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  • 1
    In: Journal of Clinical Oncology, American Society of Clinical Oncology (ASCO), Vol. 34, No. 15_suppl ( 2016-05-20), p. e23160-e23160
    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: 2016
    detail.hit.zdb_id: 2005181-5
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  • 2
    In: Journal of Clinical Oncology, American Society of Clinical Oncology (ASCO), Vol. 33, No. 15_suppl ( 2015-05-20), p. 10550-10550
    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: 2015
    detail.hit.zdb_id: 2005181-5
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  • 3
    Online Resource
    Online Resource
    American Association for Cancer Research (AACR) ; 2019
    In:  Cancer Research Vol. 79, No. 13_Supplement ( 2019-07-01), p. 1291-1291
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 79, No. 13_Supplement ( 2019-07-01), p. 1291-1291
    Abstract: Notch signaling pathway is a mediator of cell differentiation and is critical for normal bone development. Four functional Notch ligands DLL1 and DLL4, and JAG1 and JAG2 showed various levels of affinity for Notch1-4 receptors. Dose dependent Notch signaling activation or blocking is attributed to anchored or soluble form of Notch ligands binding. Interestingly, Notch pathway is shown to play a dual role, either oncogenic or tumor suppressive, depending on signal dose and tissue-context. To understand Notch signaling activities in osteosarcoma (OS), we first studied the cell surface levels of Notch receptor expression in OS cell lines and patient derived xenograft (pdx) models. Cytometry based screening of NOTCH1-4 receptors showed NOTCH2 as a predominant surface expressed protein in most of the samples. Interestingly, the canonical Notch target genes HES1 and DTX1 were higher (~5-fold) in OS cells compared to mesenchymal cells (MSC). Subsequently, we evaluated selected Notch pathway gene expression in 48 patients with recurrent/metastatic OS by RNAseq analysis. High expression of Notch pathway-related genes was seen in a subset of patients. NOTCH2 expression was comparable between primary and metastatic OS specimens, highest as compared to other Notch receptors and was significantly higher than normal tissue. Thus we aimed to elucidate soluble Notch ligands mediated blocking of Notch signaling using immunoglobulin-G bound DLL-1, -3, and -4 and JAG-1, and -2 in in vitro studies using OS cells. Soluble DLL1-Fc treatment increased OS cell death as compared to the other Notch ligands as well as control-Fc cells. Addition of soluble DLL1 resulted in the decreased expression of Notch downstream genes such as HES1, DTX1 and HEY1. Taken together, these findings identify soluble DLL1 as a potent Notch pathway inhibitor in OS in vitro and support further exploration of NOTCH2 as a potential therapeutic target in OS. Citation Format: Sankaranarayanan Kannan, John A. Livingston, Michael Roth, Jonathan Benjamin, Yifei Wang, Zhongting Zhang, Wendong Zhang, Chia-Chin Wu, Hannah Beird, Andrew Futreal, Richard Gorlick. Notch2 inhibition as a therapeutic intervention in osteosarcoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1291.
    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: 2019
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    detail.hit.zdb_id: 1432-1
    detail.hit.zdb_id: 410466-3
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  • 4
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 80, No. 16_Supplement ( 2020-08-15), p. 5704-5704
    Abstract: Brain metastases (BM) occur in 10-30% of patients with cancer. Approximately 200,000 new cases of brain metastases are diagnosed in the United States annually, with median survival after diagnosis ranging from 3 to 27 months. Recently, studies have identified significant genetic differences between BM and their corresponding primary tumors. It has been shown that BM harbor clinically actionable mutations that are distinct from those in the primary tumor samples. Additional genomic profiling of BM will provide deeper understanding of the pathogenesis of BM and suggest new therapeutic approaches. We performed whole-exome sequencing of BM and matched tumors from 41 patients collected from renal cell carcinoma (RCC), breast cancer, lung cancer, and melanoma, which are known to be more likely to develop BM. We profiled total 126 fresh-frozen tumor samples and performed subsequent analyses of BM in comparison to paired primary tumor and extracranial metastases (ECM). We found that lung cancer shared the largest number of mutations between BM and matched tumors (83%), followed by melanoma (74%), RCC (51%), and Breast (26%), indicating that cancer type with high tumor mutational burden share more mutations with BM. Mutational signatures displayed limited differences, suggesting a lack of mutagenic processes specific to BM. However, point-mutation heterogeneity revealed that BM evolve separately into different subclones from their paired tumors regardless of cancer type, and some cancer driver genes were found in BM-specific subclones. These models and findings suggest that these driver genes may drive prometastatic subclones that lead to BM. 32 curated cancer gene mutations were detected and 71% of them were shared between BM and primary tumors or ECM. 29% of mutations were specific to BM, implying that BM often accumulate additional cancer gene mutations that are not present in primary tumors or ECM. Co-mutation analysis revealed a high frequency of TP53 nonsense mutation in BM, mostly in the DNA binding domain, suggesting TP53 nonsense mutation as a possible prerequisite for the development of BM. Copy number alteration analysis showed statistically significant differences between BM and their paired tumor samples in each cancer type (Wilcoxon test, p & lt; 0.0385 for all). Both copy number gains and losses were consistently higher in BM for breast cancer (Wilcoxon test, p =1.307e-5) and lung cancer (Wilcoxon test, p =1.942e-5), implying greater genomic instability during the evolution of BM. Our findings highlight that there are more unique mutations in BM, with significantly higher copy number alterations and tumor mutational burden. These genomic analyses could provide an opportunity for more reliable diagnostic decision-making, and these findings will be further tested with additional transcriptomic and epigenetic profiling for better characterization of BM-specific tumor microenvironments. Citation Format: Olivia W. Lee, Akash Mitra, Won-Chul Lee, Kazutaka Fukumura, Hannah Beird, Miles Andrews, Grant Fischer, John N. Weinstein, Michael A. Davies, Jason Huse, P. Andrew Futreal. Pan-cancer genomic characterization of patient-matched primary, extracranial, and brain metastases [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5704.
    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: 2020
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  • 5
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 80, No. 16_Supplement ( 2020-08-15), p. 1516-1516
    Abstract: Chemotherapy/ targeted therapy are both known to trigger evolution of treatment resistant clones that can lead to relapse. Allogeneic stem cell transplant (alloSCT) for refractory Chronic Lymphocytic Leukemia (CLL) patients is associated with better outcomes. We hypothesized that allogeneic T-cell immunotherapies, including alloSCT and donor lymphocyte infusion (DLI) would impact tumor evolution through the application of selective immunologic pressure with reciprocal changes in the T-cell compartment. Here, we tested a cohort of 24 heavily pre-treated CLL patients treated. Treatments consisted of alloSCT alone, or with follow-up DLI, which are two established mediators of effective Graft versus Leukemia (GVL). Our cohort included 11 patients who relapsed (denoted as non-responder, NR) after alloSCT and 13 patients who had complete response (CR) after alloSCT, with 11/13 patients showing durable CR with a median post-transplant overall survival (OS) of 9.8 years. We mapped the evolutionary trajectories of tumor cells by whole exome sequencing (WES) of sort purified CLL in post-transplant relapsed patients. To investigate changes in immune repertoire and gene expression post-transplant, CD3 positive T-cells from peripheral blood and bone marrows of CLL patients at complete donor chimerism were analyzed both at bulk and at the single cell level. We found evidence of subclonal leukemic evolution in the majority of our CLL patient cohort after nonmyeloablative HLA-matched alloSCT. Different patterns of CLL evolution were observed, and these changes included putative CLL drivers in every case. In all of the 11 patients with longitudinal post-alloSCT samples available, we observed branched CLL evolution in 4 patients, linear evolution in 4 patients, and no evolution in 3 patients. These data suggest that differential sensitivity of leukemic subclones to allogeneic T cell killing may underlie the branched and linear evolution that we observed, and therefore can shape leukemic subclonal architecture after transplant. Of note, we found that clonal CLL was more responsive to alloSCT in comparison to CLL with subclonal disease architecture.To identify T-cells with GVL potential, we first cataloged potential neoantigens by screening mutated regions in CLL with in silico HLA binding prediction models. Neoantigen specific T-cells were then sorted from longitudinal peripheral blood samples using tetramers, followed by identification of GVL specific TCR in both bulk and single cell setting. We were able to identify T-cells that coevolved with specific tumorigenic lesions in a subset of CLL patients. Taken together, our results suggest that donor-derived antigen-specific T-cells mediate clonal selection of CLL with concurrent changes in allogeneic T-cells, and that these changes can be monitored in longitudinal patient samples. Citation Format: Celine Kerros, John P. Miller, Xizeng Mao, Haven R. Garber, Hannah C. Beird, Jianhua Zhang, Jason Roszik, Paul Leonard, Li Zhao, Sahil Seth, Pei Lin, Huandong Sun, William G. Wierda, Issa F. Khouri, Karen Clise-Dwyer, Andrew Futreal, Shoudan Liang, Koppikar Priya, Jeffrey Molldrem. Deep profiling of T-cell repertoire and tumor heterogeneity in chronic lymphocytic leukemia patients following allogeneic T-cell therapy [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 1516.
    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: 2020
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    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. 83, No. 11_Supplement ( 2023-06-02), p. A082-A082
    Abstract: Desmoplastic small round cell tumor (DSRCT) is a rare, usually incurable, aggressive sarcoma subtype that occurs predominantly in adolescent and young adult (AYA) males. At diagnosis, most present with hundreds of intraabdominal nodules composed of malignant cells that harbor a EWSR1-WT1 chromosomal translocation and resultant fusion protein (FP). It was shown that a subset of DSRCT cells (mostly of epithelial histotype) highly express the androgen receptor (AR), a key epigenetic driver of prostate cancer (PC). Given the male predilection and the high expression of AR, we sought to assess the role of AR more comprehensively in DSRCT and ask if this tumor shared AR resistance mechanism to PC. We tested if AR antagonists curb cell proliferation and tumor growth, where both enzalutamide and AR-antisense therapy blocked DHT-induced cell proliferation and reduced xenograft tumor burden. Next, to mechanistically interrogate AR’s oncogenic effects, we performed single-nuclei RNA-seq (snRNA-eq) and chromatin immunoprecipitation sequencing (ChIP-seq) on frozen patient specimens. Those studies revealed a surprising epigenetic similarity between DSRCT to PC. Though overlap exists in the DNA binding MOTIFs of AR in DSRCT and PC, our ChIP-seq resultsrevealed DSRCT-specific AR DNA binding sites adjacent to key oncogenic regulators, including FOXF1 and WT1 (the C-terminal partner of the pathognomonic FP). To our surprise, we identified a subset of DSRCT samples that underwent partial neuroendocrine (NE) epigenetic reprogramming, akin to what occurs in ~1/3 of castrate-resistant PC (CRPC). Since androgen deprivation therapy (ADT) isn’t yet a standard treatment for DSRCT, it remains an enigma why DSRCT would undergo NE reprogramming or how this may affect ADT sensitivity. To address this, nine DSRCT patient samples were profiled using snRNA-seq. Sub-clustering revealed epithelial, mesenchymal, or NE signatures and marked inter-patient and intra-tumoral heterogeneity. Notably, five of nine patients exhibited NE markers (SYP, ENO2, CHGA, FOXA2, ASCL1, and SOX2), while three expressed epithelial markers (MUC1, MUC6, KRT18, KRT23, CDH1). One patient exhibited a hybrid AR indifferent phenotype. While strikingly different from PC morphologically and phenotypically, our data suggest that DSRCT is a second androgen-stimulated malignancy (third if we consider breast cancers that rely on shared nuclear receptor family signaling). Shared dependence upon AR for tumor growth and survival provides an exciting opportunity to prospectively study AR signaling in a different cancer type and younger DSRCT-stricken patient population. Ongoing work will determine if DSRCT undergoes dedifferentiation towards a more stem-like cell as an intermediary step before undergoing neural lineage commitment or transdifferentiation directly from an epithelial cell type towards a neuroendocrine cell fate. We are also exploring if the FP acts as a Pioneer factor to direct AR towards DSRCT-specific androgen response elements that explain this sarcoma subtype’s unique clinical presentation. Citation Format: Danh D. Truong, Salah-Eddine Lamhamedi-Cherradi, Mayinuer Maitituoheti, Hannah C. Beird, Chia-Chin Wu, Sandhya Krishnan, Davis Ingram, P. Andrew Futreal, Mark Titus, Alexander Lazar, Kunal Rai, A. Robert MacLeod, Najat C. Daw, Andrea Hayes, Joseph Ludwig. The epigenetic impact and therapeutic opportunity of AR-directed therapy for desmoplastic small round cell tumor [abstract] . In: Proceedings of the AACR Special Conference: Advances in Prostate Cancer Research; 2023 Mar 15-18; Denver, Colorado. Philadelphia (PA): AACR; Cancer Res 2023;83(11 Suppl):Abstract nr A082.
    Type of Medium: Online Resource
    ISSN: 1538-7445
    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2023
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    detail.hit.zdb_id: 410466-3
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  • 7
    In: Blood, American Society of Hematology, Vol. 132, No. Supplement 1 ( 2018-11-29), p. 3899-3899
    Abstract: Background: Blastic plasmacytoid dendritic cell neoplasm (BPDCN) is a rare hematologic neoplasm involving skin lesions and disseminated disease into bone marrow, peripheral blood, and lymph nodes, characterized by poor clinical outcomes and no standard therapeutic approaches. BPDCN is characterized by the malignant proliferation of precursor plasmacytoid dendritic cells (pDCs). It is now classified by WHO 2016 as a separate entity under myeloid malignancies owing to its unique clinico-pathologic nature, greater understanding of its distinct clinical course, but with some noted clinical, morphologic, and molecular similarities to AML and myelodysplastic syndrome (MDS). One of the most common molecular mutations observed by next-generation sequencing in the vast majority of patients with BPDCN has been the presence of TET2 mutations and variants. Notably, somatic missense and truncating mutations in TET2 have been reported in patients with both BPDCN and AML, yet their differential responses to similar therapeutic regimens in clinical trial testing indicates that there are likely key underlying etiologies that are yet to be determined. Aims: We sought to investigate and identify critical differences between patients with BPDCN and AML at the molecular level, utilizing a series of advanced analyses including transcriptome microarray, serum multiplex immunoassays and cytokine analysis. Methods: In order to discern these differences, we profiled bone marrow, peripheral blood and serum samples from primary patients samples with BPDCN (N = 16) and TET2-mutated AML (AMLTET2m) (N = 9) using 3 different assays. We first ascertained somatic point mutations and copy number alterations of 300 genes in our BPDCN specimens using an in-house hematologic malignancy panel ("T300" panel). Next, we confirmed the prevalence of compound truncating TET2 mutations in patients with BPDCN and few copy number alterations in the genes profiled. We then used the transcriptome microarray (ThermoFisher Scientific ClariomTM D Pico Assay, and serum multiplex immunoassays (Cytokine/Chemokine/Growth Factor 45-Plex Human ProcartaPlex™ Panel 1 (ThermoFisher Scientific, formerly Affymetrix) with the addition of IL-3 Human ProcartaPlex™ Simplex Kit, formerly Affymetrix) to compare BPDCN specimens against those from TET2-mutated AML patients. Results: With the microarray analysis, we found 920 genes to be up-regulated and 791 genes down-regulated in BPDCN specimens as compared to AMLTET2m. We corroborated known differentially expressed marker genes: higher levels of IL3Ra and TCL1A and lower levels of MPO in BPDCN as compared to AMLTET2m specimens. Genes specific to dendritic cells (PTPRS, LTK, LAMP5) were highly expressed in BPDCN than in AMLTET2m specimens. Of interest, two of these genes, PTPRS and LTK, provide possible links to the skin lesions as PTPRS is implicated in the progression of melanoma and LTK is involved in pigmentation of melanocytes. The serum cytokine profile analysis showed significantly elevated levels of eotaxin and RANTES in the BPDCN cohort as compared to the AMLTET2m cohort (Figure 1a,b). Both of these are implicated in allergic and autoimmune reactions by behaving as eosinophil chemo-attractants. Along with the higher levels of PTPRS and dendritic nature of the tumor cells, these findings suggest a possible autoimmune background which exists in the context of disease. Conclusions: In this novel analysis, we observed elevated levels of eotaxin and RANTES in patients with BPDCN as compared to AMLTET2m. These findings may represent an important aspect of pDC functioning even outside of BPDCN, as pDCs may contribute to the pathogenesis of systemic lupus erythematosus (SLE), an autoimmune disorder with hallmark cutaneous lesions. Moreover, autoimmune pathologies have been hypothesized to damage the bone marrow and induce destruction of myeloid precursor cells. This may incorporate some of the dendritic cell nature since in its natural context, as pDCs serve to recognize foreign particles such as viruses and synthetic oligonucleotides through Toll-like Receptors TLR7/9. These findings suggest that further study into these markers are warranted in patients with BPDCN. Figure 1. Differential serum cytokine levels between BPDCN and AMLTET2m (a) Eotaxin (pg/mL), Wilcox rank test P 〈 0.01 (b) RANTES (pg/mL), Wilcox rank test P 〈 0.05. Disclosures Konopleva: Stemline Therapeutics: Research Funding. Pemmaraju:stemline: Consultancy, Honoraria, Research Funding; plexxikon: Research Funding; SagerStrong Foundation: Research Funding; daiichi sankyo: Research Funding; celgene: Consultancy, Honoraria; Affymetrix: Research Funding; samus: Research Funding; cellectis: Research Funding; abbvie: Research Funding; novartis: Research Funding.
    Type of Medium: Online Resource
    ISSN: 0006-4971 , 1528-0020
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    Language: English
    Publisher: American Society of Hematology
    Publication Date: 2018
    detail.hit.zdb_id: 1468538-3
    detail.hit.zdb_id: 80069-7
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  • 8
    In: Journal of Clinical Oncology, American Society of Clinical Oncology (ASCO), Vol. 36, No. 15_suppl ( 2018-05-20), p. 11522-11522
    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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  • 9
    Online Resource
    Online Resource
    Springer Science and Business Media LLC ; 2022
    In:  Nature Reviews Disease Primers Vol. 8, No. 1 ( 2022-12-08)
    In: Nature Reviews Disease Primers, Springer Science and Business Media LLC, Vol. 8, No. 1 ( 2022-12-08)
    Type of Medium: Online Resource
    ISSN: 2056-676X
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2022
    detail.hit.zdb_id: 2819522-X
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  • 10
    Online Resource
    Online Resource
    Springer Science and Business Media LLC ; 2022
    In:  Nature Reviews Disease Primers Vol. 8, No. 1 ( 2022-12-30)
    In: Nature Reviews Disease Primers, Springer Science and Business Media LLC, Vol. 8, No. 1 ( 2022-12-30)
    Type of Medium: Online Resource
    ISSN: 2056-676X
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2022
    detail.hit.zdb_id: 2819522-X
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