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.

Artificial intelligence uncovers carcinogenic human metabolites.

The genome of a eukaryotic cell is often vulnerable to both intrinsic and extrinsic threats owing to its constant exposure to a myriad of heterogeneous compounds. Despite the availability of innate DNA damage responses, some genomic lesions trigger malignant transformation of cells. Accurate prediction of carcinogens is an ever-challenging task owing to the limited information about bona fide (non-)carcinogens. We developed Metabokiller, an ensemble classifier that accurately recognizes carcinogens by quantitatively assessing their electrophilicity, their potential to induce proliferation, oxidative stress, genomic instability, epigenome alterations, and anti-apoptotic response. Concomitant with the carcinogenicity prediction, Metabokiller is fully interpretable and outperforms existing best-practice methods for carcinogenicity prediction. Metabokiller unraveled potential carcinogenic human metabolites. To cross-validate Metabokiller predictions, we performed multiple functional assays using Saccharomyces cerevisiae and human cells with two Metabokiller-flagged human metabolites, namely 4-nitrocatechol and 3,4-dihydroxyphenylacetic acid, and observed high synergy between Metabokiller predictions and experimental validations.

Treatment conundrums in osteosarcoma of the breast: Case report of two cases from a tertiary care cancer center in India.

Extraosseous sarcoma of the breast is an infrequent entity and a harbinger of poor prognosis. Histogenesis of this tumor is uncertain, and it can arise both in denovo and metastatic settings. Morphologically, it is indistinguishable from its skeletal counterpart and clinically, it presents like any other subtype of breast cancer. Tumor recurrence with a propensity for hematogenous rather than lymphatic spread plagues with this malicious disease. Treatment guidelines are mainly extrapolations from those of treatment of other extra-skeletal sarcomas as literature is limited in this context. In this study, it was aimed to present two clinical cases with similar clinical profiles and different treatment outcomes. The intent of this case report is to contribute to the limited database available for management of this rare disease.

Salivary protein kinase C alpha and novel microRNAs as diagnostic and therapeutic resistance markers for oral squamous cell carcinoma in Indian cohorts.

Oral squamous cell carcinoma (OSCC) is the second leading cause of cancer-related morbidity and mortality in India. Tobacco, alcohol, poor oral hygiene, and socio-economic factors remain causative for this high prevalence. Identification of non-invasive diagnostic markers tailored for Indian population can facilitate mass screening to reduce overall disease burden. Saliva offers non-invasive sampling and hosts a plethora of markers for OSCC diagnosis. Here, to capture the OSCC-specific salivary RNA markers suitable for Indian population, we performed RNA-sequencing of saliva from OSCC patients (n = 9) and normal controls (n = 5). Differential gene expression analysis detected an array of salivary RNAs including mRNAs, long non-coding RNAs, transfer-RNAs, and microRNAs specific to OSCC. Computational analysis and functional predictions identified protein kinase c alpha (PRKCA), miR-6087, miR-449b-5p, miR-3656, miR-326, miR-146b-5p, and miR-497-5p as potential salivary indicators of OSCC. Notably, higher expression of PRKCA, miR-6087 and miR-449b-5p were found to be associated with therapeutic resistance and poor survival, indicating their prognostic potential. In addition, sequencing reads that did not map to the human genome, showed alignments with microbial reference genomes. Metagenomic and statistical analysis of these microbial reads revealed a remarkable microbial dysbiosis between OSCC patients and normal controls. Moreover, the differentially abundant microbial taxa showed a significant association with tumor promoting pathways including inflammation and oxidative stress. Summarily, we provide an integrated landscape of OSCC-specific salivary RNAs relevant to Indian population which can be instrumental in devising non-invasive diagnostics for OSCC.

A multi-institutional real world data study from India of 3453 non-metastatic breast cancer patients undergoing upfront surgery.

The present analysis reports the clinical, pathological, treatment profile and overall survival (OS) and disease-free survival (DFS) outcomes of consecutive breast cancer patients from three Indian centres, who underwent curative surgery as their first treatment. Among the 3453 patients, stage I, II, and III cases were 11.75%, 66.79%, and 21.64%, respectively while hormone receptor positive/HER2 negative, triple negative (TNBC) and hormone receptor any/HER2 positive cases were 55.2%, 24.2% and 20.6%, respectively. The five-year OS in the entire cohort, node-negative and node-positive patients were 94.1% (93.25-94.98), 96.17% (95.2-97.15) and 91.83% (90.36-93.31), respectively, and the corresponding DFS were 88.1% (86.96-89.31), 92.0% (90.64-93.39) and 83.93% (82.03-85.89), respectively. The five-year OS in hormone receptor positive/HER2 negative, TNBC and HER2 subgroups were 96.11% (95.12-97.1), 92.74% (90.73-94.8) and 90.62% (88.17-93.15), respectively, and the corresponding DFS were 91.59% (90.19-93.02), 85.46% (82.79-88.22) and 81.29% (78.11-84.61), respectively. This is the largest dataset of early breast cancer patients from India with survival outcome analysis and can therefore serve as a benchmark for future studies.

Case report of everolimus-induced sustained partial response in metastatic renal epithelioid angiomyolipoma.

Epithelioid variant of angiomyolipoma (EAML) is a newly defined entity and a close mimicker of renal cell carcinoma. There is a growing body of evidence to suggest its aggressive behavior in terms of local recurrence, metastasis and death. The treatment for this subset of patients has posed challenges for the experts. Chemotherapy plays little active role and so molecular profiling to identify genomic alterations amenable to targeted therapies has paved the way. Recently, tyrosine kinase inhibitors and mTOR inhibitors have been utilised both in adjuvant and neoadjuvant settings and have shown promising results in terms of survival. We present a case of a metastatic epithelioid angiomyolipoma treated sequentially with imatinib, crizotinib and now maintaining a sustained partial response with everolimus.

Malignant Sertoli cell tumor of the testis masquerading as seminoma with bone metastasis.

Sex cord-stromal tumors of the testes are rare malignancies as compared to germ cell tumors. Pure Sertoli cell tumors are still rare representing <1% of testicular cancers and the malignant forms are too rare. Furthermore, the occurrence of metastasis in such cases is extremely rare with <30 cases reported in literature so far to the best of our knowledge. We present herein a case of malignant Sertoli cell tumor in a 48-year-old male who was initially misdiagnosed as seminoma based on histology and clinical presentation. Four months later, he presented with symptoms due to bony metastasis and found to have widespread metastatic disease which is a very rare presentation of Sertoli cell tumors. Diagnosis of sex cord-stromal tumor requires high index of suspicion as these tumors are most of the times misdiagnosed as germ cell tumors due to their rare incidence and atypical presentation leading to mismanagement. Timely diagnosis at an early stage can provide therapeutic benefit due to lack of well-defined treatment options at advanced stages.

Treatment conundrums in osteosarcoma of the breast: Two clinical cases from a tertiary care cancer center in India.

Extraosseous sarcoma of the breast occurs infrequently and is a harbinger of poor prognosis. The histogenesis of this tumor is ambiguous, and it can arise both in de novo and metastatic settings. Morphologically, it is indistinguishable from its skeletal counterpart, and clinically, it presents similarly to any other subtype of breast cancer. Tumor recurrence with a propensity for hematogenous rather than lymphatic spread plagues this malicious disease. The treatment guidelines are mainly derived from the those of other extraskeletal sarcomas as the literature is limited in this context. We hereby present 2 clinical cases with similar clinical profiles and different treatment outcomes. The intent of this case report is to contribute to the limited database available for the management of this rare disease.

Genetic variations of IL-10: Identification of novel variations and evaluation of the impact of the SNPs/haplotype in the promoter region with the progression of Oral Squamous Cell Carcinoma in Indian population.

The correlation of interleukin 10 (IL-10) with the outbreak and progression of cancer has been well established as it contributes to tumor immune evasion. Convincing number of evidences has been accumulated to reflect the critical correlation between IL-10 polymorphism and tumorogenesis. Several polymorphic sites at promoter regions have been reported to be associated with cancer susceptibility. The purpose of this study was to examine the effect of modulated genotypes in the promoter region of IL-10 gene with life-style habits in oral squamous cell carcinoma (OSCC) in the Indian population. A total of 300 subjects (100 OSCC, 50 precancer and 150 healthy controls) were recruited in this study. The IL-10 promoter region was amplified in 14 overlapping fragments by PCR and further screened through the high throughput technique of denaturing high-performance liquid chromatography (dHPLC) followed by sequencing. We identified three novel variations at positions (-924, -1045 & -1066); we also found some known SNPs (-592C/A, -657G/A, -851G/A, -819C/T, -1082A/G). The identified novel variations were submitted to the NCBI Gene Bank (accession numbers KT153594, KT291742 and KT291743). We also noticed a significant association of polymorphisms (-592C/A, -819C/T and -1082A/G) individually as well as in combination (haplotypes) along with lifestyle habits for the risk of oral carcinoma (p<0.0001). We have reported three novel SNPs in the Indian population for the first time, and these SNPs may be associated with OSCC. Besides, we showed the first evidence of IL-10 haplotypes, i.e., CCG and CTG, may act as a biomarker for early detection of oral pre-cancerous/cancerous lesions or treatment management of oral carcinoma.

Indian Council of Medical Research Consensus Document for the Management of Non-Hodgkin's Lymphoma (High Grade).

This consensus document is based on the guidelines related to the management of Non Hodgkin's Lymphoma (High grade) in the Indian population as proposed by the core expert committee. Accurate diagnosis in hematolymphoid neoplasm requires a combination of detailed history,clinical examination, and various investigations including routine laboratory tests, good quality histology section (of tumor and also bone marrow aspirate/biopsy), immunostaining, cytogenetic and molecular studies and radiology investigations. The staging system used for adult high grade lymphomas is based on the Ann Arbor system and includes various parameters like clinical, haematology, biochemistry, serology and radiology. Response should be evaluated with radiological evaluation after 3-4 cycles and at the end of treatment based on criteria including and excluding PET. Treatment of high grade lymphomas is based on histologic subtype, extent of disease, and age of the patient. Autologous stem cell transplantation after high dose chemotherapy is effective in the treatment of relapsed NHL. Newer RT techniques like 3 dimensional conformal radiation therapy (3D-CRT) and intensity modulated radiation therapy (IMRT) can significantly reduce radiation doses to surrounding normal tissues in lymphoma patients. Patients should be followed up every 3 to 4 months for the first 2 years, followed by 6 monthly for the next 3 years and then annually.