Vivek Kumar

Diagnostics and Therapeutic Potential of miR-205 and miR-34a in Ovarian Cancer Management: A miRNA-Target-Based Analysis

Epithelial ovarian cancer (EOC) treatment strategies mainly focused on surgery combined with chemotherapy. Recent targeted therapy techniques emerge as milestone and could be used for management of ovarian cancer (OC) progression with more efficacy. The aim is to evaluate the therapeutic and diagnostic potential of microRNA (miRNA) in management of EOC using in silico and quantitative real-time PCR (qRT-PCR) expression analysis. We performed functional enrichment and miRNA-Target genes expression analysis in 48 EOC and 22 normal tissue samples using qRT-PCR and correlated with miRNA expression data in matched samples to evaluate the diagnostic and therapeutic potential of miRNA in OC management. In silico functional enrichment analysis revealed miRNA association with disease. Target genes of miRNAs participate in several biologically important pathways leading to cancer progression. Targets of miRNA-205 and miRNA-34a were significantly downregulated, and upregulated, respectively, in EOC. Moreover, significant negative correlation between relative expression of miRNA-205 and target genes (BCL2, ZEB1, E2F1, and TP53) was observed with r  = −0.813; r  = −0.755; r  = −0.559; and r  = −0.767, respectively. Similarly, miRNA-34a also showed higher negative correlation with target genes (MDM4, MAPK3, BRCA1, AREG) with r  = −0.840; r  = −0.870; r  = −0.622; and r  = −0.623, respectively. In addition, receiver operating characteristics analysis of combined miRNA panel, miRNA-205-Target gene panel, and miRNA-34a-Target gene panel exhibited higher diagnostics value with area under the curve (AUC) of 92.7 ( p  < 0.0001), 94.8 ( p  < 0.0001), and 98.3 ( p  < 0.0001), respectively. Negative Correlation between miRNA and target genes expression data in matched samples highlights therapeutic potential of miRNA in EOC management. Moreover, combined diagnostic potential of miRNA-target gene panel could predict risk of EOC with higher AUC, sensitivity, and specificity.

Diagnostic performance of microRNA-34a, let-7f and microRNA-31 in epithelial ovarian cancer prediction

To correlate the genome-wide methylation signature of microRNA genes with dysregulated expression of selected candidate microRNA in tissue and serum samples of epithelial ovarian cancer (EOC) and control using quantitative reverse transcription polymerase chain reaction (qRT-PCR), and evaluation of EOC predictive value of candidate microRNA at an early stage. We performed Methylated DNA Immunoprecipitation coupled with NGS (MeDIP-NGS) sequencing of 6 EOC and 2 normal tissue samples of the ovary. Expression of selected microRNA from tissue (EOC=85, normal=30) and serum (EOC=50, normal=15) samples was evaluated using qRT-PCR. We conducted bioinformatics analysis to identify the candidate miRNA's potential target and functional role. MeDIP-NGS sequencing revealed hypermethylation of several microRNAs gene promoters. Three candidate microRNAs were selected (microRNA-34a, let-7f, and microRNA-31) from MeDIP-NGS data analysis based on log2FC and P-value. The relative expression level of microRNA-34a, let-7f, and microRNA-31 was found to be significantly reduced in early-stage EOC tissues and serum samples (p<0.0001). The receiver operating characteristic analysis of microRNA-34a, let-7f and miR-31 showed improved diagnostic value with area under curve(AUC) of 92.0 (p<0.0001), 87.9 (p<0.0001), and 85.6 (p<0.0001) and AUC of 82.7 (p<0.0001), 82.0 (p<0.0001), and 81.0 (p<0.0001) in stage III-IV and stage I-II EOC serum samples respectively. The integrated diagnostic performance of microRNA panel (microRNA-34a+let-7f+microRNA-31) in late-stage and early-stage serum samples was 95.5 and 96.9 respectively. Our data correlated hypermethylation-associated downregulation of microRNA in EOC. In addition, a combined microRNA panel from serum could predict the risk of EOC with greater AUC, sensitivity, and specificity.

Dosimetric analysis of cervical cancer stage IIB patients treated with volumetric modulated arc therapy using plan uncertainty parameters module of Varian Eclipse treatment planning system

Abstract Introduction . The present study aims to investigate the dosimetric and radiobiological impact of patient setup errors (PSE) on the target and organs at risk (OAR) of the cervix carcinoma stage IIB patients treated with volumetric-modulated arc therapy (VMAT) delivery technique using plan uncertainty parameters module of Varian Eclipse treatment planning system and in-house developed DVH Analyzer program. Materials and Methods . A total of 976 VMAT plans were generated to simulate the PSE in the base plan that varies from −10 mm to 10 mm in a step size of 1 mm in x– (lateral), y– (craniocaudal), and z– (anteroposterior) directions. The different OAR and tumor (PTV) volumes were delineated in each case. Various plan quality metrics, such as conformity index (CI) and homogeneity index (HI), as well as radiobiological quantities, such as tumor control probability (TCP) and normal tissue control probability (NTCP), were calculated from the DVH bands generated from the cohort of treatment plans associated with each patient case, using an in-house developed ‘DVH Analyzer’ program. The extracted parameters were statistically analyzed and compared with the base plan’s dosimetric parameters having no PSE. Results . The maximum variation of (i) 2.4%, 21.5%, 0.8%, 2.5% in D 2cc of bladder, rectum, small bowel and sigmoid colon respectively; (ii) 19.3% and 18.9% in D max of the left and right femoral heads (iii) 16.9% in D 95% of PTV (iv) 12.1% in NTCP of sigmoid colon were observed with change of PSE in all directions. TCP was found to be considerably affected for PSEs larger than 4 mm in x + , y + , z + directions and 7 mm in x - , y - and z - directions, respectively. Conclusion . This study presents the effect of PSE on TCP and NTCP for the cervix carcinoma cases treated with VMAT technique and also recommends daily image guidance to mitigate the effects of PSE.