Comprehensively Analyzed Macrophage-Regulated Genes Indicate That PSMA2 Promotes Colorectal Cancer Progression

Mesenchymal stromal/stem cells promote intestinal epithelium regeneration after chemotherapy-induced damage

BACKGROUND

Allogeneic hematopoietic stem cell transplantation (HSCT) is a curative treatment for leukemia and a range of non-malignant disorders. The success of the therapy is hampered by occurrence of acute graft-versus-host disease (aGvHD); an inflammatory response damaging recipient organs, with gut, liver, and skin being the most susceptible. Intestinal GvHD injury is often a life-threatening complication in patients unresponsive to steroid treatment. Allogeneic mesenchymal stromal/stem cell (MSC) infusions are a promising potential treatment for steroid-resistant aGvHD. Data from our institution and others demonstrate rescue of approximately 40-50% of aGvHD patients with MSCs in Phase I, II studies and minor side effects. Although promising, better understanding of MSC mode of action and patient response to MSC-based therapy is essential to improve this lifesaving treatment.

METHODS

Single cell human small intestine organoids were embedded in Matrigel, grown for 5 days and treated with busulfan for 48 h. Organoids damaged by treatment with busulfan or control organoids were co-cultured with 5000, 10,000, and 50,000 MSCs for 24 h, 48 h or 7 days and the analyses such as surface area determination, proliferation and apoptosis assessment, RNA sequencing and proteomics were performed.

RESULTS

Here, we developed a 3D co-culture model of human small intestinal organoids and MSCs, which allows to study the regenerative effects of MSCs on intestinal epithelium in a more physiologically relevant setting than existing in vitro systems. Using this model we mimicked chemotherapy-mediated damage of the intestinal epithelium. The treatment with busulfan, the chemotherapeutic commonly used as conditioning regiment before the HSCT, affected pathways regulating epithelial to mesenchymal transition, proliferation, and apoptosis in small intestinal organoids, as shown by transcriptomic and proteomic analysis. The co-culture of busulfan-treated intestinal organoids with MSCs reversed the effects of busulfan on the transcriptome and proteome of intestinal epithelium, which we also confirmed by functional evaluation of proliferation and apoptosis.

CONCLUSIONS

Collectively, we demonstrate that our in vitro co-culture system is a new valuable tool to facilitate the investigation of the molecular mechanisms behind the therapeutic effects of MSCs on damaged intestinal epithelium. This could benefit further optimization of the use of MSCs in HSCT patients.

Iron Supplementation Increases Tumor Burden and Alters Protein Expression in a Mouse Model of Human Intestinal Cancer

Iron supplements are widely consumed. However, excess iron may accelerate intestinal tumorigenesis. To determine the effect of excess iron on intestinal tumor burden and protein expression changes between tumor and normal tissues, ApcMin/+ mice were fed control (adequate) and excess iron (45 and 450 mg iron/kg diet, respectively; n = 9/group) for 10 wk. Tumor burden was measured, and two-dimensional fluorescence difference gel electrophoresis was used to identify differentially expressed proteins in tumor and normal intestinal tissues. There was a significant increase (78.3%; p ≤ 0.05) in intestinal tumor burden (mm2/cm) with excess iron at wk 10. Of 980 analyzed protein spots, 69 differentially expressed (p ≤ 0.05) protein isoforms were identified, representing 55 genes. Of the isoforms, 56 differed (p ≤ 0.05) between tumor vs. normal tissues from the adequate iron group and 23 differed (p ≤ 0.05) between tumors from the adequate vs. excess iron. Differentially expressed proteins include those involved in cell integrity and adaptive response to reactive oxygen species (including, by gene ID: ANPEP, DPP7, ITGB1, PSMA1 HSPA5). Biochemical pathway analysis found that iron supplementation modulated four highly significant (p ≤ 0.05) functional networks. These findings enhance our understanding of interplay between dietary iron and intestinal tumorigenesis and may help develop more specific dietary guidelines regarding trace element intake.

An immune-related exosome signature predicts the prognosis and immunotherapy response in ovarian cancer

BACKGROUND

Cancer-derived exosomes contribute significantly in intracellular communication, particularly during tumorigenesis. Here, we aimed to identify two immune-related ovarian cancer-derived exosomes (IOCEs) subgroups in ovarian cancer (OC) and establish a prognostic model for OC patients based on immune-related IOCEs.

METHODS

The Cancer Genome Atlas (TCGA) database was used to obtain RNA-seq data, as well as clinical and prognostic information. Consensus clustering analysis was performed to identify two IOCEs-associated subgroups. Kaplan-Meier analysis was used to compare the overall survival (OS) between IOCEs-high and IOCEs-low subtype. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were conducted to investigate the mechanisms and biological effects of differentially expressed genes (DEGs) between the two subtypes. Besides, an IOCE-related prognostic model of OC was constructed by Lasso regression analysis, and the signature was validated using GSE140082 as the validation set.

RESULTS

In total, we obtained 21 differentially expressed IOCEs in OC, and identified two IOCE-associated subgroups by consensus clustering. IOCE-low subgroup showed a favorable prognosis while IOCE-high subgroup had a higher level of immune cell infiltration and immune response. GSEA showed that pathways in cancer and immune response were mainly enriched in IOCE-high subgroup. Thus, IOCE-high subgroup may benefit more in immunotherapy treatment. In addition, we constructed a risk model based on nine IOCE-associated genes (CLDN4, AKT2, CSPG5, ALDOC, LTA4H, PSMA2, PSMA5, TCIRG1, ANO6).

CONCLUSION

We developed a novel stratification system for OV based on IOCE signature, which could be used to estimate the prognosis as well as immunotherapy for OC patient.

MiR-128-3p promotes the progression of deep venous thrombosis through binding SIRT1

OBJECTIVES

This research aimed to study the effect of microRNA-128-3p (miR-128-3p) on deep venous thrombosis (DVT).

METHOD

The 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay, Transwell chamber method, and flow cytometry technique were used in the cell experiments. Potential interconnection between miR-128-3p and silent information regulator sirtuin 1 (SIRT1) was revealed by luciferase activity. The concentration of miR-128-3p and mRNA SIRT1 was assessed by quantitative reverse transcription polymerase chain reaction (qRT-PCR). The receiver operating characteristic (ROC) curve was used to test the predictive effect of miR-128-3p in DVT.

RESULTS

Decreased miR-128-3p expression was beneficial to cell proliferation and migration and inhibited inflammation, apoptosis, and adhesion of human umbilical vein endothelial cells (HUVECs). The impacts of miR-128-3p on HUVECs were achieved by targeting SIRT1. MiR-128-3p was upregulated in patients with DVT, and it was of great significance in differentiating patients with DVT.

CONCLUSION

Overexpression of miR-128-3p might become a biomarker for patients with DVT.

Analysis of prognostic biomarker models and immune microenvironment in acute myeloid leukemia by integrative bioinformatics

BACKGROUND

Acute myeloid leukemia (AML) is a hematological cancer driven on by aberrant myeloid precursor cell proliferation and differentiation. A prognostic model was created in this study to direct therapeutic care.

METHODS

Differentially expressed genes (DEGs) were investigated using the RNA-seq data from the TCGA-LAML and GTEx. Weighted Gene Coexpression Network Analysis (WGCNA) examines the genes involved in cancer. Find the intersection genes and construct the PPI network to discover hub genes and remove prognosis-related genes. A nomogram was produced for predicting the prognosis of AML patients using the risk prognosis model that was constructed using COX and Lasso regression analysis. GO, KEGG, and ssGSEA analysis were used to look into its biological function. TIDE score predicts immunotherapy response.

RESULTS

Differentially expressed gene analysis revealed 1004 genes, WGCNA analysis revealed 19,575 tumor-related genes, and 941 intersection genes in total. Twelve prognostic genes were found using the PPI network and prognostic analysis. To build a risk rating model, RPS3A and PSMA2 were examined using COX and Lasso regression analysis. The risk score was used to divide the patients into two groups, and Kaplan-Meier analysis indicated that the two groups had different overall survival rates. Univariate and multivariate COX studies demonstrated that risk score is an independent prognostic factor. According to the TIDE study, the immunotherapy response was better in the low-risk group than in the high-risk group.

CONCLUSIONS

We eventually selected out two molecules to construct prediction models that might be used as biomarkers for predicting AML immunotherapy and prognosis.

Impact of mini-driver genes in the prognosis and tumor features of colorectal cancer samples: a novel perspective to support current biomarkers

Background

Colorectal cancer (CRC) is the second leading cause of cancer-related deaths, and its development is associated with the gains and/or losses of genetic material, which leads to the emergence of main driver genes with higher mutational frequency. In addition, there are other genes with mutations that have weak tumor-promoting effects, known as mini-drivers, which could aggravate the development of oncogenesis when they occur together. The aim of our work was to use computer analysis to explore the survival impact, frequency, and incidence of mutations of possible mini-driver genes to be used for the prognosis of CRC.

Methods

We retrieved data from three sources of CRC samples using the cBioPortal platform and analyzed the mutational frequency to exclude genes with driver features and those mutated in less than 5% of the original cohort. We also observed that the mutational profile of these mini-driver candidates is associated with variations in the expression levels. The candidate genes obtained were subjected to Kaplan-Meier curve analysis, making a comparison between mutated and wild-type samples for each gene using a p-value threshold of 0.01.

Results

After gene filtering by mutational frequency, we obtained 159 genes of which 60 were associated with a high accumulation of total somatic mutations with Log₂ (fold change) > 2 and p values < 10^-5. In addition, these genes were enriched to oncogenic pathways such as epithelium-mesenchymal transition, hsa-miR-218-5p downregulation, and extracellular matrix organization. Our analysis identified five genes with possible implications as mini-drivers: DOCK3, FN1, PAPPA2, DNAH11, and FBN2. Furthermore, we evaluated a combined classification where CRC patients with at least one mutation in any of these genes were separated from the main cohort obtaining a p-value < 0.001 in the evaluation of CRC prognosis.

Conclusion

Our study suggests that the identification and incorporation of mini-driver genes in addition to known driver genes could enhance the accuracy of prognostic biomarkers for CRC.

Evaluating the Prognostic and Therapeutic Potentials of the Proteasome 26S Subunit, ATPase (PSMC) Family of Genes in Lung Adenocarcinoma: A Database Mining Approach

This study explored the prognostic and therapeutic potentials of multiple Proteasome 26S Subunit, ATPase (PSMC) family of genes (PSMC1-5) in lung adenocarcinoma (LUAD) diagnosis and treatment. All the PSMCs were found to be differentially expressed (upregulated) at the mRNA and protein levels in LUAD tissues. The promoter and multiple coding regions of PSMCs were reported to be differentially and distinctly methylated, which may serve in the methylation-sensitive diagnosis of LUAD patients. Multiple somatic mutations (alteration frequency: 0.6–2%) were observed along the PSMC coding regions in LUAD tissues that could assist in the high-throughput screening of LUAD patients. A significant association between the PSMC overexpression and LUAD patients’ poor overall and relapse-free survival (p < 0.05; HR: >1.3) and individual cancer stages (p < 0.001) was discovered, which justifies PSMCs as the ideal targets for LUAD diagnosis. Multiple immune cells and modulators (i.e., CD274 and IDO1) were found to be associated with the expression levels of PSMCs in LUAD tissues that could aid in formulating PSMC-based diagnostic measures and therapeutic interventions for LUAD. Functional enrichment analysis of neighbor genes of PSMCs in LUAD tissues revealed different genes (i.e., SLIRP, PSMA2, and NUDSF3) previously known to be involved in oncogenic processes and metastasis are co-expressed with PSMCs, which could also be investigated further. Overall, this study recommends that PSMCs and their transcriptional and translational products are potential candidates for LUAD diagnostic and therapeutic measure discovery.

Prognostic and Genomic Analysis of Proteasome 20S Subunit Alpha (PSMA) Family Members in Breast Cancer

The complexity of breast cancer includes many interacting biological processes, and proteasome alpha (PSMA) subunits are reported to be involved in many cancerous diseases, although the transcriptomic expression of this gene family in breast cancer still needs to be more thoroughly investigated. Consequently, we used a holistic bioinformatics approach to study the PSMA genes involved in breast cancer by integrating several well-established high-throughput databases and tools, such as cBioPortal, Oncomine, and the Kaplan–Meier plotter. Additionally, correlations of breast cancer patient survival and PSMA messenger RNA expressions were also studied. The results demonstrated that breast cancer tissues had higher expression levels of PSMA genes compared to normal breast tissues. Furthermore, PSMA2, PSMA3, PSMA4, PSMA6, and PSMA7 showed high expression levels, which were correlated with poor survival of breast cancer patients. In contrast, PSMA5 and PSMA8 had high expression levels, which were associated with good prognoses. We also found that PSMA family genes were positively correlated with the cell cycle, ubiquinone metabolism, oxidative stress, and immune response signaling, including antigen presentation by major histocompatibility class, interferon-gamma, and the cluster of differentiation signaling. Collectively, these findings suggest that PSMA genes have the potential to serve as novel biomarkers and therapeutic targets for breast cancer. Nevertheless, the bioinformatic results from the present study would be strengthened with experimental validation in the future by prospective studies on the underlying biological mechanisms of PSMA genes and breast cancer.