Quantification Of Expression Levels Research Articles

LAG-3 Expression, γδ-T cell/MHC-I Interactions and Prognosis in Merkel Cell Carcinoma

Merkel Cell Carcinoma (MCC) is an aggressive cutaneous malignancy with a poor prognosis. One of the major mechanisms of immune evasion in MCC involves downregulation of MHC-I. Anti-PD-1/PD-L1 checkpoint inhibitors (CKIs) have revolutionized treatment for MCC, producing objective responses in ∼50% of patients, and are now standard of care; however, a substantial proportion of patients either fail to respond or develop resistance to CKIs. Given these recent successes, identification of other targetable immune checkpoints in the MCC tumor microenvironment (TME) is of great interest. Additionally, γ-delta (γδ) T cells may play critical roles in the response to MHC-I deficient cancers; therefore, evaluating γδ-T cells as a prognostic biomarker is warranted. We characterized the expression of PD-L1, PD-1, CD3, CD8, LAG-3, MHC-I, and γδ-T cells by IHC in a pre-immunotherapy retrospective cohort of 54 cases of MCC, and quantified expression levels and marker density via HALO. The increased density of LAG-3 and γδ-T cells correlated with other markers of an inflamed TME, with significant positive associations across all six markers (p<.002). Reflective of their putative role in the response to MHC-I suppressed cancers, cases with low HLA-I density showed a trend towards a higher ratio of γδ-T cells:CD3+ T cells (Spearman's r=-0.1582, p=0.21). Importantly, high CD3 density (HR=0.23, p=0.002), LAG-3 density (HR=0.47, p=0.037), γδ-T cell density (HR=0.26, p=0.02), and CD8 density (HR=0.27, p=0.03) showed associations with improved progression-free survival. Conditional tree analysis demonstrated that high CD8 and TCRδ expression were non-significant predictors of improved PFS and OS. Overall, LAG-3 is expressed in MCC infiltrates and is prognostic in pre-immunotherapy MCC, suggesting a potential role for LAG-3 inhibition in MCC. Additionally, CD8 and γδ-T cells may play a critical role in the response to MCC, and γδ-T cell density may represent a novel biomarker in MCC.

Insulin-like growth factor binding protein 2 predicts course of concomitant right-ventricular dilation and tricuspid regurgitation after transcatheter edge-to-edge mitral valve repair

Abstract Aims Right ventricular (RV) dilation and secondary tricuspid regurgitation (TR) are highly prevalent comorbidities in patients with mitral regurgitation and are associated with a worse prognosis. TR improvement after successful transcatheter edge-to-edge mitral valve repair (M-TEER) is reported regularly, however specific factors contributing to the recovery of RV function and TR after M-TEER are poorly understood. Particularly the role of serum biomarkers in this context is unclear. We aimed to identify specific biomarkers associated with the course of concomitant RV dilation and TR after M-TEER. Methods and Results We prospectively included 242 patients undergoing M-TEER at our center and obtained pre-procedural blood samples for biomarker analysis. A commercial multiplex protein assay (Cardiovascular III, Olink, Uppsala, Sweden) was used to quantify expression levels of 92 defined biomarkers. We then analyzed differences in biomarker expression between patients with and without right ventricular reverse remodeling (RVRR) as defined by improvement of concomitant TR by at least one grade and/or downsizing of the basal RV diameter of at least 10%. 242 patients were included in this analysis, 94 had no/mild concomitant TR at baseline, 148 had moderate/severe TR. RV diameters correlated with TR severity and were significantly larger in patients with moderate/severe TR. At baseline, expression of numerous cardiometabolic biomarkers was significantly higher in patients with moderate/severe TR. These included NT-proBNP (1.9-fold, p &amp;lt; 0.001), matrix metalloproteinase 2 (1.4-fold, p &amp;lt; 0.001) as well as insulin-like growth factor binding proteins 1 (1.7-fold, p &amp;lt; 0.001), -2 (1.3-fold, p = 0.001) and -7 (1.4-fold, p &amp;lt; 0.001). Follow-up analysis was performed in patients with initial moderate/severe TR. The course of TR and RV dimensions three months after M-TEER could be assessed in 99 patients (56 with moderate TR, 43 with severe TR). RVRR had occurred in 50 patients (50.5%). Patients without RVRR had a higher prevalence of chronic pulmonary disease (24.5 vs. 2.2%, p &amp;lt; 0.001). No further differences in clinical characteristics were found. Specifically, RV diameter, systolic pulmonary artery pressure (sPAP) and right-ventricular systolic function did not differ substantially between both groups. Strikingly however, the expression of insulin-like growth factor binding protein 2 (IGFBP-2) was significantly higher in patients, who did not develop RVRR (fold change 1.3 compared to patients with RVRR, p = 0.022). After adjustment for covariates IGFBP-2 was independently associated with absence of RVRR (Odds Ratio 2.078, 95% Confidence interval 1.108 – 3.897, p = 0.023). Conclusions In patients undergoing M-TEER with concomitant moderate or severe TR, numerous cardiometabolic biomarkers including IGFBP-2 are upregulated. Higher levels of IGFBP-2 at baseline are independently associated with persistent TR and/or RV dilation after M-TEER.

CSTB, FABP4, IBP-1 and ST2 are strong predictors of mortality after transcatheter edge-to-edge mitral valve repair

Abstract Introduction Various clinical characteristics have emerged as prognostic factors in patients undergoing transcatheter edge-to-edge mitral valve repair (M-TEER). The use of biomarkers for outcome prediction has enormous potential. The goal of this study was to identify novel biomarkers linked with adverse events after M-TEER. Methods We prospectively included 242 patients undergoing M-TEER at our center and obtained pre-procedural blood samples for biomarker analysis. Additionally, 94 follow-up samples were taken three months after M-TEER. A commercial multiplex protein assay (Cardiovascular III, Olink, Uppsala, Sweden) was used to quantify expression levels of 92 defined biomarkers. We analyzed differences in biomarker expression levels between patients that had died within one year after M-TEER and patients that had survived. Results 39 patients (16.3%) had died within one year after M-TEER. In these patients the most significantly upregulated biomarkers were NT-proBNP (expression 3.0-fold compared to survivors, p &amp;lt; 0.001), Cystatin B (CSTB; 2.0-fold, p &amp;lt; 0.001), fatty acid binding protein 4 (FABP4; 2.0-fold, p &amp;lt; 0.001), insulin-like growth factor-binding protein 1 (IBP-1; 1.9-fold, p &amp;lt; 0.001) and suppression of tumourigenicity 2 (ST2; 1.7-fold, p &amp;lt; 0.001). In non-survivors, expression levels of NT-proBNP (6.1-fold, p = 0.036), CSTB (3.2-fold, p = 0.050), FABP4 (3.7-fold, p = 0.037) and ST2 (2.1-fold, p = 0.017) were persistently elevated at the time of follow-up. Since its prognostic impact has already been described elsewhere, NT-proBNP was excluded from further analysis. Kaplan Meier analysis for 1-year mortality was carried out using tertiles of the respective biomarker expression levels. Mortality risk increased significantly with rising expression levels (CSTB: 3.4% in tertile 1, 12.2% in tertile 2, 37.9% in tertile 3; FABP4: 5.1%, 14.2% and 31.7%; IBP-1: 3.3%, 13.2% and 36.2%; ST2: 4.9%, 11.9% and 36.7%; p by log-rank-test &amp;lt; 0.001 for all biomarkers). Patients in which all 4 biomarkers were elevated to the highest tertile had an excessively high mortality risk of 52.9 vs. 13.5% (p by log-rank-test &amp;lt; 0.001). Receiver operating characteristic (ROC) analysis suggested higher predictive performances for mortality of all 4 biomarkers as compared to the EuroSCORE II (CSTB: area under the curve (AUC) 78.1%, 95% CI 70.7 – 85.5%; FABP4: AUC 71.6%, 95% CI 63.1 – 80.0%; IBP-1: AUC 73.9%, 95% CI 65.7 – 82.1%; ST2: AUC 76.2%, 95% CI 68.5 – 84.0%; EuroSCORE II: AUC 68.4%, 95% CI 59.3 – 77.5%). Conclusion This analysis has revealed novel biomarkers (CSTB, FABP4, IBP-1, ST2), which so far have not been characterized in M-TEER and suggests significant prognostic implications. Predictive performance of each of the respective biomarkers was superior to the most commonly used pre-operative risk stratification tool: the surgical EuroSCORE II. This hypothesis-generating study warrants further examination of these promising biomarkers.

GGTLC1 knockdown inhibits the progression of endometrial cancer by regulating the TGF-β/Smad signaling pathway

PurposeEndometrial cancer (EC) poses a serious risk to females worldwide; thus, a deep understanding of EC is urgently required. The role and mechanisms of gamma-glutamyltransferase light chain 1 (GGTLC1) in EC remain obscure. This study aims to elucidate the function and mechanisms underlying GGTLC1's involvement in EC. MethodsBioinformatic tools and databases were used to analyze GGTLC1 and its associated gene expression in EC tissues. Functional enrichment explorations and immune infiltration analyses were conducted, together with investigation into the methylation status of GGTLC1. Western blotting and Quantitative real-time PCR quantified expression levels. Additional experimental methodologies elucidated the role of GGTLC1 in EC progression. Transcriptome sequencing identified potential regulatory pathways for GGTLC1, and tumor growth was evaluated in vivo using HEC-1A cells in nude mice. ResultsGGTLC1 was upregulated and negatively correlated with immune cell infiltration and DNA methylation in EC. Cell migration and proliferation were reduced following GGTLC1 knockdown, together with arrest at the G0/G1 phase and an upsurge in apoptosis. Compared to the knockdown group, TGF-β/Smad signaling pathway was up-regulated in the negative control group of EC cells by transcriptome analysis. The levels of TGF-β, pSmad2, and pSmad3 followed the same decreasing trend, whereas Smad3 and Smad2 protein levels remained unchanged. ConclusionKnockdown of GGTLC1 attenuates EC development through the TGF-β/Smad pathway, positioning GGTLC1 as a promising target for EC treatment.

Antiretroviral Therapy Suppresses RNA N6-Methyladenosine Modification in Peripheral Blood Mononuclear Cells from HIV-1-Infected Individuals.

RNA N6-methyladenosine (m6A) modification is important for regulating gene expression and innate immune responses to viral infection. HIV-1 in vitro infection induces a significant increase in m6A modification of cellular RNA; however, whether m6A levels of cellular RNA are affected by HIV-1 replication or by antiretroviral therapy (ART) in infected individuals remains unknown. Using dot blot or enzyme-linked immunosorbent assay, we measured RNA m6A levels of peripheral blood mononuclear cells (PBMCs) from healthy donors or HIV-1-infected individuals with or without ART. Using a reverse transcription-quantitative polymerase chain reaction array, we quantified expression levels of 84 type-I interferon (IFN-I)-responsive genes in PBMCs from some individuals of these three groups. RNA m6A levels in PBMCs from HIV-1 viremic patients (n = 10) were significantly higher (p ≤ .0001) compared with ART-treated individuals (n = 22) or 1.5-fold higher compared with healthy donors (n = 14). However, the increase in RNA m6A levels did not correlate with changes in the expression of 10 m6A-regulatory genes. We found significant upregulation and downregulation in the expression of several IFN-I-responsive genes from HIV-1 viremic patients (n = 4) and ART-treated patients (n = 6) compared with healthy donors (n = 5), respectively. Our results suggest that post-transcriptional m6A modification may contribute to the regulation of IFN-I-responsive gene expression during HIV-1 infection and ART.

Determination of Early Diagnostic Biomarkers of Renal Dysfunction After Cardiopulmonary Bypass: miR-21 and miR10a Mediated Postoperative Inflammation

Objective: Acute renal failure (ARF) prevalence is high among patients who undergo cardiopulmonary bypass (CPB), and this condition can only be diagnosed via serum creatinine level (sCr) conventionally within 48 hours. Therefore, we need early novel diagnosis biomarkers to start preventive treatment of ARF. For that reason, we aimed to analyze if plasma miR-21 derived from heart, correlates with kidney- enriched miR-10a during inflammatory IL-6, IL-1β, and TNF-α response in terms of acute renal failure 30 minutes after CPB.&#x0D; Methods: Patients (n=46, Female:8 and Male:38), aged 61.08±9.41, who underwent CPB surgery were included. Blood samples were collected during the pre – and post-CPB (30 minutes after CPB). Demographic data of all cases were collected. Quantification of expression levels of miR-21 and miR-10a was done via quantitative PCR (qPCR). Determination of plasma concentration of relevant cytokines, IL-6, IL-1β, and TNF-α was done via ELISA.&#x0D; Results: The circulating level of miR-21 during post-CPB period (-11.78±6.98) was significantly higher (p≤0.05) than pre-CPB period (-6.55±7.11), but there was no significant change (p&gt;0.05) in the circulating level of miR-10a between pre – (-12.22±3.55) and post-CPB (-11.60±3.36) periods. When we compared the mean ΔΔCt values of miR-21 and miR-10a, downregulation was observed in the expression level of miR-10a (0.62±3.77) whilst the expression level of miR-21 (-5.22±7.25) was upregulated (p≤0.05). The levels of plasma concentration of IL-6 (2.74±2.50 ng/l) and TNF-α (83.63±9.33 ng/l) were increased during post-CPB period (both were ***p

Discovering common pathogenetic processes between tuberculosis and COVID-19 by bioinformatics and system biology approach

BackgroundSARS-CoV-2, the cause of the COVID-19 pandemic, poses a significant threat to humanity. Individuals with pulmonary tuberculosis (PTB) are at increased risk of developing severe COVID-19, due to long-term lung damage that heightens their susceptibility to full-blown disease. MethodsThree COVID-19 datasets (GSE157103, GSE166253, and GSE171110) and one PTB dataset (GSE83456) were obtained from the Gene Expression Omnibus databases. Subsequently, data were subjected to weighted gene co-expression network analysis(WGCNA)followed by functional enrichment analysis using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway databases. These analyses revealed two overlapping disease-specific modules, each comprising co-regulated genes with potentially related biological functions. Using Cytoscape, we visualised the interaction network containing common disease-related genes found within the intersection between modules and predicted transcription factors (TFs). Real-time qPCR was conducted to quantify expression levels of these genes in blood samples from COVID-19 and PTB patients. Finally, DisGeNET and the Drug Signatures database were employed to analyze these common genes, unveiling their connections to clinical disease features and potential drug treatments. ResultsExamination of the overlap between COVID-19 and PTB gene modules unveiled 11 common genes. Functional enrichment analyses using KEGG and GO shed light on potential functional relationships among these genes, providing insights into their potential roles in the heightened mortality of PTB patients due to SARS-CoV-2 infection. Furthermore, results of various bioinformatics-based analyses of common TFs and target genes led to identification of shared pathways and therapeutic targets for PTB patients with COVID-19, along with potential drug treatments for these patients. ConclusionOur results unveiled a potential biological connection between COVID-19 and PTB, as supported by results of functional enrichment analysis that highlighted potential biological processes and signaling pathways shared by both diseases. Building on these findings, we propose potential drug treatments for PTB patients with COVID-19, pending verification of drug safety and efficacy through laboratory and multicentre studies before clinical use.

Abstract 1024: Differential gene expression of colorectal cancer biomarkers in Hispanic individuals

Abstract Colorectal cancer (CRC) is a leading cause of cancer death among men and women in Puerto Rico and the United States. About 60-70% of CRC cases are found at advanced stages (III/IV), suggesting limited adherence to available screening methods. Several molecular biomarkers have been identified as discriminatory for CRC (e.g., KRAS, NRAS, MSI), improving CRC management and patient outcomes. This study evaluates the differential expression patterns of DKK3, PKM2, IGFBP2, and SEPT9 genes between matched CRC tumors and adjacent mucosa samples. The secondary outcome was to examine the association between the presence of the selected biomarkers in tissue compared to blood samples. Using a retrospective study design, we examined 112 tissue samples of Hispanic individuals with a pathology-confirmed CRC diagnosis recruited throughout the Puerto Rico Familial Colorectal Cancer Registry (PURIFICAR). We quantified expression levels of target genes by RT-qPCR normalized with endogenous control GAPDH, using TaqMan Gene Expression Assay in the QuantStudio 3 (Applied Biosystems). Wilcoxon signed-rank test was used to calculate differences between gene expression from tumor and adjacent mucosal tissue samples. Additionally, 39 paired blood and tissue samples were analyzed to explore the association between biomarkers in these two types of samples. Protein biomarkers were measured using a commercially available ELISA kit according to manufacturer protocols (Thermo Scientific Federick, MD and Biosource San Diego, CA). mSEPT9 was measured using the Epi proColon® 2.0 CE test. The association between biomarker presence in tissue and blood samples was assessed using the Chi-square test of independence, with biomarker concentrations dichotomized at the median value. Statistical analyses were performed using Stata 17 and R version 4.3.1. DKK3 and IGFBP2 expression levels were higher among CRC tumor samples. However, expression levels of PKM2 and SEPT9 genes were slightly lower. DKK3 was the only target gene significantly different (p&amp;lt;0.05) when comparing overall gene expression between the matched samples. Upon comparison between early and advanced CRC stages, DKK3 expression levels were higher in advanced-stage tumor samples when compared to adjacent mucosal tissue samples (p&amp;lt;0.05). Moreover, a significant association between IGFBG2 presence in tissue compared to blood was detected at a 90% confidence level (p-value&amp;lt;0.10). This association was evident in early-stage CRC cases; there is a relationship between IGFBG2 biomarker presence in tissue and IGFBG2 biomarker presence in blood (p&amp;lt;0.05). Our findings indicate DKK3 and IGFBP2 as potential biomarkers for CRC progression and early detection. The study’s insights into the differential expression patterns of these biomarkers can inform targeted screening strategies. Further research is needed to assess their potential to enhance early tumor detection in Hispanics. Citation Format: Elba V. Caraballo-Rivera, Hilmaris Centeno-Girona, Gabriel De Jesus-Astacio, Camille Zenon-Melendez, Brenda Torres-Velasquez, Madeline Martir-Ocasio, Marcia R. Cruz-Correa. Differential gene expression of colorectal cancer biomarkers in Hispanic individuals [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 1024.

An RNA-Seq Data Analysis Pipeline.

In this chapter, we present an established pipeline for analyzing RNA-Seq data, which involves a step-by-step flow starting from raw data obtained from a sequencer and culminating in the identification of differentially expressed genes with their functional characterization. The pipeline is divided into three sections, each addressing crucial stages of the analysis process. The first section covers the initial steps of the pipeline, including downloading of the data of interest and performing quality control assessment. Assessment ensures that the data used for analysis is reliable and suitable for downstream analyses. In the second section, gene-level quantification is performed, which entails quantification of expression levels of genes in the samples. The third and final section is focused on differential expression analysis, which involves comparing gene expression levels between two or more conditions. This step helps identify genes that show significant differences in expression levels under different experimental conditions. To facilitate accessibility and reproducibility, we have provided an online repository containing all scripts and files. Additionally, custom scripts are available, enabling users to modify the pipeline's output for various downstream analyses. By following this pipeline, researchers can effectively analyze RNA-Seq data and gain valuable insights into gene expression patterns and, furthermore, the understanding of biological processes.

Auxin-responsive ROS homeostasis genes display dynamic expression pattern during rice crown root primordia morphogenesis

Reactive oxygen species (ROS) are generated continuously as a by-product of aerobic metabolism in plants. While excessive ROS cause oxidative stresses in cells, they act as signaling molecules when maintained at an optimum concentration through the dynamic equilibrium of ROS metabolizing mechanisms to regulate growth, development and response to environmental stress. Auxin and its crosstalk with other signaling cascades are crucial for maintaining ROS homeostasis and orchestrating root architecture but dissecting the underlying mechanism requires detailed investigation at the molecular level. Rice fibrous root system is primarily composed of shoot-derived adventitious roots (also called crown roots). Here, we uncover auxin-ROS cross-talk during initiation and growth of rice roots. Potassium iodide treatment changes ROS levels that results in an altered rice root architecture. We reveal that auxin induction recover root growth and development defects by recouping level of hydrogen peroxide. By comparing global datasets previously generated by auxin induction and laser capture microdissection-RNA sequencing, we identify the redox-related antioxidants genes from peroxidase, glutathione reductase, glutathione S-transferase, and thioredoxin reductase families whose expression is regulated by the auxin signaling and also display dynamic expression patterns during crown root primordia morphogenesis. The auxin-mediated differential transcriptome data were validated by quantifying expression levels of a set of genes upon auxin induction. Further, in-depth spatio-temporal expression pattern analysis by RNA in situ hybridization shows the spatially restricted expression of selected genes in the developing crown root primordia. Together, our findings uncover molecular components of auxin-ROS crosstalk involved in root organogenesis.

Long noncoding RNA MALAT1; A novel and potential therapeutic target for Alzheimer’s disease

AbstractBackgroundAlzheimer disease (AD) is the most common form of dementia, characterized pathologically by amyloid plaques and neurofibrillary tangles. Despite considerable advances in the knowledge of AD pathogenesis, we know little about preventing or delaying the ongoing neurodegenerative process, indicating that there remain critical gaps in our understanding of disease mechanisms and opportunities for new treatment approaches. Long noncoding RNAs (lncRNAs) are larger than 200 nucleotides, structurally resemble mRNAs but do not encode proteins. LncRNAs participate in regulation of several physiological and pathophysiological processes by modulating gene expression and have been documented in several neurodegenerative diseases. Among them, metastasis associated lung adenocarcinoma transcript 1 (MALAT1) is a highly abundant and evolutionary conserved lncRNA and regulates a subset of genes involved in synaptic plasticity, cognitive function and memory.MethodTo test the hypothesis that lncRNA MALAT1 plays an important role in AD pathology, we quantified expression levels of lncRNA MALAT1 in the brains of age‐matched AD patients and cognitively normal controls (Non‐AD) by QRT‐PCR and RNAScope in situ hybridization assays, respectively. We further examined the lncRNA MALAT1 expressions and AD‐related neuropathology in the brains of 5XFAD transgenic mouse model of AD and their WT littermates using dual RNAScope/Immunofluorescence technique.ResultWe observed reduced expressions of lncRNA MALAT1 in the hippocampus of AD brains compared to the non‐AD control brains. Next, we found marked reduced expression of lncRNA MALAT1 in the brain of 5xFAD mice compared to non‐transgenic mice. Interestingly, decreased expression levels of lncRNA MALAT1 are correlated with AD‐related neuropathology and memory deficits in 5xFAD mice.ConclusionThese findings provided compelling evidence that AD is associated with altered expression of lncRNA MALAT1 which may influence several pathways related to neural damage and memory deficits in AD. Because expression patterns, interacting proteins, pathways, and biological functions of lncRNA MALAT1 are remain largely unexplored in AD, understanding how lncRNA MALAT1 regulates AD‐related neuropathology may allow development of effective therapies for this incurable disease.

Elevated expression of Axin2 in intestinal metaplasia and gastric cancers.

The Wnt signaling pathway regulates crucial cellular processes, including stem cell development and tissue repair. Dysregulation of this pathway, particularly β-catenin stabilization, is linked to colorectal carcinoma and other tumors. Axin2, a critical component in the pathway, plays a role in β-catenin regulation. This study examines Axin2 expression in normal gastric mucosa and various gastric pathologies. Formalin-fixed and paraffin-embedded tissue samples from normal stomach, gastritis, intestinal metaplasia (IM), and gastric carcinoma were collected. Axin2 and β-catenin expression were evaluated using RNA in situ hybridization and immunohistochemistry, respectively. Histo-scores (H-scores) were calculated to quantify expression levels of Axin2. Associations between Axin2 expression and clinicopathological variables were examined. Axin2 expression was examined in normal stomach, gastritis, and IM tissues. Axin2 expression was mainly observed in the surface and isthmus areas in the normal stomach and gastritis, whereas Axin2 expression was markedly higher at the bases of IM. Axin2 H-scores were significantly elevated in IM (mean ± standard deviation [SD], 87.0 ± 38.9) compared to normal (mean ± SD, 18.0 ± 4.5) and gastritis tissues (mean ± SD, 33.0 ± 18.6). In total, 30% of gastric carcinomas showed higher Axin2 expression. Axin2 expression did not have significant associations with age, sex, Lauren classification, histological differentiation, invasion depth, and lymph node metastasis. However, a strong positive correlation was observed between Axin2 and nuclear β-catenin in gastric carcinomas (p < .001). Axin2 expression was significantly increased in IM compared to normal and gastritis cases. In addition, Axin2 showed a strong positive association with nuclear β-catenin expression in gastric carcinomas, demonstrating a close relationship with abnormal Wnt/β-catenin signaling pathway.

Effect of stimulation intensity of a differential target multiplexed SCS program in an animal model of neuropathic pain.

Spinal cord stimulation (SCS) has been proven to be an effective treatment for patients suffering from intractable chronic neuropathic pain. Recent advances in the field include the utilization of programs that multiplex various signals to target different neural structures in the dorsal spinal cord associated with the painful area. Preclinical studies have been fundamental in understanding the mechanism by which this differential target multiplexed programming (DTMP) SCS approach works. Transcriptomic- and proteomic-based studies demonstrated that DTMP can modulate expression levels of genes and proteins involved in pain-related processes that have been affected by a neuropathic pain model. This work studied the effect of the intensity of DTMP signals on mechanical hypersensitivity and cell-specific transcriptomes. The spared nerve injury model (SNI) of neuropathic pain was induced in 20 animals which were 1:1 randomized into two SCS groups in which the intensity of the DTMP was adjusted to either 70% or 40% of the motor threshold (MT). SCS was applied continuously for 48 h via a quadripolar lead implanted in the dorsal epidural space of animals. Controls, which included a group of implanted SNI animals that received no SCS and a group of animals naive to the SNI, were assessed in parallel to the SCS groups. Mechanical hypersensitivity was assessed before SNI, before SCS, and at 48 h of SCS. At the end of SCS, the stimulated segment of the dorsal spinal cord was dissected and subjected to RNA sequencing to quantify expression levels in all experimental groups. Differential effects were assessed via fold-change comparisons of SCS and naive groups versus the no-SCS group for transcriptomes specific to neurons and glial cells. Standard statistical analyses were employed to assess significance of the comparisons (p < 0.05). SCS treatments provided significant improvement in mechanical sensitivity relative to no SCS treatment. However, the change in the intensity did not provide a significant difference in the improvement of mechanical sensitivity. DTMP regulated expression levels back toward those found in the naive group in the cell-specific transcriptomes analyzed. There were no significant differences related to the intensity of the stimulation in terms of the percentage of genes in each transcriptome in which expression levels were reversed toward the naive state. DTMP when applied at either 40% MT or 70% MT provided similar reduction of pain-like behavior in rats and similar effects in neuron- and glia-specific transcriptomes.

Identification and validation of reference genes for qRT-PCR analyses under different experimental conditions in Allium wallichii

Himalayan onion (Allium wallichii) is a perennial bulbous herb with high ornamental value and has long been used as traditional medicines in Nepal and China because of the anti-cancer and anti-microbial activities. Wild Allium wallichii features different flower colors, including purple, pink, deep purple and white. However, little is known about the molecular mechanisms of color formation during A. wallichii flower development stages due to the lack of optimal reference genes. Quantitative real-time polymerase chain reaction (qRT-PCR) is a powerful tool for quantifying expression levels of target genes. The accuracy of qRT-PCR analyses is largely dependent on the identification of stable reference genes for data normalization. The stability of reference gene expression may vary with plant species and environmental conditions. The aim of this study was to select stable reference genes for qRT-PCR analyses of target genes at flower development stages, in different flower colors and organs for Allium wallichii. The CDSs of eight potential reference genes (TUB2, ACT1, GAPC, EF1α, UBQ, UBC, SAND and CYP1) were cloned and their stability was evaluated by four programs (Delta Ct, geNorm, NormFinder and BestKeeper), and the results were further integrated into a comprehensive rank by RefFinder. The results showed that TUB2 and GAPC were the most stable two reference genes at different developmental stages of purple- and white-flower genotypes and across all samples. UBC and TUB2 expression was stable at different developmental stages of purple flowers. CYP1 and TUB2 were stably expressed at different developmental stages of white flowers. GAPC and SAND showed the highest rankings in different flower colors. TUB2 and EF1α performed the best in different tissues. ACT1 was the least stable gene in all tested samples. Moreover, DIHYDROFLAVONOL-4-REDUCTASE (DFR) gene that involved in anthocyanin synthesis was used to evaluate the effectiveness of the selected candidates. This study identified the first set of suitable reference genes for qRT-PCR analyses, which will lay the foundation for gene function study in A. wallichii.

A Multiplex Gene Expression Assay for Direct Measurement of RNA Transcripts in Crude Lysates of the Nematode Caenorhabditis elegans Used as a Bioanalytical Tool.

Gene expression profiling in Caenorhabditis elegans has been demonstrated to be a potential bioanalytical tool to detect the toxic potency of environmental contaminants. The RNA transcripts of genes responding to toxic exposure can be used as biomarkers for detecting these toxins. For routine application in environmental quality monitoring, an easy-to-use multiplex assay is required to reliably quantify expression levels of these biomarkers. In the present study, a bead-based assay was developed to fingerprint gene expression in C. elegans by quantitating messenger RNAs (mRNAs) of multiple target genes directly from crude nematode lysates, circumventing RNA extraction and purification steps. The assay uses signal amplification rather than target amplification for direct measurement of toxin-induced RNA transcripts. Using a 50-gene panel, the expression changes of four candidate reference genes and 46 target mRNAs for various contaminants and wastewaters were successfully measured, and the expression profiles indicated the type of toxin present. Moreover, the multiplex assay response was in line with previous results obtained with more time-consuming reverse-transcription quantitative polymerase chain reaction and microarray analyses. In addition, the transcriptomic profiles of nematodes exposed to wastewater samples and extracts prepared from tissues of swimming crabs were evaluated. The profiles indicated the presence of organic pollutants. The present study illustrates the successful development of a multiplex fluorescent bead-based approach using nematode C. elegans crude lysates for gene expression profiling of target RNAs. This method can be used to routinely fingerprint the presence of toxic contaminants in environmental samples and to identify the most biologically active fraction of the contaminant mixture in a toxicity identification and evaluation approach. Environ Toxicol Chem 2023;42:130-142. © 2022 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC.

Biomarker discovery for practice of precision medicine in hypopharyngeal cancer: a theranostic study on response prediction of the key therapeutic agents

BackgroundHypopharyngeal cancer is a relatively rare malignancy with poor prognosis. Current chemotherapeutic algorithm is still far from personalized medicine, and the identification of the truly active therapeutic biomarkers and/or targets is eagerly awaited.MethodsVenturing to focus on the conventional key chemotherapeutic drugs, we identified the most correlative genes (and/or proteins) with cellular sensitivity to docetaxel (TXT), cisplatin (CDDP) and 5-fluorouracil (5-FU) in the expression levels, through 3 steps approach: genome-wide screening, confirmation study on the quantified expression levels, and knock-down and transfection analyses of the candidates. The probable action pathways of selected genes were examined by Ingenuity Pathway Analysis using a large-scale database, The Cancer Genome Atlas.ResultsThe first genome-wide screening study derived 16 highly correlative genes with cellular drug sensitivity in 15 cell lines (|R| > 0.8, P < 0.01 for CDDP and 5-FU; |R| > 0.5, P < 0.05 for TXT). Among 10 genes the observed correlations were confirmed in the quantified gene expression levels, and finally knock-down and transfection analyses provided 4 molecules as the most potent predictive markers-AGR2 (anterior gradient 2 homolog gene), and PDE4D (phosphodiesterase 4D, cAMP-specific gene) for TXT; NINJ2 (nerve Injury-induced protein 2); CDC25B (cell division cycle 25 homolog B gene) for 5-FU- in both gene and protein expression levels. Overexpression of AGR2, PDE4D signified worse response to TXT, and the repressed expression sensitized TXT activity. Contrary to the findings, in the other 2 molecules, NINJ2 and CDC25, there observed opposite relationship to cellular drug response to the relevant drugs. IPA raised the potential that each selected molecule functionally interacts with main action pathway (and/or targets) of the relevant drug such as tubulin β chain genes for TXT, DNA replication pathway for CDDP, and DNA synthesis pathway and thymidylate synthetase gene for 5-FU.ConclusionWe newly propose 4 molecules -AGR2, PDE4D,NINJ2 and CDC25B) as the powerful exploratory markers for prediction of cellular response to 3 key chemotherapeutic drugs in hypopharyngeal cancers and also suggest their potentials to be the therapeutic targets, which could contribute to the development of precision medicine of the essential chemotherapy in hypopharyngeal patients. (339 words).

Incidence and Prognostic Impact of WT-1 Gene Exon7 and 9 Mutations in Acute Promyelocytic Leukemia

Background: Wilms’ tumor suppressor gene 1 (WT1) gene mutation has been reported to be a prognostic factor in normal-cytogenetic acute myeloid leukemia (AML) patients. Higher rates of mutation in the WT1 gene have been reported in several tumors including normal-cytogenetic AML patients. Data regarding WT1 mutations in acute promyelocytic leukemia (APL) is very scarce. In this study, we evaluated the incidence and impact of WT1 mutation on the outcome of APL patients. Materials and Methods: A total of 92 patients diagnosed with APL were studied in three distinct groups: early mortality, relapsed, and persistent complete remission. Genomic DNA of bone marrow samples of patients was analyzed. For quantification of expression levels of the WT1 gene, real-time quantitative PCR (rqPCR) was performed by a real-time PCR system. WT1 mutation and its impact on prognosis were considered the primary endpoint of the study. Statistical analysis was performed with STATA. Results: WT1 mutation frequency was 6.25% in the early mortality group (1/16 patients), 13.16% in the relapse group (5/38 patients), and 7.89% in the persistent complete remission group (3/38 patients). 8 mutations were in exon 7 and one mutation in exon 9. WT1 mutation in the relapse group was associated with a trend toward worse disease-free survival (DFS) while overall survival (OS) was not affected by WT1 mutation in univariate analysis. Patients with no mutations in WT1 and FLT3/ITD had better overall survival and disease-free survival compared to patients with mutations in the WT1 gene or FLT3/ITD in the relapse group. Conclusion: The frequency of WT1 gene mutations does not differ significantly between patients with early mortality, relapse, and persistent complete remission. The presence of WT1 mutation is associated with higher relapse and lower survival rates in relapse group patients.

Impact of gene annotation choice on the quantification of RNA-seq data

BackgroundRNA sequencing is currently the method of choice for genome-wide profiling of gene expression. A popular approach to quantify expression levels of genes from RNA-seq data is to map reads to a reference genome and then count mapped reads to each gene. Gene annotation data, which include chromosomal coordinates of exons for tens of thousands of genes, are required for this quantification process. There are several major sources of gene annotations that can be used for quantification, such as Ensembl and RefSeq databases. However, there is very little understanding of the effect that the choice of annotation has on the accuracy of gene expression quantification in an RNA-seq analysis.ResultsIn this paper, we present results from our comparison of Ensembl and RefSeq human annotations on their impact on gene expression quantification using a benchmark RNA-seq dataset generated by the SEQC consortium. We show that the use of RefSeq gene annotation models led to better quantification accuracy, based on the correlation with ground truths including expression data from >800 real-time PCR validated genes, known titration ratios of gene expression and microarray expression data. We also found that the recent expansion of the RefSeq annotation has led to a decrease in its annotation accuracy. Finally, we demonstrated that the RNA-seq quantification differences observed between different annotations were not affected by the use of different normalization methods.ConclusionIn conclusion, our study found that the use of the conservative RefSeq gene annotation yields better RNA-seq quantification results than the more comprehensive Ensembl annotation. We also found that, surprisingly, the recent expansion of the RefSeq database, which was primarily driven by the incorporation of sequencing data into the gene annotation process, resulted in a reduction in the accuracy of RNA-seq quantification.

Matrix Metalloproteinase-1 (MMP1) Upregulation through Promoter Hypomethylation Enhances Tamoxifen Resistance in Breast Cancer.

Simple SummaryCancer recurrence caused by tamoxifen resistance hampers chemotherapy in breast cancer patients. The reasons behind the resistance were investigated by screening epigenetically regulated genes through analysis of methylation data from tamoxifen-resistant MCF-7 cells. MMP1 locus was found to be hypomethylated at a promoter CpG site and its expression was upregulated in the cell line, which was verified by the drug-resistant tumor tissues from breast cancer patients (n = 28). Downregulating MMP1 using a short hairpin RNA inhibited the growth of resistant cells and increased sensitivity to tamoxifen in vitro as well as in a xenografted mouse model in vivo. This study suggests that MMP1 is potentially a target gene to control tamoxifen resistance in breast cancer.Background: Tamoxifen (tam) is widely used to treat estrogen-positive breast cancer. However, cancer recurrence after chemotherapy remains a major obstacle to achieve good patient prognoses. In this study, we aimed to identify genes responsible for epigenetic regulation of tam resistance in breast cancer. Methods: Methylation microarray data were analyzed to screen highly hypomethylated genes in tam resistant (tamR) breast cancer cells. Quantitative RT-PCR, Western blot analysis, and immunohistochemical staining were used to quantify expression levels of genes in cultured cells and cancer tissues. Effects of matrix metalloproteinase-1 (MMP1) expression on cancer cell growth and drug resistance were examined through colony formation assays and flow cytometry. Xenografted mice were generated to investigate the effects of MMP1 on drug resistance in vivo. Results: MMP1 was found to be hypomethylated and overexpressed in tamR MCF-7 (MCF-7/tamR) cells and in tamR breast cancer tissues. Methylation was found to be inversely associated with MMP1 expression level in breast cancer tissues, and patients with lower MMP1 expression exhibited a better prognosis for survival. Downregulating MMP1 using shRNA induced tam sensitivity in MCF-7/tamR cells along with increased apoptosis. The xenografted MCF-7/tamR cells that stably expressed short hairpin RNA (shRNA) against MMP1 exhibited retarded tumor growth compared to that in cells expressing the control shRNA, which was further suppressed by tam. Conclusions: MMP1 can be upregulated through promoter hypomethylation in tamR breast cancer, functioning as a resistance driver gene. MMP1 can be a potential target to suppress tamR to achieve better prognoses of breast cancer patients.

The neuronal retromer can regulate both neuronal and microglial phenotypes of Alzheimer's disease.

SUMMARYDisruption of retromer-dependent endosomal trafficking is considered pathogenic in late-onset Alzheimer’s disease (AD). Here, to investigate this disruption in the intact brain, we turn to a genetic mouse model where the retromer core protein VPS35 is depleted in hippocampal neurons, and then we replete VPS35 using an optimized viral vector protocol. The VPS35 depletion-repletion studies strengthen the causal link between the neuronal retromer and AD-associated neuronal phenotypes, including the acceleration of amyloid precursor protein cleavage and the loss of synaptic glutamate receptors. Moreover, the studies show that the neuronal retromer can regulate a distinct, dystrophic, microglia morphology, phenotypic of hippocampal microglia in AD. Finally, the neuronal and, in part, the microglia responses to VPS35 depletion were found to occur independent of tau. Showing that the neuronal retromer can regulate AD-associated pathologies in two of AD’s principal cell types strengthens the link, and clarifies the mechanism, between endosomal trafficking and late-onset sporadic AD.