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  • 1
    In: Clinical Genitourinary Cancer, Elsevier BV, Vol. 15, No. 4 ( 2017-08), p. e727-e734
    Type of Medium: Online Resource
    ISSN: 1558-7673
    Language: English
    Publisher: Elsevier BV
    Publication Date: 2017
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  • 2
    In: Scientific Reports, Springer Science and Business Media LLC, Vol. 6, No. 1 ( 2016-12-23)
    Abstract: DNA focused panel sequencing has been rapidly adopted to assess therapeutic targets in advanced/refractory cancer. Integrated Genomic Profiling (IGP) utilising DNA/RNA with tumour/normal comparisons in a Clinical Laboratory Improvement Amendments (CLIA) compliant setting enables a single assay to provide: therapeutic target prioritisation, novel target discovery/application and comprehensive germline assessment. A prospective study in 35 advanced/refractory cancer patients was conducted using CLIA-compliant IGP. Feasibility was assessed by estimating time to results (TTR), prioritising/assigning putative therapeutic targets, assessing drug access, ascertaining germline alterations, and assessing patient preferences/perspectives on data use/reporting. Therapeutic targets were identified using biointelligence/pathway analyses and interpreted by a Genomic Tumour Board. Seventy-five percent of cases harboured 1–3 therapeutically targetable mutations/case (median 79 mutations of potential functional significance/case). Median time to CLIA-validated results was 116 days with CLIA-validation of targets achieved in 21/22 patients. IGP directed treatment was instituted in 13 patients utilising on/off label FDA approved drugs (n = 9), clinical trials (n = 3) and single patient IND (n = 1). Preliminary clinical efficacy was noted in five patients (two partial response, three stable disease). Although barriers to broader application exist, including the need for wider availability of therapies, IGP in a CLIA-framework is feasible and valuable in selection/prioritisation of anti-cancer therapeutic targets.
    Type of Medium: Online Resource
    ISSN: 2045-2322
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2016
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  • 3
    In: PLOS ONE, Public Library of Science (PLoS), Vol. 12, No. 8 ( 2017-8-25), p. e0183871-
    Type of Medium: Online Resource
    ISSN: 1932-6203
    Language: English
    Publisher: Public Library of Science (PLoS)
    Publication Date: 2017
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  • 4
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 73, No. 8_Supplement ( 2013-04-15), p. 1911-1911
    Abstract: Pancreatic cancer (PC) is a heterogeneous disease. Several mutations have been reported to develop along the path of PC evolution, and it is important to identify targets for potential therapy. CGH and IHC analysis of pancreatic tumor samples may reveal prognostic and predictive markers. Methods: We evaluated tumor samples of patients (n=35) who were accrued to a phase II molecular profiling study (Ramanathan RK et al.12-LB-8953-AACR 2012). All subjects, with metastatic PC, with progression after 1st line of therapy had a core biopsy for CGH, IHC, and microarray analysis. Samples interrogated by CGH were flow sorted prior to analysis. Treatment recommendations were based on the IHC panel (Target Now®, Caris Life Sciences, Irving, TX). Results: In 30 patients, adequate tumor was available for CGH. We identified 9 long term survivors, living & gt; 18 months from first diagnosis of mPC. Of the 9 patients, 5 had available CGH data. (1) had two distinct aneuploid tumor cell populations. There was evidence suggestive of increased WNT signaling based on amplicon targeting FZD3;. IHC identified TS and SPARC as potential targets. Recommended treatment: Capecitabine and Nab-Paclitaxel (2) had a focal amplicon targeting WNT6 and WNT10A suggestive of increased WNT signaling, and homozygous deletions targeting RB1 and PARD3B. An intragenic break within NOTCH2 was also observed. IHC identified TS and TOPO1 as potential targets. Recommended treatment: FOLFIRI (3) was identified (and confirmed to be) KRAS wild-type, but had a homozygous deletion of RASA1, the gene that codes for p120-RasGAP a known negative regulator of KRAS signaling. Commonly seen deletions of CDKN2A and SMAD4 were not observed. IHC identified TS and ERCC1 as potential targets. Recommended treatment: FOLFOX (4) had an amplification of a PARP gene (PARP8) and of a base excision enzyme (NEIL2), chromosomal copy number changes to genes involved in chromatin regulation (LCMT, EZH2, KLF13) and EMT with dedifferentiation (ZNF703). IHC identified MGMT as a potential target. Recommended treatment: Temazolamide. (5) had amplifications of PIK3CA and of KRAS, and a homozygous deletion of CDKN2A. IHC identified TOPO2 as a potential target. Recommended treatment: Doxorubicin Conclusion: Due to the heterogeneity of the genome, even in a select group with long term survival, each patient may require an individualized treatment plan. Pathway analysis of all patients treated in the study is ongoing. Treatment strategies to focus on the stroma and of methylation of the genome are being explored to circumvent the genetic heterogeneity. (Supported by a SU2C pancreatic dream team grant) Citation Format: Safi Shahda, Michael T. Barrett, Elizabeth Lenkiewicz, Lisa Evers, Richard G. Posner, Meraj Aziz, Glen J. Weiss, Gayle Jameson, Daniel D. Von Hoff, Ramesh K. Ramanathan. Analysis of the pancreatic cancer (PC) genome by immunohistochemistry (IHC) and comparative genome hybridization (CGH) in patients with long term survival with metastatic disease (mPC) treated on a phase II molecular profiling trial. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 1911. doi:10.1158/1538-7445.AM2013-1911
    Type of Medium: Online Resource
    ISSN: 0008-5472 , 1538-7445
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    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2013
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  • 5
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 73, No. 8_Supplement ( 2013-04-15), p. 798-798
    Abstract: A fundamental challenge for the study and translation of pancreatic ductal adenocarcinoma (PDA) genomes in patients in vivo is the presence of varied admixtures of reactive stroma, inflammatory cells, and necrosis within the tumor. Furthermore biopsies frequently contain multiple clonal populations of neoplastic cells that cannot be distinguished on the basis of morphology alone. To overcome the limitations of histopathology based methods we are using DNA content based flow cytometry to identify and purify distinct clonal PDA populations from over 60 surgical samples from a Stand up to Cancer (SU2C) sponsored clinical trial. Sorted tumor populations from each patient have been interrogated with CGH arrays and whole exome sequencing. In addition we have interrogated the genomes of sorted PDA populations from a SU2C phase II trial of liver metastases from 35 patients with advanced previously treated disease, as well as those from a series of rapid autopsy samples. The genes targeted by the somatic aberrations in each tumor genome are overlaid onto a collection of 33 PDA specific maps, containing 763 genes of interest, developed as part of the Metaminer Oncology initiative. An example of the translational potential of these data includes the detection of a homozygous deletion of STAG2 in an aneuploid tumor population present in the primary and in each metastatic site of a rapid autopsy case. Targeted resequencing identified somatic mutations in a small number of additional sorted samples from our patient cohorts. Strikingly genetic and histopathologic analysis of tumors induced by transposon insertion in a KrasG12D genetically engineered mouse model showed that disruption of STAG2 promotes the development of PDA and its progression to metastatic disease. To assess the clinically significance of STAG2 expression in human tumors we screened a TMA containing a collection of 344 specimens obtained from resected patients. In normal tissue nearly all ductal cells stained with a high intensity. There was a statistically significant loss of STAG2 expression in the tumor tissue (Wilcoxon-Rank test). In univariate Kaplan Meier analysis nearly complete STAG2 positive staining ( & gt; 95% of nuclei positive) was associated with a survival benefit of median survival of 6.41 months (p = 0.031). Interestingly, the survival benefit of adjuvant chemotherapy was only identified in the group of patients with a STAG2 staining of less than 95% (median survival benefit 7.65 months; p = 0.028). Multivariate Cox Regression analysis showed that STAG2 is an independent prognostic factor for survival in PDA patients. We propose that our unbiased clonal profiling of PDA genomes provides a unique and highly efficient framework to identify clinically relevant genomic events in PDA Citation Format: Michael T. Barrett, Elizabeth Lenkiewicz, Evers Lisa, Pedro Perez-Mancera, David Tuveson, Daniela Aust, Christian Pilarsky, Meraj Aziz, Richard Posner, Ramesh Ramanathan, Victor Velculescu, Amy Kramer, Jeffrey Drebin, Daniel D. Von Hoff. Clonal analysis and clinical translation of pancreatic adenocarcinoma genomes. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 798. doi:10.1158/1538-7445.AM2013-798
    Type of Medium: Online Resource
    ISSN: 0008-5472 , 1538-7445
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    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2013
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  • 6
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 75, No. 15_Supplement ( 2015-08-01), p. 619-619
    Abstract: Pancreatic adenocarcinoma has the worst overall mortality of any solid tumor, with only 6% of patients surviving after 5 years. To evaluate the clinical implications of genomic alterations in this low cellularity tumor type, we deeply sequenced the genomes of 134 enriched pancreatic adenocarcinomas from patients who underwent potentially curative resections. Given the low neoplastic cellularity of pancreatic cancers, we enriched for neoplastic cells either by macrodissection of primary tumors or by flow-sorting of tumor nuclei, and performed deep sequencing (high coverage) of these enriched samples using next-generation sequencing approaches. We obtained a total of & gt;1Tb of sequence data, resulting in an average coverage within the target regions of & gt;200-fold for each tumor analyzed by whole-exome sequencing and & gt;750-fold for each tumor analyzed by targeted cancer gene sequencing. These approaches allowed us to identify sequence changes, including single base and small insertion or deletion mutations, as well as copy number alterations in & gt;20,000 genes in the whole-exome analyses and in 116 specific genes in the targeted analyses. These analyses revealed that somatic mutation of chromatin remodeling genes were associated with improved progression-free and overall survival. Alterations in genes with potential clinical utility were observed in a majority of cases and included alterations of AKT1, AKT2, BRCA2, ERBB2, KIT, and PIK3CA. Non-invasive liquid biopsy analyses were performed before and after surgery to evaluate the presence of circulating tumor DNA in the plasma of 83 patients. Through these approaches, we were able to diagnose early stage pancreatic tumors in the majority of patients and to detect the presence of circulating tumor DNA prior to clinical relapse. These observations provide genetic markers of clinical outcome in pancreatic cancer and suggest new avenues for personalized therapy. Citation Format: Mark Sausen, Jillian Phallen, Vilmos Adleff, Siân Jones, Rebecca J. Leary, Karli Lytle, Sonya Parpart-Li, Derek Murphy, Michael T. Barrett, David C. Linehan, Anirban Maitra, Ralph Hruban, Daniel D. Von Hoff, Julia S. Johansen, Luis A. Diaz, Jeffrey A. Drebin, Victor E. Velculescu. Identification of clinically actionable genomic alterations in the tumor and circulation of pancreatic cancer patients. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 619. doi:10.1158/1538-7445.AM2015-619
    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: 2015
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  • 7
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 80, No. 20 ( 2020-10-15), p. 4324-4334
    Abstract: Adenosquamous cancer of the pancreas (ASCP) is a subtype of pancreatic cancer that has a worse prognosis and greater metastatic potential than the more common pancreatic ductal adenocarcinoma (PDAC) subtype. To distinguish the genomic landscape of ASCP and identify actionable targets for this lethal cancer, we applied DNA content flow cytometry to a series of 15 tumor samples including five patient-derived xenografts (PDX). We interrogated purified sorted tumor fractions from these samples with whole-genome copy-number variant (CNV), whole-exome sequencing, and Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) analyses. These identified a variety of somatic genomic lesions targeting chromatin regulators in ASCP genomes that were superimposed on well-characterized genomic lesions including mutations in TP53 (87%) and KRAS (73%), amplification of MYC (47%), and homozygous deletion of CDKN2A (40%) that are common in PDACs. Furthermore, a comparison of ATAC-seq profiles of three ASCP and three PDAC genomes using flow-sorted PDX models identified genes with accessible chromatin unique to the ASCP genomes, including the lysine methyltransferase SMYD2 and the pancreatic cancer stem cell regulator RORC in all three ASCPs, and a FGFR1-ERLIN2 fusion associated with focal CNVs in both genes in a single ASCP. Finally, we demonstrate significant activity of a pan FGFR inhibitor against organoids derived from the FGFR1-ERLIN2 fusion–positive ASCP PDX model. Our results suggest that the genomic and epigenomic landscape of ASCP provide new strategies for targeting this aggressive subtype of pancreatic cancer. Significance: These data provide a unique description of the ASCP genomic and epigenomic landscape and identify candidate therapeutic targets for this dismal cancer.
    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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  • 8
    In: Nature Communications, Springer Science and Business Media LLC, Vol. 14, No. 1 ( 2023-09-06)
    Abstract: Pancreatic ductal adenocarcinoma (PDAC) is a lethal malignancy in need of new therapeutic options. Using unbiased analyses of super-enhancers (SEs) as sentinels of core genes involved in cell-specific function, here we uncover a druggable SE-mediated RNA-binding protein (RBP) cascade that supports PDAC growth through enhanced mRNA translation. This cascade is driven by a SE associated with the RBP heterogeneous nuclear ribonucleoprotein F, which stabilizes protein arginine methyltransferase 1 (PRMT1) to, in turn, control the translational mediator ubiquitin-associated protein 2-like. All three of these genes and the regulatory SE are essential for PDAC growth and coordinately regulated by the Myc oncogene. In line with this, modulation of the RBP network by PRMT1 inhibition reveals a unique vulnerability in Myc-high PDAC patient organoids and markedly reduces tumor growth in male mice. Our study highlights a functional link between epigenetic regulation and mRNA translation and identifies components that comprise unexpected therapeutic targets for PDAC.
    Type of Medium: Online Resource
    ISSN: 2041-1723
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2023
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  • 9
    In: JAMA Oncology, American Medical Association (AMA), Vol. 6, No. 1 ( 2020-01-01), p. 125-
    Type of Medium: Online Resource
    ISSN: 2374-2437
    Language: English
    Publisher: American Medical Association (AMA)
    Publication Date: 2020
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  • 10
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 75, No. 15_Supplement ( 2015-08-01), p. LB-003-LB-003
    Abstract: Background: The genomes of metastatic pancreatic cancers contain a myriad of intrachromosomal aberrations indicating a likely high prevalence of DNA repair deficiencies indicating sensitivity to DNA damaging agents such as the platinum’s. Because of this, the drug cisplatin was added to an albumin-bound paclitaxel + gemcitabine regimen, which has already been determined to improve survival over gemcitabine alone in a randomized phase III trial (NEJM 2013; 369:1691-1703). Objectives: To determine the efficacy and safety of albumin-bound paclitaxel and gemcitabine plus cisplatin for patients with advanced pancreatic cancer Methods: Eligibility criteria included Stage IV pancreatic cancer, no prior chemotherapy for systemic disease, KPS ≥ 70; life expectancy ≥ 12 weeks and measurable disease. The doses were albumin-bound paclitaxel 125 mg/m2 undiluted, gemcitabine 1000 mg/m2 in 500 ml of normal saline (NS), each infused over 30 minutes on days 1 and 8 of a 21 day cycle, along with 3 different dose levels of cisplatin (25, 37.5 or 50 mg/m2) in 500 ml of NS infused over 60 minutes, after the nab-paclitaxel infusion. Pre and post cisplatin hydration was given. Results: To date, 10 patients have been entered on study with all patients being evaluable, (baseline and at least one follow up CT scans completed). There have been 2 complete responses (20%), 6 partial responses (PR), (60%), 1 stable disease (10%), and 1 patient with progressive disease (10%), by RECIST 1.1 criteria. An exponential decrease in CA19-9 correlating with the t1/2 of the marker was noted. Response was seen rapidly with PR observed at the first staging evaluation at 9 weeks in 7 of 10 patients. The 8th patient achieved a PR at 18 weeks. Serious adverse events occurred in 4 patients: non-neutropenic sepsis/pneumonia (n = 1), and non-neutropenic bacteremia (n = 1) in the cisplatin 25 mg/m2 cohort; clostridium difficile colitis (n = 1) with cisplatin 37.5 mg/m2; and neutropenic fever/pneumonia (n = 1) with cisplatin 50mg/m2. Discussion: The study has completed phase Ib and will be expanded at the phase II dose of cisplatin 25 mg/m2 for a total of 25 patients. If this favorable response rate is confirmed, this 3 drug regimen could be further developed both for patients with advanced disease as well as in neoadjuvant and adjuvant settings. Supported by grants from the Seena Magowitz Foundation and the SU2C Dream Team Citation Format: Gayle S. Jameson, Erkut Borazanci, Elizabeth Poplin, Michael T. Barrett, John Crowley, Adam Rosenthal, Amy Stoll-D'Astice, Karen L. Ansaldo, Steven Boone, Leticia Lebron, Ramesh K. Ramanathan, Ronald L. Korn, Daniel D. Von Hoff. High complete and partial response rate in a phase Ib pilot trial with cisplatin plus albumin-bound paclitaxel and gemcitabine in patients with advanced pancreatic cancer. [abstract] . In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr LB-003. doi:10.1158/1538-7445.AM2015-LB-003
    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: 2015
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