The IS6110 belongs to the family of insertion sequences (IS) of the IS3 category. This insertion sequence was reported to be specific for Mycobacterium tuberculosis complex and hence is extensively exploited for laboratory detection of the agent of tuberculosis and for epidemiological investigations based on polymerase chain reaction. IS6110 is 1361-bp long and within this sequence different regions have been utilized as targets in the identification of M. tuberculosis by PCR. However, the results are not always consistent, specific and sensitive. In recent years, a few clinical investigations raised concerns over IS6110 specificity and sensitivity in the diagnosis of tuberculosis due to false-positive (homology with other target DNA besides M. tuberculosis) or false negative (due to absence of copies of IS6110) results with IS6110 specific primers. To unravel the variations in IS6110 sequences, an insilico analysis of IS6110 sequence of different strains of M. tuberculosis was carried out. Our results of comparative analysis of IS6110 insertion sequences of M. tuberculosis complex suggests that, IS6110 insertion sequences harbored variations in its sequence, which is evident from the phylogenetic analysis. Importantly, IS6110 sequence has divergence within the copies of same strain and formed different clusters. A list of IS6110 specific primers used in various clinical investigation of tuberculosis was obtained from the literature and their performance scrutinized. Our study emphasizes the need to develop PCR assays (multiplex format) targeting more than one region of the genome of M. tuberculosis.

This report describes the molecular detection of M. tuberculosis in patients' sputum samples tested by the nPCR format, using IS6110 as a target sequence. A high prevalence of pulmonary tuberculosis was identified by the nPCR assay, which was shown to have a significantly higher detection rate than conventional smear staining.

The non-nested TRC 4 PCR showed inability for accurate detection of M. tuberculosis in sputum samples. The study concluded that the nPCR targeting IS6110 is superior and more sensitive than TRC 4 PCR.

Background: Emerging clinical evidence using immunotherapy in recent years has demonstrated its power to suppress tumor growth by releasing the brakes on the immune system. For example, blockade of immune checkpoints, such as PD-1, has revolutionized treatment options for patients with aggressive cancers such as head and neck squamous cell carcinoma (HNSCC). However, clinical responses to PD-1 inhibition vary widely among patients while majority of them do not show any anti-tumor response. Multiple FDA-approved drugs against the same immune checkpoints have resulted in globally distinct outcomes in the clinic. There is a huge unmet need to understand these disparities at the individual patient level and to maximize the clinical benefits of these agents. Methods: Here, we employed a patient-derived ex vivo model, CANScript™ (Majumder B et al. Nature Commun 2015 Feb 27;6:6169 and Goldman A et al. Nature Commun 2015 Feb 11;6:6139), which recreates the native 3D tumor microenvironment, autocrine-paracrine dynamic and response to therapy by incorporating fresh tumor tissue and autologous immune cells with immunotherapy agents. Utilizing late stage HNSCC (N=50) we interrogated phenotypic response to two FDA-approved PD-1 inhibitors, Pembrolizumab (KEYTRUDA) and Nivolumab (OPDIVO). To do this, we used a comprehensive panel of immunological assays to evaluate changes in the immune compartments by flowcytometry and immunohistochemistry (primarily CD8, CD45, FOXP3, CXCR4, CD68, PDL1, PD1), multiplex cytokine profiling (IL6, IL8, IFN-g, IL10, IL12, Perforin, GranzymeB), along with functional/phenotypic effects including tumor proliferation, histological changes and cell death. Results: The data demonstrated that CANScript™ preserves the tumor-immune contexture and native heterogeneity across different clinical stages and patients. Importantly, we observed that PD-1 blockade resulted in patient-specific therapeutic response, which was characterized by differential distribution and maintenance of infiltrating CD8+ and CD4+ lymphocytes, distinct patterning of cytokines linked to functional dysregulation, and changes in tumor proliferation and apoptosis. Interestingly, data suggest that both Pembrolizumab and Nivolumab act on the same immune network axis but trigger functionally diverse phenotypes in the tumor immune compartment and distinct antitumor effects within an individual patient tumor. Conclusion: Together, these findings demonstrate the utility of CANScript™ as an ex vivo platform to predict therapeutic response of immune checkpoint inhibitors at the individual patient level. It also highlights mechanistic variations that could impact clinical outcome of these agents having the same molecular target. Such information can re-shape our understanding of patient selection and rational combinations for novel immune checkpoint inhibitors. Citation Format: Padhma Radhakrishnan, Vasanthakumar Sekar, Nilesh Brijwani, Priyanka Chevour, Babu Balakrishnan, Dency D Pinto, Muthusami Oliyarasi, Debapriya G. Mehrotra, Manjusha Biswas, Sabitha K S, Kodaganur S. Gopinath, Arkasubhra Ghosh, M s Ganesh, Ashok M. Shenoy, Saravanan Thiyagarajan, Biswanath Majumder, Aaron Goldman. A patient derived ex vivo platform CANScript™ predicts distinct therapeutic outcomes to multiple PD-1 checkpoint inhibitors in single tumor biopsies [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 3681. doi:10.1158/1538-7445.AM2017-3681