Comprehensive Drug Testing of Patient-derived Conditionally Reprogrammed Cells from Castration-resistant Prostate Cancer

Background: Technology development to enable the culture of human prostate cancer (PCa) progenitor cells is required for the identification of new, potentially curative therapies for PCa. Objective: We established and characterized patient-derived conditionally reprogrammed cells (CRCs) to assess their biological properties and to apply these to test the efficacies of drugs. Design, setting, and participants: CRCs were established from seven patient samples with disease ranging from primary PCa to advanced castration-resistant PCa (CRPC). The CRCs were characterized by genomic, transcriptomic, protein expression, and drug profiling. Outcome measurements and statistical analysis: The phenotypic quantification of the CRCs was done based on immunostaining followed by image analysis with Advanced Cell Classifier using Random Forest supervised machine learning. Copy number aberrations (CNAs) were called from whole-exome sequencing and transcriptomics using in-house pipelines. Dose-response measurements were used to generate multiparameter drug sensitivity scores using R-statistical language. Results and limitations: We generated six benign CRC cultures which all had an androgen receptor-negative, basal/transit-amplifying phenotype with few CNAs. In three-dimensional cell culture, these cells could re-express the androgen receptor. The CRCs from a CRPC patient (HUB.5) displayed multiple CNAs, many of which were shared with the parental tumor. We carried out high-throughput drug-response studies with 306 emerging and clinical cancer drugs. Using the benign CRCs as controls, we identified the Bcl-2 family inhibitor navitoclax as the most potent cancer-specific drug for the CRCs from a CRPC patient. Other drug efficacies included taxanes, mepacrine, and retinoids. Conclusions: Comprehensive cancer pharmacopeia-wide drug testing of CRCs from a CRPC patient highlighted both known and novel drug sensitivities in PCa, including navitoclax, which is currently being tested in clinical trials of CRPC. Patient summary: We describe an approach to generate patient-derived cancer cells from advanced prostate cancer and apply such cells to discover drugs that could be applied in clinical trials for castration-resistant prostate cancer. Proof-of-concept study with the aim of generating patient-derived ex vivo models of prostate cancer combined with high-throughput drug testing to identify potential efficacies among 306 existing and emerging cancer drugs highlighting the effect of navitoclax in an advanced disease model. © 2016 European Association of Urology

Systematic drug screening reveals specific vulnerabilities and co-resistance patterns in endocrine-resistant breast cancer

Background: The estrogen receptor (ER) inhibitor tamoxifen reduces breast cancer mortality by 31 % and has served as the standard treatment for ER-positive breast cancers for decades. However, 50 % of advanced ER-positive cancers display de novo resistance to tamoxifen, and acquired resistance evolves in 40 % of patients who initially respond. Mechanisms underlying resistance development remain poorly understood and new therapeutic opportunities are urgently needed. Here, we report the generation and characterization of seven tamoxifen-resistant breast cancer cell lines from four parental strains.Methods: Using high throughput drug sensitivity and resistance testing (DSRT) with 279 approved and investigational oncology drugs, exome-sequencing and network analysis, we for the first time, systematically determine the drug response profiles specific to tamoxifen resistance.Results: We discovered emerging vulnerabilities towards specific drugs, such as ERK1/2-, proteasome-and BCL-family inhibitors as the cells became tamoxifen-resistant. Co-resistance to other drugs such as the survivin inhibitor YM155 and the chemotherapeutic agent paclitaxel also occurred.Conclusion: This study indicates that multiple molecular mechanisms dictate endocrine resistance, resulting in unexpected vulnerabilities to initially ineffective drugs, as well as in emerging co-resistances. Thus, combatting drug-resistant tumors will require patient-tailored strategies in order to identify new drug vulnerabilities, and to understand the associated co-resistance patterns

Enhanced sensitivity to glucocorticoids in cytarabine-resistant AML

We sought to identify drugs that could counteract cytarabine resistance in acute myeloid leukemia (AML) by generating eight resistant variants from MOLM-13 and SHI-1 AML cell lines by long-term drug treatment. These cells were compared with 66 ex vivo chemorefractory samples from cytarabine-treated AML patients. The models and patient cells were subjected to genomic and transcriptomic profiling and high-throughput testing with 250 emerging and clinical oncology compounds. Genomic profiling uncovered deletion of the deoxycytidine kinase (DCK) gene in both MOLM-13- and SHI-1-derived cytarabine-resistant variants and in an AML patient sample. Cytarabine-resistant SHI-1 variants and a subset of chemorefractory AML patient samples showed increased sensitivity to glucocorticoids that are often used in treatment of lymphoid leukemia but not AML. Paired samples taken from AML patients before treatment and at relapse also showed acquisition of glucocorticoid sensitivity. Enhanced glucocorticoid sensitivity was only seen in AML patient samples that were negative for the FLT3 mutation (P = 0.0006). Our study shows that development of cytarabine resistance is associated with increased sensitivity to glucocorticoids in a subset of AML, suggesting a new therapeutic strategy that should be explored in a clinical trial of chemorefractory AML patients carrying wild-type FLT3.Peer reviewe

Autoimmunity, hypogammaglobulinemia, lymphoproliferation and mycobacterial disease in patients with dominant activating mutations in STAT3

The signal transducer and activator of transcription (STAT) family of transcription factors orchestrate hematopoietic cell differentiation. Recently, mutations in STAT1, STAT5B, and STAT3 have been linked to development of IPEX-like syndrome. Here, we immunologically characterized three patients with de novo activating mutations in the DNA binding or dimerization domains of STAT3 (p.K392R, p.M394T and p.K658N, respectively). The patients displayed multi-organ autoimmunity, lymphoproliferation, and delayed-onset mycobacterial disease. Immunologically, we noted hypogammaglobulinemia with terminal B cell maturation arrest, dendritic cell deficiency, peripheral eosinopenia, increased double-negative (CD4-CD8-) T cells, and decreased NK, Th17, and regulatory T cell numbers. Notably, the patient harboring the K392R mutation developed T cell LGL leukemia at age 14. Our results broaden the spectrum of phenotypes caused by activating STAT3 mutations, highlight the role of STAT3 in the development and differentiation of multiple immune cell lineages, and strengthen the link between the STAT family of transcription factors and autoimmunity.The signal transducer and activator of transcription (STAT) family of transcription factors orchestrate hematopoietic cell differentiation. Recently, mutations in STAT1, STAT5B, and STAT3 have been linked to development of IPEX-like syndrome. Here, we immunologically characterized three patients with de novo activating mutations in the DNA binding or dimerization domains of STAT3 (p.K392R, p.M394T and p.K658N, respectively). The patients displayed multi-organ autoimmunity, lymphoproliferation, and delayed-onset mycobacterial disease. Immunologically, we noted hypogammaglobulinemia with terminal B cell maturation arrest, dendritic cell deficiency, peripheral eosinopenia, increased double-negative (CD4-CD8-) T cells, and decreased NK, Th17, and regulatory T cell numbers. Notably, the patient harboring the K392R mutation developed T cell LGL leukemia at age 14. Our results broaden the spectrum of phenotypes caused by activating STAT3 mutations, highlight the role of STAT3 in the development and differentiation of multiple immune cell lineages, and strengthen the link between the STAT family of transcription factors and autoimmunity.The signal transducer and activator of transcription (STAT) family of transcription factors orchestrate hematopoietic cell differentiation. Recently, mutations in STAT1, STAT5B, and STAT3 have been linked to development of IPEX-like syndrome. Here, we immunologically characterized three patients with de novo activating mutations in the DNA binding or dimerization domains of STAT3 (p.K392R, p.M394T and p.K658N, respectively). The patients displayed multi-organ autoimmunity, lymphoproliferation, and delayed-onset mycobacterial disease. Immunologically, we noted hypogammaglobulinemia with terminal B cell maturation arrest, dendritic cell deficiency, peripheral eosinopenia, increased double-negative (CD4-CD8-) T cells, and decreased NK, Th17, and regulatory T cell numbers. Notably, the patient harboring the K392R mutation developed T cell LGL leukemia at age 14. Our results broaden the spectrum of phenotypes caused by activating STAT3 mutations, highlight the role of STAT3 in the development and differentiation of multiple immune cell lineages, and strengthen the link between the STAT family of transcription factors and autoimmunity.The signal transducer and activator of transcription (STAT) family of transcription factors orchestrate hematopoietic cell differentiation. Recently, mutations in STAT1, STAT5B, and STAT3 have been linked to development of IPEX-like syndrome. Here, we immunologically characterized three patients with de novo activating mutations in the DNA binding or dimerization domains of STAT3 (p.K392R, p.M394T and p.K658N, respectively). The patients displayed multi-organ autoimmunity, lymphoproliferation, and delayed-onset mycobacterial disease. Immunologically, we noted hypogammaglobulinemia with terminal B cell maturation arrest, dendritic cell deficiency, peripheral eosinopenia, increased double-negative (CD4-CD8-) T cells, and decreased NK, Th17, and regulatory T cell numbers. Notably, the patient harboring the K392R mutation developed T cell LGL leukemia at age 14. Our results broaden the spectrum of phenotypes caused by activating STAT3 mutations, highlight the role of STAT3 in the development and differentiation of multiple immune cell lineages, and strengthen the link between the STAT family of transcription factors and autoimmunity.The signal transducer and activator of transcription (STAT) family of transcription factors orchestrate hematopoietic cell differentiation. Recently, mutations in STAT1, STAT5B, and STAT3 have been linked to development of IPEX-like syndrome. Here, we immunologically characterized three patients with de novo activating mutations in the DNA binding or dimerization domains of STAT3 (p.K392R, p.M394T and p.K658N, respectively). The patients displayed multi-organ autoimmunity, lymphoproliferation, and delayed-onset mycobacterial disease. Immunologically, we noted hypogammaglobulinemia with terminal B cell maturation arrest, dendritic cell deficiency, peripheral eosinopenia, increased double-negative (CD4-CD8-) T cells, and decreased NK, Th17, and regulatory T cell numbers. Notably, the patient harboring the K392R mutation developed T cell LGL leukemia at age 14. Our results broaden the spectrum of phenotypes caused by activating STAT3 mutations, highlight the role of STAT3 in the development and differentiation of multiple immune cell lineages, and strengthen the link between the STAT family of transcription factors and autoimmunity.The signal transducer and activator of transcription (STAT) family of transcription factors orchestrate hematopoietic cell differentiation. Recently, mutations in STAT1, STAT5B, and STAT3 have been linked to development of IPEX-like syndrome. Here, we immunologically characterized three patients with de novo activating mutations in the DNA binding or dimerization domains of STAT3 (p.K392R, p.M394T and p.K658N, respectively). The patients displayed multi-organ autoimmunity, lymphoproliferation, and delayed-onset mycobacterial disease. Immunologically, we noted hypogammaglobulinemia with terminal B cell maturation arrest, dendritic cell deficiency, peripheral eosinopenia, increased double-negative (CD4-CD8-) T cells, and decreased NK, Th17, and regulatory T cell numbers. Notably, the patient harboring the K392R mutation developed T cell LGL leukemia at age 14. Our results broaden the spectrum of phenotypes caused by activating STAT3 mutations, highlight the role of STAT3 in the development and differentiation of multiple immune cell lineages, and strengthen the link between the STAT family of transcription factors and autoimmunity.The signal transducer and activator of transcription (STAT) family of transcription factors orchestrate hematopoietic cell differentiation. Recently, mutations in STAT1, STAT5B, and STAT3 have been linked to development of IPEX-like syndrome. Here, we immunologically characterized three patients with de novo activating mutations in the DNA binding or dimerization domains of STAT3 (p.K392R, p.M394T and p.K658N, respectively). The patients displayed multi-organ autoimmunity, lymphoproliferation, and delayed-onset mycobacterial disease. Immunologically, we noted hypogammaglobulinemia with terminal B cell maturation arrest, dendritic cell deficiency, peripheral eosinopenia, increased double-negative (CD4-CD8-) T cells, and decreased NK, Th17, and regulatory T cell numbers. Notably, the patient harboring the K392R mutation developed T cell LGL leukemia at age 14. Our results broaden the spectrum of phenotypes caused by activating STAT3 mutations, highlight the role of STAT3 in the development and differentiation of multiple immune cell lineages, and strengthen the link between the STAT family of transcription factors and autoimmunity.The signal transducer and activator of transcription (STAT) family of transcription factors orchestrate hematopoietic cell differentiation. Recently, mutations in STAT1, STAT5B, and STAT3 have been linked to development of IPEX-like syndrome. Here, we immunologically characterized three patients with de novo activating mutations in the DNA binding or dimerization domains of STAT3 (p.K392R, p.M394T and p.K658N, respectively). The patients displayed multi-organ autoimmunity, lymphoproliferation, and delayed-onset mycobacterial disease. Immunologically, we noted hypogammaglobulinemia with terminal B cell maturation arrest, dendritic cell deficiency, peripheral eosinopenia, increased double-negative (CD4-CD8-) T cells, and decreased NK, Th17, and regulatory T cell numbers. Notably, the patient harboring the K392R mutation developed T cell LGL leukemia at age 14. Our results broaden the spectrum of phenotypes caused by activating STAT3 mutations, highlight the role of STAT3 in the development and differentiation of multiple immune cell lineages, and strengthen the link between the STAT family of transcription factors and autoimmunity.The signal transducer and activator of transcription (STAT) family of transcription factors orchestrate hematopoietic cell differentiation. Recently, mutations in STAT1, STAT5B, and STAT3 have been linked to development of IPEX-like syndrome. Here, we immunologically characterized three patients with de novo activating mutations in the DNA binding or dimerization domains of STAT3 (p.K392R, p.M394T and p.K658N, respectively). The patients displayed multi-organ autoimmunity, lymphoproliferation, and delayed-onset mycobacterial disease. Immunologically, we noted hypogammaglobulinemia with terminal B cell maturation arrest, dendritic cell deficiency, peripheral eosinopenia, increased double-negative (CD4-CD8-) T cells, and decreased NK, Th17, and regulatory T cell numbers. Notably, the patient harboring the K392R mutation developed T cell LGL leukemia at age 14. Our results broaden the spectrum of phenotypes caused by activating STAT3 mutations, highlight the role of STAT3 in the development and differentiation of multiple immune cell lineages, and strengthen the link between the STAT family of transcription factors and autoimmunity.The signal transducer and activator of transcription (STAT) family of transcription factors orchestrate hematopoietic cell differentiation. Recently, mutations in STAT1, STAT5B, and STAT3 have been linked to development of IPEX-like syndrome. Here, we immunologically characterized three patients with de novo activating mutations in the DNA binding or dimerization domains of STAT3 (p.K392R, p.M394T and p.K658N, respectively). The patients displayed multi-organ autoimmunity, lymphoproliferation, and delayed-onset mycobacterial disease. Immunologically, we noted hypogammaglobulinemia with terminal B cell maturation arrest, dendritic cell deficiency, peripheral eosinopenia, increased double-negative (CD4-CD8-) T cells, and decreased NK, Th17, and regulatory T cell numbers. Notably, the patient harboring the K392R mutation developed T cell LGL leukemia at age 14. Our results broaden the spectrum of phenotypes caused by activating STAT3 mutations, highlight the role of STAT3 in the development and differentiation of multiple immune cell lineages, and strengthen the link between the STAT family of transcription factors and autoimmunity.The signal transducer and activator of transcription (STAT) family of transcription factors orchestrate hematopoietic cell differentiation. Recently, mutations in STAT1, STAT5B, and STAT3 have been linked to development of IPEX-like syndrome. Here, we immunologically characterized three patients with de novo activating mutations in the DNA binding or dimerization domains of STAT3 (p.K392R, p.M394T and p.K658N, respectively). The patients displayed multi-organ autoimmunity, lymphoproliferation, and delayed-onset mycobacterial disease. Immunologically, we noted hypogammaglobulinemia with terminal B cell maturation arrest, dendritic cell deficiency, peripheral eosinopenia, increased double-negative (CD4-CD8-) T cells, and decreased NK, Th17, and regulatory T cell numbers. Notably, the patient harboring the K392R mutation developed T cell LGL leukemia at age 14. Our results broaden the spectrum of phenotypes caused by activating STAT3 mutations, highlight the role of STAT3 in the development and differentiation of multiple immune cell lineages, and strengthen the link between the STAT family of transcription factors and autoimmunity.The signal transducer and activator of transcription (STAT) family of transcription factors orchestrate hematopoietic cell differentiation. Recently, mutations in STAT1, STAT5B, and STAT3 have been linked to development of IPEX-like syndrome. Here, we immunologically characterized three patients with de novo activating mutations in the DNA binding or dimerization domains of STAT3 (p.K392R, p.M394T and p.K658N, respectively). The patients displayed multi-organ autoimmunity, lymphoproliferation, and delayed-onset mycobacterial disease. Immunologically, we noted hypogammaglobulinemia with terminal B cell maturation arrest, dendritic cell deficiency, peripheral eosinopenia, increased double-negative (CD4-CD8-) T cells, and decreased NK, Th17, and regulatory T cell numbers. Notably, the patient harboring the K392R mutation developed T cell LGL leukemia at age 14. Our results broaden the spectrum of phenotypes caused by activating STAT3 mutations, highlight the role of STAT3 in the development and differentiation of multiple immune cell lineages, and strengthen the link between the STAT family of transcription factors and autoimmunity.The signal transducer and activator of transcription (STAT) family of transcription factors orchestrate hematopoietic cell differentiation. Recently, mutations in STAT1, STAT5B, and STAT3 have been linked to development of IPEX-like syndrome. Here, we immunologically characterized three patients with de novo activating mutations in the DNA binding or dimerization domains of STAT3 (p.K392R, p.M394T and p.K658N, respectively). The patients displayed multi-organ autoimmunity, lymphoproliferation, and delayed-onset mycobacterial disease. Immunologically, we noted hypogammaglobulinemia with terminal B cell maturation arrest, dendritic cell deficiency, peripheral eosinopenia, increased double-negative (CD4-CD8-) T cells, and decreased NK, Th17, and regulatory T cell numbers. Notably, the patient harboring the K392R mutation developed T cell LGL leukemia at age 14. Our results broaden the spectrum of phenotypes caused by activating STAT3 mutations, highlight the role of STAT3 in the development and differentiation of multiple immune cell lineages, and strengthen the link between the STAT family of transcription factors and autoimmunity.The signal transducer and activator of transcription (STAT) family of transcription factors orchestrate hematopoietic cell differentiation. Recently, mutations in STAT1, STAT5B, and STAT3 have been linked to development of IPEX-like syndrome. Here, we immunologically characterized three patients with de novo activating mutations in the DNA binding or dimerization domains of STAT3 (p.K392R, p.M394T and p.K658N, respectively). The patients displayed multi-organ autoimmunity, lymphoproliferation, and delayed-onset mycobacterial disease. Immunologically, we noted hypogammaglobulinemia with terminal B cell maturation arrest, dendritic cell deficiency, peripheral eosinopenia, increased double-negative (CD4-CD8-) T cells, and decreased NK, Th17, and regulatory T cell numbers. Notably, the patient harboring the K392R mutation developed T cell LGL leukemia at age 14. Our results broaden the spectrum of phenotypes caused by activating STAT3 mutations, highlight the role of STAT3 in the development and differentiation of multiple immune cell lineages, and strengthen the link between the STAT family of transcription factors and autoimmunity.The signal transducer and activator of transcription (STAT) family of transcription factors orchestrate hematopoietic cell differentiation. Recently, mutations in STAT1, STAT5B, and STAT3 have been linked to development of IPEX-like syndrome. Here, we immunologically characterized three patients with de novo activating mutations in the DNA binding or dimerization domains of STAT3 (p.K392R, p.M394T and p.K658N, respectively). The patients displayed multi-organ autoimmunity, lymphoproliferation, and delayed-onset mycobacterial disease. Immunologically, we noted hypogammaglobulinemia with terminal B cell maturation arrest, dendritic cell deficiency, peripheral eosinopenia, increased double-negative (CD4-CD8-) T cells, and decreased NK, Th17, and regulatory T cell numbers. Notably, the patient harboring the K392R mutation developed T cell LGL leukemia at age 14. Our results broaden the spectrum of phenotypes caused by activating STAT3 mutations, highlight the role of STAT3 in the development and differentiation of multiple immune cell lineages, and strengthen the link between the STAT family of transcription factors and autoimmunity.The signal transducer and activator of transcription (STAT) family of transcription factors orchestrate hematopoietic cell differentiation. Recently, mutations in STAT1, STAT5B, and STAT3 have been linked to development of IPEX-like syndrome. Here, we immunologically characterized three patients with de novo activating mutations in the DNA binding or dimerization domains of STAT3 (p.K392R, p.M394T and p.K658N, respectively). The patients displayed multi-organ autoimmunity, lymphoproliferation, and delayed-onset mycobacterial disease. Immunologically, we noted hypogammaglobulinemia with terminal B cell maturation arrest, dendritic cell deficiency, peripheral eosinopenia, increased double-negative (CD4-CD8-) T cells, and decreased NK, Th17, and regulatory T cell numbers. Notably, the patient harboring the K392R mutation developed T cell LGL leukemia at age 14. Our results broaden the spectrum of phenotypes caused by activating STAT3 mutations, highlight the role of STAT3 in the development and differentiation of multiple immune cell lineages, and strengthen the link between the STAT family of transcription factors and autoimmunity.</p

Aggressive natural killer-cell leukemia mutational landscape and drug profiling highlight JAK-STAT signaling as therapeutic target

Aggressive natural killer-cell (NK-cell) leukemia (ANKL) is an extremely aggressive malignancy with dismal prognosis and lack of targeted therapies. Here, we elucidate the molecular pathogenesis of ANKL using a combination of genomic and drug sensitivity profiling. We study 14 ANKL patients using whole-exome sequencing (WES) and identify mutations in STAT3 (21%) and RAS-MAPK pathway genes (21%) as well as in DDX3X (29%) and epigenetic modifiers (50%). Additional alterations include JAK-STAT copy gains and tyrosine phosphatase mutations, which we show recurrent also in extranodal NK/T-cell lymphoma, nasal type (NKTCL) through integration of public genomic data. Drug sensitivity profiling further demonstrates the role of the JAK-STAT pathway in the pathogenesis of NK-cell malignancies, identifying NK cells to be highly sensitive to JAK and BCL2 inhibition compared to other hematopoietic cell lineages. Our results provide insight into ANKL genetics and a framework for application of targeted therapies in NK-cell malignancies

Precision systems medicine in urological Tumors – Molecular profiling and functional testing

Background: Most precision cancer medicine efforts are based on the identification of oncogenic driver mutations by genome sequencing. We believe and have emerging evidence that this will miss therapeutic opportunities and additional technologies, such as cell-based functional testing should be included. Pioneering studies in leukemia indicate the value of ex-vivo drug testing to identify novel, clinically actionable therapeutic opportunities. Methods: Using conditional re-programming technology, we established patient-derived cells (PDCs) from castration-resistant prostate cancer (CRPC)3 and renal cell cancer (RCC) in order to pilot precision systems medicine in solid tumours. The PDCs were compared with primary tumour tissue by genomic profiling and then subjected to drug sensitivity profiling with >306 approved and investigational oncology drugs. Results: Here, we generated both benign and malignant PDCs from prostate tissue, including six benign PDCs that were androgen receptor (AR)-negative, basal/transit-amplifying phenotype, but could re-express AR in 3D-culture. The PDCs from a CRPC patient displayed multiple CNAs, some of which were shared with the parental tumor. The cancer-selective drug profile for these PDCs showed sensitivity to taxanes, navitoclax, bexarotene, tretinoin, oxaliplatin and mepacrine3. RCC displays extensive intra-tumour heterogeneity and clonal evolution. There is, however, very little information on how much this impacts drug sensitivities. Therefore, we generated several PDCs from each RCC patient across multiple tumour regions. We verified their clonal relationship with the uncultured tumour tissue by NGS and performed drug sensitivity profiling. The PDCs retained CNAs and driver mutations in e.g. VHL, PBRM1, PIK3C2A, KMD5C, TSC2 genes present in the original tumour tissue. Drug testing with 461 oncology drugs identified shared vulnerability among the multiple PDCs to pazopanib and temsirolimus that inhibit well-established renal cancer pathways EGFR/PDGFR/ FGFR and mTOR. Importantly, however, the individual PDC from different regions in one patient also showed distinct drug response profiles, confirming that genomic heterogeneity leads to variability in drug responses. Conclusions: Our aim is to generate molecular profiles and drug testing data using representative PDCs from each patient to help clinicians in treatment decision and to facilitate the early selection of the best drug candidates for clinical development. We believe this approach will help to personalize treatment, prioritize drugs for clinical testing, provide for intelligent selection of drug combinations and improve treatment outcomes.Non peer reviewe