteomics and phosphoproteomics. We successfully identified 165 differentially expressed proteins and 266 differentially expressed phosphosites in H9c2 cells following SAL treatment under hypoxic conditions. Bioinformatics analysis and biological experiment validation revealed that SAL significantly antagonized CoCl2-mediated cell cycle arrest by downregulating CCND1 expression and upregulating AURKA, AURKAB, CCND3 and PLK1 expression. Additionally, SAL can stabilize the cytoskeleton through upregulating the Kinesin Family (KIF) members expression. Our study systematically revealed that SAL had the ability to protect myocardial cells against CoCl2-induced hypoxia through multiple biological pathways, including enhancing the spindle stability, maintaining the cell cycle, relieving DNA damage, and antagonizing cell apoptosis. This study supplies a comprehension perspective on the alterations at protein and protein phosphorylation levels induced by SAL treatment, thereby expanded our knowledge of the anti-hypoxic mechanisms of SAL. Moreover, this study provides a valuable resource for further investigating the effects of SAL.

The role of histone H1.2 in pancreatic cancer metastasis and chemoresistance

AIMS

Pancreatic cancer (PC) is a highly metastatic malignant tumor of the digestive system. Drug resistance frequently occurs during cancer treatment process. This study aimed to explore the link between chemoresistance and tumor metastasis in PC and its possible molecular and cellular mechanisms.

METHODS

A Metastasis and Chemoresistance Signature (MCS) scoring system was built and validated based on metastasis- and chemoresistance-related genes using gene expression data of PC, and the model was applied to single-cell RNA sequencing data. The influence of linker histone H1.2 (H1-2) on PC was explored through in vitro and in vivo experiments including proliferation, invasion, migration, drug sensitivity, rescue experiments and immunohistochemistry, emphasizing its regulation with c-MYC signaling pathway.

RESULTS

A novel MCS scoring system accurately predicted PC patient survival and was linked to chemoresistance and epithelial-mesenchymal transition (EMT) in PC single-cell RNA sequencing data. H1-2 emerged as a significant prognostic factor, with its high expression indicating increased chemoresistance and EMT. This upregulation was mediated by c-MYC, which was also found to be highly expressed in PC tissues.

CONCLUSION

The MCS scoring system offers insights into PC chemoresistance and metastasis potential. Targeting H1-2 could enhance therapeutic strategies and improve PC patient outcomes.

Involvement of RFC3 in tamoxifen resistance in ER-positive breast cancer through the cell cycle

Since the establishment of the molecular subtyping system, ER positive breast cancer was considered to be the most prevalent type of breast cancer, and endocrine therapy was a very important solution. However, numerous studies have shown that the cell cycle plays a key role in the progression and metastasis of breast cancer. The present study showed that RFC3 was involved in the cell cycle through DNA replication. Furthermore, RFC3 expression was significantly higher in breast cancer-resistant cells than in parental cells, which correlated with the cell cycle. We confirmed these results by established drug-resistant cell lines for breast cancer, raw letter analysis and immunohistochemical analysis of primary and recurrent tissues from three ER+ breast cancers. In addition, analysis of the results through an online database revealed that RFC3 expression was significantly associated with poor prognosis in ER+ breast cancer. We also demonstrated that in ER positive breast cancer-resistant cells, knockdown of RFC3 blocked the S-phase of cells and significantly attenuated cell proliferation, migration and invasion. Furthermore, RFC3 overexpression in ER positive breast cancer cells enhanced cell proliferation, migration and invasion. Taking all these findings into account, we could conclude that RFC3 was involved in endocrine resistance in breast cancer through the cell cycle. Thus, RFC3 may be a target to address endocrine therapy resistance in ER positive breast cancer and may be an independent prognostic factor in ER positive breast cancer.

Cancer: Phosphodiesterase type 4C (PDE4C), the forgotten subfamily as a therapeutic target

Phosphodiesterase type 4 (PDE4) enzymes specifically hydrolyse cAMP in many cell signalling systems that are transduced by hormones and other primary messengers. The physiological function of the four PDE4 subfamilies (A, B, C and D) are numerous and varied due to the differentially localised plethora of isoforms that can be detected in cardiovascular, CNS and immune systems. Of the four subfamilies, least is known about PDE4C probably due to its restricted distribution pattern, scarcity of selective inhibitors and the lack of developed research tools. Here, for the first time, we chart the discovery of PDE4C, describe its regulation and highlight cancers where future development of PDE4C selective small molecules may have potential.

The new ceRNA crosstalk between mRNAs and miRNAs in intervertebral disc degeneration

Degeneration of the intervertebral disc has been linked to lower back pain. To date, pathophysiological mechanisms of intervertebral disc degeneration (IDD) remain unclear; it is meaningful to find effective diagnostic biomarkers and new therapeutic strategies for IDD. This study aimed to reveal the molecular mechanism of IDD pathogenesis from the multidimensional transcriptomics perspective. Here, we acquired IDD bulk omics datasets (GSE67567 and GSE167199) including mRNA, microRNA expression profiles, and single-cell RNA sequencing (GSE199866) from the public Gene Expression Omnibus (GEO) database. Through principal component analysis and Venn analysis, we found different expression patterns in the IDD transcription level and identified 156 common DEGs in both bulk datasets. GO and KEGG functional analyses showed these dysregulators were mostly enriched in the collagen-containing extracellular matrix, cartilage development, chondrocyte differentiation, and immune response pathways. We also constructed a potentially dysregulated competing endogenous RNA (ceRNA) network between mRNAs and miRNAs related to IDD based on microRNA target information and co-expression analysis of RNA profiles and identified 36 ceRNA axes including ZFP36/miR-155-5p/FOS, BTG2/hsa-miR-185-5p/SOCS3, and COL9A2/hsa-miR-664a-5p/IBA57. Finally, in integrating bulk and single-cell transcriptome data analyses, a total of three marker genes, COL2A1, PAX1, and ZFP36L2, were identified. In conclusion, the key genes and the new ceRNA crosstalk we identified in intervertebral disc degeneration may provide new targets for the treatment of IDD.