Candidate Biomarkers For Early Detection Research Articles

Metabolomics for early pancreatic cancer detection in plasma samples from a Swedish prospective population-based biobank.

Pancreatic ductal adenocarcinoma (pancreatic cancer) is often detected at late stages resulting in poor overall survival. To improve survival, more patients need to be diagnosed early when curative surgery is feasible. We aimed to identify circulating metabolites that could be used as early pancreatic cancer biomarkers. We performed metabolomics by liquid and gas chromatography-mass spectrometry in plasma samples from 82 future pancreatic cancer patients and 82 matched healthy controls within the Northern Sweden Health and Disease Study (NSHDS). Logistic regression was used to assess univariate associations between metabolites and pancreatic cancer risk. Least absolute shrinkage and selection operator (LASSO) logistic regression was used to design a metabolite-based risk score. We used receiver operating characteristic (ROC) analyses to assess the discriminative performance of the metabolite-based risk score. Among twelve risk-associated metabolites with a nominal P value <0.05, we defined a risk score of three metabolites [indoleacetate, 3-hydroxydecanoate (10:0-OH), and retention index (RI): 2,745.4] using LASSO. A logistic regression model containing these three metabolites, age, sex, body mass index (BMI), smoking status, sample date, fasting status, and carbohydrate antigen 19-9 (CA 19-9) yielded an internal area under curve (AUC) of 0.784 [95% confidence interval (CI): 0.714-0.854] compared to 0.681 (95% CI: 0.597-0.764) for a model without these metabolites (P value =0.007). Seventeen metabolites were significantly associated with pancreatic cancer survival [false discovery rate (FDR) <0.1]. Indoleacetate, 3-hydroxydecanoate (10:0-OH), and RI: 2,745.4 were identified as the top candidate biomarkers for early detection. However, continued efforts are warranted to determine the usefulness of these metabolites as early pancreatic cancer biomarkers.

Synaptic proteins in pre‐symptomatic Alzheimer’s disease: biomarkers for early detection of Cognitive Decline

AbstractBackgroundSynaptic proteins in the cerebrospinal fluid (CSF) may reveal changes in the pre‐symptomatic stages of Alzheimer’s disease (AD), thus may be candidate biomarkers for early detection of the disease.MethodThe PREVENT‐AD cohort includes symptom‐free (upon enrolment) elderly participants who are at risk of developing AD from their family history. We used enzyme‐linked immunosorbent assay kits to assess CSF samples from 129 such participants for the “classical” AD biomarkers total tau, phosphorylated (181) tau and Aβ42. We also used neuroimaging data (MRI, PET) and neuropsychological assessments (MMSE, RBANS) as potential indicators disease progression. We then used in the CSF samples to measure the soluble synaptic biomarkers ADAM 22 (post‐synaptic), ADAM23 (pre‐synaptic). Immunoprecipitated SYT1 (pre‐synaptic) from CSF were analyyzed using high‐resolution selected ion monitoring analyses on a quadrupole–orbitrap mass spectrometer Q Exactive. Statistical analysis of the association of these markers with evidence of disease in analyses were done included sex and APOE e4 status as covariates.ResultAmong participants who remained cognitively unimpaired, we observed significant correlations between baseline CSF ADAM 22 levels and t‐tau (R2 = 0.22, p &lt; 0.0001), p‐tau (R2 = 0.22, p &lt; 0.0001), and Aβ42 (R2 = 0.06, p = 0.01488). We also found similarly suggestive correlations also between CSF ADAM 23, CSF SYT1 and the same disease markers. Covariate analyses suggested little or no variation in the associations between these synaptic proteins with t‐tau and p‐tau by sex, APOE e4 status, negative PET amyloid positivity (standardized uptake value ratio ≤ 1.37) and negative CSF total tau positivity (≤ 335pg/ul). PET amyloid positivity was significantly associated with ADAM22 and p‐tau interactions whereas SYT1 was significantly associated with t‐tau and p‐tau in CSF tau‐positive participants. In linear regression analyses, baseline CSF ADAM22 levels correlated with the language cognitive performance trajectory slopes estimated over the course of 5 to 8 years on the RBANS (R2 = 0.04, p = 0.03912). We found no significant interaction between other baseline CSF synaptic protein levels and other subscales of the RBANS.ConclusionCSF synaptic protein levels show promising correlation with landmark AD proteins and emerging cognitive deficits.

Investigating the importance of EGFR (− 216G/T), Exo1 (K589E) and LEP (− 2548G/A) gene polymorphisms with risk of lung cancer as potential diagnostic biomarker in Iranian population

BackgroundIn Iran, lung cancer is the third most common type of cancer and its prevalence is increasing rapidly. Identification informative genetic polymorphisms in cancer causing genes including epidermal growth factor receptor (EGFR) as key gene in control of cellular proliferation via intrinsic tyrosine/kinase activity, exonuclease 1 (EXO1) as one of the upregulated gene in different human malignancies and leptin (LEP) participate in carcinogenesis in lung cancer appears to be used as potential genetic markers for predicting lung cancer risk. There is no study about investigate association of the EGFR (− 216G/T), Exo1 (K589E) and LEP (− 2548G/A) gene polymorphisms with risk of lung cancer in Iranian population. The aim of this study was investigating the association of EGFR (− 216G/T), Exo1 (K589E) and LEP (− 2548G/A) gene polymorphisms with risk of lung cancer as a potentially diagnostic biomarker in Iranian population.MethodsIn this case–control study, A total of 100 patients with lung cancer and 100 age and gender-matched healthy controls were recruited into this study and the association between EGFR (− 216G/T), Exo1 (K589E) and LEP (− 2548G/A) gene polymorphisms with the risk of lung cancer was investigated by using PCR–RFLP technique and bioinformatics approach.ResultsThe rs712829 of EGFR gene show that a significant statistical difference between G allele and risk of lung cancer (P = 0.001, OR = 2.976, CI = 95%, 1.557–5.691), in contrast, the T allele and TT genotype show a protective role against the risk of lung cancer. Result of in silico analysis indicated that the rs712829 alter splicing and promoter regulation of EGFR gene and associated with the risk of lung cancer. PCR–RFLP result for rs1047840 of Exo1 gene showed that the AA genotype and A allele of this polymorphism associated with risk of lung cancer, whereas the GG genotype show a protective effect against the risk of lung cancer (P = 0.004, OR = 5.391, CI = 95%, 1.690–17.200). On the other hand, in silico analysis showed that the existence of rs1047840 in Exo1 gene influence lung cancer susceptibility. For rs7799039 of LEP gene, PCR–RFLP analysis showed that, there is no significant association between this polymorphism and the risk of lung cancer.ConclusionThe rs712829 of EGFR gene and rs1047840 of Exo1 are associated with risk of lung cancer among Iranian population and can be used as a potentially candidate biomarker for early detection and primary prevention.

Systematic Analysis of Tissue-Derived and Biofluid Extracellular Vesicle miRNAs Associated with Prostate Cancer.

Extracellular vesicles (EVs) are emerging as biomarker candidates for early detection of prostate cancer. Studies compare EV-microRNA (miRNA) expression in individuals with prostate cancer (PCa) with cancer-free samples for diagnostic purposes. The aim of this study is to review miRNA signatures to investigate the overlap between miRNAs enriched in PCa tissue and miRNAs enriched in EVs isolated from subjects with PCa biofluids (i.e., urine, serum, and plasma). Signatures dysregulated in EVs from PCa biofluids and tissue are potentially associated with the primary tumor site and might be more indicative of PCa at an early stage. A systematic review of EV-derived miRNAs and a reanalysis of PCa tissue miRNA sequencing data for comparison is presented. Articles in the literature are screened for validated miRNA dysregulation in PCa and compared with TCGA primary PCa tumor data using DESeq2. This resulted in 190 dysregulated miRNAs being identified. Thirty-one eligible studies are identified, indicating 39 dysregulated EV-derived miRNAs. The top ten markers identified as significantly dysregulated in the PCa tissue dataset TCGA (e.g., miR-30b-3p, miR-210-3p, miR-126-3p, and miR-196a-5p) have a significant expression change in EVs with the same directionality in one or several statistically significant results. This analysis highlights several less frequently studied miRNAs in PCa literature.

Serum stratifin and presepsin as candidate biomarkers for early detection of COVID-19 disease progression

The prognosis of patients with severe cases of COVID-19 is poor; thus, biomarkers for earlier prediction of COVID-19 progression are vital. We measured levels of five lung injury-related biomarkers, SP-D, KL-6, presepsin, kallistatin and stratifin, in serum samples collected serially during hospitalization from 31 patients with mild/moderate or severe/critical COVID-19 pneumonia, and their predictive performances were compared. Like the previously reported presepsin, a new biomarker candidate, stratifin, was significantly elevated with the onset of severe or critical symptoms in COVID-19 patients and decreased with symptom improvement. Notably, changes in stratifin and presepsin levels were distinctly earlier than those in SP-D, KL-6 and even SpO2/FiO2 values. Furthermore, serum levels of these biomarkers were significantly higher at the pre-severe stage (before the start of oxygen support) of patients who eventually advanced to severe/critical stages than in the patients who remained at the mild/moderate stage. These results were confirmed in an independent cohort, including 71 mild/moderate and 14 severe/critical patients, for whom the performance of stratifin and presepsin in discriminating between mild/moderate and pre-severe conditions of COVID-19 patients was superior to that of the SpO2/FiO2 ratio. Therefore, we concluded that stratifin and presepsin could be used as prognostic biomarkers for severe COVID-19 progression.

Circulating exosomal hsa_circRNA_0039480 is highly expressed in gestational diabetes mellitus and may be served as a biomarker for early diagnosis of GDM

BackgroundGestational diabetes mellitus (GDM) seriously affects the health of mothers and babies, and there are still no effective early diagnostic markers. Therefore, it is necessary to find diagnostic biomarkers for screening GDM in early pregnancy. Circular RNA (circRNA) is more stable than linear RNA, and can be encapsulated in exosomes and participate in the pathological process of various diseases, which makes it a better candidate biomarker for various diseases. In this study, we attempted to identify the exosomal circRNA biomarkers for detecting early GDM.MethodsWe performed microarray analysis to compare the plasma exosomal circRNA expression profiles of three GDM patients 48 h before and 48 h after delivery. The repeatability of the expression of circRNAs were randomly validated by RT-PCR analysis. Pearson correlation analysis was applied to evaluate the correlation between circRNAs and OGTT level. ROC curve was established to assess the diagnostic value of circRNAs for GDM at different stages.ResultsPlasma exosomal hsa_circRNA_0039480 and hsa_circRNA_0026497 were highly expressed in GDM patients before delivery (P < 0.05). The hsa_circRNA_0039480 expression was higher for GDM group than NGT group at different stages, and was also positively correlated with OGTT during the second trimester (P < 0.05). The expression of hsa_circRNA_0026497 was higher for GDM group during the third, and second trimesters. And there was a strong correlation between two circRNAs in GDM patients during the first-trimester (r = 0.496, P = 0.014). Hsa_circRNA_0039480 showed significant diagnostic value in the first, second, and third trimesters of pregnancy (AUC = 0.704, P = 0.005; AUC = 0.898, P < 0.001 and AUC = 0.698, P = 0.001, respectively). Notably, the combination of hsa_circRNA_0039480 and hsa_circRNA_0026497 exhibited promising discriminative effect on GDM in the first trimesters (AUC = 0.754, P < 0.001).ConclusionPlasma exosomal hsa_cirRNA_0039480 is highly expressed in GDM patients at different stages and may be served as a candidate biomarker for early detection of GDM.

Acylcarnitines: Can They Be Biomarkers of Diabetic Nephropathy?

Diabetic nephropathy (DN), one of the most serious microvascular complications of diabetes mellitus (DM), may progress to end-stage renal disease (ESRD). Current biochemical biomarkers, such as urinary albumin excretion rate (UAER), have limitations for early screening and monitoring of DN. Recent studies have identified some metabolites as candidate biomarkers for early detection of DN. In this review, we summarize the role of dysregulated acylcarnitines (AcylCNs) in DN pathophysiology. Lower abundance of short- and medium-chain AcylCNs and higher long-chain AcylCNs often occurred in DM with normal albuminuria and microalbuminuria, compared with advanced stages of DN. The increase of long-chain AcylCNs was supposed to be an adaptive compensation in fat acids (FAs) oxidation in the early stage of DN. Conversely, the decrease of long-chain AcylCNs was due to incomplete oxidation of FAs in advanced stage of DN. Thus, AcylCNs may serve as sensitive biomarkers in predicting the risk of DN.

Predicting acute kidney injury and future cardiac events using urinary liver-type fatty acid-binding protein in patients with acute myocardial infarction

Abstract Background Urinary liver-type fatty acid-binding protein (L-FABP) has been known as a candidate biomarker for early detection of acute kidney injury (AKI). It has also been suggested to have an effective predictive value for cardiovascular mortality in patients. Therefore, this study aimed to examine the ability of urinary L-FABP in predicting AKI and future cardiovascular events in patients with acute myocardial infarction (AMI). Methods We evaluated consecutive 258 patients with AMI. Urinary L-FABP was measured at admission and a 2-year follow-up was performed. AKI was defined as an increase of &amp;gt;0.3 mg/dl in serum creatinine level within 2 days after emergency percutaneous coronary intervention. The composite endpoint was cardiovascular death, nonfatal myocardial infarction, nonfatal stroke, or hospitalization for heart failure. Results AKI was detected in 20 patients (7.8%). Patients with AKI had significantly higher urinary L-FABP levels (68.0 μg/gCr vs 3.1 μg/gCr, p&amp;lt;0.001) compared to those with non-AKI. Receiver operating characteristic analysis showed urinary L-FABP levels exhibited 85.7% sensitivity and 96.0% specificity, at a cutoff value of 29.7 μg/gCr. We used propensity score analyses to balance measurable confounders between patients with and without AKI, including age, left ventricular ejection fraction, an inflammation marker, renal function, and albuminuria. In logistic regression adjustment with the propensity score, urinary L-FABP level of &amp;gt;29.7 μg/gCr was an independent predictor of AKI (p=0.001). Furthermore, high urinary L-FABP (&amp;gt;29.7 μg/gCr) on admission correlated with an increased risk of the composite endpoints during 2-year follow-up in the Kaplan–Meier analysis (p&amp;lt;0.001). Conclusions Urinary L-FABP level may be a useful biomarker for predicting not only the onset of AKI but also adverse cardiovascular events in patients with AMI. Funding Acknowledgement Type of funding sources: None.

Lipidomic Profiles of Plasma Exosomes Identify Candidate Biomarkers for Early Detection of Hepatocellular Carcinoma in Patients with Cirrhosis.

Novel biomarkers for HCC surveillance in cirrhotic patients are urgently needed. Exosomes and their lipid content in particular represent potentially valuable noninvasive diagnostic biomarkers. We isolated exosomes from plasma of 72 cirrhotic patients, including 31 with HCC. Exosomes and unfractionated plasma were processed for untargeted lipidomics using ultra-high-resolution mass spectrometry. A total of 2,864 lipid species, belonging to 52 classes, were identified. Both exosome fractionation and HCC diagnosis had significant impact on the lipid profiles. Ten lipid classes were enriched in HCC exosomes compared with non-HCC exosomes. Dilysocardiolipins were detected in 35% of the HCC exosomes but in none of the non-HCC exosomes (P < 0.001). Cardiolipins and sphingosines had the highest differential effects (fold change of 133.08, q = 0.001 and 38.57, q < 0.001, respectively). In logistic regression analysis, high abundances of exosomal sphingosines, dilysocardiolipins, lysophosphatidylserines, and (O-acyl)-1-hydroxy fatty acids were strongly associated with HCC [OR (95% confidence interval (CI)), 271.1 (14.0-5,251.9), P < 0.001; 46.5 (2.3-939.9), P = 0.012; 14.9 (4.3-51.2), P < 0.001; 10.3 (3.2-33.1), P < 0.001]. Four lipid classes were depleted in HCC exosomes compared with non-HCC exosomes. In logistic regression analysis, lack of detection of sulfatides and acylGlcSitosterol esters was strongly associated with HCC [OR (95% CI): 215.5 (11.5-4,035.9), P < 0.001; 26.7 (1.4-528.4), P = 0.031]. These HCC-associated changes in lipid composition of exosomes reflected alterations in glycerophospholipid metabolism, retrograde endocannabinoid signaling, and ferroptosis. In conclusion, this study identified candidate biomarkers for early detection of HCC as well as altered pathways in exosomes that may contribute to tumor development and progression. PREVENTION RELEVANCE: This study identifies lipids in circulating exosomes, that could serve as biomarkers for the early detection of hepatocellular carcinoma as well as altered pathways in exosomes that may contribute to tumor development and progression.

Identification of Translational microRNA Biomarker Candidates for Ketoconazole-Induced Liver Injury Using Next-Generation Sequencing.

Drug-induced liver injury (DILI) is a leading cause of acute liver failure. Reliable and translational biomarkers are needed for early detection of DILI. microRNAs (miRNAs) have received wide attention as a novel class of potential DILI biomarkers. However, it is unclear how DILI drugs other than acetaminophen may influence miRNA expression or which miRNAs could serve as useful biomarkers in humans. We selected ketoconazole (KCZ), a classic hepatotoxin, to study miRNA biomarkers for DILI as a proof of concept for a workflow that integrated in vivo, in vitro, and bioinformatics analyses. We examined hepatic miRNA expression in KCZ-treated rats at multiple doses and durations using miRNA-sequencing and correlated our results with conventional DILI biomarkers such as liver histology. Significant dysregulation of rno-miR-34a-5p, rno-miR-331-3p, rno-miR-15b-3p, and rno-miR-676 was associated with cytoplasmic vacuolization, a phenotype in rat livers with KCZ-induced injury, which preceded the elevation of serum liver transaminases (ALT and AST). Between rats and humans, miR-34a-5p, miR-331-3p, and miR-15b-3p were evolutionarily conserved with identical sequences, whereas miR-676 showed 73% sequence similarity. Using quantitative PCR, we found that the levels of hsa-miR-34a-5p, hsa-miR-331-3p, and hsa-miR-15b-3p were significantly elevated in the culture media of HepaRG cells treated with 100 µM KCZ (a concentration that induced cytotoxicity). Additionally, we computationally characterized the miRNA candidates for their gene targeting, target functions, and miRNA/target evolutionary conservation. In conclusion, we identified miR-34a-5p, miR-331-3p, and miR-15b-3p as translational biomarker candidates for early detection of KCZ-induced liver injury with a workflow applicable to computational toxicology studies.

Evaluation of paraneoplastic antigens reveals TRIM21 autoantibodies as biomarker for early detection of ovarian cancer in combination with autoantibodies to NY-ESO-1 and TP53.

The majority of ovarian cancer cases are diagnosed at an advanced stage with poor prognosis. This study evaluates autoantibodies against tumor antigens to identify candidate biomarkers for early detection of ovarian cancer in women at increased risk. To assess the immunoreactivity of paraneoplastic antigens and tumor associated antigens with high-grade serous ovarian cancer (HGSOC) samples. Five paraneoplastic antigens along with three tumor-associated antigens were evaluated with HGSOC patient serum samples. Validation screening was performed with n= 164 serum samples consisting of: 50 late stage HGSOC, 14 early stage HGSOC, 50 benign ovarian cyst, and 50 healthy control samples on ELISA and western blot. The four markers TRIM21, NY-ESO-1, TP53, and PAX8 were evaluated on a second validation serum set, n= 150. TRIM21 achieved the highest sensitivity in the first validation screening of 33% with 100% specificity. Combining TRIM21 with NY-ESO-1, TP53, and PAX8 provided 67% sensitivity with 94% specificity, and 56% sensitivity at 98% specificity. These four markers resulted in 46% sensitivity with 98% specificity in the second validation cohort; TRIM21 achieved the highest individual sensitivity of 36%. Autoantibodies to TRIM21, NY-ESO-1, and TP53 may complement CA125 in screening of women at genetic risk for ovarian cancer.

APC and AXIN2 Are Promising Biomarker Candidates for the Early Detection of Adenomas and Hyperplastic Polyps.

Aberrant activation of the WNT/CTNNB1 pathway is notorious in colorectal cancer (CRC). Here, we demonstrate that the expression of specific and crucial WNT signaling pathway genes is linked to disease progression in colonic adenomatous (AP) and hyperplastic (HP) polyps in an Iranian patient population. Thus, we highlight potential gene expression profiles as candidate novel biomarkers for the early detection of CRC. From a 12-month study (2016-2017), 44 biopsy samples were collected during colonoscopy from the patients with colorectal polyps and 10 healthy subjects for normalization. Clinical and demographic data were collected in all cases, and mRNA expression of APC, CTNNB1, CDH1, AXIN1, and AXIN2 genes was investigated using real-time polymerase chain reaction (PCR). CTNNB1 and CDH1 expression levels were unaltered in AP and HP subjects, whereas mRNA expression of APC was decreased in AP contrasted with HP subjects, with a significant association between APC downregulation and polyp size. Although AXIN1 showed no changes between AP and HP groups, a significant association between AXIN1 and dysplasia grade was found. Also, significant upregulation of AXIN2 in both AP and HP subjects was detected. In summary, we have shown increased expression of AXIN2 and decreased expression of APC correlating with grade of dysplasia and polyp size. Hence, AXIN2 and APC should be explored as biomarker candidates for early detection of AP and HP polyps in CRC.

Salivary proteins from dysplastic leukoplakia and oral squamous cell carcinoma and their potential for early detection

Dysplastic leukoplakia (LP) of the oral cavity is a potentially malignant condition for oral squamous cell carcinoma (OSCC), early detection of which remains an unmet clinical need. In an effort to develop non-invasive biomarker based method for early detection of the disease, differential proteomic profiling was carried out with the saliva from patients with risk habits and diagnosed with LP and those with lymph node negative and positive OSCC in comparison to healthy controls with risk habits. Ninety three proteins were observed at elevated level (≥1.5 fold), and 30 were prioritized based on a scoring system comprising of confidence of identification, presence in the various specimen groups, functional relevance, and their secretory potential. Verification was carried out in independent patient cohorts for 8 selected, representative, upregulated proteins using ELISA. Three of them CD44, S100A7, and S100P were significantly altered in patients with LP as well as OSCC and can be regarded as a panel of biomarker candidates for early detection of the malignancy. Other members may also be investigated in a targeted manner to expand the portfolio of biomarkers for early detection. The mass spectrometry data are available via ProteomeXchange with identifier PXD015722. SignificanceThere is an unmet clinical need for non-invasive, biomarker based methods for the improved early detection and the subsequent management of oral cancer. The study represents differential proteome profiling of the saliva of patients with oral dysplastic leukoplakia (LP) – a potentially malignant lesion, patients diagnosed with oral squamous cell carcinoma (OSCC), and healthy controls to identify potential markers for the purpose of early detection of malignancy. From among the matched and prioritized proteins with elevated levels in the saliva of patients with LP and those with OSCC, eight were verified. Three of them – CD44, S100A7 and S100P appeared promising candidates as biomarkers for early detection of the neoplastic predisposition and may form the basis of clinical assays for this purpose.

Personalizing Gastric Cancer Screening With Predictive Modeling of Disease Progression Biomarkers.

Gastric cancer (GC) remains the third most common cause of cancer-related death worldwide. Infection with Helicobacter pylori is responsible for over 70% of GC incidence; colonization induces chronic inflammation, which can facilitate progression to intestinal metaplasia, dysplasia, and GC (Correa pathway). Although H. pylori eradication is a necessary first step in GC prevention, some patients continue to progress to advanced stage disease if substantial tissue damage has occurred or inflammation persists. This progression is often asymptomatic until cancer reaches stage IV, yet efficient, cost-effective screening protocols for patients who present with early stages of the Correa pathway do not exist. Given the high interpatient heterogeneity in progression time through this pathway, such screening protocols must necessarily be personalized. This requires the identification of reliable and longitudinally assessable biomarkers of patient-specific progression. Several gastric stem cell (GSC) markers including CD44, CD133, and Lgr5 are upregulated in GC. Here we show a significant stepwise increase in immunohistochemical staining for these markers in biopsies at different stages of the Correa pathway, suggesting GSC fraction to be a promising candidate biomarker for early detection of malignant transformation. We present a mathematical model capable of both simulating clinically observed increases in GSC fraction in longitudinal biopsy samples of individual patients, and forecasting patient-specific disease progression trajectories based only on characteristics identified from immunohistochemistry at initial presentation. From these forecasts, personalized screening schedules may be identified that would allow early stratification of high-risk patients, and potentially earlier detection of dysplasia or early-stage GC.

Epigenetic Alterations of Wnt Signaling Pathways in Nasopharyngeal Carcinoma

The purpose of this study is to discuss the epigenetic alterations of Wnt signaling pathways in nasopharyngeal carcinoma. Methylomic analyses have revealed that in nasopharyngeal carcinoma, numerous genes in Wnt signaling pathways are hypermethylated, which results in the inactivation of tumor-suppressor genes and aberrant activation of Wnt signaling. Reactivation of the tumor-suppressor genes by demethylation or ectopic expression inhibits the proliferation, metastasis, or stemness of nasopharyngeal carcinoma cells. Epigenetic alterations of Wnt signaling pathways contribute to cancer-cell stemness, epithelial-mesenchymal transition, and metastasis during the tumorigenesis of nasopharyngeal carcinoma. Methylated DNAs of Wnt signaling factors hold considerable potential as candidate biomarkers for early detection of nasopharyngeal carcinoma.

Abstract 2573: Selection of candidate biomarkers for aggressive prostate cancer based on targeted proteomics

Abstract Mass spectrometry based targeted proteomics such as selected reaction monitoring (SRM) provides an effective, antibody-independent strategy for sensitive, specific and multiplexed verification of genomics biomarker candidates at the protein level. In order to identify a panel of proteins with the potential to predict prostate cancer progression, we have selected 52 protein candidates from existing prostate cancer genomics data sets and validated cancer drivers, and performed quantitative proteomics analysis in tissue samples using the highly sensitive PRISM (high-pressure, high-resolution separations coupled with intelligent selection and multiplexing)-SRM approach. PRISM-SRM assays have been developed for the 52 prostate cancer biomarker candidates including: prostate cancer relevant genes and common cancer drivers. One set of 105 formalin-fixed paraffin-embedded (FFPE) whole mount prostate tissue specimens were analyzed using PRISM-SRM with heavy isotope-labeled synthetic peptides as internal standards: 20 primary tumors from patients showing metastatic progression, 37 primary tumors from patients who showed biochemical recurrence (BCR), and 48 primary tumors from patients with no BCR or metastatic progression after more than ten years of follow-up after radical prostatectomy. Overall, PRISM-SRM analyses of the FFPE tissue samples enabled the detection of 42 out of 52 biomarker candidates; in comparison regular LC-SRM without the front-end chromatographic enrichment could detect only 21 of these candidates at the protein level. Kruskal-Wallis test of the PRISM-SRM results provided a statistical evaluation of comparison of relative protein levels among the “no progression”, BCR and “metastatic progression” groups. Prostate differentiation/AR signaling related proteins (FOLH1, PSA and NCOA) or tumor progression (TGFB1, CCND1 and SPRC) were significantly different between the three groups. These promising biomarker candidates for early detection of aggressive prostate cancer are being further evaluated, individually and in panels, in an independent cohort of 234 samples for their potential prognostic applications. In summary, PRISM-SRM provides a highly sensitive method for quantification and rapid screening of promising cancer biomarker candidates defined by multiomics platforms. Citation Format: Yuqian Gao, Hui Wang, Jennifer Cullen, Yongmei Chen, Athena Schepmoes, Gyorgy Petrovics, Thomas Fillmore, Tujin Shi, Wei-Jun Qian, Richard Smith, Sudhir Srivastava, Jacob Kagan, Albert Dobi, Karin Rodland, Shiv Srivastava, Tao Liu. Selection of candidate biomarkers for aggressive prostate cancer based on targeted proteomics [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 2573.

Abstract 1559: Proteogenomic analysis of alternative splicing in colorectal adenoma-to-carcinoma progression

Abstract Background Early diagnosis of colorectal cancer (CRC) and identification of its precursor lesions (adenomas) is crucial in reducing CRC mortality rates. The fecal immunochemical test (FIT) is a non-invasive CRC screening test that detects human protein hemoglobin. Although FIT is beneficial in its current form with a sensitivity of ~65% for detection of CRC and ~27% for adenomas, its performance is still suboptimal and needs to be further improved. Adenoma-to-carcinoma progression is accompanied by alternative splicing, which results in expression of tumor-specific protein variants. These may yield novel biomarkers suitable for improving detection of progressive adenomas and CRCs. Aim We aim to identify novel biomarkers to improve early detection of CRC. Materials and methods RNA was isolated from 3D organoid cultures derived from 5 adenomas and 4 CRC tissues. RNA and proteins were isolated from 18 healthy human colon tissues, 30 adenomas and 30 CRCs. Samples were analyzed by RNA sequencing (Illumina) and in-depth tandem mass spectrometry proteomics (QExactive). For both organoid- and tissue-datasets differential splicing analysis was performed on RNA level to enrich the sequence database, against which mass spectra were searched, with predicted protein isoforms. Results Comparative splicing analysis between CRC and adenoma organoids revealed ~90 differentially spliced genes, yielding candidate biomarkers from epithelial origin. In the tissues, differential splicing analysis between CRCs and controls and between CRCs and adenomas identified over 1000 of splice variants. These include known alternatively spliced genes involved in cancer such as CD44 and VEGFA and a number of candidates overlapping with the isoforms derived from the organoids. Proteomics analysis revealed that approximately 150 of the splice variants were expressed on protein level. Conclusion and Discussion We have confirmed that adenoma-to-carcinoma progression is accompanied by aberrant splicing. Analysis of the organoid cultures allowed us to identify gene isoforms from (neoplastic) epithelial origin. Tissue analysis yielded tumor-specific splice variants that represent novel protein candidate biomarkers for early detection of CRC. The diagnostic performance of these splice variant proteins will be validated in series of stool and FIT samples. Citation Format: Malgorzata A. Komor, Thang V. Pham, Sander R. Piersma, Anne S. Bolijn, Tim Schelfhorst, Pien M. Delis-van Diemen, Marianne Tijssen, Annemieke C. Hiemstra, Meike de Wit, Beatriz Carvalho, Gerrit A. Meijer, Connie R. Jimenez, Remond J. Fijneman. Proteogenomic analysis of alternative splicing in colorectal adenoma-to-carcinoma progression [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 1559. doi:10.1158/1538-7445.AM2017-1559

Combined detection of plasma miR-127-3p and HE4 improves the diagnostic efficacy of breast cancer.

To explore the diagnostic value of combined detection of plasma miR-127-3p and HE4 for breast cancer (BC). Included in this study were 102 patients with pathologically confirmed BC who received treatment in the affiliated hospital of Nantong University between March 2015 and April 2016, 87 patients with benign breast tumors, and 90 healthy volunteers as control. Plasma miR-127-3p was detected by SYBR Green RT-qPCR, and plasma HE4 was detected by chemiluminescent immunoassay. The diagnostic efficacy of miR-127-3p alone, HE4 alone and combined detection of miR-127-3p and HE4 in BC women patients was evaluated by ROC curve analysis. The relative expression quantity (RQ) of plasma miR-127-3p and HE4 in BC patients was 13.561 (3.345∼18.281) pmol/L and 105.42 (40.28∼156.31) pmol/L. The RQ of plasma miR-127-3p in BC patients was significantly higher than that in benign breast tumor patients and healthy individuals (both P< 0.001), and there was no significant difference between benign breast tumor patients and healthy individuals (P> 0.05). There was no significant correlation between plasma miR-127-3p and HE4 levels (r2= 0.086, P= 0.471). ROC curve analysis on the diagnostic efficacy of plasma miR-127-3p and HE4 in BC diagnosis showed that the cut-off value of miR-127-3p and HE4 in BC diagnosis was 3.471 and 63.21 pmol/L; AUC was 0.767 and 0.670; sensitivity was 78.2% and 64.6%; specificity was 79.1% and 69.3%; accuracy was 73.2% and 65.1%, respectively. Prediction probability (P) obtained from the miR-127-3p and HE4 model established by logistic regression was P= 1/ [1 + exp (-0.142miR-127-3p-0.024HE4 + 2.875)]. AUC calculated from ROC was 0.825 and the sensitivity was increased to 87.4%. Combined detection of plasma miR-127-3p and HE4 greatly improved the sensitivity of BC diagnosis and may prove to be a candidate biomarker for early detection and diagnosis of BC.

MicroRNAs for Detection of Pancreatic Neoplasia: Biomarker Discovery by Next-generation Sequencing and Validation in 2 Independent Cohorts.

The aim of our study was to analyze the miRNome of pancreatic ductal adenocarcinoma (PDAC) and its preneoplastic lesion intraductal papillary mucinous neoplasm (IPMN), to find new microRNA (miRNA)-based biomarkers for early detection of pancreatic neoplasia. Effective early detection methods for PDAC are needed. miRNAs are good biomarker candidates. Pancreatic tissues (n = 165) were obtained from patients with PDAC, IPMN, or from control individuals (C), from Hospital Clínic of Barcelona. Biomarker discovery was done using next-generation sequencing in a discovery set of 18 surgical samples (11 PDAC, 4 IPMN, 3 C). MiRNA validation was carried out by quantitative reverse transcriptase PCR in 2 different set of samples. Set 1-52 surgical samples (24 PDAC, 7 IPMN, 6 chronic pancreatitis, 15 C), and set 2-95 endoscopic ultrasound-guided fine-needle aspirations (60 PDAC, 9 IPMN, 26 C). In all, 607 and 396 miRNAs were significantly deregulated in PDAC and IPMN versus C. Of them, 40 miRNAs commonly overexpressed in both PDAC and IPMN were selected for further validation. Among them, significant up-regulation of 31 and 30 miRNAs was confirmed by quantitative reverse transcriptase PCR in samples from set 1 and set 2, respectively. miRNome analysis shows that PDAC and IPMN have differential miRNA profiles with respect to C, with a large number of deregulated miRNAs shared by both neoplastic lesions. Indeed, we have identified and validated 30 miRNAs whose expression is significantly increased in PDAC and IPMN lesions. The feasibility of detecting these miRNAs in endoscopic ultrasound-guided fine-needle aspiration samples makes them good biomarker candidates for early detection of pancreatic cancer.

Abstract 4773: Aberrant methylation at chromosome 6p as novel biomarkers for diagnosis and prognosis of nasopharyngeal carcinoma

Abstract Background: Nasopharyngeal carcinoma (NPC) has the highest incidence in Guangdong province and Hong Kong in Southern China. Early detection of NPC is necessary to improve patient survival. Although aberrant methylation at promoter region of the tumour suppressors were often reported in NPC, genome-wide methylation changes have not been comprehensively investigated. Aim: We aimed to examine the methylation profile of NPC patient tumours using a high-throughput approach to discover candidate biomarkers for early detection of NPC. Methods: We systematically analyzed methylome data in the primary tumours and matched normal adjacent tissues from 25 NPC patients collected by Area of Excellence (AoE) NPC Tissue Bank using the Illumina HumanMethylation450 BeadChip platform. Comparatively, methylome data of solid tumours including prostate cancer, invasive breast cancer, pancreatic cancer, kidney cancer, thyroid cancer, liver cancer, rectal cancer, colon cancer, head and neck cancer, lung adenocarcinoma and lung squamous cell carcinoma collected by The Cancer Genome Atlas (TCGA) were examined. A quantitative method, bisulfite pyrosequencing, was applied to evaluate the aberrant methylation in an independent NPC patient cohort. Results: In NPC, the hypermethylation pattern was more dominant than hypomethylation, where over 90% of the differentially methylated loci were hypermethylated within or close to CpG islands in tumours. The comparative methylome analysis reveals aberrant methylation at chromosome 6p frequently occurred in NPC (FDR = 1.33×10-9), but was rare in other types of solid tumours. Evident enrichment of the repressive mark H3K27me3 was found at this region, indicating both DNA methylation and histone modification function together, leading to epigenetic deregulation. Bisulfite pyrosequencing results further confirmed the aberrant methylation at 6p in an additional patient cohort, and 76.9% of the early-stage NPC patients can be detected by aberrant methylation on 6p. Furthermore, aberrant methylation at this region was observed in NPC recurrent tumours and matched metastatic lymph nodes, indicating the potential use of genes in this region for prognosis. Conclusion: Our study highlights the importance of epigenetic deregulation in NPC. A novel genomic region on 6p with aberrant methylation was identified. This region contains several important genes that have great potential to be used as biomarkers for NPC early detection. The global genome-wide unbiased approach is useful to discover potential biomarkers for early diagnosis and prognosis in cancers. Acknowledgements: NPC AoE funding was provided by the Hong Kong Research Grants Council (AoE/M-06/08) to MLL and HKU Small Project Funding to WD. Citation Format: Wei Dai, Arthur Kwok Leung Cheung, Josephine Mun Yee Ko, Hong Zheng, Yue Cheng, Roger Kai Cheong Ngan, Wai Tong Ng, Anne Wing Mui Lee, Chun Chung Yau, Victor Ho Fu Lee, Maria Li Lung. Aberrant methylation at chromosome 6p as novel biomarkers for diagnosis and prognosis of nasopharyngeal carcinoma. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 4773. doi:10.1158/1538-7445.AM2015-4773