Chirayu Chokshi

A phylogenomic and molecular markers based analysis of the phylum Chlamydiae: proposal to divide the class Chlamydiia into two orders, Chlamydiales and Parachlamydiales ord. nov., and emended description of the class Chlamydiia

The phylum Chlamydiae contains nine ecologically and genetically diverse families all placed within a single order. In this work, we have completed a comprehensive comparative analysis of 36 sequenced Chlamydiae genomes in order to identify shared molecular characteristics, namely conserved signature insertions/deletions (CSIs) and conserved signature proteins (CSPs), which can serve as distinguishing characteristics of supra-familial clusters within the phylum Chlamydiae. Our analysis has led to the identification of 32 CSIs which are specific to clusters within the phylum Chlamydiae at various phylogenetic depths. Importantly, 17 CSIs and 98 CSPs were found to be specific for the family Chlamydiaceae while another 3 CSI variants and 15 CSPs were specific for a grouping of the families Criblamydiaceae, Parachlamydiaceae, Simkaniaceae and Waddliaceae. These two clusters were also found to be distinguishable in 16S rRNA based phylogenetic trees, concatenated protein based phylogenetic trees, character compatibility based phylogenetic analyses, and on the basis of 16S rRNA gene sequence identity and average amino acid identity values. On the basis of the identified molecular characteristics, branching in phylogenetic trees, and the genetic distance between the two clusters within the phylum Chlamydiae we propose a division of the class Chlamydiia into two orders: an emended order Chlamydiales, containing the family Chlamydiaceae and the closely related Candidatus family Clavichlamydiaceae, and the novel order Parachlamydiales ord. nov. containing the families Parachlamydiaceae, Simkaniaceae and Waddliaceae and the Candidatus families Criblamydiaceae, Parilichlamydiaceae, Piscichlamydiaceae, and Rhabdochlamydiaceae. We also include a brief discussion of the reunification of the genera Chlamydia and Chlamydophila.

Introduction to Cancer Stem Cells: Past, Present, and Future

The Cancer Stem Cell (CSC) hypothesis postulates the existence of a small population of cancer cells with intrinsic properties allowing for resistance to conventional radiochemotherapy regiments and increased metastatic potential. Clinically, the aggressive nature of CSCs has been shown to correlate with increased tumor recurrence, metastatic spread, and overall poor patient outcome across multiple cancer subtypes. Traditionally, isolation of CSCs has been achieved through utilization of cell surface markers, while the functional differences between CSCs and remaining tumor cells have been described through proliferation, differentiation, and limiting dilution assays. The generated insights into CSC biology have further highlighted the importance of studying intratumoral heterogeneity through advanced functional assays, including CRISPR-Cas9 screens in the search of novel targeted therapies. In this chapter, we review the discovery and characterization of cancer stem cells populations within several major cancer subtypes, recent developments of novel assays used in studying therapy resistant tumor cells, as well as recent developments in therapies targeted at cancer stem cells.

Development of a Patient-Derived Xenograft Model Using Brain Tumor Stem Cell Systems to Study Cancer

Patient-derived xenograft (PDX) models provide an excellent platform to understand cancer initiation and development in vivo. In the context of brain tumor initiating cells (BTICs), PDX models allow for characterization of tumor formation, growth, and recurrence, in a clinically relevant in vivo system. Here, we detail procedures to harvest, culture, characterize, and orthotopically inject human BTICs derived from patient samples.

Cotargeting Ephrin Receptor Tyrosine Kinases A2 and A3 in Cancer Stem Cells Reduces Growth of Recurrent Glioblastoma

Glioblastoma (GBM) carries a dismal prognosis and inevitably relapses despite aggressive therapy. Many members of the Eph receptor tyrosine kinase (EphR) family are expressed by GBM stem cells (GSC), which have been implicated in resistance to GBM therapy. In this study, we identify several EphRs that mark a therapeutically targetable GSC population in treatment-refractory, recurrent GBM (rGBM). Using a highly specific EphR antibody panel and CyTOF (cytometry by time-of-flight), we characterized the expression of all 14 EphR in primary and recurrent patient-derived GSCs to identify putative rGBM-specific EphR. EPHA2 and EPHA3 coexpression marked a highly tumorigenic cell population in rGBM that was enriched in GSC marker expression. Knockdown of EPHA2 and EPHA3 together led to increased expression of differentiation marker GFAP and blocked clonogenic and tumorigenic potential, promoting significantly higher survival in vivo Treatment of rGBM with a bispecific antibody against EPHA2/A3 reduced clonogenicity in vitro and tumorigenic potential of xenografted recurrent GBM in vivo via downregulation of AKT and ERK and increased cellular differentiation. In conclusion, we show that EPHA2 and EPHA3 together mark a GSC population in rGBM and that strategic cotargeting of EPHA2 and EPHA3 presents a novel and rational therapeutic approach for rGBM.Significance: Treatment of rGBM with a novel bispecific antibody against EPHA2 and EPHA3 reduces tumor burden, paving the way for the development of therapeutic approaches against biologically relevant targets in rGBM. Cancer Res; 78(17); 5023-37. ©2018 AACR.

Abstract 3844: Identification and validation of novel therapeutic targets driving clonal heterogeneity in treatment-refractory GBM

Glioblastoma (GBM) is the most common primary adult brain tumor, characterized by extensive cellular and genetic heterogeneity. Even with surgery, standard chemotherapy with temozolomide (TMZ), and radiation, tumor re-growth (or recurrence) and patient relapse are inevitable. Patients face a median survival of Potential therapeutic targets were validated by their effect on self-renewal and proliferation of patient-derived BTIC lines of human GBM in vitro and in vivo. Using CRISPR Cas9, potential targets were knocked out in patient-derived BTIC lines of human GBM in order to characterize the effect on sphere formation and proliferation in vitro, and tumor formation in vivo. Following validation of new therapeutic targets of treatment-refractor GBM, we aim to build novel biotherapeutics against highly validated cell surface targets, and establish preclinical testing protocols using our novel patient-derived and therapy-adapted xenograft model of treatment-resistant GBM. Citation Format: Chirayu Chokshi, Nick Yelle, Parvez Vora, Chitra Venugopal, Maleeha Qazi, Mohini Singh, Minomi Subapanditha, Avrilynn Ding, Sheila K. Singh. Identification and validation of novel therapeutic targets driving clonal heterogeneity in treatment-refractory GBM [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 3844. doi:10.1158/1538-7445.AM2017-3844

Abstract 3758: The efficacy of CD133 BiTEs and CAR-T cells in preclinical model of glioblastoma

Glioblastoma (GBM) is a uniformly fatal primary brain tumor, characterized by a diverse cellular phenotype and genetic heterogeneity. Despite the use of multi-modal treatment including surgical resection, radiotherapy and chemotherapy, the outcome of patients with GBM remains poor. Numerous studies have implicated CD133+ brain tumor initiating cells (BTICs) as drivers of chemo- and radio-resistance in GBM. We recently demonstrated that a CD133-driven gene signature is predictive of poor overall survival and targeting CD133+ treatment-refractory cells may be an effective strategy to block GBM recurrence. Chimeric antigen receptors (CARs) and bispecific T-Cell engaging antibodies (BiTEs) present promising immunotherapeutic approaches that have not yet been validated for recurrent GBM. Using CellectSeq, a novel methodology that combines use of phage-displayed synthetic antibody libraries and DNA sequencing, we developed the CD133-specific monoclonal antibody ‘RW03’. We constructed CD133-specific BiTEs that consist of two arms; one arm recognizes the tumor antigen (CD133) while the second is specific to CD3 antigen. The dual binding specificity was confirmed using flow cytometry. Using CD133high and CD133low primary GBM lines, we validated the binding of BiTEs to CD133+ cells. Further analysis showed binding of BiTEs to human T cells known to express CD3 within a population of healthy donor peripheral blood mononuclear cells. We observed BiTEs redirecting T cells to kill GBMs, with greater efficiency observed in CD133high GBMs, validating BiTE target specificity. Incubating T-cells with BiTEs and the CD133high GBMs resulted in increased expression of T cell activation markers. In parallel, we derived the single chain variable fragment (scFv) from previously generated RW03 and generated a second-generation CAR. Anti-CD133 scFv with a myc tag was cloned in frame with a human CD8 leader sequence, CD8a transmembrane domain, CD28, and hCD3ζ signaling tail in the lentiviral construct pCCL-ΔNGFR. Following lentiviral packaging, the T cells isolated from PBMCs were transduced with CD133 CAR construct. After successful T cell engineering, the expression of ΔNGFR and myc tag was analyzed using flow cytometry to confirm the efficiency of transduction and surface expression of anti-CD133 respectively. CD133-specific CAR-T cells were cytotoxic to CD133+ GBMs. Co-culturing CD133 CAR-T cells with GBMs triggered T cell activation and proliferation. Treatment of GBM tumor-bearing mice with CD133-specific CAR-T cells yielded extended survival in mice and significant reductions in brain tumor burden. The results of this study will establish a translational research program that will form the basis of early phase clinical trials of a promising CD133-based therapeutic strategy for patients with GBM. Citation Format: Parvez Vora, Chirayu Chokshi, Maleeha Qazi, Mohini Singh, Chitra Venugopal, Sujeivan Mahendram, Jarrett Adams, David Bakhshinyan, Max London, Jess Singh, Minomi Subapanditha1,, Nicole McFarlane, James Pan, Jonathan Bramson, Sachdev Sidhu, Jason Moffat, Sheila Singh. The efficacy of CD133 BiTEs and CAR-T cells in preclinical model of glioblastoma [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 3758. doi:10.1158/1538-7445.AM2017-3758

Abstract B092: Therapeutic targeting of tumorigenic EphA2+/EphA3+ brain tumor initiating cells with bi-specific antibody in glioblastoma

Glioblastoma (GBM), the most aggressive primary human brain tumor, carrier a dismal prognosis and is increasingly characterized by cellular and genetic intra-tumoral heterogeneity (ITH). Many of the 14 members of the erythropoietin-producing hepatocellular carcinoma receptor (EphR) family and their ephrin ligands are expressed in GBM cells and constitute potential molecular targets for novel therapeutic agents. We hypothesize that multiple members of the EphR family play a critical role in orchestrating the clonal evolution of GBM progression. Individual Eph receptor targeting strategies have shown only modest pre-clinical success, likely because single agent therapy cannot target the degree of ITH in GBM. Using a highly specific human Eph receptor monoclonal antibody (mAb) panel (EphR profiler), we identified five Eph receptors with dysregulated expression in recurrent GBM as compared to primary GBM. With our unique chemoradiotherapy-adapted, patient-derived xenograft model of GBM, we identified EphA2 and EphA3 expression to be upregulated after therapy. Here we show that EphA2 and EphA3 co-expression marks a highly tumorigenic cell population in recurrent GBM with higher in vitro and in vivo self-renewal and proliferation capacity as compared to EphA2+/EphA3-, EphA2-/EphA3+ or EphA2-/EphA3- cells. Lentiviral mediated knockdown of EphA2 and EphA3 blocks this self-renewal and proliferation capacity in recurrent GBM. Through further characterization using mass cytometry (CyTOF) assay, we find that EphA2 and EphA3 is co-expressed with multiple brain tumor initiating cell (BTIC) markers (CD133, CD15, Bmi1, Sox2, Integrin α6 and FoxG1). Considering the important role of EphA2+/EphA3+ cells in GBM tumorigenesis and recurrence, we generated a bi-specific antibody (bsIgG) that co-targets EphA2 and EphA3. In vitro treatment of GBM with bsEphA2/A3 IgG led to pharmacological blockade of phosphorylated EphA2. We then assessed the in vivo efficacy of the bsEphA2/A3 IgG to block GBM tumor growth in our PDX model, and found that treatment with intracranial bsIgG resulted in non-invasive and significantly smaller lesions. The striking reduction in tumor burden in recurrent GBM after co-targeting of EphA2 and EphA3 validates the premise of our therapeutic strategy of targeting multiple EphRs. Discovering the clonal composition of recurrent GBM will enable us to target cellular subpopulations, and this ITH, with selective compounds that inhibit BTIC and Eph receptor activity with minimal off-target effects. Comprehensive Eph receptor profiling of individual patient-derived GBM will allow us to develop a therapeutic strategy for each patient9s tumor, employing polytherapy with mAbs against Eph receptors expressed at recurrence. Citation Format: Parvez Vora, Maleeha Qazi, Chirayu Chokshi, Chitra Venugopal, Max London, Amy Hu, Nicole McFarlane, Minomi Subapanditha, Mohini Singh, Sujeivan Mahendram, Jarrett Adams, Jason Moffat, Sachdev Sidhu, Sheila Singh. Therapeutic targeting of tumorigenic EphA2+/EphA3+ brain tumor initiating cells with bi-specific antibody in glioblastoma [abstract]. In: Proceedings of the Second CRI-CIMT-EATI-AACR International Cancer Immunotherapy Conference: Translating Science into Survival; 2016 Sept 25-28; New York, NY. Philadelphia (PA): AACR; Cancer Immunol Res 2016;4(11 Suppl):Abstract nr B092.

Abstract B079: The efficacy of CD133 BiTEs and CAR-T cells in preclinical model of recurrent glioblastoma

Glioblastoma (GBM) is a uniformly fatal primary brain tumor, characterized by a diverse cellular phenotype and genetic heterogeneity. Despite the use of aggressive cellular multi-modal treatment including surgical resection, radiotherapy and chemotherapy, the outcome of patients with GBM has failed to improve significantly. Numerous studies have implicated CD133+ brain tumor initiating cells (BTICs) as drivers of chemo- and radio-resistance in GBM. We have recently demonstrated that a CD133-driven gene signature is predictive of poor overall survival and targeting CD133+ treatment-refractory cells may be an effective strategy to block GBM recurrence. Chimeric antigen receptors (CARs) and bispecific T-Cell engaging antibodies (BiTEs) present promising immunotherapeutic approaches that have not yet been validated for recurrent GBM. Using CellectSeq, a novel methodology that combines use of phage-displayed synthetic antibody libraries and DNA sequencing, we developed the CD133-specific monoclonal antibody ‘RW03’. We constructed CD133-specific BiTEs or RW03xCD3 that consist of two arms; one arm recognizes the tumor antigen (CD133) while the second is specific to CD3 antigen. The BiTEs were constructed in four different conformations and dual binding specificity was confirmed using flow cytometry. Using CD133high and CD133low primary GBM lines, we validated the binding of BiTEs to CD133+ cells. Further analysis showed binding of BiTEs to human T cells known to express CD3 within a population of healthy donor peripheral blood mononuclear cells. We observed BiTEs redirecting T cells to kill GBMs, with greater efficiency observed in CD133high GBMs, validating BiTE target specificity. Incubating T-cells with BiTEs and the CD133high GBMs resulted in increased expression of T cell activation markers. In parallel, we derived the single chain variable fragment (scFv) from previously generated RW03 and generated a second-generation CAR. Anti-CD133 scFv with a myc tag was cloned in frame with a human CD8 leader sequence, CD8a transmembrane domain, CD28, and hCD3ζ signaling tail in the lentiviral construct pCCL-ΔNGFR vector in two different orientations: Light chain-linker-Heavy chain (CD133 CAR-LH) and Heavy chain-linker-Light chain (CD133 CAR-HL). Following lentiviral preparation, the T cells isolated from PBMCs were transduced with CD133 CAR-LH and CD133 CAR-VH constructs. After successful T cell engineering, the expression of ΔNGFR and myc tag was analyzed using flow cytometry to confirm the efficiency of transduction and surface expression of anti-CD133 respectively. CD133-specific CAR-T cells were cytotoxic to CD133+ GBMs. Co-culturing CD133 CAR-T cells with GBMs triggered T cell activation and proliferation. Treatment of GBM tumor-bearing mice with CD133-specific CAR-T cells yielded extended survival in mice and significant reductions in brain tumor burden. Furthermore, we uniquely adapted the existing chemoradiotherapy protocol for GBM patients for treatment of immunocompromised mice engrafted with human GBMs. Within this model, we have initiated treatment of recurrent GBM directed against CD133+ BTICs, to allow for a direct prospective comparison of toxicity and efficacy of BiTEs and CAR T cell strategies. Citation Format: Parvez Vora, Chirayu Chokshi, Maleeha Qazi, Chitra Venugopal, Sujeivan Mahendram, Mohini Singh, Jarrett Adams, David Bakhshinyan, Max London, Minomi Subapanditha, Nicole McFarlane, James Pan, Jonathan Bramson, Jason Moffat, Sachdev Sidhu, Sheila Singh. The efficacy of CD133 BiTEs and CAR-T cells in preclinical model of recurrent glioblastoma [abstract]. In: Proceedings of the Second CRI-CIMT-EATI-AACR International Cancer Immunotherapy Conference: Translating Science into Survival; 2016 Sept 25-28; New York, NY. Philadelphia (PA): AACR; Cancer Immunol Res 2016;4(11 Suppl):Abstract nr B079.

Abstract 2300: Human CD133-specific chimeric antigen receptor (CAR) modified T cells target patient-derived glioblastoma brain tumors

Glioblastoma (GBM), an aggressive primary brain tumor in adults, is feared for its near uniformly fatal prognosis and is characterized by a diverse cellular phenotype and genetic heterogeneity. Despite the use of aggressive multi-modal treatment including surgical resection, radiotherapy and chemotherapy, the outcome of patients with GBM has failed to improve significantly. We developed patient-derived brain tumor initiating cell (BTIC) early passage lines that describe the extent of intertumoral heterogeneity, presenting a powerful preclinical model of GBM. Numerous studies have implicated CD133+ BTICs as drivers of chemo- and radio-resistance in GBM. CD133 expression correlates with disease progression, recurrence, and poor overall survival of GBM patients. Here, we describe the preclinical evaluation of chimeric antigen receptor (CAR) T-cell strategy that specifically targets CD133+ GBM cells. From the previously generated CD133-specific humanized monoclonal antibody, we derived the single chain variable fragment (scFv) and cloned it into an antigen-specific second-generation CAR. Anti-CD133 scFv with a myc tag was cloned in frame with a human CD8 leader sequence, CD8a transmembrane domain, CD28, and hCD3ζ signaling tail in the lentiviral construct pCCL-ΔNGFR vector in two different orientations: Light chain-linker-Heavy chain (CD133 CAR-LH) and Heavy chain-linker-Light chain (CD133 CAR-HL). Following lentiviral preparation, the T cells isolated from PBMCs were transduced with CD133 CAR-LH and CD133 CAR-VH constructs. After successful T cell engineering, the expression of ΔNGFR and myc tag was analyzed using flow cytometry to confirm the efficiency of transduction and surface expression of anti-CD133 respectively. While expression of ΔNGFR was observed in all CAR T cells (including controls), we found expression of the myc tag in both variations of CARs, CD133 CAR-HL and CD133 CAR-LH. Furthermore, we used Presto Blue-based killing assays to test the ability of CD133 CARs to selectively bind and kill CD133+ GBM BTICs. Our data shows that CD133-specific CAR T cells not only recognized, but killed the CD133+ GBM cells selectively, validating this adoptive T-cell therapeutic strategy. CAR-expressing T cells were activated in presence of CD133high GBM cells showed increase surface expression of activation markers CD69 and CD25. Both, CD4+ and CD8+ CD133-specific CAR-T cells showed upregulation in surface expression levels of activation markers. This rigorously obtained data offers compelling evidence that CAR-T induced cytotoxicity against treatment-resistant and evasive CD133+ GBM BTICs could provide a very potent, specific and novel therapeutic strategy for GBM patients. Citation Format: Parvez Vora, Chitra Venugopal, Sujeivan Mahendram, Chirayu Chokshi, Maleeha Qazi, Minomi Subapanditha, Mohini Singh, David Bakhshinyan, Ksenia Bezverbnaya, Jarrett Adams, Nicole McFarlane, Sachdev Sidhu, Jason Moffat, Jonathan Bramson, Sheila Singh. Human CD133-specific chimeric antigen receptor (CAR) modified T cells target patient-derived glioblastoma brain tumors. [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 2300.

Abstract 1481: Preclinical validation of a novel CD133/CD3 bispecific T-cell engager (BiTE) antibody to target patient-derived glioblastoma cells

Glioblastoma (GBM), an aggressive primary brain tumor in adults, is feared for its near uniformly fatal prognosis and is characterized by a diverse cellular phenotype and genetic heterogeneity. Despite the use of aggressive multi-modal treatment including surgical resection, radiotherapy and chemotherapy, the outcome of patients with GBM has failed to improve significantly. We developed patient-derived brain tumor initiating cell (BTIC) early passage lines that describe the extent of intertumoral heterogeneity, presenting a powerful preclinical model of GBM. Numerous studies have implicated CD133+ BTICs as drivers of chemo- and radio-resistance in GBM. CD133 expression correlates with disease progression, recurrence, and poor overall survival of GBM patients. Here, we describe the preclinical evaluation of a recombinant RW03xCD3 bispecific T-cell engager (BiTE) antibody that redirects human polyclonal T cells to CD133+ GBM cells, inducing very potent anti-tumor response. Using CellectSeq, a novel methodology that combines use of phage-displayed synthetic antibody libraries and high-throughput DNA sequencing technology, we developed the CD133-specific monoclonal antibody ‘RW03’. We constructed CD133-specific BiTEs or RW03xCD3 that consist of two arms; one arm recognizes the tumor antigen (CD133) while the second is specific to CD3 antigen. The BiTEs were constructed in four different conformations and dual binding specificity was confirmed using flow cytometry. Using CD133high and CD133low primary GBM lines, we validated the binding of BiTEs to CD133+ cells. Further analysis showed binding of BiTEs to human T cells known to express CD3 within a population of healthy donor peripheral blood mononuclear cells. In order to test the ability of BiTEs to functionally elicit CD133-specific cytotoxic responses in vitro, we performed Presto blue-based killing assays. We observed CD133-specific BiTEs redirect T cells to kill CD133-expressing GBM cells in a coculture of T cells and GBM cells. The killing was more efficient in CD133high GBMs compared to CD133low GBMs, validating its specificity to target CD133+ BTICs. Incubating T cells with BiTEs and GBMs resulted in increased surface expression of T-cell activation markers CD69 and CD25 in both, CD4+ and CD8+ T cells populations. Treatment with BiTEs yielded extended survival in mice and significant reductions in brain tumor burden. This rigorously obtained data offers compelling evidence that BiTE-mediated cytotoxicity against treatment-resistant and evasive CD133+ GBM BTICs could provide a very potent, specific and novel therapeutic strategy for GBM patients. Citation Format: Parvez Vora, Chitra Venugopal, Jarrett Adams, James Pan, Chirayu Chokshi, Maleeha Qazi, Minomi Subapanditha, Mohini Singh, David Bakhshinyan, Ksenia Bezverbnaya, Nicole McFarlane, Jonathan Bramson, Sachdev Sidhu, Jason Moffat, Sheila Singh. Preclinical validation of a novel CD133/CD3 bispecific T-cell engager (BiTE) antibody to target patient-derived glioblastoma cells. [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 1481.