Marker-free characterization of full-length transcriptomes of single live circulating tumor cells.

The identification and characterization of circulating tumor cells (CTCs) are important for gaining insights into the biology of metastatic cancers, monitoring disease progression, and medical management of the disease. The limiting factor in the enrichment of purified CTC populations is their sparse availability, heterogeneity, and altered phenotypes relative to the primary tumor. Intensive research both at the technical and molecular fronts led to the development of assays that ease CTC detection and identification from peripheral blood. Most CTC detection methods based on single-cell RNA sequencing (scRNA-seq) use a mix of size selection, marker-based white blood cell (WBC) depletion, and antibodies targeting tumor-associated antigens. However, the majority of these methods either miss out on atypical CTCs or suffer from WBC contamination. We present unCTC, an R package for unbiased identification and characterization of CTCs from single-cell transcriptomic data. unCTC features many standard and novel computational and statistical modules for various analyses. These include a novel method of scRNA-seq clustering, named deep dictionary learning using k-means clustering cost (DDLK), expression-based copy number variation (CNV) inference, and combinatorial, marker-based verification of the malignant phenotypes. DDLK enables robust segregation of CTCs and WBCs in the pathway space, as opposed to the gene expression space. We validated the utility of unCTC on scRNA-seq profiles of breast CTCs from six patients, captured and profiled using an integrated ClearCell FX and Polaris workflow that works by the principles of size-based separation of CTCs and marker-based WBC depletion.

piRNAQuest V.2: an updated resource for searching through the piRNAome of multiple species.

PIWI interacting RNAs (piRNAs) have emerged as important gene regulators in recent times. Since the release of our first version of piRNAQuest in 2014, lots of novel piRNAs have been annotated in different species other than human, mouse and rat. Such new developments in piRNA research have led us to develop an updated database piRNAQuest V.2. It consists of 92,77,689 piRNA entries for 25 new species of different phylum along with human, mouse and rat. Besides providing primary piRNA features which include their genomic location, with further information on piRNAs overlapping with repeat elements, pseudogenes and syntenic regions, etc., the novel features of this version includes (i) density based cluster prediction, (ii) piRNA expression profile across various healthy and disease systems and (iii) piRNA target prediction. The concept of density-based piRNA cluster identification is robust as it does not consider parametric distribution in its model. The piRNA expression profile for 21 disease systems including cancer have been hosted in addition to 32 tissue specific piRNA expression profile for various species. Further, the piRNA target prediction section includes both predicted and curated piRNA targets within eight disease systems and developmental stages of mouse testis. Further, users can visualize the piRNA-target duplex structure and the ping-pong signature pattern for all the ping-pong piRNA partners in different species. Overall, piRNAQuest V.2 is an updated user-friendly database which will serve as a useful resource to survey, search and retrieve information on piRNAs for multiple species. This freely accessible database is available at http://dibresources.jcbose.ac.in/zhumur/pirnaquest2.

The effect of intrauterine misoprostol on blood loss during caesarean section.

Excessive bleeding during and after caesarean section is a major cause of maternal morbidity and mortality, especially in low resource countries. This study evaluates the effect of intrauterine misoprostol with oxytocin in comparison with oxytocin alone on blood loss during caesarean section. A retrospective data analysis of 160 women who underwent lower segment caesarean section was conducted. Eighty-five out of 160 (53%) women received tablet misoprostol 800 µg by intrauterine route after delivery of a baby in addition to routine oxytocin infusion (group A), while 75 women (47%) received only oxytocin (group B). Blood loss, Haemoglobin (Hb) difference (pre-operative Hb - post-operative Hb) and need of any other oxytocic were compared in both the groups. Demographic variables such as mean age, parity, and an indication of caesarean section were comparable in both the groups. Mean blood loss during caesarean section was lower in group A (680 ± 202 mL) than group B (740 ± 228 mL) (p = .08). Higher Hb difference was noted in group B (1.03 ± 0.83 gm%) than group A (0.93 ± 0.68 gm%) (p = .41). No patient required additional oxytocic and no patient had postpartum haemorrhage in both the groups. The use of misoprostol by the intrauterine route in addition to routine oxytocin infusion during caesarean section is associated with a clinically significant reduction in intra-operative and post-operative blood loss. IMPACT STATEMENT What is already known on this subject? The role of misoprostol in the prevention and treatment of haemorrhage during and after caesarean section is well known and well studied. It is a better alternative to oxytocin in low resource settings. Various routes of misoprostol, with or without oxytocin, and its effect on intrapartum and postpartum haemorrhage are described in the literature. Misoprostol is an autocoid substance and acts better if it is close to the target organ (uterus). The use of misoprostol by the intrauterine route during caesarean section has not been well explored. What do the results of this study add? The use of misoprostol by intrauterine route in addition to routine oxytocin infusion during caesarean section is associated with decreased intra-operative and post-operative -blood loss. What are the implications of these findings for clinical practice and/or further research? The findings of this study reveal that misoprostol is also effective by the intrauterine route. It is a convenient way to insert misoprostol during caesarean section and it can be considered to prevent intrapartum and postpartum haemorrhage. More studies including randomised controlled trials with bigger sample size are needed to reach to any firm conclusion.

Optic nerve sheath diameter measurements using ultrasonography to diagnose raised intracranial pressure in preeclampsia: an observational study

Objective: To estimate the incidence of raised intracranial pressure (ICP) as evident by enlarged optic nerve sheath diameter (ONSD) by ocular ultrasound among patients with preeclampsia and its relationship to severity of disease. Material and Methods: Sixty pregnant mothers with preeclampsia were compared to 30 normotensive, uncomplicated pregnant controls. For ONSD measurement, a 7-MHZ linear probe was used and three values from each optic nerve were taken and the mean of six values of both eyes was recorded. All study subjects were followed until seven days after delivery. Results: Two cut off values (5.8 mm and 4.6 mm) were used to compare ONSD in severe and non-severe preeclampsia with that of healthy pregnant individuals. The incidence of raised ICP among severe preeclampsia above 5.8 mm and 4.6 mm cut-off were 43.3% and 90%, respectively, before delivery. ONSD was significantly elevated among preeclampsia subjects at both cut-off values at pre-delivery (p=0.004 for ONSD >5.8 mm and p<0.001 for ONSD >4.6 mm) compared to controls. There a significant association between presence of neurological manifestations and enlarged ONSD (p<0.001 for ONSD >5.8 mm and p=0.04 for ONSD >4.6 mm) before delivery. Conclusion: Severe preeclampsia with neurological features was associated with increased ONSD, reflecting raised ICP. Further studies are needed to compare ONSD values with invasive ICP monitoring for better understanding of this relationship.

Comparison of Human Epididymis Protein 4, Cancer Antigen 125, and Ultrasound Prediction Model in Differentiating Benign from Malignant Adnexal Masses.

Background: This study aimed to compare the diagnostic performance of carcinogenic antigen (CA) 125, (HE)-4 (Human epididymis protein 4), and ultrasound (International Ovarian Tumor Analysis [IOTA]) Simple Rules individually and to derive a composite score in the differentiating ovarian cancer from benign ovarian mass. Subjects and Methods: Consecutive patients (n = 100) with pelvic mass admitted during February 2018-August 2019 were included prospectively. Patients with either known case of epithelial ovarian cancer (EOC) or metastatic EOC were excluded. The primary outcome was to assess the sensitivity and specificity of CA-125, HE-4, and IOTA Simple Rules in predicting benign from malignant mass independently, while secondary outcome was derivation of a new model incorporating these variables using multivariate logistic regression analysis to predict benign from malignant lesions. Receiver operator curve (ROC) was drawn to redefine the best-performing cutoff values and difference between area under the ROC (AUROC) were compared by DeLong's method. Results: Out of 100 cases of adnexal mass selected, the sensitivity and specificity of CA-125 were 73.8% and 77.6%, HE-4 were 90.5% and 87.9%, and IOTA Simple Rules were 92.9% and 81.0%. CA-125, HE-4, and IOTA Simple Rules were independently associated with the likelihood of malignancy/borderline (P < 0.001). The area under the curve for the "composite score" (AUC = 0.93) was the highest and was significantly better than that of CA-125 (AUC = 0.786) (P = 0.004 using DeLong's test) and comparable with HE-4 (AUROC = 0.90; P = 0.128 using DeLong's Test). Conclusion: The sensitivity and specificity of HE-4 and IOTA Simple Rules for predicting malignant ovarian tumor was better than those of CA-125. The diagnostic performance of "composite score" was comparable to those of either HE-4 or IOTA Simple Rules and significantly better than CA-125.

Gene expression based inference of cancer drug sensitivity.

Inter and intra-tumoral heterogeneity are major stumbling blocks in the treatment of cancer and are responsible for imparting differential drug responses in cancer patients. Recently, the availability of high-throughput screening datasets has paved the way for machine learning based personalized therapy recommendations using the molecular profiles of cancer specimens. In this study, we introduce Precily, a predictive modeling approach to infer treatment response in cancers using gene expression data. In this context, we demonstrate the benefits of considering pathway activity estimates in tandem with drug descriptors as features. We apply Precily on single-cell and bulk RNA sequencing data associated with hundreds of cancer cell lines. We then assess the predictability of treatment outcomes using our in-house prostate cancer cell line and xenografts datasets exposed to differential treatment conditions. Further, we demonstrate the applicability of our approach on patient drug response data from The Cancer Genome Atlas and an independent clinical study describing the treatment journey of three melanoma patients. Our findings highlight the importance of chemo-transcriptomics approaches in cancer treatment selection.

Assessment of Diagnostic Value of Serum Ca-125 and Risk of Malignancy Index Scoring in the Evaluation of Adnexal Masses.

INTRODUCTION: Adnexal masses have a wide spectrum with respect to the age of presentation, signs and symptoms, imaging findings, and histopathology report. MATERIALS AND METHODS: This is a cross-sectional diagnostic study, conducted at All India Institute of Medical Sciences, Rishikesh, Uttarakhand, India. The data were collected from department of gynecology over a period of 1½ years from June 2017 to December 2018. All women who were diagnosed to have an adnexal mass irrespective to age, parity, and menopausal status were included in the study. Ultrasonography of the abdomen with the pelvis was ordered in all patients followed by contrast-enhanced computed tomography or magnetic resonance imaging in selective patients. Tumor markers such as Ca-125 was measured, and risk of malignancy index (RMI) was calculated for each tumor. The clinical and imaging findings were correlated with intra-operative findings and finally with the histopathology examination report. RESULTS: A total of 171 women were included in the study who were diagnosed to have adnexal mass. A total of 137 women (80.1%) had benign tumor (Group B), whereas 34 women (19.9%) were found to have malignant tumor (Group M). Mean age in Group B was 35.85 ± 12.46 and in Group M was 46.12 ± 13.46 (P = 0.001). Ca-125 was significantly higher in Group M (1350 U/ml) than Group B (175 U/ml) (P = 0.008). The RMI score was also found to significantly increased in Group M than Group B (P = 0.007). CONCLUSION: With respect to adnexal masses, both Ca-125, as well as RMI scoring, are important diagnostic tools. RMI scoring has a better overall diagnostic performance than Ca-125 in predicting malignancy.