Hepatic mi<scp>R</scp>‐126 is a potential plasma biomarker for detection of hepatitis <scp>B</scp> virus infected hepatocellular carcinoma

Ghosh, Amit; Ghosh, Alip; Datta, Somenath; Dasgupta, Debanjali; Das, Soumyajit; Ray, Sukanta; Gupta, Subash; Datta, Simanti; Chowdhury, Abhijit; Chatterjee, Raghunath; Mohapatra, Saroj Kant; Banerjee, Soma

doi:10.1002/ijc.29999

Cited by 54 publications

(30 citation statements)

References 49 publications

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“…In contrast, several previous studies found significant dysregulation of miR-30c, [21,53] miR-30b [21] and miR-126 [54,55] in HCC tumor tissue and blood samples, suggesting their potential etiologic or diagnostic roles. However, none of those previous studies used global mean of miRNAs as the normalizer and did not evaluate miRNAs expression stabilities that might lead to false positive findings.…”

Section: Discussionmentioning

confidence: 61%

Evaluating normalization approaches for the better identification of aberrant microRNAs associated with hepatocellular carcinoma

Shen

Wang

Gurvich

et al. 2016

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Aim Dysregulated microRNAs (miRNAs) have been identified in hepatocellular carcinoma (HCC), but only a small proportion have been confirmed. An appropriate normalizer is crucial to determining the accuracy and reliability of data from miRNA studies. Methods Different normalization strategies were used to validate genome-wide miRNA profiles in HCC tumor and non-tumor tissues, and to determine the consistency and discrepancy of data on dysregulated miRNAs. Results Two sets of stable miRNAs (miR-30c/miR-30b and miR-30c/miR-126) were identified in HCC tissues by geNorm and NormFinder tools, respectively. The mean of global miRNAs also showed good stability for ranking the top 1-2 miRNAs, but the stabilities of the manufacturer-recommended ncRNAs controls were poor. Four panels of miRNAs were significantly associated with HCC by separately using various normalizers, and 14 miRNAs were consistently identified by three normalization strategies. Although fewer miRNAs (17-26) were dysregulated in HCC using the global mean or the 2 stable miRNAs as normalizers, perfect clustering of tissues was also obtained with only 1 to 2 misclassifications, suggesting the efficiency of the miRNA panels. Using global mean as the normalizer, the authors identified 7 miRNAs, including 2 novel (miR-324-5p and miR-550) significantly upregulated in HCC that were omitted when using 3 endogenous controls as the normalizer. Conclusion An optimal normalization strategy to identify biologically important miRNAs in HCC tissue studies of miRNA may be the combination of global mean and 2 stable miRNAs. Selection of appropriate normalization strategies to adjust miRNAs levels is particularly important for epidemiological studies dealing with large data sets and covering multiple experimental batches.

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Section: Discussionmentioning

confidence: 61%

Evaluating normalization approaches for the better identification of aberrant microRNAs associated with hepatocellular carcinoma

Shen

Wang

Gurvich

et al. 2016

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“…Serum anti-SF3B1 autoantibody is a potential diagnostic marker for HCC patients (Hwang et al, 2018). Reportedly, HSPH1 (Yang et al, 2015), APC2 (Ghosh et al, 2016), CHST4 (Gao et al, 2015), HGF (Unic et al, 2018), MTHFD2 (Liu et al, 2016), and AGO3 (Kitagawa et al, 2013) are closely related to HCC.…”

Section: Discussionmentioning

confidence: 99%

Early Diagnosis of Hepatocellular Carcinoma Using Machine Learning Method

Zhang

Tan

Wang

et al. 2020

Front. Bioeng. Biotechnol.

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Hepatocellular carcinoma (HCC) is a serious cancer which ranked the fourth in cancerrelated death worldwide. Hence, more accurate diagnostic models are urgently needed to aid the early HCC diagnosis under clinical scenarios and thus improve HCC treatment and survival. Several conventional methods have been used for discriminating HCC from cirrhosis tissues in patients without HCC (CwoHCC). However, the recognition successful rates are still far from satisfactory. In this study, we applied a computational approach that based on machine learning method to a set of microarray data generated from 1091 HCC samples and 242 CwoHCC samples. The within-sample relative expression orderings (REOs) method was used to extract numerical descriptors from gene expression profiles datasets. After removing the unrelated features by using maximum redundancy minimum relevance (mRMR) with incremental feature selection, we achieved "11-gene-pair" which could produce outstanding results. We further investigated the discriminate capability of the "11-gene-pair" for HCC recognition on several independent datasets. The wonderful results were obtained, demonstrating that the selected gene pairs can be signature for HCC. The proposed computational model can discriminate HCC and adjacent non-cancerous tissues from CwoHCC even for minimum biopsy specimens and inaccurately sampled specimens, which can be practical and effective for aiding the early HCC diagnosis at individual level.

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“…These include, but are not limited to: DCP [37,38], Glypican-3 [39], fucosylated serum paraoxonase 1 [40] and alpha-1 acid glycoprotein [41], TEMs [42], Dickkopf-1 [43] and EpCam stained circulating tumor cells [44] and staining of HCCs [45], C-reactive protein [46], alpha-L-fucosidase [47] and hepatic miRs [48]. With such a high percent of small and large HCCs having low AFP levels, novel biomarkers are clearly needed.…”

Section: Discussionmentioning

confidence: 99%

Quantum biophysics of water

Akkız

Üsküdar

et al. 2018

clinical-practice

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A large database of 1773 HCC patients in Turkey was examined. 41.9% had alpha-fetoprotein (AFP) levels <20 IU/ml and an additional 16.123% had values between 20-100 IU/ml. This 58% of the cohort (<100 IU/ml AFP levels) was examined in detail. 66% of patients with small (<5 cm) HCCs had low AFP, compared to 49% of patients with larger (>5 cm) HCCs. The mean diameter (MTD) of larger MTD, low AFP tumors was 8.4cm. Therefore, factors other than AFP must contribute to HCC tumor growth. Larger tumors in low AFP patients had both higher platelet levels and increased PVT percent. Linear regression analysis for both MTD and multifocality showed that platelet numbers and presence of PVT were significant variables; whereas for PVT, significant variables were albumin, alkaline phosphatase and MTD. Comparisons between patients with AFP levels <20, 20-<100, 100-<1000 and >1000 IU/ml showed the most significant tumor finding was an increase in PVT percent between each group, and to a lesser extent, MTD. Thus, low-or normal-AFP HCCs constitute the majority of patients and have slightly lower MTD and much lower PVT percent than HCCs associated with elevated blood AFP levels. New, non-AFP markers are thus needed, especially for small HCCs

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Hepatic miR‐126 is a potential plasma biomarker for detection of hepatitis B virus infected hepatocellular carcinoma

Cited by 54 publications

References 49 publications

Evaluating normalization approaches for the better identification of aberrant microRNAs associated with hepatocellular carcinoma

Evaluating normalization approaches for the better identification of aberrant microRNAs associated with hepatocellular carcinoma

Early Diagnosis of Hepatocellular Carcinoma Using Machine Learning Method

Quantum biophysics of water

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