Molecular Markers For Early Detection Research Articles

Plasma SARS-CoV-2 N antigen is a powerful molecular marker for early detection of severe COVID-19 in patients and monitoring disease progression

Background and aimsClear and effective indicators for early detection of severe coronavirus disease 2019 (COVID-19) are insufficient. We investigated the clinical value of the plasma SARS-CoV-2 N antigen (plasma N antigen) for severe COVID-19 early identification and disease progression monitoring. Materials and methodsA cross-sectional study compared the diagnostic value of plasma N antigen levels detected within two days after hospital admission in 957 patients with COVID-19 during the BA2.2 outbreak in Shanghai (April 6–June 15, 2022). A follow-up study analyzed the plasma N antigen prognostic value in 274 non-severe patients, and a longitudinal study evaluated its continuous monitoring value in 16 patients with COVID-19 grade changes. ResultsPlasma N antigen concentrations were significantly higher in severely ill than in non-severely ill patients. The plasma N antigen was superior to nasopharyngeal nucleic acid CT values and established COVID-19 blood biomarkers in identifying severe COVID-19. Patients with high plasma N-antigen concentrations at initial admission were more prone to developing severe COVID-19. The changes in plasma N antigen concentrations were consistent with disease progression. Two logistic regression models, including and excluding plasma N antigen, were established, with model 1 (including plasma N antigen) (AUC = 0.971, 0.958–0.980) yielding a better diagnostic value for severe COVID-19 than Model 2 (plasma N antigen excluded). ConclusionThe plasma N antigen is superior to nasopharyngeal nucleic acids and established COVID-19 blood biomarkers for severe COVID-19 early recognition and progression monitoring, enabling the most accurate patient triaging and efficient utilization of medical resources.

Identification of Molecular Markers for Early Detection of Sluggish Fermentation Associated with Heat Shock during Alcoholic Fermentation

Problematic fermentations frequently drive economic losses and logistic problems in the winemaking industry. Previous studies have determined thermal conditions leading to problematic fermentations, selecting two contrasting yeast strains for further transcriptomic analysis. Saccharomyces cerevisiae SBB11 showed strong thermosensitivity towards heat shock, while S. cerevisiae PDM was found to be thermotolerant. The aim of this study was to select genes with significantly upregulated expression to be later used as biomarkers for early detection of sluggish fermentation associated with heat shock. Candidate genes were selected from previously obtained RNA-seq data. Alcoholic fermentations were conducted with 4 S. cerevisiae strains SBB11, PDM, M2 and ICV D21. Heat shocks on day 3 of alcoholic fermentation were applied at 36 and 40 °C for 16 h. S. cerevisiae cells were collected at different times after heat shock onset for qPCR analysis of candidate gene expression over time. Three genes showed promising results; SSA1, MGA1 and OPI10 significantly increased expression with respect to the control. The selected genes showed increased expression during the first 9 h post heat shock and are proposed for early detection of sluggish fermentations associated with heat shock.

Multimerin 1 aids in the progression of ovarian cancer possibly via modulation of DNA damage response and repair pathways.

Ovarian cancer is one of the leading causes of deaths among women. Despite advances in the treatment regimes, a high rate of diagnosis in the advanced stage makes it almost an incurable malignancy. Thus, more research efforts are required to identify potential molecular markers for early detection of the disease and therapeutic targets to augment the survival rate of ovarian cancer patients. Previously, in this context, we identified dysregulated expression of multimerin 1 (MMRN1) in ovarian cancer. To elucidate the relationship between MMRN1 expression and ovarian cancer progression, siRNA-based MMRN1 knockdown was employed and various cell assays were performed to study its effect on ovarian cancer cells. In addition, network of dysregulated proteins was identified by quantitative proteomics and associated pathways were explored by bioinformatics analysis. MMRN1 silencing showed a significant reduction in cell viability, adhesion, migration, and invasion and a high frequency of cell apoptosis. Label-free quantitative proteomics and in-depth statistical analysis identified 448 dysregulated proteins, majority of which were overexpressed in MMRN1 knockdown cells. The pathways overrepresented in ovarian cancer were DNA replication, mismatch repair, nucleotide excision repair, and cell cycle regulation. Conclusively, the findings of this study suggest that MMRN1 aids in the progression of ovarian cancer via modulation of DNA damage response and repair pathways.

Phosphoproteome analysis of cerebrospinal fluid extracellular vesicles in primary central nervous system lymphoma.

Primary central nervous system lymphoma (PCNSL) is a rare but highly aggressive extra-nodal non-Hodgkin's lymphoma, mostly of the diffuse large B-cell lymphoma (DLBCL) type. The present invasive diagnosis and poor prognosis of PCNSL propose an urgent need to develop molecular markers for early detection, real-time monitoring and treatment evaluation. Cerebrospinal fluid (CSF)-derived extracellular vesicles (EVs) are promising biomarker carriers for liquid biopsy of CNS diseases and brain tumors; however, research remains challenging due to the low concentration of EVs in the limited available volume of CSF from each individual patient and the low efficiency of existing methods for EV enrichment. Here, we introduce functionalized magnetic beads called EVTRAP (extracellular vesicles total recovery and purification) for rapid and efficient EV isolation from CSF. By coupling with high-performance mass spectrometry, over 19 000 peptides representing 1841 proteins were identified from just 30 μL of CSF. Furthermore, up to 3000 phosphopeptides representing over 1000 phosphoproteins were identified from about 2 mL of CSF. Finally, we analyzed the EV phosphoproteomics of CSF samples from PCNSL patients and non-PCNSL controls. Among them, multiple phosphoproteins related to PCNSL, including SPP1, MARCKS, NPM1 and VIM, were shown to be up-regulated in the PCNSL group. These results demonstrated the feasibility of the EVTRAP-based analytical strategy in CSF EV phosphoproteomic analysis of PCNSL molecular markers.

The IGSF1, Wnt5a, FGF14, and ITPR1 Gene Expression and Prognosis Hallmark of Prostate Cancer.

Prostate cancer is considered as the second leading cause of cancer related death in men worldwide and the third frequent cancer among Iranian men. Despite the use of PSA as the only biomarker for early diagnosis of prostate cancer, its application in clinical settings is under debate. Therefore, the introduction of new molecular markers for early detection of prostate cancer is needed. In the present study we intended to evaluate the expression of IGSF1, Wnt5a, FGF14, and ITPR1 in prostate cancer specimens by real time PCR. Biopsy samples of 40 prostate cancer cases and 41 healthy Iranian men were compared to determine the relative gene expression of IGSF1, Wnt5a, FGF14, and ITPR1 by real time PCR. Our results showed that Wnt5a, FGF14, and IGSF1 were significantly overexpressed in the prostate cancer patients while the mean relative expression of ITPR1 showed a significant decrease in PCa samples compared to healthy controls. According to results of the present study, the combination panel of IGSF1, Wnt5a, FGF14, and ITPR1 genes could be considered as potential genetic markers for prostate cancer diagnosis. However further studies on larger populations and investigating the clinicopathological relevance of these genes is needed.

Dengue Virus Non-structural (NS) 1 Gene as A Molecular Marker for Early Detection of in vitro Dengue Virus Infection

Serology-based dengue assays at times produce inaccurate results especially in the early phase of disease onset. A more precise diagnostic approach detecting dengue infections in the early phase enables better management of the disease. This helps reduce dengue-associated morbidity and mortality. Besides, an early diagnosis of dengue is also very beneficial in a dengue outbreak and in endemic regions. In this light, this study aimed to determine the potential of the dengue virus (DENV) non-structural 1 (NS1) gene as an early detection biomarker. The cytopathic effects (CPE) were monitored and the cell death of DENV serotype-2 (DENV2)-infected Vero cells was evaluated for fourteen consecutive days. Only Lemos and in-house NS1-specific primer pairs showed positive amplifications in the preliminary primer validation. Thus, both of the primer pairs were then used to amplify the NS1 gene from the infected cells. The NS1 gene was detected as early as day-2 post-infection using the in-house primers. There was no amplicon produced using the Lemos primers. This is speculated to be attributable to the relatively lower complementarity of the primer sequences with that of the template and low amount of viral mRNA in the DENV2-infected cells. Conclusively, the DENV NS1 gene is a potential early detection marker, however, the NS1-specific primers should be pre-validated to ensure a reliable dengue diagnosis.

Construction and Investigation of an LINC00284-Associated Regulatory Network in Serous Ovarian Carcinoma.

The low survival rate associated with serous ovarian carcinoma (SOC) is largely due to the lack of relevant molecular markers for early detection and therapy. Increasing experimental evidence has demonstrated that long noncoding RNAs (lncRNAs) are involved in cancer initiation and development, and a competitive endogenous RNA (ceRNA) hypothesis has been formulated. Therefore, the characterization of new lncRNA and lncRNA-related networks is crucial for early diagnosis and targeted therapy of SOC. Data on lncRNAs, mRNAs, and miRNAs with differential expression in SOC, compared to normal ovarian tissue, were obtained from the Gene Expression Omnibus (GEO) database. Data on lncRNA expression and clinical data in SOC were obtained from The Cancer Genome Atlas (TCGA). lncRNA-miRNA interactions were predicted by the miRBase database. Different online tools, i.e., TargetScan, RNA22, miRmap, microT, miRanda, StarBase, and PicTar, were cooperatively utilized to predict the mRNAs targeted by miRNAs. The plugin of BiNGO in Cytoscape and KOBAS 3.0 were used to conduct the functional and pathway enrichment analyses. The lncRNA, miRNAs, and mRNAs identified to be expressed at statistically significant and different levels between SOC and healthy fallopian tube tissues were further validated using qRT-PCR. A total of 4 lncRNAs (LINC00284, HAGLR, HCAT158, and BLACAT1) and 111 mRNAs were found to be upregulated in SOC tissues compared to normal tissues, based on the GEO database. LINC00284 was found to be highly expressed in SOC, in association with the upregulation of the transcription factor SOX9. The high LINC00284 expression was associated with poor prognosis and proved to be an independent risk factor in patients with SOC, based on TCGA database. The qRT-PCR validation results closely recapitulated the expression profiles and prognostic scores of the aforementioned bioinformatic analyses. The LINC00284-related ceRNA network was found to be associated with SOC carcinogenesis by biofunctional analysis. In conclusion, the LINC00284-related ceRNA network may provide valuable information on the mechanisms of SOC initiation and progression. Importantly, LINC00284 proved to be a new potential prognostic biomarker for SOC.

Colorectal Cancer Screening Methods and Molecular Markers for Early Detection.

Colorectal cancer (CRC) is one of the most common malignant tumors in the digestive tract in humans. The development of colorectal cancer is composed of multiple stages, starting with benign adenomatous polyps in the inner wall of the large intestine and rectum, and then gradually developing. Then it developed into advanced adenomas carcinoma in situ and invasive carcinoma. Represents the distant metastasis of the most advanced development. The purpose of this review is to novel routine screening and diagnostic methods (e.g., Endoscopy and CT colonoscopy, SEPT9 methylation assay, Fecal test) and find reliable molecular markers for early diagnosis of CRC.

Identification of Differentially Up-regulated Genes in Apple with White Rot Disease.

Fuji, a major apple cultivar in Korea, is susceptible to white rot. Apple white rot disease appears on the stem and fruit; the development of which deteriorates fruit quality, resulting in decreases in farmers' income. Thus, it is necessary to characterize molecular markers related to apple white rot resistance. In this study, we screened for differentially expressed genes between uninfected apple fruits and those infected with Botryosphaeria dothidea, the fungal pathogen that causes white rot. Antimicrobial tests suggest that a gene expression involved in the synthesis of the substance inhibiting the growth of B. dothidea in apples was induced by pathogen infection. We identified seven transcripts induced by the infection. The seven transcripts were homologous to genes encoding a flavonoid glucosyltransferase, a metallothionein-like protein, a senescence-induced protein, a chitinase, a wound-induced protein, and proteins of unknown function. These genes have functions related to responses to environmental stresses, including pathogen infections. Our results can be useful for the development of molecular markers for early detection of the disease or for use in breeding white rotresistant cultivars.

Overexpression of Pin1 and rho signaling partners correlates with metastatic behavior and poor recurrence-free survival of hepatocellular carcinoma patients

BackgroundIdentification of molecular markers for early detection or prediction of metastasis is crucial for both management of HCC patient postoperative treatment and identify new therapeutic targets to inhibit HCC progression and metastasis. In the current study, we investigated the clinical correlation between Pin1, RhoA and RhoC and their association with HCC metastasis.MethodsUsing a randomized study design of primary HCC samples from 139 patients, we determined messenger RNA expression of Pin1, RhoA and RhoC and their prognostic value.ResultsOur findings demonstrated for the first time the clinical correlation of Pin1 in HCC metastasis. Pin1, RhoA and RhoC transcript levels were significantly higher in HCC specimens when compared with the paired adjacent non-tumorous liver. Pin1 overexpression was closely correlated with that of RhoA (R = 0.562, p < 0.001) and RhoC (R = 0.529, p < 0.001), and their co-overexpressions correlated with metastatic HCC (p = 0.000012) and poor recurrence-free survival of HCC patients (p < 0.00001), which showed better prognostic significance than either Pin1, RhoA or RhoC overexpression alone. Co-overexpressions of Pin1 + RhoA/RhoC were also an independent factor for predicting development of metastasis after curative resection in our multivariate regression model (p < 0.001).ConclusionPin1, RhoA and RhoC co-overexpressions are prognostic factor for metastatic HCC and predict poor recurrence-free survival.

Serum MiRNA-27a as potential diagnostic nucleic marker for breast cancer

Background Accumulating evidence reveals that microRNA 27a (miR 27a) is implicated in the pathogenesis of cancer. However, its diagnostic role in breast cancer (BC) still needs investigation. Materials and methods MiR 27a expression was assessed in serum samples from patients with primary BC (n = 100), benign breast lesions (n = 30) and control group served as healthy volunteers (n = 20) using quantitative real-time PCR. Results Both expression and mean rank of miR 27a and tumor markers among BC patients as compared to the other two groups. Clinicopathological characteristics showed significant relation with miRN 27a expression for clinical stage, histological grading, ER receptor and HER-2/neu. The diagnostic efficacy for miR 27a was superior to both tumor markers for early detection of BC especially high-risk BC groups. Conclusion Detection of miR 27a expression may serve as a potential sensitive minimally invasive molecular marker for early detection of primary BC.

Molecular alterations of mitochondrial D-loop in oral leukoplakia.

Over the years, numerous studies proposed a crucial role of mutations of nuclear DNA in the carcinogenesis process. Of late, many researchers suppose that alterations of mitochondrial DNA should not be excepted from this analysis. Mutational analysis of mitochondrial DNA displayed that mitochondrial D-loop is assessed as a hotspot for molecular alterations in various types of malignant tumors encompassing oral squamous cell carcinoma. Squamous cell carcinoma is believed to emerge through precancerous stages, which might be merely morphologic aspects of cumulative genetic variations. In keeping with this model of molecular tumor progression, this study aimed to investigate the qualitative and quantitative alterations that might occur in mitochondrial D-loop in oral leukoplakia whether dysplastic or not by semiquantitation of aproduct of the polymerase chain reaction and sequence analyses of mitochondrial D-loop gene. Statistically significant increases in the mean values of D-loop concentrations were observed across the dysplasia gradient of oral leukoplakia. Sequence analyses revealed the presence of point mutations in both dysplastic and nondysplastic oral leukoplakia but not in normal mucosa. The results of this study suggested that quantitative and qualitative alterations in mitochondrial D-loop could be a promising molecular marker for early detection and progression of the malignancy.

Abstract P1-03-11: Harnessing the distinctive properties of tumor-adjacent tissues to develop ethnicity-dependent biomarkers of breast cancer

Abstract Recent data demonstrating a correlation between lymph node positivity at the time of detection, and the probability of disease recurrence even decades post detection only solidifies the principle that the detection of breast cancer prior to lymph node metastasis can appreciably better clinical outcomes. Although radiologic methods have greatly improved early detection and remain the mainstay for detection, molecular assays to complement existing strategies will reduce number of false positives as well as enhance detection in cases that preclude conclusive diagnosis with radiologic techniques. Normal breast biology is routinely studied using tissues from reduction mammoplasty or normal tissues adjacent to tumor (NATs). However, studies have shown histologic abnormalities in reduction mammoplasty samples and DNA methylation and gene expression abnormalities in NATs due to “field” effects of the tumor. To interrogate the differences between normal breast and NATs as potential early detection markers, we created a tissue microarray (TMA) comprising breast tissues of 100 age-matched healthy women from the Komen Tissue Bank (KTB) and tumor-NAT pairs from 100 women (a total of 300 samples). Approximately 50% of women in each set were of African American (AA) ancestry and the remaining was of European decent. The TMAs was curated as such, because of our recent findings on ethnicity-dependent differences in breast stem-luminal progenitor-mature cell hierarchy. TMA was analyzed for ZEB1, an oncogenic transcription factor that is central to cell fate and stemness, and estrogen receptor alpha (ERα) and FOXA1, which are expressed predominantly in hormone-responsive mature luminal cells. ZEB1 expressing cells were localized to surrounding ductal structures of the normal breast, whereas ERα+ and FOXA1+ cells were located within the ductal compartment. KTB-normal of AA women contained significantly higher levels of ZEB1+ cells compared to KTB-normal of Caucasian women (CA). We observed only marginal increases in ZEB1+ cells in NATs or tumors of AA women. By contrast, in CA women, both NATs and tumors compared to KTB-normal contained higher levels of ZEB1+ cells. The unique localization pattern external to the ductal structures, as well as intrinsically higher expression in AA women suggest that ZEB1+ cells serve not only as stem cells from which cancers may originate but could also contribute to the microenvironment conducive for ductal tumor progression leading to aggressive and early onset of breast cancer as observed in AA women. Conversely, KTB-normal of AA showed modestly higher FOXA1 expression compared to CA women, and further, FOXA1 levels were declined in NATs of AA but not CA women. ERα levels did not change in any of our analyses, pointing to the specificity of ethnicity-dependent changes in this TMA. We also noted ethnicity-dependent variations in the levels of CD8+ T cells, PD-1+ immune cells and PD-L1+ cells but not CD68+ macrophages in NATs, suggesting distinctive immune environment in NATs. This comprehensive approach will not only serve as a platform to develop tumor-adjacent “normal” tissues as molecular markers for early detection but also provides a molecular basis for aggressive breast tumor in AA women. Citation Format: Nakshatri H, Kumar B, Burney H, Cox ML, Jacobson M, Sandusky G, D'Souza-Schorey C, Storniolo AM. Harnessing the distinctive properties of tumor-adjacent tissues to develop ethnicity-dependent biomarkers of breast cancer [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P1-03-11.

Expression of P53 Protein and Ki-67 Antigen in Oral Leukoplakia with Different Histopathological Grades of Epithelial Dysplasia.

Aims and Objective:The aim of this study is to investigate the expression of p53 protein and Ki-67 antigen in normal oral mucosa and oral leukoplakia with different grades of dysplasia using immunohistochemistry and to clarify the correlation of the expression of these cell cycle regulatory proteins.Materials and Methods:A total of 20 archival tissue blocks obtained from our department which were diagnosed as mild (n = 5), moderate (n = 5), and severe dysplasia (n = 5) with normal mucosa (n = 5) as a control. Positivity of Ki-67 and p53 was analyzed using Statistical Package for the Social Sciences (IBM Corp. Released 2013. IBM SPSS Statistics for Windows, Version 22.0 Armonk, NY:IBM Corp) software.Results:All samples showed positive staining for p53 and Ki-67. Statistically significant difference (P < 0.05) was seen between the frequency of occurrence of p53 and Ki-67 pattern of expression among all the groups. The intensity of staining was mild to intense in basal layer as there was a progression toward the severity of the disease. Almost 81.1% correlation existed between p53 and Ki-67 with high correlation and marked relationship.Conclusion:Oral leukoplakia represents the most common oral potentially malignant disorder (OPMD). Molecular biological markers such as p53 and Ki-67 are considered to be of great value in the diagnosis and prognostic evaluation of OPMD. Our results emphasize the potential use of p53 protein and Ki-67 antigen as significant molecular markers for early detection of PMDs and its risk of developing oral squamous cell carcinoma.

Epigenetic Modifications and Head and Neck Cancer: Implications for Tumor Progression and Resistance to Therapy.

Head and neck squamous carcinoma (HNSCC) is the sixth most prevalent cancer and one of the most aggressive malignancies worldwide. Despite continuous efforts to identify molecular markers for early detection, and to develop efficient treatments, the overall survival and prognosis of HNSCC patients remain poor. Accumulated scientific evidences suggest that epigenetic alterations, including DNA methylation, histone covalent modifications, chromatin remodeling and non-coding RNAs, are frequently involved in oral carcinogenesis, tumor progression, and resistance to therapy. Epigenetic alterations occur in an unsystematic manner or as part of the aberrant transcriptional machinery, which promotes selective advantage to the tumor cells. Epigenetic modifications also contribute to cellular plasticity during tumor progression and to the formation of cancer stem cells (CSCs), a small subset of tumor cells with self-renewal ability. CSCs are involved in the development of intrinsic or acquired therapy resistance, and tumor recurrences or relapse. Therefore, the understanding and characterization of epigenetic modifications associated with head and neck carcinogenesis, and the prospective identification of epigenetic markers associated with CSCs, hold the promise for novel therapeutic strategies to fight tumors. In this review, we focus on the current knowledge on epigenetic modifications observed in HNSCC and emerging Epi-drugs capable of sensitizing HNSCC to therapy.

Mitochondrial dysfunctions in bladder cancer: Exploring their role as disease markers and potential therapeutic targets.

Bladder cancer (BC) is a major cause of mortality worldwide as it currently lacks fully reliable markers of disease outcome and effective molecular targets for therapy. Mitochondria play a key role in cell metabolism but the role of mitochondrial dysfunctions in BC has been scarcely investigated. In this review, we explored current evidence for the potential role of mitochondrial DNA (mtDNA) alterations (point mutations and copy number) as disease markers in BC. Some germline mtDNA mutations detectable in blood could represent a non-invasive tool to predict the risk of developing BC. MtDNA copy number and tumor specific mtDNA mutations and RNAs showed encouraging results as novel molecular markers for early detection of BC in body fluids. Moreover, mitochondrial proteins Lon protease, Mitofusin-2, and TFAM may have prognostic/predictive value and may represent potential therapeutic targets. A deeper understanding of mitochondrial dysfunctions in BC could therefore provide novel opportunities for targeted therapeutic strategies.

Abstract 3489: Noncoding RNA distribution in clear cell renal cell cancer: small RNA-seq data

Abstract Small noncoding RNAs (sncRNAs) play pivotal roles in biological processes and may prove to be a tool in cancer diagnosis, prognosis, and treatment. Noncoding RNAs such as microRNAs (miRNAs), piwi-interacting-RNAs (piRNAs), long noncoding RNA (lncRNAs) and small nuclear/nucleolar RNAs (sn/snoRNAs) have recently been investigated to identify their role in cancer. Approximately 62,700 new cases of kidney cancer are expected each year in the United States leading to 14,240 deaths, with rates rising over the past 20 years. Nearly 90% of all kidney cancers will be renal cell carcinoma, of which 70% will be a clear cell renal cell carcinoma (ccRCC) subtype. When detected early most cases can be treated effectively, however there is a lack of early detection tests. We sought to identify molecular markers for early detection and diagnosis. We downloaded publically available (NIH bioproject PRJNA162397) ccRCC small RNA sequence raw data for noncoding RNA analysis. 22 ccRCC and 11 non-tumor renal cortex patient samples were evaluated. Data was analyzed by PartekFlow software. sRNA-seq data was annotated to miRNAs with 69 miRNAs aberrantly expressed in ccRCC with 37 being upregulated (top five: miR-122, miR-210, miR155, miR-224 and miR-21) and 32 being downregulated (top five: miR-200c, miR-502, miR-20b, miR10a and miR-204). Utilizing MetaCore software for pathway analysis the majority of expressed miRNAs were involved in metabolism related signaling pathways. Examining data for piRNAs revealed 22 which were significantly expressed (8 upregulated and 14 downregulated). Investigation of lncRNAs revealed 15 to be downregulated and 27 upregulated. We also uncovered 2 mitochondrial rRNAs, 10 miscRNAs, 1 snRNA, 7 snoRNAs, and 5 rRNAs in ccRCC samples. Our comprehensive analysis of publically available small RNA-seq data identified numerous sncRNAs associated with ccRCC. Pending further validation, they may prove useful as early detection biomarkers in this common cancer. Citation Format: Srinivas V. Koduru, Dino J. Ravnic. Noncoding RNA distribution in clear cell renal cell cancer: small RNA-seq data [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 3489. doi:10.1158/1538-7445.AM2017-3489

A bioinformatics analysis of differentially expressed genes associated with liver cancer

Objective: To investigate differentially expressed genes associated with liver cancer using bioinformatics methods, and to screen out molecular markers for early diagnosis of liver cancer and potential molecular targets for immunotherapy. Methods: The microarray data associated with liver cancer were downloaded from Gene Expression Omnibus. JMP software was used for correlation analysis of GSE datasets, Limma program in R language was used to screen out differentially expressed genes, and the Gene Ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genome (KEGG) pathway analysis were performed for differentially expressed genes. A protein-protein interaction (PPI) network was also established for analysis. An analysis of specific expression associated with liver cancer was performed with reference to RNA-seq transcriptome data for other tumors obtained from TCGA to further identify specific differentially expressed genes in liver cancer, and a survival curve analysis was performed for patients with liver cancer. Results: A total of 92 differentially expressed genes were identified, with 21 upregulated genes and 71 downregulated genes. Through the GO, KEGG, and PPI analyses, RNA-seq data verified that only glypican 3 (GPC3) was upregulated in liver cancer, and MBL2, SDS, SLCO1B3, TDO2, SAA4, and SPP2 were downregulated. Conclusions: GPC3 might act as a target for immunotherapy, and other molecular markers may become molecular markers for early detection of liver cancer and potential targets for immunotherapy.

Neuropilin-2 promotes tumourigenicity and metastasis in oesophageal squamous cell carcinoma through ERK-MAPK-ETV4-MMP-E-cadherin deregulation.

Oesophageal squamous cell carcinoma (ESCC) is the most common histological subtype of oesophageal cancer. The disease is particularly prevalent in southern China. The incidence of the disease is on the rise and its overall survival rate remains dismal. Identification and characterization of better molecular markers for early detection and therapeutic targeting are urgently needed. Here, we report levels of transmembrane and soluble neuropilin-2 (NRP2) to be significantly up-regulated in ESCC, and to correlate positively with advanced tumour stage, lymph node metastasis, less favourable R category and worse overall patient survival. NRP2 up-regulation in ESCC was in part a result of gene amplification at chromosome 2q. NRP2 overexpression promoted clonogenicity, angiogenesis and metastasis in ESCC in vitro, while NRP2 silencing by lentiviral knockdown or neutralizing antibody resulted in a contrary effect. This observation was extended in vivo in animal models of subcutaneous tumourigenicity and tail vein metastasis. Mechanistically, overexpression of NRP2 induced expression of ERK MAP kinase and the transcription factor ETV4, leading to enhanced MMP-2 and MMP-9 activity and, as a consequence, suppression of E-cadherin. In summary, NRP2 promotes tumourigenesis and metastasis in ESCC through deregulation of ERK-MAPK-ETV4-MMP-E-cadherin signalling. NRP2 represents a potential diagnostic or prognostic biomarker and therapeutic target for ESCC. Copyright © 2016 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.

RNA-seq analysis of early enteromyxosis in turbot (Scophthalmus maximus): new insights into parasite invasion and immune evasion strategies

Enteromyxum scophthalmi, an intestinal myxozoan parasite, is the causative agent of a threatening disease for turbot (Scophthalmus maximus, L.) aquaculture. The colonisation of the digestive tract by this parasite leads to a cachectic syndrome associated with high morbidity and mortality rates. This myxosporidiosis has a long pre-patent period and the first detectable clinical and histopathological changes are subtle. The pathogenic mechanisms acting in the early stages of infection are still far from being fully understood. Further information on the host–parasite interaction is needed to assist in finding efficient preventive and therapeutic measures. Here, a RNA-seq-based transcriptome analysis of head kidney, spleen and pyloric caeca from experimentally-infected and control turbot was performed. Only infected fish with early signs of infection, determined by histopathology and immunohistochemical detection of E. scophthalmi, were selected. The RNA-seq analysis revealed, as expected, less intense transcriptomic changes than those previously found during later stages of the disease. Several genes involved in IFN-related pathways were up-regulated in the three organs, suggesting that the IFN-mediated immune response plays a main role in this phase of the disease. Interestingly, an opposite expression pattern had been found in a previous study on severely infected turbot. In addition, possible strategies for immune system evasion were suggested by the down-regulation of different genes encoding complement components and acute phase proteins. At the site of infection (pyloric caeca), modulation of genes related to different structural proteins was detected and the expression profile indicated the inhibition of cell proliferation and differentiation. These transcriptomic changes provide indications regarding the mechanisms of parasite attachment to and invasion of the host. The current results contribute to a better knowledge of the events that characterise the early stages of turbot enteromyxosis and provide valuable information to identify molecular markers for early detection and control of this important parasitosis.