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  • 1
    In: Journal of Clinical Oncology, American Society of Clinical Oncology (ASCO), Vol. 36, No. 15_suppl ( 2018-05-20), p. e18042-e18042
    Type of Medium: Online Resource
    ISSN: 0732-183X , 1527-7755
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    Language: English
    Publisher: American Society of Clinical Oncology (ASCO)
    Publication Date: 2018
    detail.hit.zdb_id: 2005181-5
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  • 2
    In: Cellular Oncology, Springer Science and Business Media LLC, Vol. 40, No. 2 ( 2017-4), p. 145-155
    Type of Medium: Online Resource
    ISSN: 2211-3428 , 2211-3436
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2017
    detail.hit.zdb_id: 2595105-1
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  • 3
    In: Nature Communications, Springer Science and Business Media LLC, Vol. 6, No. 1 ( 2015-02-27)
    Abstract: Predicting clinical response to anticancer drugs remains a major challenge in cancer treatment. Emerging reports indicate that the tumour microenvironment and heterogeneity can limit the predictive power of current biomarker-guided strategies for chemotherapy. Here we report the engineering of personalized tumour ecosystems that contextually conserve the tumour heterogeneity, and phenocopy the tumour microenvironment using tumour explants maintained in defined tumour grade-matched matrix support and autologous patient serum. The functional response of tumour ecosystems, engineered from 109 patients, to anticancer drugs, together with the corresponding clinical outcomes, is used to train a machine learning algorithm; the learned model is then applied to predict the clinical response in an independent validation group of 55 patients, where we achieve 100% sensitivity in predictions while keeping specificity in a desired high range. The tumour ecosystem and algorithm, together termed the CANScript technology, can emerge as a powerful platform for enabling personalized medicine.
    Type of Medium: Online Resource
    ISSN: 2041-1723
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2015
    detail.hit.zdb_id: 2553671-0
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  • 4
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 73, No. 8_Supplement ( 2013-04-15), p. 2051-2051
    Abstract: Histone deacetylases (HDAC) have been shown to be involved in oncogenic transformation by mediating transcription factors. Although a few HDAC inhibitors (HDACi) have been shown to be effective in patients with rare leukemia, there is a need to develop best in class HDACi with higher therapeutic index in solid cancers. PAT-1102 is a novel HDACi that exhibited potent histone deacetylase inhibitory activity and growth inhibitory activity against a panel of cell lines in in vitro and in vivo models. Studies indicated that PAT-1102 mediates target modulation (histone hyperacetylation), p21 up regulation, angiogenesis inhibition, and induction of cell cycle arrest in these models. PAT-1102 possesses drug like properties including good aqueous solubility, oral absorption, metabolic stability and favorable pharmacokinetic profile in rodents. It did not show any hERG inhibitory activity, CYP liability and was well tolerated in tumor bearing mice. It had showed a dose dependent tumor growth inhibition of up to 72% in cell line based xenograft models of lung and colorectal cancer. Our data further indicated that the anti-tumor efficacy of PAT-1102 was superior to Vorinostat and comparable with Pracinostat (SB-939) while being more tolerable than Pracinostat. Although it has pan histone deacetylase properties, it showed preferential inhibition of HDAC-3 & HDAC-6. PAT-1102 efficacy was further assessed using “Oncoprint®” platform, a clinically relevant preclinical technology that has been demonstrated to have very high correlation to clinical outcome for chemotherapeutics as well as targeted drugs in multiple solid and hematological cancers (with overall sensitivity of 88% and specificity of 90% in N=500+ patients). Using Oncoprint®, PAT-1102’s efficacy was assessed in patient derived solid cancers (Pancreas, Gastric, Esophagus, Head & Neck, and Colorectal). Further we assessed the efficacy of PAT-1102 alone as well as in combination with various Standard-Of-Care drugs (SOCs) and compared the outcome with efficacy derived from the use of SOCs alone. Our study has been powered to include 75-100 patient derived refractory/recurrent tumors in each indication. Current results indicated the superiority of PAT-1102 when combined with SOCs in a subset of patients with solid cancers. Pre-clinical data shows that PAT-1102 has no toxic effect when given alone or in combination with SOC at efficacious doses . PAT-1102 has the potential to be more effective in a defined patient population than other molecules in this class. In summary, we have identified a novel, potent HDACi with drug like properties. Our data suggest PAT-1102 has the potential to be best in class HDACi when combined with SOC in solid cancers. Clinical development of PAT-1102 in solid cancers will be initiated in 2013. Citation Format: Padhma Radhakrishnan, Muthu Dhandapani, Baraneedharan Ulaganathan, Allen Thayakumar, Saravanan Thiyagarajan, Dency Pinto, D R. Vinod, Biswanath Majumder, Prasad Shivarudriaah, H Jagadheshan, Ganesh Sambasivam, Pradip K. Majumder. PAT-1102, a novel HDAC inhibitor exhibits potent anti-tumor efficacy in patient-derived refractory solid tumors. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 2051. doi:10.1158/1538-7445.AM2013-2051
    Type of Medium: Online Resource
    ISSN: 0008-5472 , 1538-7445
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    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2013
    detail.hit.zdb_id: 2036785-5
    detail.hit.zdb_id: 1432-1
    detail.hit.zdb_id: 410466-3
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  • 5
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 73, No. 8_Supplement ( 2013-04-15), p. 4947-4947
    Abstract: The PI3K/AKT/mTOR pathway is an important signaling axis that is perturbed in majority of cancers. Biomarkers such as pS6RP, GLUT1 and tumor FDG uptake are being evaluated in patient stratification for mTOR pathway inhibitors. In the absence of a clear understanding of the underlying mechanisms in tumor signaling, the biomarker strategy for patient stratification is of limited use. Here, we show that no discernible correlation exists between FDG uptake and the corresponding Ki67, GLUT1, pS6RP expression in tumor biopsies from Head and Neck Cancer (HNC) patients. Correlation between GLUT1 and pS6RP levels in tumors was observed but elevated pS6RP was noticed even in the absence of concomitant AKT activation, suggesting other downstream molecules of PI3K/AKT and/or other pathways upstream of mTOR, are active in these tumors. Using an ex-vivo platform, we identified putative responders to Rapamycin, an mTOR inhibitor in these tumors. However, Rapamycin did not induce anti-tumor effect in the majority of tumors with activated mTOR, potentially attributable to the observation that Rapamycin induces feedback activation of AKT. Accordingly, treatment of these tumors with an AKT inhibitor and Rapamycin uniformly resulted in abrogation of mTOR inhibition induced AKT activation in all tumors but failed to induce anti-tumor response in a subset. Phosphoproteomic profiling of tumors resistant to dual AKT/mTOR inhibitors revealed differential activation of multiple pathways involved in proliferation and survival. Collectively, our data suggest that in addition to biomarker based segregation, functional assessment of patient tumor prior to treatment with mTOR/AKT inhibitors might be useful for patient stratification. Citation Format: Padhma Radhakrishnan, Ulaganathan Baraneedharan, Muthu Dhandapani, Allen Thyakumar, Dency Pinto, Arun Prasath, Ayyappan Velu, A Kamal, Nilesh Brijwani, Rohini Nair, R Basavaraja, Misti Jain, Saravanan Thiyagarajan, Biswanath Majumder, Mallik Sundaram, Prasad Narayanan, Vikram D. Kekatpure, Pradip K. Majumder. Inhibition of Rapamycin induced AKT activation elicits differential anti-tumor response in head and neck cancers. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 4947. doi:10.1158/1538-7445.AM2013-4947
    Type of Medium: Online Resource
    ISSN: 0008-5472 , 1538-7445
    RVK:
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    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2013
    detail.hit.zdb_id: 2036785-5
    detail.hit.zdb_id: 1432-1
    detail.hit.zdb_id: 410466-3
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  • 6
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 75, No. 15_Supplement ( 2015-08-01), p. 1304-1304
    Abstract: Predicting clinical response to anticancer drugs remains a major challenge in the treatment of cancer. Indeed, while biomarker-guided strategies for personalizing anticancer drugs have shown strong promise in certain cases, recent studies have shown that the tumor microenvironment and heterogeneity can limit the predictive power of biomarkers alone. Here we have engineered a personalized tumor ecosystems, termed CANScript™, that contextually conserve tumor heterogeneity and phenocopy the tumor ecosystem using thin tumor explants maintained in defined tumor grade-matched matrix support and autologous ligands from patients. We then demonstrated that the CANScript™ platform can be used to predict clinical response. Specifically, functional readouts obtained by exposing the CANScript™ ecosystems from more than 1100 patients to a panel of anticancer drugs, together with the corresponding clinical outcomes, were used to train a novel machine learning algorithm; the learned model was then applied to predict clinical response to anticancer drugs in a test group comprising of 900 new patients, where it achieved 100% sensitivity in its predictions while also keeping specificity in a desired high range. We have also observed that CANScript™ retains patient tumor immune environment which is important for clinical response of not only immunomodulators but other anti-cancer drugs. Here we report the effect of immunomodulators in refractory CRC tumors which remains difficult to treat. Data demonstrates that Anti-CTLA-4 has profound antitumor effect in refractory CRC tumors by increasing cytotoxic T-Cells. In this cohort of 16 patients’ tumors CANScript™ platform identifies 31% as responders (5/16) where conventional tumor sections culture model shows only 6% as (1/16) responders. Citation Format: Biswanath Majumder, Baraneedharan Ulaganathan, Allen Thayakumar, Saravanan Thiyagarajan, Nilesh Brijwani, Biplab Tewari, Basavaraja U. Santhappa, Padhma Radhakrishnan, Pradip K. Majumder. Identification of responders for Anti-CTLA4 in refractory colorectal cancers using CANScript™ platform. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 1304. doi:10.1158/1538-7445.AM2015-1304
    Type of Medium: Online Resource
    ISSN: 0008-5472 , 1538-7445
    RVK:
    RVK:
    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2015
    detail.hit.zdb_id: 2036785-5
    detail.hit.zdb_id: 1432-1
    detail.hit.zdb_id: 410466-3
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  • 7
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 73, No. 3 ( 2013-02-01), p. 1118-1127
    Abstract: The PI3K/AKT/mTOR pathway is an important signaling axis that is perturbed in majority of cancers. Biomarkers such as pS6RP, GLUT1, and tumor FDG uptake are being evaluated in patient stratification for mTOR pathway inhibitors. In the absence of a clear understanding of the underlying mechanisms in tumor signaling, the biomarker strategy for patient stratification is of limited use. Here, we show that no discernible correlation exists between FDG uptake and the corresponding Ki67, GLUT1, pS6RP expression in tumor biopsies from patients with head and neck cancer. Correlation between GLUT1 and pS6RP levels in tumors was observed but elevated pS6RP was noticed even in the absence of concomitant AKT activation, suggesting that other downstream molecules of PI3K/AKT and/or other pathways upstream of mTOR are active in these tumors. Using an ex vivo platform, we identified putative responders to rapamycin, an mTOR inhibitor in these tumors. However, rapamycin did not induce antitumor effect in the majority of tumors with activated mTOR, potentially attributable to the observation that rapamycin induces feedback activation of AKT. Accordingly, treatment of these tumors with an AKT inhibitor and rapamycin uniformly resulted in abrogation of mTOR inhibition-induced AKT activation in all tumors but failed to induce antitumor response in a subset. Phosphoproteomic profiling of tumors resistant to dual AKT/mTOR inhibitors revealed differential activation of multiple pathways involved in proliferation and survival. Collectively, our results suggest that, in addition to biomarker-based segregation, functional assessment of a patient's tumor before treatment with mTOR/AKT inhibitors may be useful for patient stratification. Cancer Res; 73(3); 1118–27. ©2013 AACR.
    Type of Medium: Online Resource
    ISSN: 0008-5472 , 1538-7445
    RVK:
    RVK:
    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2013
    detail.hit.zdb_id: 2036785-5
    detail.hit.zdb_id: 1432-1
    detail.hit.zdb_id: 410466-3
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  • 8
    In: Nature Communications, Springer Science and Business Media LLC, Vol. 6, No. 1 ( 2015-02-11)
    Abstract: Understanding the emerging models of adaptive resistance is key to overcoming cancer chemotherapy failure. Using human breast cancer explants, in vitro cell lines, mouse in vivo studies and mathematical modelling, here we show that exposure to a taxane induces phenotypic cell state transition towards a favoured transient CD44 Hi CD24 Hi chemotherapy-tolerant state. This state is associated with a clustering of CD44 and CD24 in membrane lipid rafts, leading to the activation of Src Family Kinase (SFK)/hemopoietic cell kinase (Hck) and suppression of apoptosis. The use of pharmacological inhibitors of SFK/Hck in combination with taxanes in a temporally constrained manner, where the kinase inhibitor is administered post taxane treatment, but not when co-administered, markedly sensitizes the chemotolerant cells to the chemotherapy. This approach of harnessing chemotherapy-induced phenotypic cell state transition for improving antitumour outcome could emerge as a translational strategy for the management of cancer.
    Type of Medium: Online Resource
    ISSN: 2041-1723
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2015
    detail.hit.zdb_id: 2553671-0
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  • 9
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 74, No. 19_Supplement ( 2014-10-01), p. 3736-3736
    Abstract: Histone deacetylases (HDAC) are deregulated in many human cancers and a few HDAC inhibitors (HDACi) have been shown to be effective in patients with rare leukemia. However, clinical responses are not very promising for many HDACi in solid cancers. There is an urgent need to develop best in class HDACi with higher therapeutic index in solid cancers. At present less than 10% of anti-cancer drugs entering phase 1 clinical trials are successful in getting market approval. There are many factors for this poor clinical success for oncology therapeutics, and one of them is the lack of robust preclinical model driving clinical development. Cancer is a very heterogeneous disease and many of the present preclinical models do not represent this heterogeneity. As a result, while a candidate drug may appear good in present preclinical models, they often fail to make the cut in clinical development. To circumvent this critical problem, we have developed a robust TE (Tumor Ecosystem) platform technology using patient tumors, autologous ligands, and immune compartments from the same patients.Our TE platform preserves patient tumor heterogeneity along with other functional and genomic markers and immunogenic cytokines. Efficacy of drugs exposed to the patient's tumor tissue in our TE platform is assessed by as many as 17 orthogonal assays within a week. The results from these assays are converted into a single predictive score called the “M-Score,” and it has been clinically validated using FDA approved drugs in & gt; 1,800 patients across multiple solid and hematological cancers. Our data shows that TE platform predicts treatment outcome of FDA approved drugs in clinical setting with very high sensitivity and specificity. We have the opportunity to use this platform technology to identify cancer indications and appropriate combinations for MIT-1102, a novel HDACi that exhibited potent histone deacetylase inhibitory activity. Our data further indicates that the anti-tumor efficacy of MIT-1102 is superior to Vorinostat and comparable with Pracinostat (SB-939) while being more tolerable than Pracinostat. Results indicated the superiority of MIT-1102 when combined with SOCs in a subset of patients with gastric and pancreatic cancers. We are also using different omics to identify markers associated with response in those tumor types. MIT-1102 has the potential to be more effective in a defined patient population than other molecules in this class. In summary, we have identified a novel, potent HDACi with drug-like properties, and identified the correct cancer indications and most effective combinations using TE platform Technology. Citation Format: Mallikarjun Sundaram, Baraneedharan Ulaganathan, Muthu Dhandapani, Allen Thayakumar, Pragnashree Mukhopadhyay, Saravanan Thiyagarajan, Biswanath Majumder, Prasad Shivarudriah, H Jagadheshan, Ganesh Sambasivam, Steve Birnbuam, Padhma Radhakrishnan, Pradip K. Majumder. Application of patient tumors-derived tumor ecosystem platform for the development of novel HDAC inhibitor in solid cancers. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 3736. doi:10.1158/1538-7445.AM2014-3736
    Type of Medium: Online Resource
    ISSN: 0008-5472 , 1538-7445
    RVK:
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    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2014
    detail.hit.zdb_id: 2036785-5
    detail.hit.zdb_id: 1432-1
    detail.hit.zdb_id: 410466-3
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  • 10
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 76, No. 14_Supplement ( 2016-07-15), p. 5129-5129
    Abstract: Colorectal cancer (CRC) is one of the leading causes of cancer related mortality. Recent findings from clinical studies showed that immune checkpoint inhibitors are making good progress towards clinical practise. However, existing biomarkers and 3D platforms are not equipped to offer reliable prediction of response of these drugs. We recently engineered a personalized ex vivo systems biology based platform using patient tumors called CANScriptTM (Majumder B et al Nat. Commun. 2015, Goldman A et al Nat. Commun. 2015) and a companion in vivo patient derived immune reconstituted xenograft model (Mi-HTX) preserving multiple critical phenotypic profiles orchestrating tumor-immune cross talk and dysfunction. We further performed baseline characterization of immune markers (CD4, CD8, CD68, CXCR4 and CD45-RO). Intratumor heterogeneity of both M1 and M2 phenotypes were observed irrespective of clinico-pathological features. Baseline CD68 enrichment status was found to be correlated with therapy failure for some patients where clinical outcome (PERCIST) was available. Flow cytometry and microarray analysis showed preservation of diverse sets of functional CD4, CD8 and NK phenotypes along with degranulation markers (CD107a), IFN-γ and FoxP3 in both in vivo and ex vivo tumors reconstituted with ex vivo primed PBMC. The comparative response profiling of these models following treatment with immune checkpoint inhibitors suggested enhanced antitumor effects (as measured by multiple functional parameters like viability, proliferation, morphology and apoptosis). Together, these findings highlight the strengths of immune-competent functional testing tools to stratify patients for precision immunotherapy where direct response prediction biomarkers are still elusive. 1. Majumder B et al. Nat. Commun.6:6169 (2015). 2. Goldman A et al. Nat. Commun. 6:6139 (2015). Citation Format: Pradip K. Majumder, Nilesh Brijwani, Nikita N. Karandikar, Vinod D. Radhakrishna, Muthusamy Oliyarasi, Dency D. Pinto, Babu Balakrishnan, Vasathakumar Sekar, Manoj Rajappa, Debapriya G. Mehrotra, Priyanka Chevur, Priyanka Chevur, Arkasubhra Ghosh, Saravanan Thyiagarajan, Padhma Radhakrishnan, Biswanath Majumder. Delineating immune networks in colorectal cancers to predict effects of immune checkpoint inhibitors using CANScript platform technology preserving tumor immune microenvironment. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 5129.
    Type of Medium: Online Resource
    ISSN: 0008-5472 , 1538-7445
    RVK:
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    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2016
    detail.hit.zdb_id: 2036785-5
    detail.hit.zdb_id: 1432-1
    detail.hit.zdb_id: 410466-3
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