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  • 1
    In: Molecular Cell, Elsevier BV, Vol. 34, No. 1 ( 2009-04), p. 104-114
    Type of Medium: Online Resource
    ISSN: 1097-2765
    Language: English
    Publisher: Elsevier BV
    Publication Date: 2009
    detail.hit.zdb_id: 2001948-8
    SSG: 12
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  • 2
    Online Resource
    Online Resource
    Springer Science and Business Media LLC ; 2015
    In:  Genome Medicine Vol. 7, No. 1 ( 2015-12)
    In: Genome Medicine, Springer Science and Business Media LLC, Vol. 7, No. 1 ( 2015-12)
    Type of Medium: Online Resource
    ISSN: 1756-994X
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2015
    detail.hit.zdb_id: 2484394-5
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  • 3
    In: Future Science OA, Future Science Ltd, Vol. 7, No. 2 ( 2021-02)
    Abstract: Lay abstract MET is a receptor for growth signals that keeps cells alive and healthy. However, some tumors have changes in MET that allow for uncontrollable cell growth. Patients with MET-altered tumors may benefit from treatments targeting this gene, but eventually they become resistant to the treatments. Thus, there is a need to identify additional therapies for this patient population. The authors tested immune gene expression in tumors with MET alterations to determine if these patients would benefit from a new class of treatments called immunotherapies and found that patients with and without MET changes had differences in immune gene expression.
    Type of Medium: Online Resource
    ISSN: 2056-5623
    Language: English
    Publisher: Future Science Ltd
    Publication Date: 2021
    detail.hit.zdb_id: 2863457-3
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  • 4
    In: Clinical Cancer Research, American Association for Cancer Research (AACR), Vol. 24, No. 15_Supplement ( 2018-08-01), p. IA12-IA12
    Abstract: High-grade serous ovarian cancer (HGSC) was one of the first cancer types subjected to comprehensive genomic analysis, and over the last 5-7 years gene expression and DNA sequence data have been generated from hundreds of samples. A large majority of this data has been obtained from surgical samples collected following primary debulking surgery or following a few cycles of neoadjuvant chemotherapy. By contrast, comparatively little data exist from patients who have been extensively treated with chemotherapy or newer targeted agents, such as antiangiogenics or PARP inhibitors (PARPi). Of particular interest are samples collected from patients whose cancer was initially responsive to treatment but has become resistant to therapy (acquired resistance) at the time of collection. The presentation will describe data obtained from whole-genome (N=73 samples, 36 patients) and targeted (N=65 samples, 48 patients) sequence analysis of recurrent or end-stage HGSC samples, focusing in particular on two mechanisms of acquired resistance–fusions involving the ABCB1 gene and reversion of germline BRCA1/2 mutations. ABCB1 encodes the multidrug resistance transporter MDR1, also known as P-glycoprotein. Data will be presented on the frequency and mechanisms of ABCB1 deregulation in recurrent HGSC, and approaches to clinical intervention in fusion-positive patients. Reversions in BRCA1/2 appear to render tumors that were defective in homologous recombination (HR) repair, HR proficient and therefore may have important implications for likely treatment response. The presentation will also discuss approaches to evaluating reversion status in patients with mutation in BRCA1/2. Citation Format: Elizabeth L. Christie, Jessica Beach, Dariush Etemadmoghadam, Dale Garsed, Ann-Marie Patch, Sian Fereday, Swetansu Pattnaik, Australian Ovarian Cancer Study, Samuel Brady, Andrea Bild, David D.L. Bowtell. Acquired chemotherapy resistance in high-grade serous ovarian cancer patients. [abstract]. In: Proceedings of the AACR Conference: Addressing Critical Questions in Ovarian Cancer Research and Treatment; Oct 1-4, 2017; Pittsburgh, PA. Philadelphia (PA): AACR; Clin Cancer Res 2018;24(15_Suppl):Abstract nr IA12.
    Type of Medium: Online Resource
    ISSN: 1078-0432 , 1557-3265
    RVK:
    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2018
    detail.hit.zdb_id: 1225457-5
    detail.hit.zdb_id: 2036787-9
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  • 5
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 83, No. 7_Supplement ( 2023-04-04), p. 3129-3129
    Abstract: Breast cancer is a leading cause of global cancer-related mortality. About 75% of breast tumors are estrogen receptor-positive (ER+). Nearly 30-50% of ER+ breast cancers eventually become refractory to multiple lines of therapy and progress to an uncurable metastatic stage despite positive 5-year results on primary endocrine therapy. To uncover the malignant phenotypes underlying the development of therapeutic resistance, we performed single-cell RNA sequencing (scRNA-seq) of 219,532 cells from 80 ER+ breast cancer patients. This included 28 solid tumors and 52 metastatic fluid samples (pleural effusions and ascites). We grouped samples in three groups to study the evolution of biological phenotypes based on the number of lines of therapy administered to a patient: 1. Early (non-metastatic), 2. Advanced (metastatic with less than 3 lines of therapy), and Refractory (metastatic with 3 or more lines of therapy). We used Pareto task inference analysis to model evolutionary task trade-offs across malignant cell populations from the early, advanced, and refractory tumors. Our model revealed 5 unique phenotypic states or “archetypes” that existed across ER+ cancer cells. A multitask learning model based on group lasso revealed the specialized biological tasks associated with each archetype, including 1. Metabolism and self-renewal, 2. EGF/STAT3 signaling, 3. Estrogen signaling, 4. Apoptosis, and 5. MYC activation with rapid proliferation. We found the estrogen signaling archetype was progressively lost in advanced and refractory tumors (P=7.2x10-110), while the MYC archetype was progressively gained in the advanced and refractory tumors (P=2.45x10-9). The EGF/STAT3 archetype was unique to refractory tumors (P= 1.42x10-37). We further investigated the evolution of resistant traits by modeling the pathway phenotypes in malignant cells against the number of lines of therapy received by the patients. Patients refractive to multiple lines of therapy progressively gained mTOR signaling pathway activity concurrent with loss of estrogen-signaling. Multiple pathways that crosstalk with the mTOR pathway were activated in the tumors receiving multiple lines of therapy, including IGFR, and EGF/ERBB signaling. In comparison to early and advanced tumors, refractory tumors also gained JNK/p38 signaling (P=0.006) and activated glycolysis (P=5x10-6). This study reveals how metastatic ER+ breast cancer cells acquire capabilities for resistance to multiple lines of therapy, thus serving as a unique resource for understanding refractory ER+ breast cancer biology. Citation Format: Aritro Nath, Patrick Cosgrove, Jason Griffiths, Jeffrey Chang, Adam Cohen, Andrea Bild. Single-cell RNA sequencing of early-stage to refractory metastatic ER+ breast cancers reveal phenotypic states underlying resistance to multiple lines of therapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3129.
    Type of Medium: Online Resource
    ISSN: 1538-7445
    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2023
    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. 81, No. 13_Supplement ( 2021-07-01), p. 3141-3141
    Abstract: The evolution of resistance in high-grade serous ovarian cancer (HGSOC) cells following chemotherapy is only partially understood. To uncover phenotypic changes associated with chemotherapy resistance, we profiled single-cell RNA-sequencing (scRNA-seq) transcriptomes of HGSOC tumors collected longitudinally during patient treatment. Analysis of scRNA-seq data from two independent patient cohorts revealed that HGSOC is driven by three core archetypal phenotypes, defined as oncogenic tasks that describe the majority of the transcriptome variation. A multi-task learning approach to identify the biological tasks of each archetype identified metabolism and proliferation, cellular defense response, and DNA repair signaling. The metabolism and proliferation archetype evolved during treatment and was enriched in cancer cells from patients that received multiple-lines of treatment and had elevated tumor burden indicated by CA-125 levels. The emergence of archetypes was not consistently associated with specific whole-genome driver mutations. However, archetypes were closely associated with subclonal populations at the single-cell level, indicating that subclones within a tumor often specialize in unique biological tasks. Our study reveals the core archetypes found in progressive HGSOC and shows consistent enrichment of subclones with the metabolism archetype as resistance is acquired to multiple lines of therapy. Citation Format: Aritro Nath, Patrick Cosgrove, Benjamin Copeland, Hoda Mirsafian, Elizabeth Christie, Lance Pflieger, Sumana Majumdar, Mihaela Cristea, Ernest Han, Stephen Lee, Edward Wang, Sian Fereday, Nadia Traficante, Ravi Salgia, Theresa Werner, Adam Cohen, Phillip Moos, Jeffrey Chang, David Bowtell, Andrea Bild. Evolution of core archetypal phenotypes in progressive high grade serous ovarian cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 3141.
    Type of Medium: Online Resource
    ISSN: 0008-5472 , 1538-7445
    RVK:
    RVK:
    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2021
    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. 82, No. 4_Supplement ( 2022-02-15), p. OT2-19-07-OT2-19-07
    Abstract: Background: Cytotoxic chemotherapy is the mainstay of treatment in metastatic triple negative breast cancer (TNBC), a phenotype predictive of poor survival. Similarly, ovarian cancer is the leading cause of death from gynecologic malignancies and shares genomic similarities with TNBC. New treatment paradigms are needed for people with these malignancies. CDK4/6 (CDKi) and histone deacetylase (HDACi) inhibitors are promising treatment approaches in breast cancer though neither has been successfully translated as monotherapy in TNBC. HDACi have single-agent activity against TNBC in vivo, possibly through decreasing epithelial mesenchymal transition, migration, and metastases. CDKi cause cell cycle arrest and tumor regression in TNBC models. HDACi increase inhibitors of cell cycle progression including RB1, CDKN1A, CDKN1C, CDKN2B, and CDKN2D in TNBC in vitro. We hypothesized that HDACi would increase the sensitivity of breast cancer to CDKi. RIB + BEL demonstrated growth inhibition in TNBC cell lines with synergy seen at multiple doses. RIB and BEL are expected to be safe in combination. BEL has no effect on CYP3A4, the main metabolizing enzyme for RIB. Although RIB can inhibit CYP3A4, which partially metabolizes BEL, BEL is primarily metabolized by UGT1A1. Although both drugs can cause myelosuppression, thrombocytopenia occurs more often with BEL and leukopenia with RIB. The primary objective is to assess the maximum tolerated dose of RIB and BEL in combination. Secondary objectives include safety and efficacy. Exploratory objectives include development of a predictive biomarker, exploration of subclonal structure and phenotypic pathway activation through serial biopsies, and efficacy within RB1 mutation status subgroups. We hypothesized that RIB plus BEL will be well-tolerated and demonstrate activity in people with metastatic TNBC or recurrent ovarian cancer. Methods: This open-label, multi-center, phase I study follows a modified 3+3 dose escalation design allowing independent escalation of the dose of each of the agents with a 10 person expansion cohort at the Recommended Phase 2 Dose (RP2D). Dose escalation will be open to patients with TNBC or ovarian cancer and only TNBC will be enrolled at dose expansion. The first cohort uses RIB 200 mg daily and BEL 600 mg/m2 daily on days 1-5 of a 28 day cycle. Tumor is assessed at baseline and every 8 weeks. Biopsies occur at screening and cycle 2 day 15 to establish a predictive biomarker panel that will be validated with future study. Patients ≥ 18 years of age who have measurable and metastatic or unresectable disease are included. Patients previously treated with a CDKi or HDACi are excluded. Additional exclusion criteria include use of valproic acid during the study or within 5 days of the first dose of BEL, prolonged QTc, grade ≥2 unresolved diarrhea, or new or progressive brain metastases. Statistical analysis of safety data will be descriptive. Efficacy will be reported in the study population as well as in RB1 mutation status subgroups. PFS will be estimated using Kaplan-Meier methods. Cox regression will be used to determine if there is a relationship between biomarker predictor and PFS. The estimated duration for accrual is 18 months with patient participation of around 36 months. Enrollment began January 2021 with 2 patients currently enrolled. Clinical Trial registry Number: NCT04315233 Citation Format: Shashank Sama, Kristen Kelley, Christos Vaklavas, Andrea Bild, Kenneth Boucher, John Lamb, Julia Lehman, Philip Moos, Theresa Werner, Adam Cohen. A phase I/Ib trial of the CDK4/6 antagonist ribociclib (RIB) and the HDAC inhibitor belinostat (BEL) in patients with metastatic triple negative breast cancer and recurrent ovarian cancer with response prediction by genomics (CHARGE) [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr OT2-19-07.
    Type of Medium: Online Resource
    ISSN: 0008-5472 , 1538-7445
    RVK:
    RVK:
    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2022
    detail.hit.zdb_id: 2036785-5
    detail.hit.zdb_id: 1432-1
    detail.hit.zdb_id: 410466-3
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  • 8
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 83, No. 7_Supplement ( 2023-04-04), p. 5693-5693
    Abstract: While endocrine therapy (ET) has considerably improved Stage II/III ER+ breast cancer survival rates, resistance emerges in 30-50% of patients. Recent advances have uncovered numerous cancer intrinsic and tumor-microenvironment mediated mechanisms contributing to ET resistance. However, the predominant mechanisms that prevent cure and ultimately lead to development of terminal metastatic cancer remain unknown. To reveal the leading causes of ET resistance in early-stage ER+ breast cancers, we used single-cell RNA sequencing to profile serial tumor biopsies from a larger cohort of patients. Patients received either endocrine therapy (letrozole) alone or in combination with a CDK4/6 cell cycle inhibitor (ribociclib). We examined the evolution of tumor composition, cellular communication, and the phenotypic diversity of tumor-associated cancer and non-cancer cells throughout treatment. Our analyses reveal that ET-resistant tumors are fibroblast- and endothelial-enriched and consistently exhibit broad upregulation of growth factor signaling to cancer cells, with consistent activation of ERBB communication across patient tumors. Fibroblasts emerged as the primary source of these additional growth factor signals. Upregulation of fibroblast growth factor signaling (via NRG1/2, EGF and IGF) was commensurate with differentiation to a mesenchymal cancer-associated-fibroblast (myCAF) phenotype, which was itself stimulated by cancer cells through EGF and TGF signaling. In response to growth factor enrichment, cancer cells of ET-resistant tumors showed activation of MAPK signal transduction and downstream transcription factors promoting proliferation including FOS, JUN and TRIB1. These results indicate that ET resistance emerges in patient tumors when cancer cells subvert fibroblast function to promote a growth factor enriched tumor microenvironment permitting estrogen independent cancer proliferation. Citation Format: Jason I. Griffiths, Patrick A. Cosgrove, Eric Medina Castaneda, Aritro Nath, Jinfeng Chen, Frederick R. Adler, Jeffrey T. Chang, Qamar J. Khan, Andrea H. Bild. Cancer cells subvert fibroblast function to promote a growth factor enriched tumor microenvironment in endocrine therapy resistant ER+ breast cancer. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5693.
    Type of Medium: Online Resource
    ISSN: 1538-7445
    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2023
    detail.hit.zdb_id: 2036785-5
    detail.hit.zdb_id: 1432-1
    detail.hit.zdb_id: 410466-3
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  • 9
    In: Molecular Systems Biology, EMBO, Vol. 7, No. 1 ( 2011-01)
    Type of Medium: Online Resource
    ISSN: 1744-4292 , 1744-4292
    Language: English
    Publisher: EMBO
    Publication Date: 2011
    detail.hit.zdb_id: 2193510-5
    SSG: 12
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  • 10
    Online Resource
    Online Resource
    EMBO ; 2022
    In:  Molecular Systems Biology Vol. 18, No. 6 ( 2022-06)
    In: Molecular Systems Biology, EMBO, Vol. 18, No. 6 ( 2022-06)
    Type of Medium: Online Resource
    ISSN: 1744-4292 , 1744-4292
    Language: English
    Publisher: EMBO
    Publication Date: 2022
    detail.hit.zdb_id: 2193510-5
    SSG: 12
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