Intra-operative point-of-procedure delineation of oral cancer margins using optical coherence tomography.

ObjectivesSurgical margin status is a significant determinant of treatment outcome in oral cancer. Negative surgical margins can decrease the loco-regional recurrence by five-fold. The current standard of care of intraoperative clinical examination supplemented by histological frozen section, can result in a risk of positive margins from 5 to 17 percent. In this study, we attempted to assess the utility of intraoperative optical coherence tomography (OCT) imaging with automated diagnostic algorithm to improve on the current method of clinical evaluation of surgical margin in oral cancer.Materials and methodsWe have used a modified handheld OCT device with automated algorithm based diagnostic platform for imaging. Intraoperatively, images of 125 sites were captured from multiple zones around the tumor of oral cancer patients (n = 14) and compared with the clinical and pathologic diagnosis.ResultsOCT showed sensitivity and specificity of 100%, equivalent to histological diagnosis (kappa, ĸ = 0.922), in detection of malignancy within tumor and tumor margin areas. In comparison, for dysplastic lesions, OCT-based detection showed a sensitivity of 92.5% and specificity of 68.8% and a moderate concordance with histopathology diagnosis (ĸ = 0.59). Additionally, the OCT scores could significantly differentiate squamous cell carcinoma (SCC) from dysplastic lesions (mild/moderate/severe; p ≤ 0.005) as well as the latter from the non-dysplastic lesions (p ≤ 0.05).ConclusionThe current challenges associated with clinical examination-based margin assessment could be improved with intra-operative OCT imaging. OCT is capable of identifying microscopic tumor at the surgical margins and demonstrated the feasibility of mapping of field cancerization around the tumor

Resistance/response molecular signature for oral tongue squamous cell carcinoma

Worldwide, the incidence of oral tongue cancer is on the rise, adding to the existing burden due to prevailing low survival and high recurrence rates. This study uses high-throughput expression profiling to identify candidate markers of resistance/response in patients with oral tongue cancer. Analysis of primary and post-treatment samples (12 tumor and 8 normal) by the Affymetrix platform (HG U133 plus 2) identified 119 genes as differentially regulated in recurrent tumors. The study groups had distinct profiles, with induction of immune response and apoptotic pathways in the non-recurrent and metastatic/invasiveness pathways in the recurrent group. Validation was carried out in tissues by Quantitative Real-Time PCR (QPCR) (n = 30) and Immunohistochemistry (IHC) (n = 35) and in saliva by QPCR (n = 37). The markers, COL5A1, HBB, IGLA and CTSC individually and COL5A1 and HBB in combination had the best predictive power for treatment response in the patients. A subset of markers identified (COL5A1, ABCG1, MMP1, IL8, FN1) could be detected in the saliva of patients with oral cancers with their combined sensitivity and specificity being 0.65 and 0.87 respectively. The study thus emphasizes the extreme prognostic value of exploring markers of treatment resistance that are expressed in both tissue and saliva

A minimal set of internal control genes for gene expression studies in head and neck squamous cell carcinoma

Selection of the right reference gene(s) is crucial in the analysis and interpretation of gene expression data. The aim of the present study was to discover and validate a minimal set of internal control genes in head and neck tumor studies. We analyzed data from multiple sources (in house whole-genome gene expression microarrays, previously published quantitative real-time PCR (qPCR) data and RNA-seq data from TCGA) to come up with a list of 18 genes (discovery set) that had the lowest variance, a high level of expression across tumors, and their matched normal samples. The genes in the discovery set were ranked using four different algorithms (BestKeeper, geNorm, NormFinder, and comparative delta Ct) and a web-based comparative tool, RefFinder, for their stability and variance in expression across tissues. Finally, we validated their expression using qPCR in an additional set of tumor:matched normal samples that resulted in five genes (RPL30, RPL27, PSMC5, MTCH1, and OAZ1), out of which RPL30 and RPL27 were most stable and were abundantly expressed across the tissues. Our data suggest that RPL30 or RPL27 in combination with either PSMC5 or MTCH1 or OAZ1 can be used as a minimal set of control genes in head and neck tumor gene expression studies

Scientometric analysis of mammalian microbiome research

Over the past few decades, microbiota research has been gaining the attention of the researchers working on the concepts of health–enhancement and overall–wellbeing. The mammalian microbiome has been progressively acknowledged as a developing research area resulting in an increased number of publications. This study intends to use scientometric and bibliometric analysis to evaluate the research development and evolution of publication patterns in the field of mammalian microbiome between 2007 and 2020. 512 published articles were retrieved from the Web of Science Core Collection and were analyzed. We assessed the quantity and quality of research output through statistical methods of bibliometric indicators, comprising a number of publications, citations, productive authors, journals and countries, using a bibliometric analysis. Scientometric analysis was performed using main path analysis, bibliometric coupling, co-word co-occurrence and co-author analysis, systematically characterizing and visualizing the trend and delivering a pivotal review of the mammalian microbiome research status quo. The results identified an increase in the number of publications over time showing the rapid research growth, with top productive countries recording the highest number of research outcomes with influential research. The bibliographic coupling revealed the most shared papers that form landmark papers and the co-author analysis indicated the most influential authors in mammalian microbiome research. The evolutionary path of the mammalian microbiome research was traced using the main path analysis identifying the milestone papers. The frequently occurred words were enumerated from co-word, co-occurrence networks. The information from this study could be a transcript for a comprehensive understanding of current mammalian microbiome research and can also direct the future and emerging trends in this research realm

CORRELATION OF ANTIOXIDANT AND ANTIPROLIFERATIVE ACTIVITY OF AMLA AND GINGER

Objective: Our study focused on evaluating the anticancer property of ascorbic acid and aqueous extract of amla and ginger.Methods: Antioxidant capacity of ascorbic acid, aqueous extract of amla, and ginger was obtained by 2,2-diphenyl-1-picrylhydrazyl method and total antioxidant capacity (TAC). Vero cell line, PA-1, Cal-27, Cal-27 CisR, and DysMSCTR16 cell lines were treated with antioxidants to evaluate its antiproliferative property using 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide assay. Colony and spheroid formation assays were also carried out in the presence of extracts to assess its role in anticancer stem cell activity.Results: Two volumes of amla 5 μl (~0.016 g) and 25 μl (~0.08 g) and ginger 5 μl (~0.02 g) and 25 μl (~0.1 g) showed TAC activity equivalent to 0.25 mM and 2 mM ascorbic acid, respectively. Amla and ascorbic acid showed significant antiproliferative property in normal (Vero) p=0.05, cancer (PA-1, Cal-27) p=0.005, and resistant (Cal-27 CisR) p=0.05 cell lines and ginger extract in Vero and Cal-27 cell lines (p=0.05). In PA-1 and Cal-27 CisR cell line, ginger extract showed proliferative activity (p=0.005). Antioxidants showed no antiproliferative activity in DysMSCTR16 cells. Amla extract and ascorbic acid showed significant inhibitory effect on spheroid (p=0.005) and colony formation capacity (p=0.0005) among dysplastic, cancer, and resistant cell lines. Ginger showed inhibitory effect (p=0.05) only in colony formation capacity.Conclusion: Overall, we found a strong correlation between antioxidant and antiproliferative activity of ascorbic acid, amla, and ginger. Amla and ascorbic acid proved to be effective in controlling cell proliferation and self-renewal properties of cancer cells. However, ginger was found to have selective and less antiproliferative effect in comparison to amla

Molecular prognosticators in clinically and pathologically distinct cohorts of head and neck squamous cell carcinoma-A meta-analysis approach.

Head and neck squamous cell carcinomas (HNSCC) includes multiple subsites that exhibit differential treatment outcome, which is in turn reflective of tumor stage/histopathology and molecular profile. This study hypothesized that the molecular profile is an accurate prognostic adjunct in patients triaged based on clinico-pathological characteristics. Towards this effect, publically available micro-array datasets (n = 8), were downloaded, classified based on HPV association (n = 83) and site (tongue n = 88; laryngopharynx n = 53; oropharynx n = 51) and re-analyzed (Genespring; v13.1). The significant genes were validated in respective cohorts in The Cancer Genome Atlas (TCGA) for correlation with clinico-pathological parameters/survival. The gene entities (n = 3258) identified from HPV based analysis, when validated in TCGA identified the subset specifically altered in HPV+ HNSCC (n = 63), with three genes showing survival impact (RPP25, NUDCD2, NOVA1). Site-specific meta-analysis identified respective differentials (tongue: 3508, laryngopharynx: 4893, oropharynx: 2386); validation in TCGA revealed markers with high incidence (altered in >10% of patients) in tongue (n = 331), laryngopharynx (n = 701) and oropharynx (n = 404). Assessment of these genes in clinical sub-cohorts of TCGA indicated that early stage tongue (MTFR1, C8ORF33, OTUD6B) and laryngeal cancers (TWISTNB, KLHL13 and UBE2Q1) were defined by distinct prognosticators. Similarly, correlation with perineural/angiolymophatic invasion, identified discrete marker panels with survival impact (tongue: NUDCD1, PRKC1; laryngopharynx: SLC4A1AP, PIK3CA, AP2M1). Alterations in ANO1, NUDCD1, PIK3CA defined survival in tongue cancer patients with nodal metastasis (node+ECS-), while EPS8 is a significant differential in node+ECS- laryngopharyngeal cancers. In oropharynx, wherein HPV is a major etiological factor, distinct prognosticators were identified in HPV+ (ECHDC2, HERC5, GGT6) and HPV- (GRB10, EMILIN1, FNDC1). Meta-analysis in combination with TCGA validation carried out in this study emphasized on the molecular heterogeneity inherent within HNSCC; the feasibility of leveraging this information for improving prognostic efficacy is also established. Subject to large scale clinical validation, the marker panel identified in this study can prove to be valuable prognostic adjuncts

Novel noncoding RNA from human Y distal heterochromatic block (Yq12) generates testis-specific chimeric CDC2L2

The human Y chromosome, because it is enriched in repetitive DNA, has been very intractable to genetic and molecular analyses. There is no previous evidence for developmental stage- and testis-specific transcription from the male-specific region of the Y (MSY). Here, we present evidence for the first time for a developmental stage- and testis-specific transcription from MSY distal heterochromatic block. We isolated two novel RNAs, which localize to Yq12 in multiple copies, show testis-specific expression, and lack active X-homologs. Experimental evidence shows that one of the above Yq12 noncoding RNAs (ncRNAs) trans-splices with CDC2L2 mRNA from chromosome 1p36.3 locus to generate a testis-specific chimeric β sv13 isoform. This 67-nt 5′UTR provided by the Yq12 transcript contains within it a Y box protein-binding CCAAT motif, indicating translational regulation of the β sv13 isoform in testis. This is also the first report of trans-splicing between a Y chromosomal and an autosomal transcript

A highly conserved human gene encoding a novel member of WD-repeat family of proteins (WDR13)

We have identified and characterized a novel member of the WD-repeat motif gene family, WDR13, which contains 9 exons and 8 introns. The gene has been mapped to the genomic locus Xp11.23 by fluorescent in situ hybridization and in silico mapping. Sequence analysis has revealed a continuous open reading frame (ORF) encoding for 485 amino acids with six WD motifs. The expression of this gene has been detected in all the tissues analyzed with significantly varied expression levels among the tissues studied. Analysis of EST clones from various tissues, showing significant homology to WDR13, has identified two spliced variants. The transcription start point has been mapped. Promoter analysis has identified high activity in the 5' UTR, which interestingly showed a testis-specific activity in the transgenic animals studied. The subcellular localization of the WDR13 protein in the nucleus suggests that it may also have a regulatory role in nuclear function along with protein-protein interaction like other members of the WD family of proteins