The Identification of Blood Biomarkers of Chronic Neuropathic Pain by Comparative Transcriptomics

In this study, we recruited 50 chronic pain (neuropathic and nociceptive) and 43 pain-free controls to identify specific blood biomarkers of chronic neuropathic pain (CNP). Affymetrix microarray was carried out on a subset of samples selected 10 CNP and 10 pain-free control participants. The most significant genes were cross-validated using the entire dataset by quantitative real-time PCR (qRT-PCR). In comparative analysis of controls and CNP patients, WLS (P = 4.80 × 10–7), CHPT1 (P = 7.74 × 10–7) and CASP5 (P = 2.30 × 10–5) were highly significant, whilst FGFBP2 (P = 0.00162), STAT1 (P = 0.00223), FCRL6 (P = 0.00335), MYC (P = 0.00335), XCL2 (P = 0.0144) and GZMA (P = 0.0168) were significant in all CNP patients. A three-arm comparative analysis was also carried out with control as the reference group and CNP samples differentiated into two groups of high and low S-LANSS score using a cut-off of 12. STAT1, XCL2 and GZMA were not significant but KIR3DL2 (P = 0.00838), SH2D1B (P = 0.00295) and CXCR31 (P = 0.0136) were significant in CNP high S-LANSS group (S-LANSS score > 12), along with WLS (P = 8.40 × 10–5), CHPT1 (P = 7.89 × 10–4), CASP5 (P = 0.00393), FGFBP2 (P = 8.70 × 10–4) and FCRL6 (P = 0.00199), suggesting involvement of immune pathways in CNP mechanisms. None of the genes was significant in CNP samples with low (< 12) S-LANSS score. The area under the receiver operating characteristic (AUROC) analysis showed that combination of MYC, STAT1, TLR4, CASP5 and WLS gene expression could be potentially used as a biomarker signature of CNP (AUROC − 0.852, (0.773, 0.931 95% CI)).

AEG-1 silencing attenuates M2-polarization of glioma-associated microglia/macrophages and sensitizes glioma cells to temozolomide

Glioma is the most frequent primary malignancy in the brain; temozolomide (TMZ) is the first-line chemotherapeutic agent used to combat this tumor. We showed here that astrocyte elevated gene-1 (AEG-1) was overexpressed in glioma tissues and associated with a worse subtype and a poor prognosis. CCK-8 proliferation assays and clone formation experiments presented that AEG-1 knockdown sensitizes glioma cells to TMZ. The γH2AX foci formation assays indicated that AEG-1 silencing promotes TMZ-induced DNA damage in glioma cells. Glioma-associated microglia/macrophages (GAMs), the largest subpopulation infiltrating glioma, play important roles in the tumor microenvironment. Bioinformatics analyses and functional studies demonstrated that AEG-1 silencing decreased M2-polarization of HMC3 microglia and the secretion of tumor supportive cytokines IL-6 and TGF-β1. The expression of AEG-1 was positively associated with M2 markers in glioma tissues varified by IHC staining. Based on the results of Affymetrix microarray and GSEA analyses, Western blot and Co-Immunoprecipitation assays were conducted to show that AEG-1 activates Wnt/β-catenin signaling by directly interacting with GSK-3β. The co-localization of AEG-1 and GSK-3β in the cytoplasm of glioma cells was detected through immunofluorescence staining. This study raises the possibility that targeting AEG-1 might improve the efficiency of chemotherapy and reduce immunosuppressive M2 GAMs in glioma.

O-141 Mapping of SARS-CoV-2-associated receptors and proteases mRNA in human endometrium during natural and stimulated cycles

Study question Covid-19 pandemic has significantly affected the assisted reproductive technology (ART) practice. Understanding whether SARS-CoV-2 could infect endometrial tissues during ART is crucial for risk mitigation Summary answer Analyses of gene expression profiles of SARS-CoV-2 host entry candidates from microarray data suggest that endometrium should be considered as potential target for SARS-CoV-2 infection. What is known already Very few studies analyzed the gene expression profiles of SARS-CoV-2-associated receptors and proteases, mainly focusing on ACE2 and TMPRSS2 expression, resulting incomplete knowledge in different specimens from female genital tract. However, no studies have analyzed the potential impact of controlled ovarian stimulation (COS) protocols during ART procedure on the endometrial gene expression profiles of SARS-CoV-2-associated receptors and proteases Study design, size, duration To address this question, we retrospectively examined the gene expression profile of SARS-CoV-2-associated receptors and proteases in endometrial biopsies of a cohort of ART candidates using Affymetrix microarray data Participants/materials, setting, methods Human endometrial tissue under natural (n = 62) and COS cycles (n = 42) were analyzed. A focus was particularly made on the renin-angiotensin system relates genes with a prominent role in the virus infection, and gene expression levels of receptors and proteases closely related to SARS-CoV-2 infectionwas also studied. Main results and the role of chance Using our large cohort of endometrial samples, we reported a high prevalence of genes related to the ACE2 pathway, including AGT, AGTR1, ANPEP, CTSA, ENPEP, LNPEP, MME, NLN, THOP1, BSG and CTSL during both phases(early- and mid-secretory phase), and mainly during the mid-secretory phase for ACE2. The highest signal intensities were found for CTSA, LNPEP, MME, NLN, BSG and CTSL. The most representative of dual coexpression of SARS-CoV-2-associated receptor and protease in endometrium was BSG-CSTL and BSG-CTSA. It s also important to note high variation of SARS-CoV-2 receptors inter-patients under natural cycle.Globally, the impact of COS on endometrial gene expression profile of SARS-CoV-2-associated receptors and proteases of non Covid-19 patients is low, suggesting no additional potential risks of SARS-CoV-2 infection during stimulated ART procedure compared with natural cycles. Limitations, reasons for caution Analyses of Affymetrix microarray gene expression data were performed in non-COVID-19 patients. Whether the SARS-CoV-2 infection changes the endometrial gene expression profile of SARS-CoV-2-associated receptors and proteases is under investigation Wider implications of the findings Specimens from female genital tract may be considered as potential targets for SARS-CoV-2. Trial registration number not applicable

GIANT: galaxy-based tool for interactive analysis of transcriptomic data

Transcriptomic analyses are broadly used in biomedical research calling for tools allowing biologists to be directly involved in data mining and interpretation. We present here GIANT, a Galaxy-based tool for Interactive ANalysis of Transcriptomic data, which consists of biologist-friendly tools dedicated to analyses of transcriptomic data from microarray or RNA-seq analyses. GIANT is organized into modules allowing researchers to tailor their analyses by choosing the specific set of tool(s) to analyse any type of preprocessed transcriptomic data. It also includes a series of tools dedicated to the handling of raw Affymetrix microarray data. GIANT brings easy-to-use solutions to biologists for transcriptomic data mining and interpretation.

Astaxanthin Counteracts Vascular Calcification In Vitro Through an Early Up-Regulation of SOD2 Based on a Transcriptomic Approach

Vascular calcification (VC) is a critical contributor to the rising cardiovascular risk among at-risk populations such as those with diabetes or renal failure. The pathogenesis of VC involves an uprising of oxidative stress, for which antioxidants can be theoretically effective. However, astaxanthin, a potent antioxidant, has not been tested before for the purpose of managing VC. To answer this question, we tested the efficacy of astaxanthin against VC using the high phosphate (HP)-induced vascular smooth muscle cell (VSMC) calcification model. RNAs from treated groups underwent Affymetrix microarray screening, with intra-group consistency and inter-group differential expressions identified. Candidate hub genes were selected, followed by validation in experimental models and functional characterization. We showed that HP induced progressive calcification among treated VSMCs, while astaxanthin dose-responsively and time-dependently ameliorated calcification severities. Transcriptomic profiling revealed that 3491 genes exhibited significant early changes during VC progression, among which 26 potential hub genes were selected based on closeness ranking and biologic plausibility. SOD2 was validated in the VSMC model, shown to drive the deactivation of cellular senescence and enhance antioxidative defenses. Astaxanthin did not alter intracellular reactive oxygen species (ROS) levels without HP, but significantly lowered ROS production in HP-treated VSMCs. SOD2 knockdown prominently abolished the anti-calcification effect of astaxanthin on HP-treated VSMCs, lending support to our findings. In conclusion, we demonstrated for the first time that astaxanthin could be a potential candidate treatment for VC, through inducing the up-regulation of SOD2 early during calcification progression and potentially suppressing vascular senescence.

Dietary β-Hydroxy-β-Methylbutyrate Supplementation Promotes PDAC Response to Gemcitabine and Immunotherapy Response in Obese Mice

Objectives Late diagnosis, aggressive underlying biology, and limited treatment options contribute towards the exceptionally poor survival of pancreatic ductal adenocarcinoma (PDAC). Obesity promotes both incidence and progression of PDAC via chronic systemic inflammation, generation of an immunosuppressive tumor microenvironment, and promotion of tumor fibrosis. β-Hydroxy-β-Methylbutyrate (HMB) reduces cancer associated cachexia and promotes modest reductions in tumor growth in animal models of cancer. The objective of this study was to determine if HMB supplementation would alter therapeutic response to either gemcitabine or anti-PD1 immunotherapy. Methods C57BL/6 mice were fed either a diet induced obesity high fat diet or a matched low fat control. Following PANC02 tumor induction, animals were treated with HMB alone or in combination with gemcitabine or anti-PD1 immunotherapy. Tumor transcriptomic analysis was preformed using Affymetrix microarray, with subsequent gene set enrichment analysis. Immunohistochemistry was performed for CD3 (a T cell marker). C57BL/6 mice were fed either a diet induced obesity high fat diet or a matched low fat control. Following PANC02 tumor induction, animals were treated with HMB alone or in combination with gemcitabine or anti-PD1 immunotherapy. Tumor transcriptomic analysis was preformed using Affymetrix microarray, with subsequent gene set enrichment analysis. Immunohistochemistry was performed for CD3 (a T cell marker). Results DIO-induced immune suppression was partially reversed by HMB, with reduced tumor growth, increased T cell markers and enhanced efficacy of gemcitabine following HMB treatment in obese mice. Separately, HMB enhanced the efficacy of anti-PD1 immunotherapy. Conclusions HMB enhanced PDAC immune surveillance, augmenting both cytotoxic chemotherapy and immunotherapy. HMB-induced suppression of obesity driven PDAC tumor growth, and promotion of immune surveillance may provide extend the therapeutic index of both chemotherapies and immunotherapies in PDAC. Funding Sources This study was supported by a grant from the National Cancer Institute (R35 CA197627) to SDH.

Nucleotide, ribonucleotide and ribonucleoside binding belongs to differentially expressed genes in porcine epithelial oviductal cells during longterm primary cultivation

The oviduct play a crucial role in reproductive process, through facilitating successful embryo growth and conception. Oviduct activity is orchestrated by various factors, depending on cyclic dynamics, which crucially affect the success of reproductive function. The morphological modifications of oviducts in response to the female reproductive cycle are well established. However, detailed characterization at the molecular level is still needed. The present study, employed primary in vitro cell cultures and high-throughput transcriptome analysis via an Affymetrix microarray approach, described nucleotide, ribonucleotide and ribonucleoside binding patterns at a molecular level in oviduct epithelial cells (OECs). 222 genes were targeted belonging to four gene ontology biological process terms (GO BP): “adenyl nucleotide binding”, “adenyl ribonucleotide binding”, “ribonucleotide binding”, “ribonucleoside binding”, which showed the greatest variability in the level of mRNA expression during of long-term cultivation. In this group of genes, special attention was paid to those showing the greatest variability in relation to the reference measurement, including OASL, PIM1, ACTA2 and ABCA1.Running title: Oviductal nucleotide and nucleoside binding patterns

Biochemical properties of cofactor and coenzyme metabolism in porcine oviductal epithelial cells – a microarray study

The oviduct is a key organ responsible for ultimate oocytes maturation, transport of gametes, sperm capacitation, fertilization, as well as early embryo development. Its innermost layer, oviductal epithelium, represents a highly dynamic structure which undergoes changes in response to different physiological and pathological processes. Previously, the expression profile of genes involved in several important processes in porcine oviductal epithelial cells (OECs) during long-term primary in vitro culture. The present study further characterizes the porcine OECs model using Affymetrix microarray assay and it analyzes gene expression changes observed on the 7th, 15th and 30th day of culture. 25 genes belonging to “coenzyme metabolic process”, “cofactor biosynthetic process” and “cofactor metabolic process” GO BP terms were differentially expressed in culture. The most up-regulated genes were ALDH1L2, P2RX7, PANK1, ACSS2, SCD, AASS and PDK3. In contrast, several genes appeared to be significantly down-regulated, e.g. ACSL4 and HAAO. Considering the biological roles of the most regulated genes, it can be concluded that these changes may indicate the increased metabolic and proliferation activity of studied cells in primary in vitro culture.Running title: Cofactor and coenzyme metabolism in porcine oviductal epithelial cells

Analysis of expression of genes responsible for regulation of cellular proliferation and migration – microarray approach based on porcine oocyte model

The formation of mammalian oocytes begins in the ovary during fetal development. The proper development of oocytes requires close communication with surrounding somatic cells, the substances they emit allow proper maturation of oocytes. Somatic cumulus (CC) cells and oocytes form cumulus-oocyte (COC) complexes.In this study, the Affymetrix microarray analysis was used to investigate changes in gene expression occurring in oocytes before and after in vitro maturation (IVM). The aim of the study was to examine oocyte genes involved in two ontological groups, “regulation of cell migration” and “regulation of cell proliferation” discovered by the microarray method.We found a reduced expression of all 28 genes tested in the ontological groups: ID2, VEGFA, BTG2, CCND2, EDNRA, TGFBR3, GJA, LAMA2, RTN4, CDK6, IHH, MAGED1, INSR, CD9, PTGES, TXNIP, ITGB1, SMAD4, MAP3K1, NOTCH2 , IGFBP7, KLF10, KIT, TPM1, PLD1, BTG3, CD47 and MITF. We chose the most regulated genes down the IVM culture, and pointed out those belonging to two ontological groups.Increased expression of the described genes before IVM maturation may indicate the important role of these genes in the process of ovum maturation. After the maturation process, the proteins produced by them did not play such an important role. In summary, the study provides us with many genes that can serve as molecular markers of oocyte processes associated with in vitro maturation. This knowledge can be used for detailed studies on the regulation of oocyte maturation processes.Running title: Genes regulating cellular migration and proliferation in porcine oocytes