Interplay Between Non-Coding RNAs and Programmed Cell Death Proteins

Exploring the feasibility of using mice as a substitute model for investigating microglia in aging and Alzheimer's disease though single cell analysis

OBJECTIVE

To guide animal experiments, we investigated the similarities and differences between humans and mice in aging and Alzheimer's disease (AD) at the single-nucleus RNA sequencing (snRNA-seq) or single-cell RNA sequencing (scRNA-seq) level.

METHODS

Microglia cells were extracted from dataset GSE198323 of human post-mortem hippocampus. The distributions and proportions of microglia subpopulation cell numbers related to AD or age were compared. This comparison was done between GSE198323 for humans and GSE127892 for mice, respectively. The Seurat R package and harmony R package were used for data analysis and batch effect correction. Differentially expressed genes (DEGs) were identified by FindMarkers function with MAST test. Comparative analyses were conducted on shared genes in DEGs associated with age and AD. The analyses were done between human and mouse using various bioinformatics techniques. The analysis of genes in DEGs related to age was conducted. Similarly, the analysis of genes in DEGs related to AD was performed. Cross-species analyses were conducted using orthologous genes. Comparative analyses of pseudotime between humans and mice were performed using Monocle2.

RESULTS

(1) Similarities: The proportion of microglial subpopulation Cell_APOE/Apoe shows consistent trends, whether in AD or normal control (NC) groups in both humans and mice. The proportion of Cell_CX3CR1/Cx3cr1, representing homeostatic microglia, remains stable with age in NC groups across species. Tuberculosis and Fc gamma R-mediated phagocytosis pathways are shared in microglia responses to age and AD across species, respectively. (2) Differences: IL1RAPL1 and SPP1 as marker genes are more identifiable in human microglia compared to their mouse counterparts. Most genes of DEGs associated with age or AD exhibit different trends between humans and mice. Pseudotime analyses demonstrate varying cell density trends in microglial subpopulations, depending on age or AD across species.

CONCLUSIONS

Mouse Apoe and Cell_Apoe maybe serve as proxies for studying human AD, while Cx3cr1 and Cell_Cx3cr1 are suitable for human aging studies. However, AD mouse models (App_NL_G_F) have limitations in studying human genes like IL1RAPL1 and SPP1 related to AD. Thus, mouse models cannot fully replace human samples for AD and aging research.

Higher expression of programmed cell death 4 (PDCD4) in acute myeloid leukemia is associated with better prognosis after chemotherapy

Acute myeloid leukemia (AML) is a common heterogeneous malignancy. Novel molecular markers aid diagnosis, patient sub-categorization, and optimal clinical decisions. Here, we explored the prognostic implications associated with the expression of the programmed cell death (PDCD) family of molecules in AML patients. Based on the findings from the TCGA and OHSU cohorts, we observed that the mRNA abundance of PDCD4 is significantly higher compared to other molecules within the PDCD family. Furthermore, high expression of PDCD4 was associated with predicted long-term patient survival in diagnosed AML patients. In the chemotherapy group, patients with high PDCD4 expression showed a tendency toward longer overall survival (OS) (P = 0.0266) and event-free survival (EFS) (P = 0.0008). High PDCD4 levels served as a favorable independent predictor for both OS and EFS in AML patients. However, subgroup analyses in the hematopoietic stem cell transplantation (HSCT) group revealed no significant difference in OS or EFS between individuals with high and low PDCD4 expression. Furthermore, in the low PDCD4 expression group, AML patients who underwent HSCT experienced improved survival outcomes (P = 0.0015), helping to mitigate the unfavorable prognosis associated with PDCD4 downregulation. Conversely, in the high PDCD4 expression group, HSCT offered a notable short-term survival advantage, while patients with high PDCD4 expression responded favorably to long-term survival through chemotherapy. Biological function enrichment showed that the expression of PDCD4 was correlated with complement and coagulation cascades, cell receptor signaling pathways, and cholesterol metabolism. The findings from this study will aid in better categorizing heterogeneous AML patients and guiding more appropriate clinical decision-making.

The Dual Role of PDCD10 in Cancers: A Promising Therapeutic Target

Programmed cell death 10 (PDCD10) was initially considered as a protein associated with apoptosis. However, recent studies showed that PDCD10 is actually an adaptor protein. By interacting with multiple molecules, PDCD10 participates in various physiological processes, such as cell survival, migration, cell differentiation, vesicle trafficking, cellular senescence, neurovascular development, and gonadogenesis. Moreover, over the past few decades, accumulating evidence has demonstrated that the aberrant expression or mutation of PDCD10 is extremely common in various pathological processes, especially in cancers. The dysfunction of PDCD10 has been strongly implicated in oncogenesis and tumor progression. However, the updated data seem to indicate that PDCD10 has a dual role (either pro- or anti-tumor effects) in various cancer types, depending on cell/tissue specificity with different cellular interactors. In this review, we aimed to summarize the knowledge of the dual role of PDCD10 in cancers with a special focus on its cellular function and potential molecular mechanism. With these efforts, we hoped to provide new insight into the future development and application of PDCD10 as a clinical therapeutic target in cancers.

Interplay between programmed death-ligand 1 and non-coding RNAs

Programmed death-ligand 1 (PD-L1) is a transmembrane protein with essential roles in the suppression of adaptive immune responses. As an immune checkpoint molecule, PD-L1 can be exploited by cancer cells to evade the anti-tumor attacks initiated by the immune system. Thus, blockade of the PD1/PD-L1 axis can eliminate the suppressive signals and release the antitumor immune responses. Identification of the underlying mechanisms of modulation of the activity of the PD1/PD-L1 axis would facilitate the design of more efficacious therapeutic options and better assignment of patients for each option. Recent studies have confirmed the interactions between miRNAs/lncRNAs/circ-RNAs and the PD1/PD-L1 axis. In the current review, we give a summary of interactions between these transcripts and PD-L1 in the context of cancer. We also overview the consequences of these interactions in the determination of the response of patients to anti-cancer drugs.

DNMT3b-mediated SPAG6 promoter hypermethylation affects lung squamous cell carcinoma development through the JAK/STAT pathway

BACKGROUND

DNA methylation controls the transcription of genes and is involved in the development of lung cancer. Our preliminary bioinformatics prediction revealed that sperm associated antigen 6 (SPAG6) was considerably hypermethylated in lung squamous cell carcinoma (LUSC). Thus, this study aimed to probe the mechanism underlying its hypermethylation.

METHODS

The effect of DNA methylation of SPAG6 on its expression in LUSC was analyzed. The contributors to SPAG6 DNA hypermethylation were sought. CCK-8, EdU, and Transwell assays were carried out to assess the malignant phenotype of LUSC cells. KEGG pathway enrichment analysis was used to screen for pathways affected by SPAG6, which were confirmed by dual-luciferase assays. Bioinformatics analysis was conducted to dissect the impact of SPAG6 on the immune response and cancer cell stemness in LUSC.

RESULTS

DNA methyltransferase 3b (DNMT3b)-mediated hypermethylation of the SPAG6 promoter in LUSC led to SPAG6 downregulation. SPAG6 reverted the malignant phenotype of LUSC cells. SPAG6 regulated the JAK/STAT pathway by inhibiting the transcription of STAT1 and STAT3. The expression of SPAG6 was positively related to immune infiltration in LUSC and inversely related to the expressions of the immunosuppressive genes CTLA4 and PDCD1. SPAG6 expression was negatively correlated with cancer cell stemness in LUSC, and its expression inhibited the expressions of Nanog, ALDH1, and Sox2, markers of cancer cell stemness.

CONCLUSIONS

DNMT3b-mediated SPAG6 promoter hypermethylation activates the JAK/STAT pathway to promote LUSC progression.

Small Extracellular Vesicles and Their Involvement in Cancer Resistance: An Up-to-Date Review

In recent years, tremendous progress has been made in understanding the roles of extracellular vesicles (EVs) in cancer. Thanks to advancements in molecular biology, it has been found that the fraction of EVs called exosomes or small EVs (sEVs) modulates the sensitivity of cancer cells to chemotherapeutic agents by delivering molecularly active non-coding RNAs (ncRNAs). An in-depth analysis shows that two main molecular mechanisms are involved in exosomal modified chemoresistance: (1) translational repression of anti-oncogenes by exosomal microRNAs (miRs) and (2) lack of translational repression of oncogenes by sponging of miRs through long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs). At the cellular level, these processes increase the proliferation and survival of cancer cells and improve their ability to metastasize and resist apoptosis. In addition, studies in animal models have shown enhancing tumor size under the influence of exosomal ncRNAs. Ultimately, exosomal ncRNAs are responsible for clinically significant chemotherapy failures in patients with different types of cancer. Preliminary data have also revealed that exosomal ncRNAs can overcome chemotherapeutic agent resistance, but the results are thoroughly fragmented. This review presents how exosomes modulate the response of cancer cells to chemotherapeutic agents. Understanding how exosomes interfere with chemoresistance may become a milestone in developing new therapeutic options, but more data are still required.

Dissecting the Roles of PDCD4 in Breast Cancer

The human programmed cell death 4 (PDCD4) gene was mapped at chromosome 10q24 and encodes the PDCD4 protein comprised of 469 amino acids. PDCD4 inhibits protein translation PDCD4 inhibits protein translation to suppress tumor progression, and its expression is frequently decreased in breast cancer. PDCD4 blocks translation initiation complex by binding eIF4A via MA-3 domains or by directly binding 5’ mRNA internal ribosome entry sites with an RNA binding domain to suppress breast cancer progression and proliferation. Numerous regulators and biological processes including non-coding RNAs, proteasomes, estrogen, natural compounds and inflammation control PDCD4 expression in breast cancer. Loss of PDCD4 expression is also responsible for drug resistance in breast cancer. HER2 activation downregulates PDCD4 expression by activating MAPK, AKT, and miR-21 in aromatase inhibitor-resistant breast cancer cells. Moreover, modulating the microRNA/PDCD4 axis maybe an effective strategy for overcoming chemoresistance in breast cancer. Down-regulation of PDCD4 is significantly associated with short overall survival of patients, which suggests that PDCD4 may be an independent prognostic marker for breast cancer.