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Pernar Kovač M, Tadić V, Kralj J, Duran GE, Stefanelli A, Stupin Polančec D, Dabelić S, Bačić N, Tomicic MT, Heffeter P, Sikic BI, Brozovic A. Carboplatin-induced upregulation of pan β-tubulin and class III β-tubulin is implicated in acquired resistance and cross-resistance of ovarian cancer. Cell Mol Life Sci 2023; 80:294. [PMID: 37718345 PMCID: PMC11071939 DOI: 10.1007/s00018-023-04943-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 08/28/2023] [Accepted: 08/29/2023] [Indexed: 09/19/2023]
Abstract
Resistance to platinum- and taxane-based chemotherapy represents a major obstacle to long-term survival in ovarian cancer (OC) patients. Here, we studied the interplay between acquired carboplatin (CBP) resistance using two OC cell models, MES-OV CBP and SK-OV-3 CBP, and non-P-glycoprotein-mediated cross-resistance to paclitaxel (TAX) observed only in MES-OV CBP cells. Decreased platination, mesenchymal-like phenotype, and increased expression of α- and γ-tubulin were observed in both drug-resistant variants compared with parental cells. Both variants revealed increased protein expression of class III β-tubulin (TUBB3) but differences in TUBB3 branching and nuclear morphology. Transient silencing of TUBB3 sensitized MES-OV CBP cells to TAX, and surprisingly also to CBP. This phenomenon was not observed in the SK-OV-3 CBP variant, probably due to the compensation by other β-tubulin isotypes. Reduced TUBB3 levels in MES-OV CBP cells affected DNA repair protein trafficking and increased whole-cell platination level. Furthermore, TUBB3 depletion augmented therapeutic efficiency in additional OC cells, showing vice versa drug-resistant pattern, lacking β-tubulin isotype compensation visible at the level of total β-tubulin (TUBB) in vitro and ex vivo. In summary, the level of TUBB in OC should be considered together with TUBB3 in therapy response prediction.
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Affiliation(s)
- Margareta Pernar Kovač
- Division of Molecular Biology, Ruđer Bošković Institute, Bijenička Str. 54, 10000, Zagreb, Croatia
| | - Vanja Tadić
- Division of Molecular Biology, Ruđer Bošković Institute, Bijenička Str. 54, 10000, Zagreb, Croatia
| | - Juran Kralj
- Division of Molecular Biology, Ruđer Bošković Institute, Bijenička Str. 54, 10000, Zagreb, Croatia
| | - George E Duran
- Division of Oncology, Stanford University School of Medicine, 269 Campus Dr., 94305, Stanford, CA, USA
| | - Alessia Stefanelli
- Center for Cancer Research, Medical University of Vienna, Borschkegasse 8a, 1090, Vienna, Austria
| | | | - Sanja Dabelić
- Faculty of Pharmacy and Biochemistry, University of Zagreb, Ante Kovačića 1, 10000, Zagreb, Croatia
| | - Niko Bačić
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička Str. 54, 10000, Zagreb, Croatia
| | - Maja T Tomicic
- Institute of Toxicology, University Medical Center Mainz, Obere Zahlbacher Str. 67, 55131, Mainz, Germany
| | - Petra Heffeter
- Center for Cancer Research, Medical University of Vienna, Borschkegasse 8a, 1090, Vienna, Austria
| | - Branimir I Sikic
- Division of Oncology, Stanford University School of Medicine, 269 Campus Dr., 94305, Stanford, CA, USA
| | - Anamaria Brozovic
- Division of Molecular Biology, Ruđer Bošković Institute, Bijenička Str. 54, 10000, Zagreb, Croatia.
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Smith MA, Van Alsten SC, Walens A, Damrauer JS, Maduekwe UN, Broaddus RR, Love MI, Troester MA, Hoadley KA. DNA Damage Repair Classifier Defines Distinct Groups in Hepatocellular Carcinoma. Cancers (Basel) 2022; 14:cancers14174282. [PMID: 36077818 PMCID: PMC9454479 DOI: 10.3390/cancers14174282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 08/27/2022] [Accepted: 08/29/2022] [Indexed: 12/02/2022] Open
Abstract
Simple Summary DNA repair pathways have been implicated in hepatocellular carcinoma outcomes. We found that hepatocellular carcinomas (HCC) could be separated into two groups (high and low) based on the overall expression of genes involved in DNA repair. Among the low repair group, there were three subgroups, one of which shared features of the high repair group. Given the important role of liver in metabolism and detoxification and its regenerative capacity, proliferation and DNA damage responses are critical in subdividing major biological categories of liver tumors. High repair samples showed more proliferative and regenerative signatures and had poorer outcomes versus the low repair that were more associated with the genes involved in normal liver biology. These biological groups suggest that dysregulation in endogenous liver processes promotes a pro-tumorigenic microenvironment that may facilitate tumor progression or identify tumors that require more substantial clinical intervention. Abstract DNA repair pathways have been associated with variability in hepatocellular carcinoma (HCC) clinical outcomes, but the mechanism through which DNA repair varies as a function of liver regeneration and other HCC characteristics is poorly understood. We curated a panel of 199 genes representing 15 DNA repair pathways to identify DNA repair expression classes and evaluate their associations with liver features and clinicopathologic variables in The Cancer Genome Atlas (TCGA) HCC study. We identified two groups in HCC, defined by low or high expression across all DNA repair pathways. The low-repair group had lower grade and retained the expression of classical liver markers, whereas the high-repair group had more clinically aggressive features, increased p53 mutant-like gene expression, and high liver regenerative gene expression. These pronounced features overshadowed the variation in the low-repair subset, but when considered separately, the low-repair samples included three subgroups: L1, L2, and L3. L3 had high DNA repair expression with worse progression-free (HR 1.24, 95% CI 0.81–1.91) and overall (HR 1.63, 95% CI 0.98–2.71) survival. High-repair outcomes were also significantly worse compared with the L1 and L2 groups. HCCs vary in DNA repair expression, and a subset of tumors with high regeneration profoundly disrupts liver biology and poor prognosis.
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Affiliation(s)
- Markia A. Smith
- Department of Pathology and Laboratory Medicine, School of Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Sarah C. Van Alsten
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Andrea Walens
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Jeffrey S. Damrauer
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Ugwuji N. Maduekwe
- Department of Surgery, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Russell R. Broaddus
- Department of Pathology and Laboratory Medicine, School of Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Michael I. Love
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Melissa A. Troester
- Department of Pathology and Laboratory Medicine, School of Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Katherine A. Hoadley
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Correspondence:
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Gould AL, Campbell RK, Loewy JW, Beckman RA, Dey J, Schiel A, Burman CF, Zhou J, Antonijevic Z, Miller ER, Tang R. A framework for assessing the impact of accelerated approval. PLoS One 2022; 17:e0265712. [PMID: 35749431 PMCID: PMC9231718 DOI: 10.1371/journal.pone.0265712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 03/07/2022] [Indexed: 01/26/2023] Open
Abstract
The FDA's Accelerated Approval program (AA) is a regulatory program to expedite availability of products to treat serious or life-threatening illnesses that lack effective treatment alternatives. Ideally, all of the many stakeholders such as patients, physicians, regulators, and health technology assessment [HTA] agencies that are affected by AA should benefit from it. In practice, however, there is intense debate over whether evidence supporting AA is sufficient to meet the needs of the stakeholders who collectively bring an approved product into routine clinical care. As AAs have become more common, it becomes essential to be able to determine their impact objectively and reproducibly in a way that provides for consistent evaluation of therapeutic decision alternatives. We describe the basic features of an approach for evaluating AA impact that accommodates stakeholder-specific views about potential benefits, risks, and costs. The approach is based on a formal decision-analytic framework combining predictive distributions for therapeutic outcomes (efficacy and safety) based on statistical models that incorporate findings from AA trials with stakeholder assessments of various actions that might be taken. The framework described here provides a starting point for communicating the value of a treatment granted AA in the context of what is important to various stakeholders.
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Affiliation(s)
- A. Lawrence Gould
- Methodology Research, BARDS, Merck & Co., Inc., Kenilworth, New Jersey, United States of America
- * E-mail:
| | - Robert K. Campbell
- Molecular Pharmacology, Physiology and Biotechnology, Brown University, Providence, Rhode Island, United States of America
| | - John W. Loewy
- DataForethought, Winchester, Massachusetts, United States of America
| | - Robert A. Beckman
- Lombardi Comprehensive Cancer Center and Innovation Center for Biomedical Informatics, Georgetown University Medical Center, Washington, DC, United States of America
| | - Jyotirmoy Dey
- Data and Statistical Sciences, AbbVie, North Chicago, Illinois, United States of America
| | - Anja Schiel
- Department for Pharmacoeconomics, Norwegian Medicines Agency, Oslo, Norway
| | | | - Joey Zhou
- Xcovery Pharmaceuticals, Palm Beach Gardens, Florida, United States of America
| | | | - Eva R. Miller
- Independent Biostatistical Consultant, Middletown Twp, Pennsylvania, United States of America
| | - Rui Tang
- Methodology and Data Visualization, Biostatistics Department, Servier Pharmaceuticals US, Boston, Massachusetts, United States of America
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Georgescu MM, Islam MZ, Li Y, Circu ML, Traylor J, Notarianni CM, Kline CN, Burns DK. Global activation of oncogenic pathways underlies therapy resistance in diffuse midline glioma. Acta Neuropathol Commun 2020; 8:111. [PMID: 32680567 PMCID: PMC7367358 DOI: 10.1186/s40478-020-00992-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 07/08/2020] [Indexed: 12/18/2022] Open
Abstract
Diffuse midline gliomas (DMGs) are aggressive pediatric brain tumors with dismal prognosis due to therapy-resistant tumor growth and invasion. We performed the first integrated histologic/genomic/proteomic analysis of 21 foci from three pontine DMG cases with supratentorial dissemination. Histone H3.3-K27M was the driver mutation, usually at high variant allele fraction due to recurrent chromosome 1q copy number gain, in combination with germline variants in ATM, FANCM and MYCN genes. Both previously reported and novel recurrent copy number variations and somatic pathogenic mutations in chromatin remodeling, DNA damage response and PI3K/MAPK growth pathways were variably detected, either in multiple or isolated foci. Proteomic analysis showed global upregulation of histone H3, lack of H3-K27 trimethylation, and further impairment of polycomb repressive complex 2 by ASXL1 downregulation. Activation of oncogenic pathways resulted from combined upregulation of N-MYC, SOX2, p65/p50 NF-κB and STAT3 transcription factors, EGFR, FGFR2, PDGFRα/β receptor tyrosine kinases, and downregulation of PHLPP1/2, PTEN and p16/INK4A tumor suppressors. Upregulation of SMAD4, PAI-1, CD44, and c-SRC in multiple foci most likely contributed to invasiveness. This integrated comprehensive analysis revealed a complex spatiotemporal evolution in diffuse intrisic pontine glioma, recommending pontine and cerebellar biopsies for accurate populational genetic characterization, and delineated common signaling pathways and potential therapeutic targets. It also revealed an unsuspected activation of a multitude of oncogenic pathways, including cancer cell reprogramming, explaining the resistance of DMG to current therapies.
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The Validity and Predictive Value of Blood-Based Biomarkers in Prediction of Response in the Treatment of Metastatic Non-Small Cell Lung Cancer: A Systematic Review. Cancers (Basel) 2020; 12:cancers12051120. [PMID: 32365836 PMCID: PMC7280996 DOI: 10.3390/cancers12051120] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 04/21/2020] [Accepted: 04/27/2020] [Indexed: 12/11/2022] Open
Abstract
With the introduction of targeted therapies and immunotherapy, molecular diagnostics gained a more profound role in the management of non-small cell lung cancer (NSCLC). This study aimed to systematically search for studies reporting on the use of liquid biopsies (LB), the correlation between LBs and tissue biopsies, and finally the predictive value in the management of NSCLC. A systematic literature search was performed, including results published after 1 January 2014. Articles studying the predictive value or validity of a LB were included. The search (up to 1 September 2019) retrieved 1704 articles, 1323 articles were excluded after title and abstract screening. Remaining articles were assessed for eligibility by full-text review. After full-text review, 64 articles investigating the predictive value and 78 articles describing the validity were included. The majority of studies investigated the predictive value of LBs in relation to therapies targeting the epidermal growth factor receptor (EGFR) or anaplastic lymphoma kinase (ALK) receptor (n = 38). Of studies describing the validity of a biomarker, 55 articles report on one or more EGFR mutations. Although a variety of blood-based biomarkers are currently under investigation, most studies evaluated the validity of LBs to determine EGFR mutation status and the subsequent targeting of EGFR tyrosine kinase inhibitors based on the mutation status found in LBs of NSCLC patients.
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Kancherla J, Rao S, Bhuvaneshwar K, Riggins RB, Beckman RA, Madhavan S, Corrada Bravo H, Boca SM. Evidence-Based Network Approach to Recommending Targeted Cancer Therapies. JCO Clin Cancer Inform 2020; 4:71-88. [PMID: 31990579 PMCID: PMC6995264 DOI: 10.1200/cci.19.00097] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/04/2019] [Indexed: 12/30/2022] Open
Abstract
PURPOSE In this work, we introduce CDGnet (Cancer-Drug-Gene Network), an evidence-based network approach for recommending targeted cancer therapies. CDGnet represents a user-friendly informatics tool that expands the range of targeted therapy options for patients with cancer who undergo molecular profiling by including the biologic context via pathway information. METHODS CDGnet considers biologic pathway information specifically by looking at targets or biomarkers downstream of oncogenes and is personalized for individual patients via user-inputted molecular alterations and cancer type. It integrates a number of different sources of knowledge: patient-specific inputs (molecular alterations and cancer type), US Food and Drug Administration-approved therapies and biomarkers (curated from DailyMed), pathways for specific cancer types (from Kyoto Encyclopedia of Genes and Genomes [KEGG]), gene-drug connections (from DrugBank), and oncogene information (from KEGG). We consider 4 different evidence-based categories for therapy recommendations. Our tool is delivered via an R/Shiny Web application. For the 2 categories that use pathway information, we include an interactive Sankey visualization built on top of d3.js that also provides links to PubChem. RESULTS We present a scenario for a patient who has estrogen receptor (ER)-positive breast cancer with FGFR1 amplification. Although many therapies exist for patients with ER-positive breast cancer, FGFR1 amplifications may confer resistance to such treatments. CDGnet provides therapy recommendations, including PIK3CA, MAPK, and RAF inhibitors, by considering targets or biomarkers downstream of FGFR1. CONCLUSION CDGnet provides results in a number of easily accessible and usable forms, separating targeted cancer therapies into categories in an evidence-based manner that incorporates biologic pathway information.
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Tesauro C, Simonsen AK, Andersen MB, Petersen KW, Kristoffersen EL, Algreen L, Hansen NY, Andersen AB, Jakobsen AK, Stougaard M, Gromov P, Knudsen BR, Gromova I. Topoisomerase I activity and sensitivity to camptothecin in breast cancer-derived cells: a comparative study. BMC Cancer 2019; 19:1158. [PMID: 31783818 PMCID: PMC6884793 DOI: 10.1186/s12885-019-6371-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 11/18/2019] [Indexed: 12/30/2022] Open
Abstract
Background Camptothecin (CPT) and its derivatives are currently used as second- or third-line treatment for patients with endocrine-resistant breast cancer (BC). These drugs convert nuclear enzyme DNA topoisomerase I (TOP1) to a cell poison with the potential to damage DNA by increasing the half-life of TOP1-DNA cleavage complexes (TOP1cc), ultimately resulting in cell death. In small and non-randomized trials for BC, researchers have observed extensive variation in CPT response rates, ranging from 14 to 64%. This variability may be due to the absence of reliable selective parameters for patient stratification. BC cell lines may serve as feasible models for generation of functional criteria that may be used to predict drug sensitivity for patient stratification and, thus, lead to more appropriate applications of CPT in clinical trials. However, no study published to date has included a comparison of multiple relevant parameters and CPT response across cell lines corresponding to specific BC subtypes. Method We evaluated the levels and possible associations of seven parameters including the status of the TOP1 gene (i.e. amplification), TOP1 protein expression level, TOP1 activity and CPT susceptibility, activity of the tyrosyl-DNA phosphodiesterase 1 (TDP1), the cellular CPT response and the cellular growth rate across a representative panel of BC cell lines, which exemplifies three major BC subtypes: Luminal, HER2 and TNBC. Results In all BC cell lines analyzed (without regard to subtype classification), we observed a significant overall correlation between growth rate and CPT response. In cell lines derived from Luminal and HER2 subtypes, we observed a correlation between TOP1 gene copy number, TOP1 activity, and CPT response, although the data were too limited for statistical analyses. In cell lines representing Luminal and TNBC subtypes, we observed a direct correlation between TOP1 protein abundancy and levels of enzymatic activity. In all three subtypes (Luminal, HER2, and TNBC), TOP1 exhibits approximately the same susceptibility to CPT. Of the three subtypes examined, the TNBC-like cell lines exhibited the highest CPT sensitivity and were characterized by the fastest growth rate. This indicates that breast tumors belonging to the TNBC subtype, may benefit from treatment with CPT derivatives. Conclusion TOP1 activity is not a marker for CPT sensitivity in breast cancer.
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Affiliation(s)
- Cinzia Tesauro
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Anne Katrine Simonsen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark.,Present Address: Department of Biology, Copenhagen University, Copenhagen, Denmark
| | - Marie Bech Andersen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | | | - Emil Laust Kristoffersen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark.,Present Address: MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Line Algreen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | | | - Anne Bech Andersen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | | | - Magnus Stougaard
- Department of Pathology, Aarhus University Hospital, Aarhus, Denmark
| | - Pavel Gromov
- Genome Integrity Unit, Breast Cancer Biology Group, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Birgitta R Knudsen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark.
| | - Irina Gromova
- Genome Integrity Unit, Breast Cancer Biology Group, Danish Cancer Society Research Center, Copenhagen, Denmark.
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Weinberg BA, Xiu J, Lindberg MR, Shields AF, Hwang JJ, Poorman K, Salem ME, Pishvaian MJ, Holcombe RF, Marshall JL, Morse MA. Molecular profiling of biliary cancers reveals distinct molecular alterations and potential therapeutic targets. J Gastrointest Oncol 2019; 10:652-662. [PMID: 31392046 DOI: 10.21037/jgo.2018.08.18] [Citation(s) in RCA: 94] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Background Biliary tract cancers (BTCs) are a heterogeneous group of aggressive, rare malignancies with limited standard chemotherapeutic options for advanced disease. Recent studies have demonstrated potential novel biliary cancer targets and a possible role for immunotherapy in the treatment of patients with this disease. Intrahepatic cholangiocarcinoma (IHCC), extrahepatic cholangiocarcinoma (EHCC), and gallbladder carcinoma (GBC) are frequently grouped together in clinical trials despite differences in tumor biology. Methods To further investigate tumor biology differences, we profiled 1,502 BTCs using next-generation sequencing (NGS), immunohistochemistry, in situ hybridization, and RNA sequencing. Results IHCCs had higher rates of IDH1, BAP1, and PBRM1 mutations and FGFR2 fusions; EHCCs had higher rates of KRAS, CDKN2A, and BRCA1 mutations; and GBCs had higher rates of homologous recombination repair deficiency and Her2/neu overexpression and amplification. IHCCs and GBCs had higher rates of potential positive predictive biomarkers for immune checkpoint inhibition (PD-L1 expression, high microsatellite instability, and high tumor mutational burden) than EHCCs. Conclusions These findings support clinical molecular profiling of BTCs to inform potential therapeutic selection and clinical trial design based on the primary tumor's site of origin within the biliary tree.
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Affiliation(s)
- Benjamin A Weinberg
- Ruesch Center for the Cure of Gastrointestinal Cancers, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, USA
| | | | - Michael R Lindberg
- Ruesch Center for the Cure of Gastrointestinal Cancers, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, USA
| | - Anthony F Shields
- Department of Oncology, Karmanos Cancer Institute, Wayne State University, Detroit, MI, USA
| | - Jimmy J Hwang
- Levine Cancer Institute, Carolinas HealthCare System, Charlotte, NC, USA
| | | | - Mohamed E Salem
- Levine Cancer Institute, Carolinas HealthCare System, Charlotte, NC, USA
| | - Michael J Pishvaian
- Ruesch Center for the Cure of Gastrointestinal Cancers, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, USA
| | | | - John L Marshall
- Ruesch Center for the Cure of Gastrointestinal Cancers, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, USA
| | - Michael A Morse
- Division of Medical Oncology, Duke Cancer Institute, Duke University Medical Center, Durham, NC, USA
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Tesfaye AA, Wang H, Hartley ML, He AR, Weiner L, Gabelia N, Kapanadze L, Shezad M, Brody JR, Marshall JL, Pishvaian MJ. A Pilot Trial of Molecularly Tailored Therapy for Patients with Metastatic Pancreatic Ductal Adenocarcinoma. J Pancreat Cancer 2019; 5:12-21. [PMID: 31065624 PMCID: PMC6503449 DOI: 10.1089/pancan.2019.0003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Purpose: Despite the wide adoption of tumor molecular profiling, there is a dearth of evidence linking molecular biomarkers for treatment selection to prediction of treatment outcomes in patients with metastatic pancreatic cancer. We initiated a pilot study to test the feasibility of designing a larger phase II trial of molecularly tailored treatment for metastatic pancreatic cancer. Methods: Our study aimed to assess the feasibility of following a treatment algorithm based on the expression of three published predictive markers of response to chemotherapy: ribonucleotide reductase catalytic subunit M1 (for gemcitabine); excision repair cross-complementation group 1 (for platinum agents); and thymidylate synthase (for 5-fluorouracil) in patients with untreated, metastatic pancreatic cancer. Results of the tumor biopsy analysis were used to assign patients to one of seven doublet regimens. Key secondary objectives included response rate (RR), disease control rate (DCR), progression-free survival (PFS), and overall survival (OS). Results: Between December 2012 and March 2015, 30 patients were enrolled into the study. Ten patients failed screening primarily due to inadequate tumor tissue availability. Of the remaining 20 patients, 19 were assigned into 6 different chemotherapy doublets, and achieved an RR of 28%, with a DCR rate of 78%. The median PFS and OS were 5.78 and 8.21 months, respectively. Conclusions: The incorporation of biomarkers into a treatment algorithm is feasible and resulted in a PFS and OS similar to other doublet therapies for patients with metastatic pancreatic cancer. Based on the results from this pilot study, a larger phase II randomized trial of molecularly targeted therapy versus physicians' choice of standard of care has been initiated in the second-line setting (NCT02967770).
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Affiliation(s)
- Anteneh A Tesfaye
- Karmanos Cancer Institute, Wayne State University, Detroit, Michigan
| | - Hongkun Wang
- Lombardi Comprehensive Cancer Center, Georgetown University, Washington, District of Columbia
| | - Marion L Hartley
- Lombardi Comprehensive Cancer Center, Georgetown University, Washington, District of Columbia
| | - Aiwu Ruth He
- Lombardi Comprehensive Cancer Center, Georgetown University, Washington, District of Columbia
| | - Louis Weiner
- Lombardi Comprehensive Cancer Center, Georgetown University, Washington, District of Columbia
| | - Nina Gabelia
- Lombardi Comprehensive Cancer Center, Georgetown University, Washington, District of Columbia
| | - Lana Kapanadze
- Lombardi Comprehensive Cancer Center, Georgetown University, Washington, District of Columbia
| | - Muhammad Shezad
- Lombardi Comprehensive Cancer Center, Georgetown University, Washington, District of Columbia
| | - Jonathan R Brody
- Department of Surgery, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - John L Marshall
- Lombardi Comprehensive Cancer Center, Georgetown University, Washington, District of Columbia
| | - Michael J Pishvaian
- Lombardi Comprehensive Cancer Center, Georgetown University, Washington, District of Columbia
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Shi S, Yu X. Selecting chemotherapy for pancreatic cancer: Far away or so close? Semin Oncol 2018; 46:39-47. [PMID: 30611527 DOI: 10.1053/j.seminoncol.2018.12.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 01/26/2018] [Accepted: 12/19/2018] [Indexed: 02/06/2023]
Abstract
Pancreatic cancer is a lethal disease with a very poor prognosis. In contrast to treatments for many other tumor types, cytotoxic agents are still the first-line drugs for pancreatic cancer in both the palliative and adjuvant settings. Some progress has been made in recent years, but most large phase 3 studies have not shown significant improvements in survival. Because the available drugs and regimens are limited in both type and effect, the selection of chemotherapy based on clinicopathologic characteristics may be consequential for pancreatic cancer. In the present report, we focused on 7 landmark clinical trials for pancreatic cancer. We observed that FOLFIRINOX (oxaliplatin, irinotecan, fluorouracil, and leucovorin) and NG (nab-paclitaxel and gemcitabine), 2 first-line regimens, exerted opposite effects on metastatic pancreatic cancer patients with different baseline carbohydrate antigen 19-9 (CA19-9) levels. This suggested that not only the performance status but possibly also CA19-9 levels should be considered when making a therapeutic choice for patients with advanced pancreatic cancer. Moreover, we found that patients with a diagnosis of pancreatic cancer who have undergone a surgical resection with a negative margin (R0) may benefit more from fluorouracil and/or oral prodrugs of fluorouracil-based adjuvant therapy than from gemcitabine. Conversely, gemcitabine or gemcitabine-based regimens may be more effective for patients with a positive resection margin (R1). Based on these findings, we propose flowcharts for selecting chemotherapy for both advanced and resected pancreatic cancer. Furthermore, we present possible mechanisms and interpretations underlying the selection of chemotherapy for pancreatic cancer and propose the tumor burden as a key variable in this process. Regardless of the possible bias and exact treatment selection process, this study offers an opportunity to improve patient outcomes by using agents currently used in the therapy of pancreatic cancer. Although these conclusions are based on indirect evidence, we provide insights and possibilities to drive the selection of chemotherapy for pancreatic cancer.
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Affiliation(s)
- Si Shi
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China; Pancreatic Cancer Institute, Fudan University, Shanghai, China
| | - Xianjun Yu
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China; Pancreatic Cancer Institute, Fudan University, Shanghai, China.
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Sharma V, Fong A, Beckman RA, Rao S, Boca SM, McGarvey PB, Ratwani RM, Madhavan S. Eye-Tracking Study to Enhance Usability of Molecular Diagnostics Reports in Cancer Precision Medicine. JCO Precis Oncol 2018; 2:1-11. [PMID: 35135129 DOI: 10.1200/po.17.00296] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
PURPOSE We conducted usability studies on commercially available molecular diagnostic (MDX) test reports to identify strengths and weaknesses in content and form that drive clinical decision making. Given routine genomic testing in cancer medicine, oncologists must interpret MDX reports as well as evidence concerning clinical utility of biomarkers accurately for treatment or trial selection. This work aims to evaluate effectiveness of MDX reports in facilitating cancer treatment planning. METHODS Fourteen clinicians at an academic tertiary care medical facility, with a wide range of experience in oncology and in the use of molecular testing, participated in this study. Three commercially available, widely used, Clinical Laboratory Improvement Amendments (CLIA)-certified, College of American Pathologists (CAP)-accredited test reports (labeled Laboratories A, B, and C) were used. Eye tracking, surveys, and think-aloud protocols were used to collect usability data for these MDX reports focusing on ease of comprehension and actionability. RESULTS Clinicians found two primary areas in molecular diagnostic reports most useful for patient care: therapy options with benefit or lack of benefit to patients, including enrolling clinical trials; and pathogenic tumor molecular anomalies detected. Therapeutic implications and therapy classes such as US Food and Drug Administration-approved off-label, on-label, clinical trials were critical for decision making. However, all reports had usability and comprehension issues in these areas and could be improved. CONCLUSION Focused usability studies can help drive our understanding of the clinical workflow for use of molecular diagnostic tests in cancer care. This in turn can have major effects on quality of care, outcomes, costs, and patient satisfaction. This study demonstrates the use of specific usability techniques (eye tracking and think-aloud protocols) to help clinical laboratories improve MDX report design in a precision oncology treatment setting.
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Affiliation(s)
- Vishakha Sharma
- Vishakha Sharma, Robert A. Beckman, Shruti Rao, Simina M. Boca, Peter B. McGarvey, and Subha Madhavan, Georgetown University; Vishakha Sharma, Robert A. Beckman, Simina M. Boca, and Subha Madhavan, Georgetown University Medical Center; Allan Fong and Raj M. Ratwani, National Center for Human Factors in Healthcare, MedStar Health; and Raj M. Ratwani, Georgetown University School of Medicine, Washington, DC
| | - Allan Fong
- Vishakha Sharma, Robert A. Beckman, Shruti Rao, Simina M. Boca, Peter B. McGarvey, and Subha Madhavan, Georgetown University; Vishakha Sharma, Robert A. Beckman, Simina M. Boca, and Subha Madhavan, Georgetown University Medical Center; Allan Fong and Raj M. Ratwani, National Center for Human Factors in Healthcare, MedStar Health; and Raj M. Ratwani, Georgetown University School of Medicine, Washington, DC
| | - Robert A Beckman
- Vishakha Sharma, Robert A. Beckman, Shruti Rao, Simina M. Boca, Peter B. McGarvey, and Subha Madhavan, Georgetown University; Vishakha Sharma, Robert A. Beckman, Simina M. Boca, and Subha Madhavan, Georgetown University Medical Center; Allan Fong and Raj M. Ratwani, National Center for Human Factors in Healthcare, MedStar Health; and Raj M. Ratwani, Georgetown University School of Medicine, Washington, DC
| | - Shruti Rao
- Vishakha Sharma, Robert A. Beckman, Shruti Rao, Simina M. Boca, Peter B. McGarvey, and Subha Madhavan, Georgetown University; Vishakha Sharma, Robert A. Beckman, Simina M. Boca, and Subha Madhavan, Georgetown University Medical Center; Allan Fong and Raj M. Ratwani, National Center for Human Factors in Healthcare, MedStar Health; and Raj M. Ratwani, Georgetown University School of Medicine, Washington, DC
| | - Simina M Boca
- Vishakha Sharma, Robert A. Beckman, Shruti Rao, Simina M. Boca, Peter B. McGarvey, and Subha Madhavan, Georgetown University; Vishakha Sharma, Robert A. Beckman, Simina M. Boca, and Subha Madhavan, Georgetown University Medical Center; Allan Fong and Raj M. Ratwani, National Center for Human Factors in Healthcare, MedStar Health; and Raj M. Ratwani, Georgetown University School of Medicine, Washington, DC
| | - Peter B McGarvey
- Vishakha Sharma, Robert A. Beckman, Shruti Rao, Simina M. Boca, Peter B. McGarvey, and Subha Madhavan, Georgetown University; Vishakha Sharma, Robert A. Beckman, Simina M. Boca, and Subha Madhavan, Georgetown University Medical Center; Allan Fong and Raj M. Ratwani, National Center for Human Factors in Healthcare, MedStar Health; and Raj M. Ratwani, Georgetown University School of Medicine, Washington, DC
| | - Raj M Ratwani
- Vishakha Sharma, Robert A. Beckman, Shruti Rao, Simina M. Boca, Peter B. McGarvey, and Subha Madhavan, Georgetown University; Vishakha Sharma, Robert A. Beckman, Simina M. Boca, and Subha Madhavan, Georgetown University Medical Center; Allan Fong and Raj M. Ratwani, National Center for Human Factors in Healthcare, MedStar Health; and Raj M. Ratwani, Georgetown University School of Medicine, Washington, DC
| | - Subha Madhavan
- Vishakha Sharma, Robert A. Beckman, Shruti Rao, Simina M. Boca, Peter B. McGarvey, and Subha Madhavan, Georgetown University; Vishakha Sharma, Robert A. Beckman, Simina M. Boca, and Subha Madhavan, Georgetown University Medical Center; Allan Fong and Raj M. Ratwani, National Center for Human Factors in Healthcare, MedStar Health; and Raj M. Ratwani, Georgetown University School of Medicine, Washington, DC
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12
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Pishvaian MJ, Bender RJ, Halverson D, Rahib L, Hendifar AE, Mikhail S, Chung V, Picozzi VJ, Sohal D, Blais EM, Mason K, Lyons EE, Matrisian LM, Brody JR, Madhavan S, Petricoin EF. Molecular Profiling of Patients with Pancreatic Cancer: Initial Results from the Know Your Tumor Initiative. Clin Cancer Res 2018; 24:5018-5027. [PMID: 29954777 DOI: 10.1158/1078-0432.ccr-18-0531] [Citation(s) in RCA: 139] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 05/04/2018] [Accepted: 06/25/2018] [Indexed: 12/30/2022]
Abstract
Purpose: To broaden access to and implementation of precision medicine in the care of patients with pancreatic cancer, the Know Your Tumor (KYT) program was initiated using a turn-key precision medicine system. Patients undergo commercially available multiomic profiling to determine molecularly rationalized clinical trials and off-label therapies.Experimental Design: Tumor samples were obtained for 640 patients from 287 academic and community practices covering 44 states. College of American Pathologists/Clinical Laboratory Improvement Amendments-accredited laboratories were used for genomic, proteomic, and phosphoprotein-based molecular profiling.Results: Tumor samples were adequate for next-generation sequencing in 96% and IHC in 91% of patients. A tumor board reviewed the results for every patient and found actionable genomic alterations in 50% of patients (with 27% highly actionable) and actionable proteomic alterations (excluding chemopredictive markers) in 5%. Actionable alterations commonly found were in DNA repair genes (BRCA1/2 or ATM mutations, 8.4%) and cell-cycle genes (CCND1/2/3 or CDK4/6 alterations, 8.1%). A subset of samples was assessed for actionable phosphoprotein markers. Among patients with highly actionable biomarkers, those who received matched therapy (n = 17) had a significantly longer median progression-free survival (PFS) than those who received unmatched therapy [n = 18; PFS = 4.1 vs. 1.9 months; HR, 0.47; 95% confidence interval (CI): 0.24-0.94; P adj = 0.03].Conclusions: A comprehensive precision medicine system can be implemented in community and academic settings, with highly actionable findings observed in over 25% of pancreatic cancers. Patients whose tumors have highly actionable alterations and receive matched therapy demonstrated significantly increased PFS. Our findings support further prospective evaluation of precision oncology in pancreatic cancer. Clin Cancer Res; 24(20); 5018-27. ©2018 AACR.
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Affiliation(s)
- Michael J Pishvaian
- Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, D.C. .,Perthera, Inc, McLean, Virginia
| | | | | | - Lola Rahib
- The Pancreatic Cancer Action Network, Manhattan Beach, California
| | | | | | | | | | | | | | | | - Emily E Lyons
- The Pancreatic Cancer Action Network, Manhattan Beach, California
| | - Lynn M Matrisian
- The Pancreatic Cancer Action Network, Manhattan Beach, California
| | - Jonathan R Brody
- The Jefferson Pancreatic, Biliary, and Related Cancer Center and the Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Subha Madhavan
- Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, D.C.,Perthera, Inc, McLean, Virginia
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13
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Rauch A, Carlstedt A, Emmerich C, Mustafa AHM, Göder A, Knauer SK, Linnebacher M, Heinzel T, Krämer OH. Survivin antagonizes chemotherapy-induced cell death of colorectal cancer cells. Oncotarget 2018; 9:27835-27850. [PMID: 29963241 PMCID: PMC6021236 DOI: 10.18632/oncotarget.25600] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 05/08/2018] [Indexed: 02/06/2023] Open
Abstract
Irinotecan (CPT-11) and oxaliplatin (L-OHP) are among the most frequently used drugs against colorectal tumors. Therefore, it is important to define the molecular mechanisms that these agents modulate in colon cancer cells. Here we demonstrate that CPT-11 stalls such cells in the G2/M phase of the cell cycle, induces an accumulation of the tumor suppressor p53, the replicative stress/DNA damage marker γH2AX, phosphorylation of the checkpoint kinases ATM and ATR, and an ATR-dependent accumulation of the pro-survival molecule survivin. L-OHP reduces the number of cells in S-phase, stalls cell cycle progression, transiently triggers an accumulation of low levels of γH2AX and phosphorylated checkpoint kinases, and L-OHP suppresses survivin expression at the mRNA and protein levels. Compared to CPT-11, L-OHP is a stronger inducer of caspases and p53-dependent apoptosis. Overexpression and RNAi against survivin reveal that this factor critically antagonizes caspase-dependent apoptosis in cells treated with CPT-11 and L-OHP. We additionally show that L-OHP suppresses survivin through p53 and its downstream target p21, which stalls cell cycle progression as a cyclin-dependent kinase inhibitor (CDKi). These data shed new light on the regulation of survivin by two clinically significant drugs and its biological and predictive relevance in drug-exposed cancer cells.
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Affiliation(s)
- Anke Rauch
- Center for Molecular Biomedicine, Institute of Biochemistry and Biophysics, Department of Biochemistry, Friedrich Schiller University Jena, 07745 Jena, Germany
| | - Annemarie Carlstedt
- Center for Molecular Biomedicine, Institute of Biochemistry and Biophysics, Department of Biochemistry, Friedrich Schiller University Jena, 07745 Jena, Germany.,Leibniz Institute on Aging, Fritz Lipmann Institute, 07745 Jena, Germany
| | - Claudia Emmerich
- Center for Molecular Biomedicine, Institute of Biochemistry and Biophysics, Department of Biochemistry, Friedrich Schiller University Jena, 07745 Jena, Germany
| | - Al-Hassan M Mustafa
- Department of Toxicology, University Medical Center of the Johannes Gutenberg University Mainz, 55131 Mainz, Germany
| | - Anja Göder
- Department of Toxicology, University Medical Center of the Johannes Gutenberg University Mainz, 55131 Mainz, Germany
| | - Shirley K Knauer
- Department of Molecular Biology, Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, 45141 Essen, Germany
| | - Michael Linnebacher
- Department of General Surgery, Molecular Oncology and Immunotherapy, University of Rostock, 18057 Rostock, Germany
| | - Thorsten Heinzel
- Center for Molecular Biomedicine, Institute of Biochemistry and Biophysics, Department of Biochemistry, Friedrich Schiller University Jena, 07745 Jena, Germany
| | - Oliver H Krämer
- Department of Toxicology, University Medical Center of the Johannes Gutenberg University Mainz, 55131 Mainz, Germany
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14
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Boca SM, Panagiotou OA, Rao S, McGarvey PB, Madhavan S. Future of Evidence Synthesis in Precision Oncology: Between Systematic Reviews and Biocuration. JCO Precis Oncol 2018; 2:PO.17.00175. [PMID: 31930186 PMCID: PMC6953752 DOI: 10.1200/po.17.00175] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Affiliation(s)
- Simina M. Boca
- Simina M. Boca, Shruti Rao, Peter B. McGarvey, and Subha Madhavan, Georgetown University Medical Center, Washington, DC; and Orestis A. Panagiotou, Brown University School of Public Health, Providence, RI
| | - Orestis A. Panagiotou
- Simina M. Boca, Shruti Rao, Peter B. McGarvey, and Subha Madhavan, Georgetown University Medical Center, Washington, DC; and Orestis A. Panagiotou, Brown University School of Public Health, Providence, RI
| | - Shruti Rao
- Simina M. Boca, Shruti Rao, Peter B. McGarvey, and Subha Madhavan, Georgetown University Medical Center, Washington, DC; and Orestis A. Panagiotou, Brown University School of Public Health, Providence, RI
| | - Peter B. McGarvey
- Simina M. Boca, Shruti Rao, Peter B. McGarvey, and Subha Madhavan, Georgetown University Medical Center, Washington, DC; and Orestis A. Panagiotou, Brown University School of Public Health, Providence, RI
| | - Subha Madhavan
- Simina M. Boca, Shruti Rao, Peter B. McGarvey, and Subha Madhavan, Georgetown University Medical Center, Washington, DC; and Orestis A. Panagiotou, Brown University School of Public Health, Providence, RI
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15
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Pishvaian MJ, Slack RS, Jiang W, He AR, Hwang JJ, Hankin A, Dorsch-Vogel K, Kukadiya D, Weiner LM, Marshall JL, Brody JR. A phase 2 study of the PARP inhibitor veliparib plus temozolomide in patients with heavily pretreated metastatic colorectal cancer. Cancer 2018; 124:2337-2346. [PMID: 29579325 DOI: 10.1002/cncr.31309] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 12/23/2017] [Accepted: 01/18/2018] [Indexed: 12/14/2022]
Abstract
BACKGROUND Poly(adenosine diphosphate ribose) polymerase (PARP) inhibitors such as veliparib are potent sensitizing agents and have been safely combined with DNA-damaging agents such as temozolomide. The sensitizing effects of PARP inhibitors are magnified when cells harbor DNA repair defects. METHODS A single-arm, open-label, phase 2 study was performed to investigate the disease control rate (DCR) after 2 cycles of veliparib plus temozolomide in patients with metastatic colorectal cancer (mCRC) refractory to all standard therapies. Fifty patients received temozolomide (150 mg/m2 /d) on days 1 to 5 and veliparib (40 mg twice daily) on days 1 to 7 of each 28-day cycle. Another 5 patients with mismatch repair-deficient (dMMR) tumors were also enrolled. Twenty additional patients were then treated with temozolomide at 200 mg/m2 /d. Archived tumor specimens were used for immunohistochemistry to assess mismatch repair, phosphatase and tensin homolog deleted on chromosome 10 (PTEN), and O(6)-methylguanine-DNA methyltransferase (MGMT) protein expression levels. RESULTS The combination was well tolerated, although some patients required dose reductions for myelosuppression. The primary endpoint was successfully met with a DCR of 24% and 2 confirmed partial responses. The median progression-free survival was 1.8 months, and the median overall survival was 6.6 months. PTEN protein expression and MGMT protein expression were not predictors of DCR. There was also a suggestion of worse outcomes for patients with dMMR tumors. CONCLUSIONS In this heavily pretreated mCRC population, a combination of veliparib and temozolomide was well tolerated with temozolomide doses up to 200 mg/m2 /d, and it was clinically active. PARP inhibitor-based therapy merits further exploration in patients with mCRC. Cancer 2018;124:2337-46. © 2018 American Cancer Society.
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Affiliation(s)
- Michael J Pishvaian
- Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC
| | - Rebecca S Slack
- The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Wei Jiang
- Carolinas Medical Center, Charlotte, North Carolina
| | - A Ruth He
- Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC
| | | | - Amy Hankin
- Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC
| | - Karen Dorsch-Vogel
- Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC
| | - Divyesh Kukadiya
- Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC
| | - Louis M Weiner
- Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC
| | - John L Marshall
- Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC
| | - Jonathan R Brody
- Jefferson Pancreas, Biliary, and Related Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania.,Department of Surgery, Thomas Jefferson University, Philadelphia, Pennsylvania.,Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
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16
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Mahmood ASMA, Rao S, McGarvey P, Wu C, Madhavan S, Vijay-Shanker K. eGARD: Extracting associations between genomic anomalies and drug responses from text. PLoS One 2017; 12:e0189663. [PMID: 29261751 PMCID: PMC5738129 DOI: 10.1371/journal.pone.0189663] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Accepted: 11/29/2017] [Indexed: 12/25/2022] Open
Abstract
Tumor molecular profiling plays an integral role in identifying genomic anomalies which may help in personalizing cancer treatments, improving patient outcomes and minimizing risks associated with different therapies. However, critical information regarding the evidence of clinical utility of such anomalies is largely buried in biomedical literature. It is becoming prohibitive for biocurators, clinical researchers and oncologists to keep up with the rapidly growing volume and breadth of information, especially those that describe therapeutic implications of biomarkers and therefore relevant for treatment selection. In an effort to improve and speed up the process of manually reviewing and extracting relevant information from literature, we have developed a natural language processing (NLP)-based text mining (TM) system called eGARD (extracting Genomic Anomalies association with Response to Drugs). This system relies on the syntactic nature of sentences coupled with various textual features to extract relations between genomic anomalies and drug response from MEDLINE abstracts. Our system achieved high precision, recall and F-measure of up to 0.95, 0.86 and 0.90, respectively, on annotated evaluation datasets created in-house and obtained externally from PharmGKB. Additionally, the system extracted information that helps determine the confidence level of extraction to support prioritization of curation. Such a system will enable clinical researchers to explore the use of published markers to stratify patients upfront for 'best-fit' therapies and readily generate hypotheses for new clinical trials.
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Affiliation(s)
- A. S. M. Ashique Mahmood
- Department of Computer and Information Science, University of Delaware, Newark, Delaware, United States of America
- * E-mail:
| | - Shruti Rao
- Innovation Center For Biomedical Informatics, Georgetown University, Washington D.C, United States of America
| | - Peter McGarvey
- Innovation Center For Biomedical Informatics, Georgetown University, Washington D.C, United States of America
- Protein Information Resource, Georgetown University Medical Center, Washington D.C, United States of America
| | - Cathy Wu
- Department of Computer and Information Science, University of Delaware, Newark, Delaware, United States of America
- Protein Information Resource, Georgetown University Medical Center, Washington D.C, United States of America
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, Delaware, United States of America
| | - Subha Madhavan
- Innovation Center For Biomedical Informatics, Georgetown University, Washington D.C, United States of America
- Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington D.C, United States of America
| | - K. Vijay-Shanker
- Department of Computer and Information Science, University of Delaware, Newark, Delaware, United States of America
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17
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Oliveira ÉAD, Lima DSD, Cardozo LE, Souza GFD, de Souza N, Alves-Fernandes DK, Faião-Flores F, Quincoces JAP, Barros SBDM, Nakaya HI, Monteiro G, Maria-Engler SS. Toxicogenomic and bioinformatics platforms to identify key molecular mechanisms of a curcumin-analogue DM-1 toxicity in melanoma cells. Pharmacol Res 2017; 125:178-187. [PMID: 28882690 DOI: 10.1016/j.phrs.2017.08.018] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Revised: 07/31/2017] [Accepted: 08/30/2017] [Indexed: 12/17/2022]
Abstract
Melanoma is a highly invasive and metastatic cancer with high mortality rates and chemoresistance. Around 50% of melanomas are driven by activating mutations in BRAF that has led to the development of potent anti-BRAF inhibitors. However resistance to anti-BRAF therapy usually develops within a few months and consequently there is a need to identify alternative therapies that will bypass BRAF inhibitor resistance. The curcumin analogue DM-1 (sodium 4-[5-(4-hydroxy-3-methoxy-phenyl)-3-oxo-penta-1,4-dienyl]-2-methoxy-phenolate) has substantial anti-tumor activity in melanoma, but its mechanism of action remains unclear. Here we use a synthetic lethal genetic screen in Saccharomyces cerevisiae to identify 211 genes implicated in sensitivity to DM-1 toxicity. From these 211 genes, 74 had close human orthologues implicated in oxidative phosphorylation, insulin signaling and iron and RNA metabolism. Further analysis identified 7 target genes (ADK, ATP6V0B, PEMT, TOP1, ZFP36, ZFP36L1, ZFP36L2) with differential expression during melanoma progression implicated in regulation of tumor progression, cell differentiation, and epithelial-mesenchymal transition. Of these TOP1 and ADK were regulated by DM-1 in treatment-naïve and vemurafenib-resistant melanoma cells respectively. These data reveal that the anticancer effect of curcumin analogues is likely to be mediated via multiple targets and identify several genes that represent candidates for combinatorial targeting in melanoma.
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Affiliation(s)
- Érica Aparecida de Oliveira
- Skin Biology Group, Clinical Chemistry and Toxicology Department, School of Pharmaceutical Sciences, University of Sao Paulo, FCF/USP, Sao Paulo, Brazil
| | - Diogenes Saulo de Lima
- Computational Systems Biology Laboratory, School of Pharmaceutical Sciences, University of Sao Paulo, FCF/USP, Sao Paulo, Brazil
| | - Lucas Esteves Cardozo
- Computational Systems Biology Laboratory, School of Pharmaceutical Sciences, University of Sao Paulo, FCF/USP, Sao Paulo, Brazil
| | | | - Nayane de Souza
- Skin Biology Group, Clinical Chemistry and Toxicology Department, School of Pharmaceutical Sciences, University of Sao Paulo, FCF/USP, Sao Paulo, Brazil
| | - Debora Kristina Alves-Fernandes
- Skin Biology Group, Clinical Chemistry and Toxicology Department, School of Pharmaceutical Sciences, University of Sao Paulo, FCF/USP, Sao Paulo, Brazil
| | - Fernanda Faião-Flores
- Skin Biology Group, Clinical Chemistry and Toxicology Department, School of Pharmaceutical Sciences, University of Sao Paulo, FCF/USP, Sao Paulo, Brazil
| | | | - Silvia Berlanga de Moraes Barros
- Skin Biology Group, Clinical Chemistry and Toxicology Department, School of Pharmaceutical Sciences, University of Sao Paulo, FCF/USP, Sao Paulo, Brazil
| | - Helder I Nakaya
- Computational Systems Biology Laboratory, School of Pharmaceutical Sciences, University of Sao Paulo, FCF/USP, Sao Paulo, Brazil
| | - Gisele Monteiro
- Biochemical Pharmaceutical Technology Department, School of Pharmaceutical Sciences, University of Sao Paulo, FCF/USP, Sao Paulo, Brazil
| | - Silvya Stuchi Maria-Engler
- Skin Biology Group, Clinical Chemistry and Toxicology Department, School of Pharmaceutical Sciences, University of Sao Paulo, FCF/USP, Sao Paulo, Brazil.
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Woldu SL, Şanli Ö, Lotan Y. Tackling non-muscle invasive bladder cancer in the clinic. Expert Rev Anticancer Ther 2017; 17:467-480. [PMID: 28359179 DOI: 10.1080/14737140.2017.1313119] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
INTRODUCTION Non-muscle invasive bladder cancer (NMIBC) is a common disease process with a high propensity for recurrence and risk of progression to muscle-invasive or systemic disease. Optimal management of NMIBC depends on appropriate resection and staging, risk-based use of intravesical therapy and tailored surveillance. Current challenges include compliance with guideline recommendations and cancers which are refractory to standard therapies. Areas covered: This review summarizes the conventional management of NMIBC - which relies on strict cystoscopic surveillance and intravesical therapies with chemotherapy and/or immunotherapy in the form of bacillus Calmette-Guerin (BCG). As many patients will be resistant to conventional treatment, investigational therapies and novel prognostic models will also be discussed. Expert commentary: For decades, the management of NMIBC has been predicated on intravesical therapies, most often through the instillation of BCG which has proven clinical efficacy over transurethral resection alone. Despite this, many patients will recur or progress after BCG therapy. While radical cystectomy remains the standard for such patients, suitable alternatives are being actively investigated. An increased interest in immunotherapy for malignancy has reinvigorated this field and on-going advances in disease prognostication are likely to improve upon the existing treatment paradigms for NMIBC.
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Affiliation(s)
- Solomon L Woldu
- a Department of Urology , University of Texas Southwestern Medical Center , Dallas , TX , USA
| | - Öner Şanli
- a Department of Urology , University of Texas Southwestern Medical Center , Dallas , TX , USA.,b Department of Urology, Istanbul Faculty of Medicine , Istanbul University , Istanbul , Turkey
| | - Yair Lotan
- a Department of Urology , University of Texas Southwestern Medical Center , Dallas , TX , USA
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