Candidate Biomarkers For Diagnosis Research Articles

Plasma thrombomodulin as a candidate biomarker for the diagnosis and prognosis of HBV-related acute-on-chronic liver failure.

Hepatitis B virus-related acute-on-chronic liver failure (HBV-ACLF) is a complicated syndrome with high short-term mortality. Effective biomarkers are required for its early diagnosis and prognosis. This study aimed to determine the diagnostic and prognostic value of thrombomodulin (TM) in patients with HBV-ACLF. The expression of TM during disease progression was evaluated through transcriptomics analysis. The plasma TM concentrations of 393 subjects with HBV-ACLF (n=213), acute-on-chronic hepatic dysfunction (ACHD, n=50), liver cirrhosis (LC, n=50) or chronic hepatitis B (CHB, n=50), and normal controls (NC, n=30) from a prospective multicenter cohort, were measured to verify the diagnostic and prognostic significance of plasma TM for HBV-ACLF patients by enzyme-linked immunosorbent assay (ELISA). TM mRNA was highly expressed in the HBV-ACLF group compared with the ACHD group (AUROC=0.710). High expression of TM predicted poor prognosis for HBV-ACLF patients at 28/90 days (AUROCs=0.823/0.788). Functional analysis showed that TM was significantly associated with complement activation and the inflammatory signaling pathway. External validation confirmed its high diagnostic accuracy for HBV-ACLF patients (AUROC=0.796). Plasma TM concentrations were correlated with organ failure, including coagulation and kidney failure. Plasma TM concentrations showed a potential prognostic value for 28-day mortality rates (AUROC=0.702). Risk stratification specifically identified HBV-ACLF patients with a high risk of death as having a plasma TM concentration of ≥8.4 ng/mL. This study reveals that the plasma TM can be a candidate biomarker for early diagnosis and prognosis of HBV-ACLF, and might play a vital role in coagulation and inflammation.

Association between Microenvironment-Related Genes and Prognosis of Primary Central Nervous System Lymphoma

Background: Comprehensive gene mutation profiling of primary central nervous system lymphoma (PCNSL) revealed genomic abnormalities associated with the NFκB signaling pathway and immune escape (Chapuy B, et al. Blood 2016). Although this has led to advances in targeted therapy, there are only a few candidate biomarkers for diagnosis and prediction of survival in PCNSL. Recurrence still occurs at high rate of over 60% and therapeutic resistance is a significant challenge in the management of recurrent PCNSL. Until now, the systemic profiling of tumor micro-environment (TME) was performed through gene expression analysis by whole transcriptome analysis (WTA) and single-cell RNA sequencing analysis (Heming M, et al. Genome medicine 2022), and stratification in PCNSL was attempted by using spatial transcriptome analysis (Xia Y, et al. Leukemia 2023). However, TME of PCNSL and their impact on prognosis remain uncertain. Objective: We performed this study to investigate the prognostic impact on survival and establish novel prognostic biomarkers in PCNSL. Methods: We analyzed the expression levels of 770 neuroinflammation-related (NFR) genes by the NanoString nCounter technology in tumor samples from 30 PNCSL patients. The clinical significance of genes and their association with prognosis were assessed. Genes related to “worse prognosis (WP)” or “better prognosis (BP)” were identified. We performed the univariable analysis using a cox proportional hazards model to evaluate the predictive value of expression of genes related to WP and clinical risk factors, such as age, sex, serum lactate dehydrogenase level, Karnofsky Performance Status (KPS), consciousness levels at diagnosis and lymphoma involvement of the deep brain structure. Gene expression data related to WP were subjected to multivariate analysis with clinical variables with p values less than 0.15 in the univariate analysis. The genes associated with WP were further validated using WTA of an independent PCNSL cohort (n=30, previously published by Fukumura K, et al. Acta neuropathologica 2016). Results: The median age at diagnosis was 69 years old (range, 32-83). The median follow-up period was 25 months (range, 1-110 months), with overall survival (OS) at 3 years of 39.7% and progression free survival at 3 years of 25.4%. Notably, 48 of 770 NFR genes were highly expressed in the WP group (3-year OS, 22.2%), compared with the BP group (3-year OS, 66.7%) (Figure 1). We found that oligodendrocyte and astrocyte-related signatures were enriched in the WP-associated gene set. Among clinical prognostic factors, KPS > 70 (p=0.0293), and consciousness levels at diagnosis (other than JCS 0-1) (p=0.104) were relatively associated with poor OS (p < 0.15) in univariate analysis. Multivariate analysis revealed that high expressions of TUBB4A (p=0.028, HR:3.88), S100B (p=0.046, HR:3.093) and SLC6A1 (p=0.034, HR:3.765) were significantly related to death independent from KPS and consciousness levels at diagnosis. Expression levels of these 3 genes were also significantly associated with poor OS in a validation cohort. Conclusion: Our observations suggest high expression of TUBB4A, S100B and SLC6A1 are the clinical indicators to predict poor prognosis in PCNSL patients. Furthermore, these data suggest that genes related to TME may play a crucial role in the pathogenesis of PCNSL, complementing the well-known involvement of the NF-kB signaling pathway. Therefore it is necessary to continue research focused on TME-targeted therapeutics to encounter drug resistance and refractoriness in PCNSL.

Epigenetic marks associated with gestational diabetes mellitus across two time points during pregnancy

An adverse intrauterine or periconceptional environment, such as hyperglycemia during pregnancy, can affect the DNA methylation pattern both in mothers and their offspring. In this study, we explored the epigenetic profile in maternal peripheral blood samples through pregnancy to find potential epigenetic biomarkers for gestational diabetes mellitus (GDM), as well as candidate genes involved in GDM development. We performed an epigenome-wide association study in maternal peripheral blood samples in 32 pregnant women (16 with GDM and 16 non-GDM) at pregnancy week 24–28 and 36–38. Biochemical, anthropometric, and obstetrical variables were collected from all the participants. The main results were validated in an independent cohort with different ethnic origin (European = 307; South Asians = 165). Two hundred and seventy-two CpGs sites remained significantly different between GDM and non-GDM pregnant women across two time points during pregnancy. The significant CpG sites were related to pathways associated with type I diabetes mellitus, insulin resistance and secretion. Cg01459453 (SELP gene) was the most differentiated in the GDM group versus non-GDM (73.6 vs. 60.9, p = 1.06E−11; FDR = 7.87E−06). Three CpG sites (cg01459453, cg15329406, and cg04095097) were able to discriminate between GDM cases and controls (AUC = 1; p = 1.26E−09). Three differentially methylated positions (DMPs) were replicated in an independent cohort. To conclude, epigenetic marks during pregnancy differed between GDM cases and controls suggesting a role for these genes in GDM development. Three CpGs were able to discriminate GDM and non-GDM groups with high specificity and sensitivity, which may be biomarker candidates for diagnosis or prediction of GDM.

Comparative proteomics identify HSP90A, STIP1 and TAGLN-2 in serum extracellular vesicles as potential circulating biomarkers for human adenomyosis.

Extracellular vesicles (EVs) carry specific proteins involved in intercellular communication. EVs with different protein contents are released into circulation in different diseases. Recent studies have identified proteins in adenomyosis (AM)-derived EVs (AMEVs) from blood as biomarkers for this disease. AM is an extension of endometrial tissue into the uterine myometrium. Magnetic resonance imaging (MRI) is the most accurate imaging tool for identifying adenomyosis. Therefore, the present study aimed to investigate the role of EVs in diagnosing AM. In the present study, tissue AMEVs (T-AMEVs) were isolated from lesion homogenates of patients with adenomyosis, and blood AMEVs (B-AMEVs) were isolated from peripheral blood of patients with AM via differential centrifugation and density gradient centrifugation. T-AMEVs and B-AMEVs were characterized by electron microscopy, western blotting and mass spectrometry and analysed using FunRich3.1.3 software. T-AMEVs (average diameter, 150.9±102.2 nm) and B-AMEVs (194.1±66.81 nm) expressed the CD9, CD63 and flotillin-2 EV markers. A total of 211 proteins expressed in T-AMEVs and B-AMEVs overlapped with Vesiclepedia database entries, including 2 epithelial-to-mesenchymal transition (EMT)-associated proteins and 6 invasion-associated proteins. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis indicated that these 211 proteins were associated with the ‘regulation of cell morphogenesis’ and ‘cytoskeletal organization’ terms, as well as the PPAR and HIF-1 signalling pathways, which are related to the proliferation and metastasis of endometrial cells that cannot invade the myometrium under normal circumstances. Among the 211 proteins, HSP90A, STIP1 and TAGLN-2 were expressed in T-AMEVs and B-AMEVs, but not in serum EVs of women without adenomyosis/endometriosis, and these proteins might be the potential biomarkers for adenomyosis. These findings provide insights into the molecular features of adenomyosis and the new candidate biomarkers for diagnosis.

Long Noncoding RNA Mediated Regulation in Human Embryogenesis, Pluripotency, and Reproduction.

Long noncoding RNAs (lncRNAs), a class of noncoding RNAs with more than 200 bp in length, are produced by pervasive transcription in mammalian genomes and regulate gene expression through various action mechanisms. Accumulating data indicate that lncRNAs mediate essential biological functions in human development, including early embryogenesis, induction of pluripotency, and germ cell development. Comprehensive analysis of sequencing data highlights that lncRNAs are expressed in a stage-specific and human/primate-specific pattern during early human development. They contribute to cell fate determination through interacting with almost all classes of cellular biomolecules, including proteins, DNA, mRNAs, and microRNAs. Furthermore, the expression of a few of lncRNAs is highly associated with the pathogenesis and progression of many reproductive diseases, suggesting that they could serve as candidate biomarkers for diagnosis or novel targets for treatment. Here, we review research on lncRNAs and their roles in embryogenesis, pluripotency, and reproduction. We aim to identify the underlying molecular mechanisms essential for human development and provide novel insight into the causes and treatments of human reproductive diseases.

Exosomal miRNA Profiling is a Potential Screening Route for Non-Functional Pituitary Adenoma.

Non-functional pituitary adenomas (NFPAs) are one of the most prevalent pituitary adenoma subtypes. The lack of reliable screening approach for NFPAs for the insidious clinical course usually leads to delays in medical therapy and consequently worse prognosis. Hence, we employed a sequence cohort (patient: control, 6:2) and a validation cohort (patient: control, 22:8) to develop a serum exosomal miRNA profile-based method for NFPA screening and prognosis prediction. We found that a total of 1,395 kinds of human miRNA were detected. Compared with healthy donors, 18 up-regulated and 36 down-regulated miRNAs showed significant expression alterations in NFPA patients. Target genes of differentially expressed miRNAs are mainly enriched in axonogenesis and cancer-associated terms. After validation, hsa-miR-486-5p, hsa-miR-151a-5p, hsa-miR-652-3p_R+1, and hsa-miR-1180-3p were promising biomarkers for NFPA, in which miR-486-5p was the most competent one. After a median of 33 months of prospective follow-up, exosomal hsa-miR-486-5p also was an efficient predictive biomarker for progression or relapse of NFPAs. By protein-protein interaction network construction of hsa-miR-486-5p targeted genes, the core modules revealed a high possibility that exosomal hsa-miR-486-5p regulated tumor progression by epigenetic regulation of MAPK signaling pathways. In conclusion, exosomal hsa-miR-486-5p, hsa-miR-151a-5p, hsa-miR-652-3p_R+1, and hsa-miR-1180-3p are candidate biomarkers for diagnosis and screening of NFPAs. More importantly, prospective follow-up reveals that hsa-miR-486-5p can be regarded as a significant predictor for prognosis of NFPAs.

The Role and Clinical Potentials of Circular RNAs in Prostate Cancer.

Globally, prostate cancer (PCa) is the second most commonly diagnosed cancer in men globally. Early diagnosis may help in promoting survival in the affected patients. Circular RNAs (circRNAs) are a novel class of non-coding RNAs (ncRNAs) which have been found to show extensive dysregulation in a handful of human diseases including cancers. Progressions in RNA identification techniques have provided a vast number of circRNAs exhibiting either up-regulation or down-regulation in PCa tissues compared to normal adjacent tissues. The mechanism of action is not clear for most of dysregulated circRNAs. Among them, function of a number of newly identified dysregulated circRNAs have been assessed in PCa cells. Increase in cell proliferation, migration, invasion, and metastasis have been reported for up-regulated circRNAs which suggest their role as oncogenes. On the other hand, down-regulated circRNAs have shown tumor suppressing actions in experimental studies. Furthermore, in a majority of studies, circRNAs have been found to sponge microRNAs (miRNAs), negatively regulating expression or activity of the downstream miRNAs. Additionally, they have been identified in interaction with regulatory proteins. This axis consequently regulates a signaling pathway, a tumor suppressor, or an oncogene. Easy, quick, and reliable detection of circRNAs in human body fluids also suggests their potentials as biomarker candidates for diagnosis and prediction of prognosis in PCa patients. In this review, we have discussed the role and potentials of a number of dysregulated circRNAs in PCa.

Assessment of Tau Pathology as Measured by 18F-THK5317 and 18F-Flortaucipir PET and Their Relation to Brain Atrophy and Cognition in Alzheimer's Disease.

Background:In Alzheimer’s disease (AD), the abnormal aggregation of hyperphosphorylated tau leads to synaptic dysfunction and neurodegeneration. Recently developed tau PET imaging tracers are candidate biomarkers for diagnosis and staging of AD.Objective:We aimed to investigate the discriminative ability of 18F-THK5317 and 18F-flortaucipir tracers and brain atrophy at different stages of AD, and their respective associations with cognition.Methods:Two cohorts, each including 29 participants (healthy controls [HC], prodromal AD, and AD dementia patients), underwent 18F-THK5317 or 18F-flortaucipir PET, T1-weighted MRI, and neuropsychological assessment. For each subject, we quantified regional 18F-THK5317 and 18F-flortaucipir uptake within six bilateral and two composite regions of interest. We assessed global brain atrophy for each individual by quantifying the brain volume index, a measure of brain volume-to-cerebrospinal fluid ratio. We then quantified the discriminative ability of regional 18F-THK5317, 18F-flortaucipir, and brain volume index between diagnostic groups, and their associations with cognition in patients.Results:Both 18F-THK5317 and 18F-flortaucipir outperformed global brain atrophy in discriminating between HC and both prodromal AD and AD dementia groups. 18F-THK5317 provided the highest discriminative ability between HC and prodromal AD groups. 18F-flortaucipir performed best at discriminating between prodromal and dementia stages of AD. Across all patients, both tau tracers were predictive of RAVL learning, but only 18F-flortaucipir predicted MMSE.Conclusion:Our results warrant further in vivo head-to-head and antemortem-postmortem evaluations. These validation studies are needed to select tracers with high clinical validity as biomarkers for early diagnosis, prognosis, and disease staging, which will facilitate their incorporation in clinical practice and therapeutic trials.

Identification of heterogeneous nuclear ribonucleoprotein as a candidate biomarker for diagnosis and prognosis of hepatocellular carcinoma.

Hepatocellular carcinoma (HCC) is the most common type of liver cancer with a high mortality rate. However, spliceosomal genes are still lacking in the diagnosis and prognosis of HCC. Identification of differentially expressed genes (DEGs) was performed using the limma package in R software. Modules highly related to HCC were obtained by weighted gene co-expression network analysis (WGCNA), and the module genes were analyzed using the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway. The biomarker for diagnosing HCC was determined by receiver operating characteristic (ROC) curve analysis, and the effect of the biomarker in the diagnosis of HCC was evaluated by performing five-fold cross-validation with logistic regression. HCC specimens from preoperatively treated patients were tested for biomarker by real-time quantitative polymerase chain reaction (RT-qPCR). Kaplan-Meier analysis was used to assess the relationship between biomarker and patient survival. The role of biomarker was evaluated using ESTIMATE analysis in the tumor microenvironment. In this study, 389 DEGs were screened out from three Gene Expression Omnibus (GEO) datasets. We also found that the turquoise module of 123 genes from The Cancer Genome Atlas (TCGA) data was the key module with the highest correlation with HCC traits. Then, 123 genes were analyzed using the KEGG enrichment pathway, and eight genes were found to be most significantly related to the spliceosome pathway. We selected 8 genes and 389 DEGs shared genes, and finally got the only gene, heterogeneous nuclear ribonucleoprotein (hnRNPU). The high expression of hnRNPU was associated with poor prognosis of HCC, and hnRNPU was a biomarker for diagnosing HCC. In the tissues of patients with excellent HCC treatment hnRNPU messenger RNA (mRNA) was lower than in the tissues of patients with poor HCC treatment. High expression of hnRNPU was significantly increased in HCC patients with low stromal (P<0.05), low immune (P<0.05), and low estimation scores (P<0.05), and with high tumor purity (P<0.05) and high malignant progression (P<0.05) of the HCC. The hnRNPU gene identified in this study may become a new biomarker for the diagnosis and prognosis of HCC.

Identification of clinical trait-related small RNA biomarkers with weighted gene co-expression network analysis for personalized medicine in endocervical adenocarcinoma.

Endocervical adenocarcinoma (EAC) is an aggressive type of endocervical cancer. At present, molecular research on EAC mainly focuses on the genome and mRNA transcriptome, the investigation of small RNAs in EAC has not been fully described. Here, we systematically explored small RNAs in 14 EAC patients with different subtypes using small RNA sequencing. MiRNAs and tRNA-derived RNAs (tDRs) accounted for the majority of mapped reads and the total number of miRNAs and tDRs maintained a relative balance. To explore the correlations between small RNAs expression and EAC with different clinical characteristics, we performed the weighted gene co-expression network analysis (WGCNA) and screened for hub small RNAs. From the key modules, we identified 9 small RNAs that were significantly related to clinical characteristics in EAC patients. Gene ontology and pathway analyses revealed that these molecules were involved in the pathogenesis of EAC. Our work provided new insights into EAC pathogenesis and successfully identified several small RNAs as candidate biomarkers for diagnosis and prognosis of EAC.

ECT2 overexpression promotes the polarization of tumor-associated macrophages in hepatocellular carcinoma via the ECT2/PLK1/PTEN pathway

Hepatocellular carcinoma (HCC) is a common high-mortality cancer, mainly due to diagnostic difficulties during its early clinical stages. In this study, we aimed to identify genes that are important for HCC diagnosis and treatment, and we investigated the underlying mechanism of prognostic differences. Differentially expressed genes (DEGs) were identified by using the limma package, and receiver operating characteristic curve analysis was performed to identify diagnostic markers for HCC. Bioinformatics and clinical specimens were used to assess epithelial cell transforming 2 (ECT2) in terms of expression, prognostic value, pathways, and immune correlations. In vitro experiments were used to investigate the underlying mechanism and function of ECT2, and the results were confirmed through in vivo experiments. The integrated analysis revealed 53 upregulated DEGs, and one candidate biomarker for diagnosis (ECT2) was detected. High expression of ECT2 was found to be an independent prognostic risk factor for HCC. ECT2 expression showed a strong correlation with tumor-associated macrophages. We found that ECT2 overexpression increased the migration and proliferation of HCC cells. It also promoted the expression of PLK1, which subsequently interacted with PTEN and interfered with its nuclear translocation, ultimately enhancing aerobic glycolysis and promoting M2 macrophage polarization. M2 macrophages suppress the functions of NK cells and T cells, and this was confirmed in the in vivo experiments. Overall, ECT2 may promote the polarization of M2 macrophages by enhancing aerobic glycolysis and suppressing the functions of immune cells. ECT2 could serve as a candidate diagnostic and prognostic biomarker for HCC.

Peripheral blood and tissue assessment highlights differential tumor-circulatory gradients of IL2 and MIF with prognostic significance in resectable pancreatic ductal adenocarcinoma

ABSTRACT Various reports have pointed out the potential of cytokines as diagnostic and prognostic biomarkers for pancreatic ductal adenocarcinoma (PDA). Nonetheless, the evidence is contradictory and the role of chronic inflammation and relationship between circulatory and corresponding tumoral cytokine levels remain elusive. Utilizing a broad array of cytokines, we identified two opposing parameters: serum levels of interleukin 2 (IL2) and macrophage migration inhibitory factor (MIF) are diagnostic and prognostic factors. While low IL2 levels are associated with PDA, they also relate to a favorable prognosis of patients. In contrast, high MIF levels are associated with PDA and simultaneously related to an unfavorable outcome. MIF levels are associated with the intratumoral density of M2 macrophages (CD163+). Focusing on the tumor-to-serum gradient, we unveiled a different pattern of compartmental cytokine expression between IL2 and MIF. Our findings indicate that an extra-tumoral source of IL2 exists in PDA patients leading to increased detectability in the circulatory system. In case of MIF, the tumor microenvironment is presumably the main site of production and thereby reflected by serum measurements. Taken together, our study describes IL2 and MIF levels as biomarker candidates for diagnosis and prognosis of PDA, highlighting the need for compartmental cytokine analyses. From the perspective of tumor immunobiology, we identify multiple inflammatory states (proposed as types I–III) and see that systemic chronic dysregulation, independent of tumor microenvironment, can be measured and is a possible tool for stratification. Thus, direct correlation of local cytokine levels to peripheral blood levels needs to be regarded with caution.

ASTN1 is associated with immune infiltrates in hepatocellular carcinoma, and inhibits the migratory and invasive capacity of liver cancer via the Wnt/β‑catenin signaling pathway.

Astrotactin 1 (ASTN1) is known to serve a physiological role in neuronal migration; however its role in liver cancer remains to be determined. In the present study, ASTN1 levels were lower in liver cancer tissues compared with those in matching normal tissue. ASTN1 levels were negatively associated with microscopic vascular invasion, advanced clinical stage and a less favorable prognosis in patients with hepatocellular carcinoma (HCC). Furthermore, ASTN1 overexpression in a liver cancer cell line reduced the migratory and invasive capacity of the cells. Based on bioinformatics analysis, ASTN1 levels were negatively associated with the Wnt signaling pathway. In addition, ASTN1 downregulated the protein expression levels of β-catenin, T-cell factor (TCF)1, TCF4, Jun proto-oncogene (C-jun), Myc proto-oncogene (C-myc), cyclooxygenase-2 (COX2), metalloproteinase (MMP)2, MMP9 and vascular endothelial growth factor (VEGF) protein levels, indicative of suppression of Wnt signaling. Furthermore, XAV939-induced Wnt signaling suppression reversed the ASTN1-mediated inhibition of invasion and migration in cells. Overexpression of ASTN1 in xenografts reduced cancer development as well as Wnt signaling. TIMER analysis showed that ASTN1 expression was negatively correlated with B cell, macrophage and neutrophil infiltrating levels in HCC. Together, the results of the present study showed that ASTN1 reduced the migratory and invasive capacity of liver cancer cells, potentially served as a candidate biomarker for diagnosis and prediction of the prognosis of HCC, and was associated with immune infiltration. Understanding the underlying mechanisms of action of ASTN1 may facilitate the development of novel strategies for prevention and treatment of liver cancer.

The expanding role of CDR1‐AS in the regulation and development of cancer and human diseases

CircRNAs are a superabundant and highly conserved group of noncoding RNAs (ncRNAs) that are characterized by their high stability and integrity compared with linear forms of ncRNAs. Recently, theircritical rolein gene expression regulation has been shown; thus, it is not far-fetched to believe that their abnormal expression can be a cause of different kinds of diseases such as cancer, neurodegenerative, and autoimmune diseases. They can have a function in variety of biological processes such as microRNA (miRNA) sponging, interacting with RNA-binding proteins, or even an ability to translate to proteins. A huge challengein finding diagnostic biomarkers isfinding noninvasive biomarkers that can be detected in human fluids, especially blood samples. CircRNAs are becoming candidate biomarkers for diagnosis and prognosis of these diseases through their ability to transverse from the blood-brain barrier and their broad presence in circulating exosomes. The circRNA for miRNA-7 (ciRS-7) is newly recognized, and acknowledged to being related to human pathology and cancer progression. In this review, we first briefly summarizethe latest studies about their characteristics, biogenesis, and their mechanisms of action in the regulation and development of human diseases. Finally, we providea list of diseases that are linked to one memberofthis novel class of ncRNAs called ciRS-7.

M &lt;sup&gt;6&lt;/sup&gt;A Signature and Tumour Immune Microenvironment for Predicting Prognostic Value in Gliomas

Background: Gliomas comprise about 80 per cent of all malignant brain tumours. Current gliomas staging alone cannot adequately predict prognosis between Glioblastoma multiforme (GBM) and low-grade gliomas (LGG). This study aims to explore effective diagnostic and prognostic biomarkers for gliomas. Methods: We performed consensus clustering to m6A RNA methylation regulators in TCGA-GBM/LGG datasets. The tumour-infiltrating immune cells of The Cancer Genome Atlas (TCGA) gliomas cohort was analyzed by single-sample gene set enrichment analysis (ssGSEA). Four hub gene were identified via weighted gene co-expression network analysis (WGCNA) and least absolute shrinkage, and selection operator (LASSO). The diagnostic and prognostic value were validated by risk score analysis, Kaplan-Meier and ROC. Finding: We identified two glioma subgroups (cluster 1/2) by applying consensus clustering to m6A RNA methylation regulators in 665 gliomas (TCGA-GBM and TCGA-LGG). The cluster 1 subgroup was associated with a poorer prognosis and a higher WHO classification than the cluster 2 subgroup. We performed chi-square test between m6A cluster subgroup and immune infiltration subgroup, the results indicated that the characteristics of the tumor-associated immune infiltration are significantly enriched in the cluster 1 subgroup. These findings suggest that m6A RNA methylation regulators are related to immune infiltration. In order to explore potential hub genes, we performed WGCNA between high/low immune infiltration and m6A cluster 1/2 groups. LASSO was utilized for the hub genes, and four immune and m6A related genes TAGLN2, PDPN, TIMP1, EMP3 were identified as biomarkers for glioma prognosis. Moreover, the 4-gene signature achieved AUC values of 0.80, 0.79, 0.67 and 0.72 in TCGA, Rembrandt, GSE16011 and Chinese Glioma Genome Atlas (CGGA), respectively. Interpretation: These findings provide new insight into gliomas prognosis and identify four genes (TAGLN2, PDPN, TIMP1 and EMP3) as candidate biomarkers for diagnosis and prognosis of glioma. Funding Statement: This work was supported by National Natural Science Foundation of China (no.81701359), Natural science foundation of Shanghai (18ZR1430400), and the Cross Research Fund of Medicine and Engineering of Shanghai Jiaotong University (No. YG2016QN32, YG2019QNA67). Declaration of Interests: The authors have declared that no conflict of interest exists. Ethics Approval Statement: Not required.

Abstract GMM-044: IDENTIFICATION OF A NOVEL CANDIDATE BIOMARKER FOR DIAGNOSIS AND THERAPEUTIC OVARIAN CANCER TARGET

Abstract Ovarian cancer is the most fatal gynecological cancer with high mortality. It still has no reliable diagnostic marker and effective treatment due to its high drug resistance and high recurrence. To develop a novel biomarker for diagnosis and therapeutic target of intractable ovarian cancer, we selected for an upregulated gene in serous ovarian tumors compared with normal ovary counterparts by microarray analysis and confirmed its elevated mRNA expression in ovarian tumors by RT-PCR. Consistent with its high mRNA level, tumor-specific preferential high expression of candidate protein was detected in the cytoplasm of the ovarian tumor tissues by immunohistochemistry. To our surprise, indirect immunofluorescence staining revealed an unexpected cytoplasmic subcellular localization of a candidate protein. Furthermore, forced expression of a candidate gene in cultured cells with no detectable level showed a marked inhibition of cell proliferation. To address these unexpected findings, we set out to identify a candidate interacting protein by yeast 2-hybrid screening to explore a novel function and its underlying mechanism. Among them, one of cell death associated protein was identified as a novel interacting partner of a candidate protein and their physical interaction in mammalian cells was confirmed by co-immunoprecipitation assay and confocal microscopy. Further domain mapping analysis should reveal critical domains for their interaction and would provide fundamental and pivotal information for a novel function and an underlying molecular mechanism of a candidate gene. This research was supported by Basic Science Research Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Education (2018R1D1A1B07047640). Citation Format: Kyoungsook Park, Chaeyeon Son, Sang Yong Song. IDENTIFICATION OF A NOVEL CANDIDATE BIOMARKER FOR DIAGNOSIS AND THERAPEUTIC OVARIAN CANCER TARGET [abstract]. In: Proceedings of the 12th Biennial Ovarian Cancer Research Symposium; Sep 13-15, 2018; Seattle, WA. Philadelphia (PA): AACR; Clin Cancer Res 2019;25(22 Suppl):Abstract nr GMM-044.

Identification of hub genes in prostate cancer using robust rank aggregation and weighted gene co-expression network analysis.

The pathogenic mechanisms of prostate cancer (PCa) remain to be defined. In this study, we utilized the Robust Rank Aggregation (RRA) method to integrate 10 eligible PCa microarray datasets from the GEO and identified a set of significant differentially expressed genes (DEGs) between tumor samples and normal, matched specimens. To explore potential associations between gene sets and PCa clinical features and to identify hub genes, we utilized WGCNA to construct gene co-expression networks incorporating the DEGs screened with the use of RRA. From the key module, we selected LMNB1, TK1, ZWINT, and RACGAP1 for validation. We found that these genes were up-regulated in PCa samples, and higher expression levels were associated with higher Gleason scores and tumor grades. Moreover, ROC and K-M plots indicated these genes had good diagnostic and prognostic value for PCa. On the other hand, methylation analyses suggested that the abnormal up-regulation of these four genes likely resulted from hypomethylation, while GSEA and GSVA for single hub gene revealed they all had a close association with proliferation of PCa cells. These findings provide new insight into PCa pathogenesis, and identify LMNB1, TK1, RACGAP1 and ZWINT as candidate biomarkers for diagnosis and prognosis of PCa.

Zinc-α2-glycoprotein 1 promotes EMT in colorectal cancer by filamin A mediated focal adhesion pathway.

Liver metastasis is the main reason for the poor prognosis of colorectal cancer, and identifying molecules involved in liver metastases of colorectal cancer may provide effective therapeutic targets. Zinc-α2-glycoprotein 1(AZGP1) is a candidate biomarker for diagnosis and prognosis in cancer. However, its function and molecular mechanism in metastatic colorectal cancer remains largely unknown. We previously found that up-regulated AZGP1 promotes proliferation, migration and invasion in colorectal cancer cell line, here we elucidated the mechanism of AZGP1 in regulating metastasis. In this article, we found that AZGP1 was also highly expressed in colorectal cancer tissues with liver metastasis relative to those without metastasis, and abundant expression of AZGP1 was associated with poor prognosis, also, AZGP1 down regulation prevented cell metastasis in vivo and in vitro. We further demonstrated that AZGP1 promotes metastasis by regulating the epithelial-mesenchymal transition (EMT) and associating with molecules involved in the focal adhesion pathway, including the adhesion molecule FLNA, which acts as an important protein interactor. More importantly, AZGP1 down regulation inhibited the phosphorylation of FLNA mediated by the restrain of PAK2 kinase, thereby inducing its proteolysis and subsequently affecting its subcellular localization, where it regulates the EMT and promotes metastasis. Collectively, these results highlight AZGP1 as a new and promising therapeutic molecule for liver metastatic colorectal cancer.

Role of differentially expressed genes and long non-coding RNAs in papillary thyroid carcinoma diagnosis, progression, and prognosis.

Currently, the combination of ultrasonography and fine-needle aspiration biopsy (FNAB) can not discriminate between benign and malignant tumor of thyroid in some cases. The main issue in assessing the patients with thyroid nodules is to distinguish thyroid cancer from benign nodules, and reduce diagnostic surgery. To identify potential molecular biomarkers for patients with indeterminate FNAB, we explored the differentially expressed genes (DEGs) and differentially expressed long non-coding RNAs (DElncRNAs) in TCGA database between 318 papillary thyroid carcinoma (PTC) tissues and 35 normal thyroid gland tissues by DESeq R. Furthermore, DEGs were verified by gene expression profile GSE33630. Ten top DEGs and DElncRNAs were identified as candidate biomarkers for diagnosis and Lasso (Least Absolute Shrinkage and Selection Operator) logistic regression analysis were performed to improve the diagnostic accuracy of them. Besides, partial molecular biomarkers of top DEGs and DElncRNAs were closely related to the tumor stage (T), lymph node metastasis (N), metastasis (M) and pathological stage of PTC, which could reflect behavior of tumor progression. According to multivariate Cox analysis, the combination of two DEGs (METTL7B and KCTD16) and two DElncRNAs (LINC02454 and LINC02471) could predict the outcome in a more exact way. In conclusion, top DEGs and DElncRNAs could raise diagnosis of PTC in indeterminate FNAB specimens, and some could function as molecule biomarkers for tumor progression and prognosis.

Abstract 3546: Extracellular vesicles and exosome-associated microRNAs in squamous cell carcinoma of the head and neck disrupt dendritic cell differentiation and maturation

Abstract Squamous cell carcinomas (SCCs) remain among the most common malignancies of the head and neck region. Plasma microRNAs (miRNAs) are appealing biomarker candidates for diagnosis or therapy response monitoring since they may be associated with clinical and pathological features of the disease. Increasing evidence also points to a role for these molecules, mostly when transported by extracellular vesicles (EVs), in signaling between cancer and immune cells. The aims of this study are to search for potential miRNA biomarkers for SCCs in plasma, to evaluate the presence of these markers within EVs using SCC-derived cell lines as study models and to study the effect of EVs on monocyte-derived dendritic cells functions. Total RNA was isolated from plasma samples from head and neck SCC patients and healthy donors following optimized protocols. EVs from the culture medium of SCC cell lines were collected by differential centrifugation and visualized by transmission electron microscopy. The expression profile of miRNAs in plasma and EVs was evaluated by qRT-PCR. CD14+ cells from healthy donors were selected from peripheral blood using magnetic selection columns. Monocyte-derived immature dendritic cells were obtained following CD14+ cells treatment with human recombinant IL-4 and GM-CSF for six days and the maturation signal consisted on treatment of immature dendritic cells with LPS for 24 hours. Both treatments were carried out either in the presence or absence of EVs. Immunophenotyping of monocytes and monocyte-derived dendritic cells was based on the detection and expression levels of cell surface markers CD14, CD33, CD45, CD80, CD86, CD209 and HLA-DR by flow cytometry. A subset of miRNAs was consistently detected in SCC patients' plasma and EVs. Among these, miR-24 is of special interest since it has been associated with antigen processing and presentation by dendritic cells. The percentage of CD14+ cells expressing CD33 when cultured in the presence of EVs was significantly lower, and the same effect was seen for the CD209 and CD80 markers, suggesting alterations of antigen presentation functions. The percentage of cells expressing HLA-DR was similar both when CD14+ cells were cultured in the presence or without the addition of EVs, but the level of HLA-DR expression, as measured by fluorescence intensity, was lower when EVs were present, following both differentiation and maturation signals. The detection of miRNAs both in plasma and in association with EVs corroborates their potential as cancer biomarkers but also their possible implication in cell signaling. Differences in surface markers of monocyte-derived dendritic cells in the presence of EVs suggest an effect of EV content, including miRNAs, on differentiation and maturation processes, essential aspects for the proper function of dendritic cells in the tumor microenvironment. Citation Format: Luciana C. Marti, Elisangela P. Silva, Mariana B. Rizzo, Rossana V. Lopez, Otavio A. Curioni, Raquel A. Moyses, Fabio D. Nunes, Patricia Severino. Extracellular vesicles and exosome-associated microRNAs in squamous cell carcinoma of the head and neck disrupt dendritic cell differentiation and maturation [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3546.