GAPDH and PUM1: Optimal Housekeeping Genes for Quantitative Polymerase Chain Reaction-Based Analysis of Cancer Stem Cells and Epithelial-Mesenchymal Transition Gene Expression in Rectal Tumors

The secretomes of bovine mammary epithelial cell subpopulations differentially modulate macrophage function

Bovine mammosphere-derived epithelial cell (MDEC) cultures are heterogeneous and enriched for stem and progenitor cells. We previously reported that the bovine MDEC secretome, comprised of all bioactive factors secreted by the cells, displays regenerative properties, exerts antimicrobial effects, and modulates neutrophil activity, positioning it as a promising non-antibiotic biologic therapy for infectious diseases important to the dairy industry, like mastitis. Mastitis is defined as inflammation of the udder, and it is typically caused by bacterial infection. The effect of the MDEC secretome on macrophages, a first line of defense against bacterial infections in the udder, is unknown and could impact the utility of the secretome as a therapy for mastitis. To address this, we isolated bovine monocytes from peripheral blood and maintained them as an unpolarized (M0) population or polarized them into M1 or M2 phenotypes. Macrophages cultured with the secretome of bovine MDECs were assessed for their ability to phagocytose labeled bacterial particles and accumulate reactive oxygen species (ROS). We used single-cell RNA sequencing (scRNA-seq) and fluorescence-activated cell sorting (FACS) to isolate a subpopulation of MDECs that exert enhanced effects on macrophages. We found that the secretome of MDECs that do not express cluster of differentiation (CD) 73, a cell surface enzyme used as a marker for mesenchymal stromal cells, most strongly increased macrophage phagocytosis and ROS accumulation. These findings will help optimize the generation of the bovine MDEC secretome as a suitable treatment option for mastitis.

Identification of new reference genes with stable expression patterns for cell cycle experiments in human leukemia cell lines

Cell cycle-dependent gene expression analysis is particularly important as numerous genes show tightly regulated expression patterns at different phases of the cell cycle. For cancer cells, analysis of cell cycle-related events is of paramount significance since tumorigenesis is characteristically coupled to cell cycle perturbations. RT-qPCR is a highly sensitive technique to investigate cell cycle-dependent transcriptional regulation. However, for reliable evaluation of qPCR data reference genes with stable mRNA expression are required. Although several studies investigating cell cycle-dependent gene expression employ frequently used reference genes, the suitability of these reference genes has not been thoroughly investigated so far. Moreover, such potential reference genes for cell cycle analysis have not been described in the literature. Therefore, we aimed to identify reference genes characterized with stable expression throughout the cell cycle in MOLT4 and U937 human leukemia cell lines synchronized with RO-3306 CDK1 inhibitor using RT-qPCR. Here we show that for cell cycle-dependent gene expression analysis the commonly used TBP is suitable, while the recently recognized reference genes SNW1 and CNOT4 are applicable in a cell line-dependent manner. We also suggest that proper selection of reference genes for each experimental condition is crucial for reliable normalization as these aspects can severely compromise conclusions.

Diagnostic Value of Plasma Long Non-coding SLC26A4 Antisense RNA 1 Combined with Magnetic Resonance Imaging in Rectal Cancer

Background/Aims

The prevalence of rectal cancer is increasing every year due to changes in living and eating habits. Early diagnosis contributes to the treatment and survival of patients. This study investigated the feasibility of employing SLC26A4-AS1 combined with magnetic resonance imaging (MRI) for diagnosing rectal cancer.

Materials and Methods

The current study involved 125 patients with rectal cancer and an equal number of healthy individuals. The study focused on assessing the relationship between SLC26A4-AS1 expression and clinical data among patients with rectal cancer by analyzing the expression levels. MRI blood perfusion parameters (Ktrans, Kep, Ve, and incremental area under the curve (iAUC)) were measured in the patients with rectal cancer. The regulation of SLC26A4-AS1 on the biological function of rectal cancer cells was analyzed by Cell Counting Kit-8 (CCK-8) method, flow cytometry, and Transwell assay. Furthermore, luciferase activity assays and RNA-binding protein immunoprecipitation assay (RIP) were conducted to elucidate the relationship between SLC26A4-AS1 and microRNA-3174 (miR-3174).

Results

A significant reduction in SLC26A4-AS1 expression was observed in rectal cancer alongside a significant increase in miR-3174 levels. SLC26A4-AS1 expression was negatively correlated with Ktrans and Kep values, but not with Ve or iAUC values. Cell experiments confirmed the inhibitory effect of SLC26A4-AS1 overexpression on the growth of rectal cancer cells. Additionally, SLC26A4-AS1 sponged miR-3174 mediated the progression of rectal cancer. The enriched miR-3174 may counteract the suppression of the biological activity of oe-SLC26A4-AS1 on rectal cancer cells.

Conclusion

SLC26A4-AS1 may serve as a diagnostic tool for rectal cancer, mediating tumor progression by directly targeting miR-3174.

Biological effect of ETV4 and the underlying mechanism of its regulatory effect on epithelial‑mesenchymal transition in intrahepatic cholangiocarcinoma cells

Intrahepatic cholangiocarcinoma (ICC) is a highly invasive malignant tumor. The prognosis of patients with ICC after radical surgical resection remains poor, due to local infiltration, distant metastasis, a high recurrence rate and lack of effective treatment strategies. E26 transformation-specific sequence variant 4 (ETV4) is a pro-carcinogenic factor that is upregulated in several tumors; however, the role of ETV4 in ICC is relatively unknown. The present study aimed to determine the role of ETV4 in the Hccc9810 ICC cell line and to assess how it contributes to epithelial-mesenchymal transition (EMT) in ICC. Hccc9810 cells were infected with lentiviruses to construct stable ETV4-overexpressing cells, stable ETV4 knockdown cells and corresponding control groups. The Cell Counting Kit-8 and Transwell assays were used to quantify cell proliferation, invasion and migration, and the effects on cell cycle progression and apoptosis were detected by flow cytometry. ETV4 was identified as a driver of cell growth, invasion, migration and cell cycle progression, while restraining apoptosis in Hccc9810 cells. Reverse transcription-quantitative PCR and western blotting revealed that increased ETV4 levels may drive EMT by triggering the TGF-β1/Smad signaling pathway. This cascade, in turn, may foster tumor cell proliferation, migration, invasion and cell cycle advancement, and hinder apoptosis.

FSH induces EMT in ovarian cancer via ALKBH5-regulated Snail m6A demethylation

Background: The therapeutic benefits of targeting follicle-stimulating hormone (FSH) receptor in treatment of ovarian cancer are significant, whereas the role of FSH in ovarian cancer progresses and the underlying mechanism remains to be developed. Methods: Tissue microarray of human ovarian cancer, tumor xenograft mouse model, and in vitro cell culture were used to investigate the role of FSH in ovarian carcinogenesis. siRNA, lentivirus and inhibitors were used to trigger the inactivation of genes, and plasmids were used to increase transcription of genes. Specifically, pathological characteristic was assessed by histology and immunohistochemistry (IHC), while signaling pathway was studied using western blot, quantitative RT-PCR, and immunofluorescence. Results: Histology and IHC of human normal ovarian and tumor tissue confirmed the association between FSH and Snail in ovarian cancer metastasis. Moreover, in epithelial ovarian cancer cells and xenograft mice, FSH was showed to promote epithelial mesenchymal transition (EMT) progress and metastasis of ovarian cancer via prolonging the half-life of Snail mRNA in a N6-methyladenine methylation (m6A) dependent manner, which was mechanistically through the CREB/ALKBH5 signaling pathway. Conclusions: These findings indicated that FSH induces EMT progression and ovarian cancer metastasis via CREB/ALKBH5/Snail pathway. Thus, this study provided new insight into the therapeutic strategy of ovarian cancer patients with high level of FSH.

Identification of AP002498.1 and LINC01871 as prognostic biomarkers and therapeutic targets for distant metastasis of colorectal adenocarcinoma

BACKGROUND

Increasing evidence suggests that lncRNA (Long non-coding RNA, lncRNA)-mediated ceRNA (competing endogenous RNA, ceRNA) networks are involved in the occurrence and progression of colorectal cancer (CRC). However, the roles of the lncRNA-miRNA-mRNA ceRNA network in distant metastasis of CRC are still unclear.

METHODS

In this study, we constructed a specific ceRNA network to identify potential biomarkers and therapeutic targets for distant metastasis of CRC. Specifically, RNA-Seq data from The Cancer Genome Atlas (TCGA) were used to screen for differentially expressed lncRNAs (DElncRNAs) and mRNAs (DEmRNAs) related to metastasis. After validation and selection by qRT-PCR and univariate and multivariate analysis of the metastasis- and prognosis-related lncRNAs, the regulated microRNAs (miRNAs) and coexpressed mRNAs were used to construct a ceRNA network for distant metastasis of CRC.

RESULTS

Two key distant metastasis-related DElncRNAs, AP002498.1 and LINC01871, were identified by univariate and multivariate analysis in combination with analyses of clinical data and expression levels. Furthermore, lncRNA-associated ceRNA subnetworks were constructed from the predicted miRNAs and 13 coexpressed DEmRNAs (SERPINA1, ITLN1, REG4, L1TD1, IGFALS, MUC5B, CIITA, CXCL9, CXCL10, GBP4, GNLY, IDO1, and NOS2). The AP002498.1- and LINC01871-associated ceRNA subnetworks regulated the expression of the target genes SERPINA1 and MUC5B and GNLY, respectively, through the associated miRNAs.

CONCLUSION

The DElncRNA AP002498.1 and the LINC01871/miR-4644 and miR-185-5p/GNLY axes were identified as being closely associated with distant metastasis and could represent independent prognostic biomarkers or therapeutic targets in colorectal adenocarcinoma.

Exploring novel genetic and hematological predictors of response to neoadjuvant chemoradiotherapy in locally advanced rectal cancer

Introduction: The standard treatment for locally advanced rectal cancer (LARC) is neoadjuvant chemoradiotherapy (nCRT). To select patients who would benefit the most from nCRT, there is a need for predictive biomarkers. The aim of this study was to evaluate the role of clinical, pathological, radiological, inflammation-related genetic, and hematological parameters in the prediction of post-nCRT response. Materials and methods: In silico analysis of published transcriptomics datasets was conducted to identify candidate genes, whose expression will be measured using quantitative Real Time PCR (qRT-PCR) in pretreatment formaline-fixed paraffin-embedded (FFPE) samples. In this study, 75 patients with LARC were prospectively included between June 2020-January 2022. Patients were assessed for tumor response in week 8 post-nCRT with pelvic MRI scan and rigid proctoscopy. For patients with a clinical complete response (cCR) and initially distant located tumor no immediate surgery was suggested ("watch and wait" approach). The response after surgery was assessed using histopathological tumor regression grading (TRG) categories from postoperative specimens by Mandard. Responders (R) were defined as patients with cCR without operative treatment, and those with TRG 1 and TRG 2 postoperative categories. Non-responders (NR) were patients classified as TRG 3-5. Results: Responders group comprised 35 patients (46.6%) and NR group 53.4% of patients. Analysis of published transcriptomics data identified genes that could predict response to treatment and their significance was assessed in our cohort by qRT-PCR. When comparison was made in the subgroup of patients who were operated (TRG1 vs. TRG4), the expression of IDO1 was significantly deregulated (p < 0.05). Among hematological parameters between R and NR a significant difference in the response was detected for neutrophil-to-monocyte ratio (NMR), initial basophil, eosinophil and monocyte counts (p < 0.01). According to MRI findings, non-responders more often presented with extramural vascular invasion (p < 0.05). Conclusion: Based on logistic regression model, factors associated with favorable response to nCRT were tumor morphology and hematological parameters which can be easily and routinely derived from initial laboratory results (NMR, eosinophil, basophil and monocyte counts) in a minimally invasive manner. Using various metrics, an aggregated score of the initial eosinophil, basophil, and monocyte counts demonstrated the best predictive performance.

Expression of housekeeping genes varies depending on mevalonate pathway inhibition in cancer cells

Statins have anticancer effects and may be used as anticancer agents via drug repositioning. In reverse transcription-quantitative polymerase chain reaction (RT-qPCR) assays, the internal reference gene must not be affected by any experimental conditions. As statins exert a wide range of effects on cells by inhibiting the mevalonate pathway, it is possible that statin treatment might alter the expression of housekeeping genes used as internal reference genes, thereby misleading the assessment of obtained gene expression data. Here, we evaluated the expression stability of internal reference genes in atorvastatin-treated cancer cell lines. We treated both statin-sensitive and statin-resistant cancer cell lines with atorvastatin at seven different concentrations and performed RT-qPCR on 15 housekeeping genes whose expression stability was then assessed using five different algorithms. In both statin-sensitive and statin-resistant cancer cell lines, atorvastatin affected the expression of certain internal reference genes in a dose-dependent and cancer cell line-dependent manner; therefore, caution should be exercised when comparing target gene expression between cells. Our findings emphasize the importance of the validation of internal reference genes in gene expression analyses in drug treatment-based cancer research.

A new intronic quantitative PCR method led to the discovery of transformation from human ascites to murine malignancy in a mouse model

Purpose

To establish a fast and accurate detection method for interspecies contaminations in the patient-derived xenograft (PDX) models and cell lines, and to elucidate possible mechanisms if interspecies oncogenic transformation is detected.

Methods

A fast and highly sensitive intronic qPCR method detecting Gapdh intronic genomic copies was developed to quantify if cells were human or murine or a mixture. By this method, we documented that murine stromal cells were abundant in the PDXs; we also authenticated our cell lines to be human or murine.

Results

In one mouse model, GA0825-PDX transformed murine stromal cells into a malignant tumorigenic murine P0825 cell line. We traced the timeline of this transformation and discovered three subpopulations descended from the same GA0825-PDX model: epithelium-like human H0825, fibroblast-like murine M0825, and main passaged murine P0825 displayed differences in tumorigenic capability in vivo. P0825 was the most aggressive and H0825 was weakly tumorigenic. Immunofluorescence (IF) staining revealed that P0825 cells highly expressed several oncogenic and cancer stem cell markers. Whole exosome sequencing (WES) analysis revealed that TP53 mutation in the human ascites IP116-generated GA0825-PDX may have played a role in the human-to-murine oncogenic transformation.

Conclusion

This intronic qPCR is able to quantify human/mouse genomic copies with high sensitivity and within a time frame of a few hours. We are the first to use intronic genomic qPCR for authentication and quantification of biosamples. Human ascites transformed murine stroma into malignancy in a PDX model.

Effect of bevacizumab combined with chemotherapy on SDF-1 and CXCR4 in epithelial ovarian cancer and its prognosis

BACKGROUND

The effect of bevacizumab combined with chemotherapy on the expression of stromal cell-derived factor-1 (SDF-1) and receptor CXCR4 in epithelial ovarian cancer tumor cells and its prognosis are unknown. Our work aimed to investigate the effect of chemotherapy +/- bevacizumab on these markers and the impact of this treatment modality in clinical outcomes.

METHODS

Altogether 68 patients with epithelial ovarian cancer who were treated with chemotherapy in our hospital from June 2018 to June 2019 were selected. It was an open-labeled and controlled clinical trial (ethical approval no. 20180435). The patients were grouped according to their admission order. Patients treated with paclitaxel and carboplatin were included in group A, while patients treated with bevacizumab, paclitaxel, and carboplatin were included in group B. qRT-PCR was used to detect the changes of SDF-1 and CXCR4 before and after chemotherapy. Various clinical indicators of patients in the two groups were recorded to analyze the clinical efficacy, and safety of different treatment modalities and the prognosis of the two groups was analyzed.

RESULTS

The relative expression of SDF-1 and CXCR4 was positively correlated with epithelial ovarian cancer stages (P<0.00). Together, SDF-1 and CXCR4 were positively correlated in epithelial ovarian cancer staging (P<0.001). SDF-1 and CXCR4 in both groups after chemotherapy were significantly decreased (P<0.001), and the downregulation of SDF-1 and CXCR4 expression in group B was significantly higher than that in group A after chemotherapy (P<0.001). No significant difference in the metastasis rates of the two groups before chemotherapy was observed (P>0.05), but the recurrence rate after 1 year was lower in group B than in group A (P<0.05).

CONCLUSION

Adding bevacizumab diminished the expression of related cancer markers SDF-1 and CXCR4 more than chemotherapy alone in patients with epithelial ovarian cancer. Furthermore, better rates of recurrence with no concerns regarding adverse drug reactions or quality of life were seen in bevacizumab plus chemotherapy group.

G-protein coupled receptor 34 regulates the proliferation and growth of LS174T cells through differential expression of PI3K subunits and PTEN

PURPOSE

G-protein coupled receptor (GPR 34) has been found to play important roles in some cancers and regulates the proliferation, apoptosis, and migration of these cancer cells. However, the mechanisms underlying how GPR34 functions to regulate growth and proliferation of colorectal cancer cells remains to be clarified.

METHODS

We employed stable GPR34 knockdown LS174T cell models, GPR34 Mab blocking, a CCK-8 kit, and a colony formation assay to characterize the effect of GPR34 on the proliferation of LS174T in vitro and xenograft tumor growth in vivo. The mRNA level of GPR34 was detected by RT-PCR in tumor tissues and adjacent normal tissues from 34 CRC patients.

RESULTS

Based on RT-PCR results, GPR34 exhibited high level in tumor samples compared with adjacent normal samples. Increased expression of GPR34 is more associated with poor prognosis of CRC as shown in The Cancer Genome Atlas (TCGA) dataset by Kaplan-Meier survival analysis. Furthermore, we showed that GPR34 knockdown inhibited the proliferation of LS174T colon cancer cells and related xenograft tumor growth. Searching for the distinct molecular mechanism, we identified several contributors to proliferation of LS174T colon cancer cells: PI3K subunits/PTEN, PDK1/AKT, and Src/Raf/Ras/ERK. GPR34 knockdown inhibited the proliferation of LS174T cells by upregulating expression of PTEN, and downregulating expression of PI3K subunits p110-beta.

CONCLUSION

Our findings provide direct evidence that GPR34 regulates the proliferation of LS174T cells and the growth of LS174T tumor xenografts by regulating different pathways. High expression of GPR34 mRNA could then be used to predict poor prognosis of CRC.