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Lei JT, Huang C, Srinivasan RR, Vasaikar S, Dobrolecki LE, Lewis AN, Zhao N, Cao J, Hilsenbeck SG, Osborne CK, Rimawi M, Ellis MJ, Petrosyan V, Saltzman AB, Malovannaya A, Landua JD, Wen B, Jain A, Wulf GM, Li S, Kraushaar DC, Wang T, Chen X, Echeverria GV, Anurag M, Zhang B, Lewis MT. Abstract P2-23-01: Patient-derived xenografts allow deconvolution of single agent and combination chemotherapy responses in triple-negative breast cancer. Cancer Res 2023. [DOI: 10.1158/1538-7445.sabcs22-p2-23-01] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Abstract
Abstract
Background: Triple-negative breast cancer (TNBC) patients frequently receive combination chemotherapy treatment, but a direct comparison of response to carboplatin, docetaxel, and their combination in 50 TNBC patient-derived xenografts (PDXs) showed that combination treatment was largely ineffective at generating enhanced responses over the best single agent. This suggests de-escalation of chemotherapy may be possible if molecular mechanisms and biomarkers underlying response to individual treatments can be identified. To this end, we performed multi-omics profiling for the 50 TNBC PDXs. Methods: Orthotopic TNBC PDXs were treated with four weekly cycles of docetaxel, carboplatin, or the combination. Changes in tumor volume after 4 weeks of treatment were assessed quantitatively and by modified RECIST criteria. Genomic, transcriptomic, and mass-spectrometry-based proteomic profiling were performed on baseline tumors prior to treatments to identify associations with chemotherapy response at the gene and pathway level. ProMS was used to integrate both RNA and protein data to select a 5 RNA feature combination for optimized prediction of carboplatin response in a logistic regression model. Publicly available neoadjuvant chemotherapy clinical datasets with transcriptomic data and response information used for validation/testing included TNBC samples from: GSE18864, I-SPY2 (GSE194040), and BrighTNess (GSE164458). Results: Proteogenomic profiles revealed distinct genes associated with response to each agent and their combination, respectively, suggesting distinct molecular mechanisms underlying response to each treatment. A substantial number of genes associated with single agent and combination treatment were validated in multiple independent patient cohorts receiving platinum and taxane containing neoadjuvant therapy, confirming clinical relevance of our PDX panel. For the same treatment, different types of molecular data identified distinct sets of associated genes, providing highly complementary information. At the pathway level, RNA and protein data converged to metabolic and E2F/G2M related pathways which were upregulated in PDXs resistant or responsive to all treatment types, respectively, while variable levels of MYC-related proliferation pathways were observed across all treatments suggesting pathways that are common across and unique to different treatments. Several individual genes found to be higher in PDXs with better response to either single-agent had discriminatory power in external clinical TNBC datasets treated with similar neoadjuvant chemotherapy regimens. In addition, a logistic regression-based carboplatin response prediction model trained to select a group of 5 RNA markers (TKT, MAGI2, ATF6B, MCM7, LRP6) using both RNA and protein data performed the best in predicting response to cisplatin in a clinical TNBC dataset vs predicting response to other datasets with taxane and platinum + taxane combination containing chemotherapy regimens, demonstrating specificity of the prediction model. These results suggest potential individual biomarkers or biomarker combinations to select TNBC tumors that may respond to either single agent carboplatin, docetaxel, or their combination. PDXs refractory to all treatment arms had higher levels of proteostasis-related pathways including proteasome degradation and the unfolded protein response (UPR) related to endoplasmic reticulum stress and altered levels of chromatin regulation. Subsequent pharmacological targeting of the UPR pathway and targeting HDACs enhanced chemotherapy response. Conclusion: Proteogenomic characterization identifies molecular mechanisms and putative biomarkers for stratifying TNBC tumors for single or combination chemotherapy treatments, suggests targeted therapies to augment chemotherapy response, and provides a valuable resource for researchers and clinicians.
Citation Format: Jonathan T. Lei, Chen Huang, Ramakrishnan R. Srinivasan, Suhas Vasaikar, Lacey E. Dobrolecki, Alaina N. Lewis, Na Zhao, Jin Cao, Susan G. Hilsenbeck, C. Kent Osborne, Mothaffar Rimawi, Matthew J. Ellis, Varduhi Petrosyan, Alexander B. Saltzman, Anna Malovannaya, John D. Landua, Bo Wen, Antrix Jain, Gerburg M. Wulf, Shunqiang Li, Daniel C. Kraushaar, Tao Wang, Xi Chen, Gloria V. Echeverria, Meenakshi Anurag, Bing Zhang, Michael T. Lewis. Patient-derived xenografts allow deconvolution of single agent and combination chemotherapy responses in triple-negative breast cancer [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P2-23-01.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Bo Wen
- 17Baylor College of Medicine
| | | | | | - Shunqiang Li
- 20Washington University School of Medicine in St. Louis
| | | | - Tao Wang
- 22Duncan Cancer Center-Biostatistics, Baylor College of Medicine, Houston, TX, USA
| | - Xi Chen
- 23Baylor College of Medicine
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2
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Bhat R, Thangavel H, Abdulkareem NM, Vasaikar S, De Angelis C, Bae L, Cataldo ML, Nanda S, Fu X, Zhang B, Schiff R, Trivedi MV. NPY1R exerts inhibitory action on estradiol-stimulated growth and predicts endocrine sensitivity and better survival in ER-positive breast cancer. Sci Rep 2022; 12:1972. [PMID: 35121782 PMCID: PMC8817007 DOI: 10.1038/s41598-022-05949-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 01/13/2022] [Indexed: 12/25/2022] Open
Abstract
G Protein-Coupled Receptors (GPCRs) represent the largest superfamily of cell-surface proteins. However, the expression and function of majority of GPCRs remain unexplored in breast cancer (BC). We interrogated the expression and phosphorylation status of 398 non-sensory GPCRs using the landmark BC proteogenomics and phosphoproteomic dataset from The Cancer Genome Atlas. Neuropeptide Y Receptor Y1 (NPY1R) gene and protein expression were significantly higher in Luminal A tumors versus other BC subtypes. The trend of NPY1R gene, protein, and phosphosite (NPY1R-S368s) expression was decreasing in the order of Luminal A, Luminal B, Basal, and human epidermal growth factor receptor 2 (HER2) subtypes. NPY1R gene expression increased in response to estrogen and reduced with endocrine therapy in estrogen receptor-positive (ER+) BC cells and xenograft models. Conversely, NPY1R expression decreased in ER+ BC cells resistant to endocrine therapies (estrogen deprivation, tamoxifen, and fulvestrant) in vitro and in vivo. NPY treatment reduced estradiol-stimulated cell growth, which was reversed by NPY1R antagonist (BIBP-3226) in ER+ BC cells. Higher NPY1R gene expression predicted better relapse-free survival and overall survival in ER+ BC. Our study demonstrates that NPY1R mediates the inhibitory action of NPY on estradiol-stimulated growth of ER+ BC cells, and its expression serves as a biomarker to predict endocrine sensitivity and survival in ER+ BC patients.
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Affiliation(s)
- Raksha Bhat
- Department of Pharmacy Practice and Translational Research, University of Houston College of Pharmacy, 4849 Calhoun Rd, Houston, TX, 77204, USA
| | - Hariprasad Thangavel
- Department of Pharmacy Practice and Translational Research, University of Houston College of Pharmacy, 4849 Calhoun Rd, Houston, TX, 77204, USA
| | - Noor Mazin Abdulkareem
- Department of Pharmacological and Pharmaceutical Sciences, University of Houston College of Pharmacy, Houston, TX, 77204, USA
| | - Suhas Vasaikar
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Carmine De Angelis
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Clinical Medicine and Surgery, University of Naples Federico II, 80131, Naples, Italy
| | - Leon Bae
- Department of Pharmacy Practice and Translational Research, University of Houston College of Pharmacy, 4849 Calhoun Rd, Houston, TX, 77204, USA
| | - Maria Letizia Cataldo
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Sarmistha Nanda
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Xiaoyong Fu
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, 77030, USA.,Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Bing Zhang
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, 77030, USA.,Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Rachel Schiff
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, 77030, USA.,Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Medicine, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Meghana V Trivedi
- Department of Pharmacy Practice and Translational Research, University of Houston College of Pharmacy, 4849 Calhoun Rd, Houston, TX, 77204, USA. .,Department of Pharmacological and Pharmaceutical Sciences, University of Houston College of Pharmacy, Houston, TX, 77204, USA. .,Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, 77030, USA. .,Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA. .,Department of Medicine, Baylor College of Medicine, Houston, TX, 77030, USA.
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Abstract
Cancer stem cells (CSCs) are a small subpopulation of self-renewing cancer cells that are present within tumors. CSCs possess tumor initiation potential as well as the ability to resist toxic compounds and chemotherapeutic agents through the upregulation of drug efflux transporters, DNA repair pathways, and survival cascades. Accumulating evidence suggests that CSCs are responsible for tumor relapse and resistance to chemotherapeutic agents and that targeting CSCs is critical to inhibition of cancer progression. Therefore, isolation and characterization of CSCs is important in studying tumor initiation and progression. In this chapter, we provide a detailed method for the identification and isolation of CSCs.
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Affiliation(s)
- Abhijeet P Deshmukh
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Petra den Hollander
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Nick A Kuburich
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Suhas Vasaikar
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Robiya Joseph
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sendurai A Mani
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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den Hollander P, Joseph R, Vasaikar S, Kuburich NA, Deshmukh AP, Mani SA. Limiting Dilution Tumor Initiation Assay: An In Vivo Approach for the Study of Cancer Stem Cells. Methods Mol Biol 2022; 2429:547-554. [PMID: 35507188 DOI: 10.1007/978-1-0716-1979-7_38] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Cancer stem cells (CSCs) are a small subpopulation of self-renewing cancer cells that are present within tumors. Calculating the frequency of tumor-initiating cells is important in the assessment of the number of CSCs present in a cell population. In this chapter, we present a protocol developed for quantification of CSCs from breast cancer tumors that can be adapted to CSCs from other types of tumors.
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Affiliation(s)
- Petra den Hollander
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Robiya Joseph
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Suhas Vasaikar
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Nick A Kuburich
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Abhijeet P Deshmukh
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sendurai A Mani
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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5
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Kuburich NA, den Hollander P, Deshmukh AP, Vasaikar S, Joseph R, Wicha MS, Mani SA. In Vitro Quantification of Cancer Stem Cells Using a Mammosphere Formation Assay. Methods Mol Biol 2022; 2429:509-513. [PMID: 35507185 DOI: 10.1007/978-1-0716-1979-7_35] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Cancer stem cells (CSCs) are a small subpopulation of self-renewing cancer cells that are present within tumors. In this chapter, we provide a detailed method for the quantification of CSCs in vitro through mammosphere formation.
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Affiliation(s)
- Nick A Kuburich
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Petra den Hollander
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Abhijeet P Deshmukh
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Suhas Vasaikar
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Robiya Joseph
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Max S Wicha
- Forbes Institute for Cancer Discovery, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Sendurai A Mani
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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6
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Abdulkareem NM, Bhat R, Qin L, Vasaikar S, Gopinathan A, Mitchell T, Shea MJ, Nanda S, Thangavel H, Zhang B, De Angelis C, Schiff R, Trivedi MV. A novel role of ADGRF1 (GPR110) in promoting cellular quiescence and chemoresistance in human epidermal growth factor receptor 2-positive breast cancer. FASEB J 2021; 35:e21719. [PMID: 34110646 DOI: 10.1096/fj.202100070r] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 05/16/2021] [Accepted: 05/19/2021] [Indexed: 12/25/2022]
Abstract
While G protein-coupled receptors (GPCRs) are known to be excellent drug targets, the second largest family of adhesion-GPCRs is less explored for their role in health and disease. ADGRF1 (GPR110) is an adhesion-GPCR and has an important function in neurodevelopment and cancer. Despite serving as a poor predictor of survival, ADGRF1's coupling to G proteins and downstream pathways remain unknown in cancer. We evaluated the effects of ADGRF1 overexpression on tumorigenesis and signaling pathways using two human epidermal growth factor receptor-2-positive (HER2+) breast cancer (BC) cell-line models. We also interrogated publicly available clinical datasets to determine the expression of ADGRF1 in various BC subtypes and its impact on BC-specific survival (BCSS) and overall survival (OS) in patients. ADGRF1 overexpression in HER2+ BC cells increased secondary mammosphere formation, soft agar colony formation, and % of Aldefluor-positive tumorigenic population in vitro and promoted tumor growth in vivo. ADGRF1 co-immunoprecipitated with both Gαs and Gαq proteins and increased cAMP and IP1 when overexpressed. However, inhibition of only the Gαs pathway by SQ22536 reversed the pro-tumorigenic effects of ADGRF1 overexpression. RNA-sequencing and RPPA analysis revealed inhibition of cell cycle pathways with ADGRF1 overexpression, suggesting cellular quiescence, as also evidenced by cell cycle arrest at the G0/1 phase and resistance to chemotherapy in HER2+ BC. ADGRF1 was significantly overexpressed in the HER2-enriched BC compared to luminal A and B subtypes and predicted worse BCSS and OS in these patients. Therefore, ADGRF1 represents a novel drug target in HER2+ BC, warranting discovery of novel ADGRF1 antagonists.
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Affiliation(s)
- Noor Mazin Abdulkareem
- Department of Pharmacological and Pharmaceutical Sciences, University of Houston College of Pharmacy, Houston, TX, USA
| | - Raksha Bhat
- Department of Pharmacological and Pharmaceutical Sciences, University of Houston College of Pharmacy, Houston, TX, USA.,Department of Pharmacy Practice and Translational Research, University of Houston College of Pharmacy, Houston, TX, USA
| | - Lanfang Qin
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, USA
| | - Suhas Vasaikar
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, USA
| | - Ambily Gopinathan
- Department of Pharmacy Practice and Translational Research, University of Houston College of Pharmacy, Houston, TX, USA
| | - Tamika Mitchell
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, USA
| | - Martin J Shea
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, USA
| | - Sarmistha Nanda
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, USA
| | - Hariprasad Thangavel
- Department of Pharmacy Practice and Translational Research, University of Houston College of Pharmacy, Houston, TX, USA
| | - Bing Zhang
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Carmine De Angelis
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, USA.,Department of Clinical Medicine and Surgery, University of Naples, Federico II, Naples, Italy
| | - Rachel Schiff
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA.,Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Meghana V Trivedi
- Department of Pharmacological and Pharmaceutical Sciences, University of Houston College of Pharmacy, Houston, TX, USA.,Department of Pharmacy Practice and Translational Research, University of Houston College of Pharmacy, Houston, TX, USA.,Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, USA.,Department of Medicine, Baylor College of Medicine, Houston, TX, USA
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7
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Lei JT, Huang C, Srinivasan RR, Vasaikar S, Dobrolecki LE, Lewis AN, Sallas C, Hilsenbeck SG, Osborne CK, Rimawi MF, Ellis MJ, Petrosyan V, Saltzman AB, Malovannaya A, Wulf G, Kraushaar DC, Wang T, Echeverria GV, Zhang B, Lewis MT. Abstract 2992: Proteogenomic characterization of triple-negative breast cancer patient-derived xenografts reveals molecular correlates of differential chemotherapy response and potential therapeutic targets to overcome resistance. Cancer Res 2021. [DOI: 10.1158/1538-7445.am2021-2992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Chemotherapy is essential for the management of patients with triple-negative breast cancer (TNBC). Identification of biomarkers that may indicate treatment efficacy will be critical to improve patient stratification prior to treatment. To elucidate molecular determinants underlying chemotherapy response, we conducted a proteogenomic study using TNBC patient-derived xenografts (PDXs) treated with chemotherapy.
Approach: 50 TNBC PDXs were treated with either docetaxel or carboplatin. Changes in tumor volume after 4 weeks from baseline were evaluated. Genomic, transcriptomic, and mass-spectrometry-based proteomic profiling were performed on baseline tumors prior to treatment to identify associations with chemotherapy response. Fisher's exact tests were used to test for significant enrichment of mutation and copy number events (p<0.05). Gene Set Enrichment Analysis was performed for pathway analyses.
Results: At the DNA level, genomic aberrations in BRCA2 and BCL2 were enriched in carboplatin-responsive PDXs, while ARID1B aberrations were enriched in docetaxel-responsive PDXs. Gene-drug response correlations supported by both mRNA and protein-based measurements, but not mRNA or protein alone, for both carboplatin and docetaxel treatment in PDXs were associated with prognosis from basal and claudin-low human breast tumors in receipt of any chemotherapy from the METABRIC dataset. These data suggest that the combination of mRNA and protein data increased power to identify genes related to clinical outcome in TNBC. Some of the top genes overexpressed at both mRNA and protein levels in chemoresistant PDXs are targets of approved drugs, many of which have not been evaluated for their ability to augment response to taxane- or platinum-based chemotherapies. These genes are being investigated as therapeutic targets as well as markers of chemotherapy response. At the pathway level, both RNA and protein data associated models resistant to both agents with enhanced oxidative phosphorylation and translation regulation. Protein data further associated resistant models with elevated cytoplasmic ribosomal proteins. In contrast, both RNA and protein data associated tumors sensitive to both agents with genes involved in the E2F-Rb axis and cell cycle progression. Moreover, DNA mismatch repair and mRNA processing pathways were uniquely associated with carboplatin and docetaxel sensitivity, respectively, while amino acid metabolism and MAPK signaling pathways were uniquely associated with carboplatin and docetaxel resistance, respectively.
Conclusion: Taken together, proteogenomic analysis of PDX tumors identifies diverse genes and pathways associated with chemotherapy response and further suggests potential therapeutic opportunities in TNBC.
Citation Format: Jonathan T. Lei, Chen Huang, Ramakrishnan R. Srinivasan, Suhas Vasaikar, Lacey E. Dobrolecki, Alaina N. Lewis, Christina Sallas, Susan G. Hilsenbeck, C Kent Osborne, Mothaffar F. Rimawi, Matthew J. Ellis, Varduhi Petrosyan, Alexander B. Saltzman, Anna Malovannaya, Gerburg Wulf, Daniel C. Kraushaar, Tao Wang, Gloria V. Echeverria, Bing Zhang, Michael T. Lewis. Proteogenomic characterization of triple-negative breast cancer patient-derived xenografts reveals molecular correlates of differential chemotherapy response and potential therapeutic targets to overcome resistance [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 2992.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Tao Wang
- 1Baylor College of Medicine, Houston, TX
| | | | - Bing Zhang
- 1Baylor College of Medicine, Houston, TX
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8
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Abdulkareem N, Bhat R, Qin L, Vasaikar S, Gopinathan A, Nanda S, Thangavel H, Zhang B, Angelis C, Schiff R, Trivedi M. A novel role of ADGRF1 (GPR110) in promoting cellular quiescence and chemoresistance in human epidermal growth factor receptor 2‐positive breast cancer. FASEB J 2021. [DOI: 10.1096/fasebj.2021.35.s1.00353] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Noor Abdulkareem
- Pharmacological and Pharmaceutical SciencesUniversity of HoustonHoustonTX
| | | | - Lanfang Qin
- Lester and Sue Smith Breast CenterBaylor College of MedicineHoustonTX
| | - Suhas Vasaikar
- Lester and Sue Smith Breast CenterBaylor College of MedicineHoustonTX
| | | | - Sarmistha Nanda
- Lester and Sue Smith Breast CenterBaylor College of MedicineHoustonTX
| | | | - Bing Zhang
- Lester and Sue Smith Breast CenterBaylor College of MedicineHoustonTX
| | - Carmine Angelis
- Lester and Sue Smith Breast CenterBaylor College of MedicineHoustonTX
- Baylor College of MedicineHoustonTX
| | - Rachel Schiff
- Lester and Sue Smith Breast CenterBaylor College of MedicineHoustonTX
| | - Meghana Trivedi
- University of HoustonHoustonTX
- Lester and Sue Smith Breast CenterUniversity of HoustonHoustonTX
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Anurag M, Zhu M, Huang C, Vasaikar S, Wang J, Hoog J, Burugu S, Gao D, Suman V, Zhang XH, Zhang B, Nielsen T, Ellis MJ. Immune Checkpoint Profiles in Luminal B Breast Cancer (Alliance). J Natl Cancer Inst 2021; 112:737-746. [PMID: 31665365 DOI: 10.1093/jnci/djz213] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 09/12/2019] [Accepted: 10/25/2019] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Unlike estrogen receptor (ER)-negative breast cancer, ER-positive breast cancer outcome is less influenced by lymphocyte content, indicating the presence of immune tolerance mechanisms that may be specific to this disease subset. METHODS A supervised analysis of microarray data from the ACOSOG Z1031 (Alliance) neoadjuvant aromatase inhibitor (AI) trial identified upregulated genes in Luminal (Lum) B breast cancers that correlated with AI-resistant tumor proliferation (percentage of Ki67-positive cancer nuclei, Pearson r > 0.4) (33 cases Ki67 > 10% on AI) vs LumB breast cancers that were more AI sensitive (33 cases Ki67 < 10% on AI). Overrepresentation analysis was performed using WebGestalt. All statistical tests were two-sided. RESULTS Thirty candidate genes positively correlated (r ≥ 0.4) with AI-resistant proliferation in LumB and were upregulated greater than twofold. Gene ontologies identified that the targetable immune checkpoint (IC) components IDO1, LAG3, and PD1 were overrepresented resistance candidates (P ≤ .001). High IDO1 mRNA was associated with poor prognosis in LumB disease (Molecular Taxonomy of Breast Cancer International Consortium, hazard ratio = 1.43, 95% confidence interval = 1.04 to 1.98, P = .03). IDO1 also statistically significantly correlated with STAT1 at protein level in LumB disease (Pearson r = 0.74). As a composite immune tolerance signature, expression of IFN-γ/STAT1 pathway components was associated with higher baseline Ki67, lower estrogen, and progesterone receptor mRNA levels and worse disease-specific survival (P = .002). In a tissue microarray analysis, IDO1 was observed in stromal cells and tumor-associated macrophages, with a higher incidence in LumB cases. Furthermore, IDO1 expression was associated with a macrophage mRNA signature (M1 by CIBERSORT Pearson r = 0.62 ) and by tissue microarray analysis. CONCLUSIONS Targetable IC components are upregulated in the majority of endocrine therapy-resistant LumB cases. Our findings provide rationale for IC inhibition in poor-outcome ER-positive breast cancer.
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MESH Headings
- Antigens, CD/biosynthesis
- Antigens, CD/genetics
- Antigens, CD/immunology
- Antineoplastic Agents, Hormonal/therapeutic use
- Aromatase Inhibitors/therapeutic use
- Breast Neoplasms/drug therapy
- Breast Neoplasms/genetics
- Breast Neoplasms/immunology
- Cell Proliferation/physiology
- Drug Resistance, Neoplasm
- Female
- Humans
- Immune Tolerance
- Indoleamine-Pyrrole 2,3,-Dioxygenase/biosynthesis
- Indoleamine-Pyrrole 2,3,-Dioxygenase/genetics
- Indoleamine-Pyrrole 2,3,-Dioxygenase/immunology
- Interferon-gamma/metabolism
- Letrozole/therapeutic use
- Prognosis
- Programmed Cell Death 1 Receptor/biosynthesis
- Programmed Cell Death 1 Receptor/genetics
- Programmed Cell Death 1 Receptor/immunology
- STAT1 Transcription Factor/metabolism
- Signal Transduction
- Tissue Array Analysis
- Transcriptome
- Up-Regulation
- Lymphocyte Activation Gene 3 Protein
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10
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Zheng ZY, Anurag M, Lei JT, Cao J, Singh P, Peng J, Kennedy H, Nguyen NC, Chen Y, Lavere P, Li J, Du XH, Cakar B, Song W, Kim BJ, Shi J, Seker S, Chan DW, Zhao GQ, Chen X, Banks KC, Lanman RB, Shafaee MN, Zhang XHF, Vasaikar S, Zhang B, Hilsenbeck SG, Li W, Foulds CE, Ellis MJ, Chang EC. Neurofibromin Is an Estrogen Receptor-α Transcriptional Co-repressor in Breast Cancer. Cancer Cell 2020; 37:387-402.e7. [PMID: 32142667 PMCID: PMC7286719 DOI: 10.1016/j.ccell.2020.02.003] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 11/15/2019] [Accepted: 02/06/2020] [Indexed: 12/18/2022]
Abstract
We report that neurofibromin, a tumor suppressor and Ras-GAP (GTPase-activating protein), is also an estrogen receptor-α (ER) transcriptional co-repressor through leucine/isoleucine-rich motifs that are functionally independent of GAP activity. GAP activity, in turn, does not affect ER binding. Consequently, neurofibromin depletion causes estradiol hypersensitivity and tamoxifen agonism, explaining the poor prognosis associated with neurofibromin loss in endocrine therapy-treated ER+ breast cancer. Neurofibromin-deficient ER+ breast cancer cells initially retain sensitivity to selective ER degraders (SERDs). However, Ras activation does play a role in acquired SERD resistance, which can be reversed upon MEK inhibitor addition, and SERD/MEK inhibitor combinations induce tumor regression. Thus, neurofibromin is a dual repressor for both Ras and ER signaling, and co-targeting may treat neurofibromin-deficient ER+ breast tumors.
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Affiliation(s)
- Ze-Yi Zheng
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Meenakshi Anurag
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Jonathan T Lei
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA; Interdepartmental Program in Translational Biology and Molecular Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Jin Cao
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Purba Singh
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Jianheng Peng
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA; Department of Physical Examination, the First Affiliated Hospital of Chongqing Medical University, Chongqing, P.R. China
| | - Hilda Kennedy
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Nhu-Chau Nguyen
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Yue Chen
- Adrienne Helis Malvin Medical Research Foundation, New Orleans, LA, USA
| | - Philip Lavere
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Jing Li
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Xin-Hui Du
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA; Department of Bone and Soft Tissue, Zhengzhou University Affiliated Henan Cancer Hospital and College of Basic Medical Sciences, Zhengzhou University, Zhengzhou, P. R. China
| | - Burcu Cakar
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Wei Song
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Beom-Jun Kim
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Jiejun Shi
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Sinem Seker
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Doug W Chan
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Guo-Qiang Zhao
- Department of Bone and Soft Tissue, Zhengzhou University Affiliated Henan Cancer Hospital and College of Basic Medical Sciences, Zhengzhou University, Zhengzhou, P. R. China
| | - Xi Chen
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | | | | | - Maryam Nemati Shafaee
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Xiang H-F Zhang
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Suhas Vasaikar
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Bing Zhang
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Susan G Hilsenbeck
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Wei Li
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Charles E Foulds
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA; Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX, USA
| | - Matthew J Ellis
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA; Department of Medicine, Baylor College of Medicine, Houston, TX, USA.
| | - Eric C Chang
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA.
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11
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Dou Y, Kawaler EA, Cui Zhou D, Gritsenko MA, Huang C, Blumenberg L, Karpova A, Petyuk VA, Savage SR, Satpathy S, Liu W, Wu Y, Tsai CF, Wen B, Li Z, Cao S, Moon J, Shi Z, Cornwell M, Wyczalkowski MA, Chu RK, Vasaikar S, Zhou H, Gao Q, Moore RJ, Li K, Sethuraman S, Monroe ME, Zhao R, Heiman D, Krug K, Clauser K, Kothadia R, Maruvka Y, Pico AR, Oliphant AE, Hoskins EL, Pugh SL, Beecroft SJI, Adams DW, Jarman JC, Kong A, Chang HY, Reva B, Liao Y, Rykunov D, Colaprico A, Chen XS, Czekański A, Jędryka M, Matkowski R, Wiznerowicz M, Hiltke T, Boja E, Kinsinger CR, Mesri M, Robles AI, Rodriguez H, Mutch D, Fuh K, Ellis MJ, DeLair D, Thiagarajan M, Mani DR, Getz G, Noble M, Nesvizhskii AI, Wang P, Anderson ML, Levine DA, Smith RD, Payne SH, Ruggles KV, Rodland KD, Ding L, Zhang B, Liu T, Fenyö D. Proteogenomic Characterization of Endometrial Carcinoma. Cell 2020; 180:729-748.e26. [PMID: 32059776 PMCID: PMC7233456 DOI: 10.1016/j.cell.2020.01.026] [Citation(s) in RCA: 247] [Impact Index Per Article: 61.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 11/11/2019] [Accepted: 01/16/2020] [Indexed: 02/07/2023]
Abstract
We undertook a comprehensive proteogenomic characterization of 95 prospectively collected endometrial carcinomas, comprising 83 endometrioid and 12 serous tumors. This analysis revealed possible new consequences of perturbations to the p53 and Wnt/β-catenin pathways, identified a potential role for circRNAs in the epithelial-mesenchymal transition, and provided new information about proteomic markers of clinical and genomic tumor subgroups, including relationships to known druggable pathways. An extensive genome-wide acetylation survey yielded insights into regulatory mechanisms linking Wnt signaling and histone acetylation. We also characterized aspects of the tumor immune landscape, including immunogenic alterations, neoantigens, common cancer/testis antigens, and the immune microenvironment, all of which can inform immunotherapy decisions. Collectively, our multi-omic analyses provide a valuable resource for researchers and clinicians, identify new molecular associations of potential mechanistic significance in the development of endometrial cancers, and suggest novel approaches for identifying potential therapeutic targets.
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Affiliation(s)
- Yongchao Dou
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Emily A Kawaler
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU School of Medicine, New York, NY 10016, USA
| | - Daniel Cui Zhou
- Department of Medicine and Genetics, Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Marina A Gritsenko
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Chen Huang
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Lili Blumenberg
- Department of Medicine, NYU School of Medicine, New York, NY 10016, USA
| | - Alla Karpova
- Department of Medicine and Genetics, Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Vladislav A Petyuk
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Sara R Savage
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Shankha Satpathy
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Wenke Liu
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU School of Medicine, New York, NY 10016, USA
| | - Yige Wu
- Department of Medicine and Genetics, Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Chia-Feng Tsai
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Bo Wen
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Zhi Li
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU School of Medicine, New York, NY 10016, USA
| | - Song Cao
- Department of Medicine and Genetics, Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Jamie Moon
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Zhiao Shi
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - MacIntosh Cornwell
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU School of Medicine, New York, NY 10016, USA
| | - Matthew A Wyczalkowski
- Department of Medicine and Genetics, Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Rosalie K Chu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Suhas Vasaikar
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Hua Zhou
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU School of Medicine, New York, NY 10016, USA
| | - Qingsong Gao
- Department of Medicine and Genetics, Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Ronald J Moore
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Kai Li
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sunantha Sethuraman
- Department of Medicine and Genetics, Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Matthew E Monroe
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Rui Zhao
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - David Heiman
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Karsten Krug
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Karl Clauser
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ramani Kothadia
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Yosef Maruvka
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Alexander R Pico
- Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA 94158, USA
| | - Amanda E Oliphant
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
| | - Emily L Hoskins
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
| | - Samuel L Pugh
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
| | - Sean J I Beecroft
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
| | - David W Adams
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
| | - Jonathan C Jarman
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
| | - Andy Kong
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Hui-Yin Chang
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Boris Reva
- Department of Genetics and Genomic Sciences, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Yuxing Liao
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Dmitry Rykunov
- Department of Genetics and Genomic Sciences, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Antonio Colaprico
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Division of Biostatistics, Department of Public Health Science, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Xi Steven Chen
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Division of Biostatistics, Department of Public Health Science, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Andrzej Czekański
- Department of Oncology, Wroclaw Medical University, 50-367 Wrocław, Poland; Wroclaw Comprehensive Cancer Center, 53-413 Wrocław, Poland
| | - Marcin Jędryka
- Department of Oncology, Wroclaw Medical University, 50-367 Wrocław, Poland; Wroclaw Comprehensive Cancer Center, 53-413 Wrocław, Poland
| | - Rafał Matkowski
- Department of Oncology, Wroclaw Medical University, 50-367 Wrocław, Poland; Wroclaw Comprehensive Cancer Center, 53-413 Wrocław, Poland
| | - Maciej Wiznerowicz
- Poznan University of Medical Sciences, 61-701 Poznań, Poland; University Hospital of Lord's Transfiguration, 60-569 Poznań, Poland; International Institute for Molecular Oncology, 60-203 Poznań, Poland
| | - Tara Hiltke
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Emily Boja
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Christopher R Kinsinger
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Mehdi Mesri
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Ana I Robles
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Henry Rodriguez
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - David Mutch
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Katherine Fuh
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Matthew J Ellis
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Deborah DeLair
- Department of Pathology, NYU Langone Health, New York, NY 10016, USA
| | - Mathangi Thiagarajan
- Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - D R Mani
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Gad Getz
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Michael Noble
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Alexey I Nesvizhskii
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Pei Wang
- Department of Genetics and Genomic Sciences, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Matthew L Anderson
- College of Medicine Obstetrics & Gynecology, University of South Florida Health, Tampa, FL 33620, USA
| | - Douglas A Levine
- Gynecologic Oncology, Laura and Isaac Perlmutter Cancer Center, NYU Langone Health, New York, NY 10016, USA
| | - Richard D Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Samuel H Payne
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
| | - Kelly V Ruggles
- Department of Medicine, NYU School of Medicine, New York, NY 10016, USA
| | - Karin D Rodland
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA; Department of Cell, Developmental, and Cancer Biology, Oregon Health & Science University, Portland, OR 97221, USA.
| | - Li Ding
- Department of Medicine and Genetics, Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA.
| | - Bing Zhang
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Tao Liu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA.
| | - David Fenyö
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU School of Medicine, New York, NY 10016, USA.
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12
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Satpathy S, Jaehnig E, Karsten K, Kim BJ, Saltzman A, Chan D, Holloway K, Anurag M, Huang C, Singh P, Gao A, Namai N, Dou Y, Wen B, Vasaikar S, Mutch D, Watson M, Ma C, Ademuyiwa F, Rimawi M, Hoog J, Jacobs S, Malovannaya A, Hyslop T, Mani D, Perou C, Miles G, Zhang B, Gillette M, Carr S, Ellis M. Abstract GS2-05: Microscaled proteogenomic methods for precision oncology. Cancer Res 2020. [DOI: 10.1158/1538-7445.sabcs19-gs2-05] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Cancer proteogenomics combines genomics, transcriptomics and mass spectrometry-based proteomics to gain insights into cancer biology and treatment responsiveness. While proteogenomics analyses have already shown great potential to deepen our understanding of cancer tissue complexity and signaling, how a patient’s tumor changes upon treatment has largely been the province of genomics. This is due to technical difficulties associated with doing proteogenomic analysis on clinic-derived core-needle biopsies. To address this critical need, we have developed a “microscaled” proteogenomics approach for tumor-rich OCT-embedded core needle biopsies. Tissue-sparing specimen processing (“Biopsy Trifecta EXTraction”, BioTExt) and microscaled proteomics (MiProt) methodologies allowed generation of deep-scale proteogenomics datasets, with copy number and transcript information for >20,000 genes and mass spectrometry-based identification and quantification of nearly all expressed proteins in a tumor (>10,000 proteins) and more than >20,000 phosphosites starting with just 25 micrograms of protein per sample. In order to understand the capabilities and limitations our our approach relative to more conventional deepscale proteomics requiring >10X more starting material, we compared preclinical patient derived xenograft (PDX) models at conventional scale with data obtained by core-needle biopsy of the same tissues. Comparable depth and biological insights were obtained from the cores relative to surgically resected tumors. As a proof-of-concept for implementation in clinical trials, we applied microscaled proteogenomic methods to a small-scale clinical study where biopsies were accrued from patients with ERBB2+ locally advanced breast cancer before and 48 to 72 hours after the first dose of neoadjuvant Trastuzumab-based chemotherapy. Multi-omics comparisons were conducted between samples associated with residual disease versus samples associated with complete pathological response. Integrative, microscaled proteogenomic analyses efficiently diagnosed the molecular bases of diverse candidate treatment resistance mechanisms including: 1) absence of ERBB2 amplification (false-ERBB2+); 2) insufficient ERBB2 activity for therapeutic sensitivity despite ERBB2 amplification (pseudo-ERBB2+); 3) resistance features in true-ERBB2+ cases including androgen receptor signaling, mucin expression and an inactive immune microenvironment; 4) lack of acute phospho-ERBB2 down-regulation in non-pCR cases. In summary, we have developed a robust proteogenomics pipeline well suited for large-scale cancer clinical studies to identify potential resistance mechanism in patients. We conclude that microscaled cancer proteogenomics could improve diagnostic precision in the clinical setting.
Citation Format: Shankha Satpathy, Eric Jaehnig, Krug Karsten, Beom-Jun Kim, Alexander Saltzman, Doug Chan, Kimberly Holloway, Meenakshi Anurag, Chen Huang, Purba Singh, Ari Gao, Noel Namai, Yongchao Dou, Bo Wen, Suhas Vasaikar, David Mutch, Mark Watson, Cynthia Ma, Foluso Ademuyiwa, Mothaffar Rimawi, Jeremy Hoog, Samuel Jacobs, Anna Malovannaya, Terry Hyslop, D.R Mani, Charles Perou, George Miles, Bing Zhang, Michael Gillette, Steven Carr, Matthew Ellis. Microscaled proteogenomic methods for precision oncology [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr GS2-05.
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Affiliation(s)
| | | | | | | | | | - Doug Chan
- 2Baylor College of Medicine, Houston, TX
| | | | | | - Chen Huang
- 2Baylor College of Medicine, Houston, TX
| | | | - Ari Gao
- 2Baylor College of Medicine, Houston, TX
| | - Noel Namai
- 2Baylor College of Medicine, Houston, TX
| | | | - Bo Wen
- 2Baylor College of Medicine, Houston, TX
| | | | - David Mutch
- 3Siteman Comprehensive Cancer Center and Washington University School of Medicine, St. Louis, MO
| | - Mark Watson
- 3Siteman Comprehensive Cancer Center and Washington University School of Medicine, St. Louis, MO
| | - Cynthia Ma
- 3Siteman Comprehensive Cancer Center and Washington University School of Medicine, St. Louis, MO
| | - Foluso Ademuyiwa
- 3Siteman Comprehensive Cancer Center and Washington University School of Medicine, St. Louis, MO
| | | | - Jeremy Hoog
- 3Siteman Comprehensive Cancer Center and Washington University School of Medicine, St. Louis, MO
| | - Samuel Jacobs
- 4National Surgical Adjuvant Breast and Bowel Project (NSABP) Foundation, Pittsburgh, PA
| | | | | | - D.R Mani
- 1Broad Institute of MIT and Harvard, Boston, MA
| | - Charles Perou
- 6Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | | | - Bing Zhang
- 2Baylor College of Medicine, Houston, TX
| | | | - Steven Carr
- 1Broad Institute of MIT and Harvard, Boston, MA
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13
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Seth S, Huo L, Vasaikar S, Rauch G, Lim B, White J, Adrada B, Piwnica-Worms H, Ueno NT, Thompson AM, Mittendorf E, Tripathy D, Litton JK, Symmans WF, Draetta G, Futreal A, Chang J, Moulder S. Abstract P2-16-08: Longitudinal response and selection under neoadjuvant systemic therapy (NAST) in triple-negative breast cancer (TNBC): Profiling results from a randomized, TNBC enrolling trial to confirm molecular profiling improves survival (ARTEMIS; NCT02276443). Cancer Res 2020. [DOI: 10.1158/1538-7445.sabcs19-p2-16-08] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: The heterogeneity of TNBC results in a spectrum of responses to NAST: 30-40% of patients (pts) have pathologic complete response (pCR) with excellent prognosis. Several methods have been used to measure and evaluate residual disease, including ultrasound, MRI scans, histo-pathology and transcriptional profiling (Seth, ASCO 2019). In addition, we hypothesize that integrative understanding of sub-clonal selection and changes in molecular pathways would lead to better stratification as a biomarker for chemotherapy, and subsequent targeted therapy trials. Methods: Pts with stage I-III TNBC began a planned 4 cycles of Adriamycin-based chemo (AC). Biopsies were performed pre (mandatory) and post (optional) AC. Volumetric change by ultrasound (VUS) at completion of AC (or progression) was calculated. Pts with sensitive disease received subsequent taxane-based (T) therapy. Pts with insensitive disease were offered phase II trials. Pathologic response was assessed at surgical resection in 55 pts. Matched samples, pre and post AC (N = 55 pts) underwent transcriptomic and genomic profiling. Samples were classified into six previously identified ARTEMIS subtypes of TNBC (ART-Type) and immune deconvolution and estimation was performed using RNA-Seq profiles. Somatic mutations and copy-number changes were evaluated using, Mutect, FACETS, and PyClone. Results: Predominately, tumors reacted to AC in 4 different patterns with variation in immune and EMT related pathways. Enrichment of EMT (Group 4) was associated with poor prognosis and higher RCB (10.3% vs 42% pCR rates, p<0.05). The global changes in transcription led to ART-Type switching in all subtypes (44% of pts), except LAR subtype. MYC amplification was more prevalent (40%) in Group 4, associated with higher EMT and poor prognosis than other groups (28%). Phylogenetic evaluation of selection revealed, sub-clonal selection in 22% of evaluable cases with pre and post biopsies. Conclusions: Molecular profiling of longitudinal TNBC samples reveals distinct response patterns in tumors and their micro-environments upon treatment with AC. Integrative analysis of genomic and transcriptomic changes can lead to better stratification of response to NAST. These patterns were indicative of pathologic response in this cohort; however, they require validation in a separate cohort.
Citation Format: Sahil Seth, Lei Huo, Suhas Vasaikar, Gaiane Rauch, Bora Lim, Jason White, Beatriz Adrada, Helen Piwnica-Worms, Naoto T Ueno, Alastair Mark Thompson, Elizabeth Mittendorf, Debashish Tripathy, Jennifer Keating Litton, William Fraser Symmans, Giulio Draetta, Andrew Futreal, Jeffrey Chang, Stacy Moulder. Longitudinal response and selection under neoadjuvant systemic therapy (NAST) in triple-negative breast cancer (TNBC): Profiling results from a randomized, TNBC enrolling trial to confirm molecular profiling improves survival (ARTEMIS; NCT02276443) [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P2-16-08.
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Affiliation(s)
| | - Lei Huo
- MD Anderson Cancer Center, Houston, TX
| | | | | | - Bora Lim
- MD Anderson Cancer Center, Houston, TX
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14
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Gillette M, Satpathy S, Cao S, Dhanasekaran S, Vasaikar S, Krug K, Petralia F, Li Y, Liang WW, Reva B, Hong R, Savage S, Getz G, Li Q, Zhang B, Rodriguez H, Ruggles K, Robles A, Clauser K, Govindan R, Wang P, Nesvizhskii A, Ding L, Mani D, Carr S. A02 Proteogenomic Characterization Reveals Therapeutic Vulnerabilities in Lung Adenocarcinoma. J Thorac Oncol 2020. [DOI: 10.1016/j.jtho.2019.12.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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15
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Clark DJ, Dhanasekaran SM, Petralia F, Pan J, Song X, Hu Y, da Veiga Leprevost F, Reva B, Lih TSM, Chang HY, Ma W, Huang C, Ricketts CJ, Chen L, Krek A, Li Y, Rykunov D, Li QK, Chen LS, Ozbek U, Vasaikar S, Wu Y, Yoo S, Chowdhury S, Wyczalkowski MA, Ji J, Schnaubelt M, Kong A, Sethuraman S, Avtonomov DM, Ao M, Colaprico A, Cao S, Cho KC, Kalayci S, Ma S, Liu W, Ruggles K, Calinawan A, Gümüş ZH, Geiszler D, Kawaler E, Teo GC, Wen B, Zhang Y, Keegan S, Li K, Chen F, Edwards N, Pierorazio PM, Chen XS, Pavlovich CP, Hakimi AA, Brominski G, Hsieh JJ, Antczak A, Omelchenko T, Lubinski J, Wiznerowicz M, Linehan WM, Kinsinger CR, Thiagarajan M, Boja ES, Mesri M, Hiltke T, Robles AI, Rodriguez H, Qian J, Fenyö D, Zhang B, Ding L, Schadt E, Chinnaiyan AM, Zhang Z, Omenn GS, Cieslik M, Chan DW, Nesvizhskii AI, Wang P, Zhang H. Integrated Proteogenomic Characterization of Clear Cell Renal Cell Carcinoma. Cell 2020; 180:207. [PMID: 31923397 DOI: 10.1016/j.cell.2019.12.026] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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16
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Sato S, Vasaikar S, Eskaros A, Kim Y, Lewis JS, Zhang B, Zijlstra A, Weaver AM. EPHB2 carried on small extracellular vesicles induces tumor angiogenesis via activation of ephrin reverse signaling. JCI Insight 2019; 4:132447. [PMID: 31661464 DOI: 10.1172/jci.insight.132447] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 10/23/2019] [Indexed: 12/19/2022] Open
Abstract
Angiogenesis is a key process that allows nutrient uptake and cellular trafficking and is coopted in cancer to enable tumor growth and metastasis. Recently, extracellular vesicles (EVs) have been shown to promote angiogenesis; however, it is unclear what unique features EVs contribute to the process. Here, we studied the role of EVs derived from head and neck squamous cell carcinoma (HNSCC) in driving tumor angiogenesis. Small EVs (SEVs), in the size range of exosomes (50-150 nm), induced angiogenesis both in vitro and in vivo. Proteomic analysis of HNSCC SEVs revealed the cell-to-cell signaling receptor ephrin type B receptor 2 (EPHB2) as a promising candidate cargo to promote angiogenesis. Analysis of patient data further identified EPHB2 overexpression in HNSCC tumors to be associated with poor patient prognosis and tumor angiogenesis, especially in the context of overexpression of the exosome secretion regulator cortactin. Functional experiments revealed that EPHB2 expression in SEVs regulated angiogenesis both in vitro and in vivo and that EPHB2 carried by SEVs stimulates ephrin-B reverse signaling, inducing STAT3 phosphorylation. A STAT3 inhibitor greatly reduced SEV-induced angiogenesis. These data suggest a model in which EVs uniquely promote angiogenesis by transporting Eph transmembrane receptors to nonadjacent endothelial cells to induce ephrin reverse signaling.
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Affiliation(s)
- Shinya Sato
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Suhas Vasaikar
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Adel Eskaros
- Department of Pathology, Microbiology and Immunology, and
| | - Young Kim
- Department of Otolaryngology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - James S Lewis
- Department of Pathology, Microbiology and Immunology, and
| | - Bing Zhang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | | | - Alissa M Weaver
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA.,Department of Pathology, Microbiology and Immunology, and
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17
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Clark DJ, Dhanasekaran SM, Petralia F, Pan J, Song X, Hu Y, da Veiga Leprevost F, Reva B, Lih TSM, Chang HY, Ma W, Huang C, Ricketts CJ, Chen L, Krek A, Li Y, Rykunov D, Li QK, Chen LS, Ozbek U, Vasaikar S, Wu Y, Yoo S, Chowdhury S, Wyczalkowski MA, Ji J, Schnaubelt M, Kong A, Sethuraman S, Avtonomov DM, Ao M, Colaprico A, Cao S, Cho KC, Kalayci S, Ma S, Liu W, Ruggles K, Calinawan A, Gümüş ZH, Geiszler D, Kawaler E, Teo GC, Wen B, Zhang Y, Keegan S, Li K, Chen F, Edwards N, Pierorazio PM, Chen XS, Pavlovich CP, Hakimi AA, Brominski G, Hsieh JJ, Antczak A, Omelchenko T, Lubinski J, Wiznerowicz M, Linehan WM, Kinsinger CR, Thiagarajan M, Boja ES, Mesri M, Hiltke T, Robles AI, Rodriguez H, Qian J, Fenyö D, Zhang B, Ding L, Schadt E, Chinnaiyan AM, Zhang Z, Omenn GS, Cieslik M, Chan DW, Nesvizhskii AI, Wang P, Zhang H. Integrated Proteogenomic Characterization of Clear Cell Renal Cell Carcinoma. Cell 2019; 179:964-983.e31. [PMID: 31675502 PMCID: PMC7331093 DOI: 10.1016/j.cell.2019.10.007] [Citation(s) in RCA: 357] [Impact Index Per Article: 71.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 07/15/2019] [Accepted: 10/07/2019] [Indexed: 02/07/2023]
Abstract
To elucidate the deregulated functional modules that drive clear cell renal cell carcinoma (ccRCC), we performed comprehensive genomic, epigenomic, transcriptomic, proteomic, and phosphoproteomic characterization of treatment-naive ccRCC and paired normal adjacent tissue samples. Genomic analyses identified a distinct molecular subgroup associated with genomic instability. Integration of proteogenomic measurements uniquely identified protein dysregulation of cellular mechanisms impacted by genomic alterations, including oxidative phosphorylation-related metabolism, protein translation processes, and phospho-signaling modules. To assess the degree of immune infiltration in individual tumors, we identified microenvironment cell signatures that delineated four immune-based ccRCC subtypes characterized by distinct cellular pathways. This study reports a large-scale proteogenomic analysis of ccRCC to discern the functional impact of genomic alterations and provides evidence for rational treatment selection stemming from ccRCC pathobiology.
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Affiliation(s)
- David J Clark
- Department of Pathology, Johns Hopkins University, Baltimore, MD 21231, USA
| | | | - Francesca Petralia
- Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jianbo Pan
- Department of Pathology, Johns Hopkins University, Baltimore, MD 21231, USA
| | - Xiaoyu Song
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Yingwei Hu
- Department of Pathology, Johns Hopkins University, Baltimore, MD 21231, USA
| | | | - Boris Reva
- Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Tung-Shing M Lih
- Department of Pathology, Johns Hopkins University, Baltimore, MD 21231, USA
| | - Hui-Yin Chang
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Weiping Ma
- Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Chen Huang
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Christopher J Ricketts
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lijun Chen
- Department of Pathology, Johns Hopkins University, Baltimore, MD 21231, USA
| | - Azra Krek
- Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Yize Li
- Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Dmitry Rykunov
- Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Qing Kay Li
- Department of Pathology, Johns Hopkins University, Baltimore, MD 21231, USA
| | - Lin S Chen
- Department of Public Health Sciences, University of Chicago, Chicago, IL 60637, USA
| | - Umut Ozbek
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Suhas Vasaikar
- Department of Translational Molecular Pathology, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yige Wu
- Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Seungyeul Yoo
- Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Shrabanti Chowdhury
- Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | | | - Jiayi Ji
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Michael Schnaubelt
- Department of Pathology, Johns Hopkins University, Baltimore, MD 21231, USA
| | - Andy Kong
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Dmitry M Avtonomov
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Minghui Ao
- Department of Pathology, Johns Hopkins University, Baltimore, MD 21231, USA
| | - Antonio Colaprico
- Department of Public Health Sciences, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Song Cao
- Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Kyung-Cho Cho
- Department of Pathology, Johns Hopkins University, Baltimore, MD 21231, USA
| | - Selim Kalayci
- Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Shiyong Ma
- Department of Pathology, Johns Hopkins University, Baltimore, MD 21231, USA
| | - Wenke Liu
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | - Kelly Ruggles
- Department of Medicine, New York University School of Medicine, New York, NY 10016, USA
| | - Anna Calinawan
- Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Zeynep H Gümüş
- Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Daniel Geiszler
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Emily Kawaler
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | - Guo Ci Teo
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Bo Wen
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yuping Zhang
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Sarah Keegan
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | - Kai Li
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Feng Chen
- Departments of Medicine and Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Nathan Edwards
- Department of Biochemistry and Cellular Biology, Georgetown University, Washington, DC 20007, USA
| | - Phillip M Pierorazio
- Brady Urological Institute and Department of Urology, Johns Hopkins University, Baltimore, MD 21231, USA
| | - Xi Steven Chen
- Department of Public Health Sciences, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Christian P Pavlovich
- Brady Urological Institute and Department of Urology, Johns Hopkins University, Baltimore, MD 21231, USA
| | - A Ari Hakimi
- Department of Surgery, Urology Service, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Gabriel Brominski
- Department of Urology, Poznań University of Medical Sciences, Szwajcarska 3, Poznań 61-285, Poland
| | - James J Hsieh
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Andrzej Antczak
- Department of Urology, Poznań University of Medical Sciences, Szwajcarska 3, Poznań 61-285, Poland
| | - Tatiana Omelchenko
- Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Jan Lubinski
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin 71-252, Poland
| | - Maciej Wiznerowicz
- International Institute for Molecular Oncology, Poznań 60-203, Poland; Poznań University of Medical Sciences, Poznan 60-701, Poland
| | - W Marston Linehan
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Christopher R Kinsinger
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA
| | | | - Emily S Boja
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Mehdi Mesri
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Tara Hiltke
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Ana I Robles
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Henry Rodriguez
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Jiang Qian
- Department of Ophthalmology, Johns Hopkins University, Baltimore, MD 21231, USA
| | - David Fenyö
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | - Bing Zhang
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Li Ding
- Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Eric Schadt
- Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Sema4, Stamford, CT 06902, USA
| | - Arul M Chinnaiyan
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Zhen Zhang
- Department of Pathology, Johns Hopkins University, Baltimore, MD 21231, USA
| | - Gilbert S Omenn
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA; Department of Internal Medicine, Human Genetics, and School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Marcin Cieslik
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA.
| | - Daniel W Chan
- Department of Pathology, Johns Hopkins University, Baltimore, MD 21231, USA.
| | | | - Pei Wang
- Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| | - Hui Zhang
- Department of Pathology, Johns Hopkins University, Baltimore, MD 21231, USA.
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18
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Ramirez-Peña E, Arnold J, Shivakumar V, Joseph R, Vidhya Vijay G, den Hollander P, Bhangre N, Allegakoen P, Prasad R, Conley Z, Matés JM, Márquez J, Chang JT, Vasaikar S, Soundararajan R, Sreekumar A, Mani SA. The Epithelial to Mesenchymal Transition Promotes Glutamine Independence by Suppressing GLS2 Expression. Cancers (Basel) 2019; 11:cancers11101610. [PMID: 31652551 PMCID: PMC6826439 DOI: 10.3390/cancers11101610] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2019] [Revised: 10/05/2019] [Accepted: 10/18/2019] [Indexed: 12/17/2022] Open
Abstract
Identifying bioenergetics that facilitate the epithelial to mesenchymal transition (EMT) in breast cancer cells may uncover targets to treat incurable metastatic disease. Metastasis is the number one cause of cancer-related deaths; therefore, it is urgent to identify new treatment strategies to prevent the initiation of metastasis. To characterize the bioenergetics of EMT, we compared metabolic activities and gene expression in cells induced to differentiate into the mesenchymal state with their epithelial counterparts. We found that levels of GLS2, which encodes a glutaminase, are inversely associated with EMT. GLS2 down-regulation was correlated with reduced mitochondrial activity and glutamine independence even in low-glucose conditions. Restoration of GLS2 expression in GLS2-negative breast cancer cells rescued mitochondrial activity, enhanced glutamine utilization, and inhibited stem-cell properties. Additionally, inhibition of expression of the transcription factor FOXC2, a critical regulator of EMT in GLS2-negative cells, restored GLS2 expression and glutamine utilization. Furthermore, in breast cancer patients, high GLS2 expression is associated with improved survival. These findings suggest that epithelial cancer cells rely on glutamine and that cells induced to undergo EMT become glutamine independent. Moreover, the inhibition of EMT leads to a GLS2-directed metabolic shift in mesenchymal cancer cells, which may make these cells susceptible to chemotherapies.
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Affiliation(s)
- Esmeralda Ramirez-Peña
- National Cancer Institute, Cancer Prevention Fellowship Program, Division of Cancer Prevention, Bethesda, MD 20892, USA.
| | - James Arnold
- Department of Molecular and Cell Biology, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Vinita Shivakumar
- Wiess School of Natural Sciences, Rice University, Houston, TX 77005, USA.
| | - Robiya Joseph
- Department of Translational Molecular Pathology, MD Anderson Cancer Center, Houston, TX 77030, USA.
| | | | - Petra den Hollander
- Department of Translational Molecular Pathology, MD Anderson Cancer Center, Houston, TX 77030, USA.
| | - Neeraja Bhangre
- Department of Fibrosis Biology, Gilead Sciences, Foster City, CA 94404, USA.
| | - Paul Allegakoen
- Department of Medicine, University of California-San Francisco, San Francisco, CA 94143, USA.
| | - Rishika Prasad
- Department of Translational Molecular Pathology, MD Anderson Cancer Center, Houston, TX 77030, USA.
| | - Zachary Conley
- Center for Science Outreach, Department of Teaching and Learning, Vanderbilt University, Nashville, TN 37235, USA.
| | - José M Matés
- Canceromics Lab, Department of Molecular Biology and Biochemistry, University of Málaga and Instituto de Investigación Biomedica de Málaga (IBIMA), 29071 Málaga, Spain.
| | - Javier Márquez
- Canceromics Lab, Department of Molecular Biology and Biochemistry, University of Málaga and Instituto de Investigación Biomedica de Málaga (IBIMA), 29071 Málaga, Spain.
| | - Jeffrey T Chang
- Department of Integrative Biology and Pharmacology, University of Texas Health Science Center, Houston, TX 77030, USA.
| | - Suhas Vasaikar
- Department of Translational Molecular Pathology, MD Anderson Cancer Center, Houston, TX 77030, USA.
| | - Rama Soundararajan
- Department of Translational Molecular Pathology, MD Anderson Cancer Center, Houston, TX 77030, USA.
| | - Arun Sreekumar
- Department of Molecular and Cell Biology, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Sendurai A Mani
- Department of Translational Molecular Pathology, MD Anderson Cancer Center, Houston, TX 77030, USA.
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19
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Gómez-Miragaya J, Díaz-Navarro A, Tonda R, Beltran S, Palomero L, Palafox M, Dobrolecki LE, Huang C, Vasaikar S, Zhang B, Wulf GM, Collado-Sole A, Trinidad EM, Muñoz P, Paré L, Prat A, Bruna A, Caldas C, Arribas J, Soler-Monso MT, Petit A, Balmaña J, Cruz C, Serra V, Pujana MA, Lewis MT, Puente XS, González-Suárez E. Chromosome 12p Amplification in Triple-Negative/ BRCA1-Mutated Breast Cancer Associates with Emergence of Docetaxel Resistance and Carboplatin Sensitivity. Cancer Res 2019; 79:4258-4270. [PMID: 31213465 DOI: 10.1158/0008-5472.can-18-3835] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 03/05/2019] [Accepted: 06/07/2019] [Indexed: 11/16/2022]
Abstract
Taxanes are the mainstay of treatment in triple-negative breast cancer (TNBC), with de novo and acquired resistance limiting patient's survival. To investigate the genetic basis of docetaxel resistance in TNBC, exome sequencing was performed on matched TNBC patient-derived xenografts (PDX) sensitive to docetaxel and their counterparts that developed resistance in vivo upon continuous drug exposure. Most mutations, small insertions/deletions, and copy number alterations detected in the initial TNBC human metastatic samples were maintained after serial passages in mice and emergence of resistance. We identified a chromosomal amplification of chr12p in a human BRCA1-mutated metastatic sample and the derived chemoresistant PDX, but not in the matched docetaxel-sensitive PDX tumor. Chr12p amplification was validated in a second pair of docetaxel-sensitive/resistant BRCA1-mutated PDXs and after short-term docetaxel treatment in several TNBC/BRCA1-mutated PDXs and cell lines, as well as during metastatic recurrence in a patient with BRCA1-mutated breast cancer who had progressed on docetaxel treatment. Analysis of clinical data indicates an association between chr12p amplification and patients with TNBC/basal-like breast cancer, a BRCA1 mutational signature, and poor survival after chemotherapy. Detection of chr12p amplification in a cohort of TNBC PDX models was associated with an improved response to carboplatin. Our findings reveal tumor clonal dynamics during chemotherapy treatments and suggest that a preexisting population harboring chr12p amplification is associated with the emergence of docetaxel resistance and carboplatin responsiveness in TNBC/BRCA1-mutated tumors. SIGNIFICANCE: Chr12p copy number gains indicate rapid emergence of resistance to docetaxel and increased sensitivity to carboplatin, therefore sequential docetaxel/carboplatin treatment could improve survival in TNBC/BRCA1 patients. GRAPHICAL ABSTRACT: http://cancerres.aacrjournals.org/content/canres/79/16/4258/F1.large.jpg.
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Affiliation(s)
- Jorge Gómez-Miragaya
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Avinguda de la Gran Via, 199-203, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Ander Díaz-Navarro
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología del Principado de Asturias (IUOPA), CIBERONC, Universidad de Oviedo, Oviedo, Spain
| | - Raul Tonda
- CNAG-CRG, Centre for Genomic Regulation (CRG), Institute of Science and Technology (BIST), Centre for Genomic Analysis (CNAG), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Sergi Beltran
- CNAG-CRG, Centre for Genomic Regulation (CRG), Institute of Science and Technology (BIST), Centre for Genomic Analysis (CNAG), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Luis Palomero
- Breast Cancer and Systems Biology Laboratory, Program Against Cancer Therapeutic Resistance (ProCURE), Catalan Institute of Oncology (ICO), Oncobell, Bellvitge Institute for Biomedical Research (IDIBELL), L'Hospitalet del Llobregat, Barcelona, Spain
| | - Marta Palafox
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Avinguda de la Gran Via, 199-203, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Lacey E Dobrolecki
- Departments of Molecular and Cellular Biology and Radiology, The Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas
| | - Chen Huang
- Departments of Molecular and Human Genetics, The Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas
| | - Suhas Vasaikar
- Departments of Molecular and Human Genetics, The Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas
| | - Bing Zhang
- Departments of Molecular and Human Genetics, The Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas
| | - Gerburg M Wulf
- Division of Hematology/Oncology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts
| | - Alejandro Collado-Sole
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Avinguda de la Gran Via, 199-203, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Eva M Trinidad
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Avinguda de la Gran Via, 199-203, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Purificación Muñoz
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Avinguda de la Gran Via, 199-203, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Laia Paré
- Translational Genomics and Targeted Therapeutics in Solid Tumors, Institut D'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
| | - Aleix Prat
- Translational Genomics and Targeted Therapeutics in Solid Tumors, Institut D'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
- Department of Medical Oncology, Hospital Clinic, Barcelona, Spain
| | - Alejandra Bruna
- Cancer Research UK Cancer Centre, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Carlos Caldas
- Cancer Research UK Cancer Centre, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Joaquín Arribas
- Preclinical Research Program, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | | | - Anna Petit
- Pathology Department, University Hospital of Bellvitge, IDIBELL, Barcelona, Spain
| | - Judith Balmaña
- Preclinical Research Program, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Cristina Cruz
- Preclinical Research Program, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Violeta Serra
- Preclinical Research Program, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Miguel Angel Pujana
- Breast Cancer and Systems Biology Laboratory, Program Against Cancer Therapeutic Resistance (ProCURE), Catalan Institute of Oncology (ICO), Oncobell, Bellvitge Institute for Biomedical Research (IDIBELL), L'Hospitalet del Llobregat, Barcelona, Spain
| | - Michael T Lewis
- Departments of Molecular and Cellular Biology and Radiology, The Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas
| | - Xose S Puente
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología del Principado de Asturias (IUOPA), CIBERONC, Universidad de Oviedo, Oviedo, Spain
| | - Eva González-Suárez
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Avinguda de la Gran Via, 199-203, L'Hospitalet de Llobregat, Barcelona, Spain.
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Wang J, Vasaikar S, Shi Z, Greer M, Zhang B. WebGestalt 2017: a more comprehensive, powerful, flexible and interactive gene set enrichment analysis toolkit. Nucleic Acids Res 2019; 45:W130-W137. [PMID: 28472511 PMCID: PMC5570149 DOI: 10.1093/nar/gkx356] [Citation(s) in RCA: 772] [Impact Index Per Article: 154.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 04/20/2017] [Indexed: 12/22/2022] Open
Abstract
Functional enrichment analysis has played a key role in the biological interpretation of high-throughput omics data. As a long-standing and widely used web application for functional enrichment analysis, WebGestalt has been constantly updated to satisfy the needs of biologists from different research areas. WebGestalt 2017 supports 12 organisms, 324 gene identifiers from various databases and technology platforms, and 150 937 functional categories from public databases and computational analyses. Omics data with gene identifiers not supported by WebGestalt and functional categories not included in the WebGestalt database can also be uploaded for enrichment analysis. In addition to the Over-Representation Analysis in the previous versions, Gene Set Enrichment Analysis and Network Topology-based Analysis have been added to WebGestalt 2017, providing complementary approaches to the interpretation of high-throughput omics data. The new user-friendly output interface and the GOView tool allow interactive and efficient exploration and comparison of enrichment results. Thus, WebGestalt 2017 enables more comprehensive, powerful, flexible and interactive functional enrichment analysis. It is freely available at http://www.webgestalt.org.
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Affiliation(s)
- Jing Wang
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Suhas Vasaikar
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Zhiao Shi
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Michael Greer
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37203, USA
| | - Bing Zhang
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
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21
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Zhang B, Vasaikar S, Huang C, Wang X, Petyuk VA, Savage SR, Wen B, Dou Y, Zhang Y, Shi Z, Arshad OA, Gritsenko MA, Zimmerman LJ, McDermott JE, Clauss TR, Moore RJ, Zhao R, Monroe ME, Wang YT, Chambers MC, Slebos RJ, Lau KS, Mo Q, Ding L, Ellis M, Thiagarajan M, Kinsinger CR, Rodriguez H, Smith RD, Rodland KD, Liebler DC, Liu T. Abstract LB-006: Proteogenomic characterization of human colon cancer reveals new therapeutic opportunities. Cancer Res 2019. [DOI: 10.1158/1538-7445.am2019-lb-006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
We prospectively collected matched tumor specimens, adjacent non-tumor tissues, and blood samples from 110 colon cancer patients and analyzed the samples using seven omics platforms, including whole-exome sequencing, copy number arrays, RNA-Seq, miRNA-Seq, label-free global proteomics, isobaric tandem mass tag (TMT) labeling-based global proteomics, and TMT-based phosphoproteomics. Comparative proteomic and phosphoproteomic analysis of paired tumor and adjacent normal samples produced the first comprehensive catalogue of colon cancer-associated proteins and phosphosites, including known and putative new biomarkers and drug targets. These cancer-associated proteins and phosphosites had very little overlap with known cancer genes in the Cancer Gene Census, providing a novel information layer to our knowledge about colon cancer. One notable finding in differential proteome analysis is the identification of several cancer/testis antigens that were recurrently over-expressed in tumors compared to adjacent normal tissue, including IGF2BP3 (51%), SPAG1 (14%), and ATAD2 (8%). Through integrative analysis of the whole-exome sequencing, RNA-Seq, and proteomics data, we further predicted personalized neoantigens for 38% of the patients. In total, we found proteomics-supported neoantigens or cancer/testis antigens for 78% of the tumors in this cohort, demonstrating the potential of proteogenomics in identifying tumor antigens for cancer vaccine development. Proteomics data complemented somatic copy number analysis results and showed that multiple somatic copy number deletion events converge to repress the endocytosis pathway, suggesting its tumor suppressor role in colon cancer. In addition to reinforcing or complementing genomic findings, proteogenomic integration may also contradict genomics data-based inferences and lead to unexpected discoveries and therapeutic opportunities. Proteomics data identified SOX9 as an oncogene in colon cancer, whereas it was predicted to be a tumor suppressor based on somatic mutation data in the TCGA study. Phosphoproteomics data revealed a dual role of Rb phosphorylation in promoting proliferation and repressing apoptosis in colon cancer, clarifying the long-standing puzzle of colon cancer-specific amplification of this tumor suppressor and highlighting a unique opportunity for targeting Rb phosphorylation in colon cancer. Microsatellite instability status has been approved by the FDA as a biomarker for selecting patients for checkpoint inhibitor therapy in colorectal and other solid tumors. However, many MSI-high tumors fail to respond to checkpoint inhibition. Our proteogenomic analysis identified a subtype-specific association between increased glycolysis and decreased CD8 T cell infiltration in MSI-high colon tumors, suggesting glycolysis as a target for overcoming immune evasion in this MSI-H tumors. We make the primary and processed datasets available in publicly accessible data repositories and portals to allow broad use of these datasets for new biological discoveries and therapeutic hypothesis generation.
Citation Format: Bing Zhang, Suhas Vasaikar, Chen Huang, Xiaojing Wang, Vladislav A. Petyuk, Sara R. Savage, Bo Wen, Yongchao Dou, Yun Zhang, Zhiao Shi, Osama A. Arshad, Marina A. Gritsenko, Lisa J. Zimmerman, Jason E. McDermott, Therese R. Clauss, Ronald J. Moore, Rui Zhao, Matthew E. Monroe, Yi-Ting Wang, Matthew C. Chambers, Robbert J. Slebos, Ken S. Lau, Qianxing Mo, Li Ding, Matthew Ellis, Mathangi Thiagarajan, Christopher R. Kinsinger, Henry Rodriguez, Richard D. Smith, Karin D. Rodland, Daniel C. Liebler, Tao Liu, CPTAC Investigators. Proteogenomic characterization of human colon cancer reveals new therapeutic opportunities [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr LB-006.
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Affiliation(s)
- Bing Zhang
- 1Baylor College of Medicine, HOUSTON, TX
| | | | - Chen Huang
- 1Baylor College of Medicine, HOUSTON, TX
| | | | | | | | - Bo Wen
- 1Baylor College of Medicine, HOUSTON, TX
| | | | - Yun Zhang
- 1Baylor College of Medicine, HOUSTON, TX
| | - Zhiao Shi
- 1Baylor College of Medicine, HOUSTON, TX
| | | | | | | | | | | | | | - Rui Zhao
- 2Pacific Northwest National Laboratory, Richland, WA
| | | | - Yi-Ting Wang
- 2Pacific Northwest National Laboratory, Richland, WA
| | | | | | | | | | - Li Ding
- 4Washington University in St. Louis, St. Louis, MO
| | | | | | | | | | | | | | | | - Tao Liu
- 2Pacific Northwest National Laboratory, Richland, WA
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Bhat R, Qin L, Angelis CD, Vasaikar S, Thangavel H, AbdulKareem N, Zhang B, Schiff R, Trivedi MV. Abstract 3044: The role of GPR110 in tumorigenicity, tumor cell dissemination, and cell cycle regulation in HER2+ breast cancer. Cancer Res 2019. [DOI: 10.1158/1538-7445.am2019-3044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Identification of novel drug targets to overcome anti-HER2 therapy resistance is an unmet need. Since G protein-coupled receptors (GPCRs) are known to cross-talk with the HER superfamily, it is possible that some GPCRs may signal to modulate the HER2 pathway. We have identified GPR110 (also known as ADGFR1, Adhesion G Protein-Coupled Receptor F1) as a potential target in HER2+ breast cancer (BC) based on its expression in tumorigenic and anti-HER2-resistant cells. We have also shown that GPR110 knockdown in HER2+ BC cells inhibits colony formation in soft agar assay, mammosphere formation, and invasion/migration in trans-well assay, suggesting its potential role in tumorigenesis and tumor cell dissemination. To further characterize the role of GPR110 in HER2+ BC, we generated stable cell lines of BT474 and SKBR3, two HER2+ BC cell line models, that overexpress GPR110 in Doxycycline (Dox)-inducible manner. GPR110 overexpression enhanced colony formation in soft agar assay, mammosphere formation, and number of Aldefluor+ tumorigenic cells, substantiating its role in tumorigenesis. In addition, Dox-induced GPR110 overexpression increased invasion/migration potential of clones in trans-well assay, further supporting its role in cancer cell dissemination. To understand the mechanism of GPR110-mediated tumorigenesis and tumor cell dissemination in HER2+ BC, we carried out transcriptomic and proteomic analysis of selected cell lines (with or without Dox) using RNAseq and RPPA respectively. This analysis uncovered a previously unanticipated role of GPR110 in cancer cell regulation and maintaining quiescence. Overexpression of GPR110 by Dox treatment led to downregulation of various cell cycle pathways and targets such as E2F targets, G2M checkpoint pathway and MYC targets at the transcriptomic level. Validation of RNA-Seq and RPPA candidates demonstrated lower number of proliferative Ki67+ cells and reduced NF-kB staining, and inhibited STAT3 phosphorylation. In support of these results, GPR110 overexpression also led to cell cycle arrest at G0/G1 phase, when analyzed by the DNA content analysis with propidium iodide using flow cytometry. Ongoing in vivo studies will further elucidate the exact and overall role of GPR110 in HER2+ BC. In summary, our results demonstrate a previously uncovered role of GPR110 in tumorigenesis and metastasis as well as cell cycle regulation in HER2+ BC.
Citation Format: Raksha Bhat, Lanfang Qin, Carmine De Angelis, Suhas Vasaikar, Hariprasad Thangavel, Noor AbdulKareem, Bing Zhang, Rachel Schiff, Meghana V. Trivedi. The role of GPR110 in tumorigenicity, tumor cell dissemination, and cell cycle regulation in HER2+ breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3044.
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Affiliation(s)
| | | | | | | | | | | | - Bing Zhang
- 2Baylor College of Medicine, Houston, TX
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Thangavel H, Angelis CD, Vasaikar S, Bhat R, Jolly MK, Dobrolecki LE, George JT, Giuliano M, Lewis M, Levine H, Zhang B, Schiff R, Trivedi MV. Abstract 2783: OMICS analysis of breast cancer PDX tumors to determine CTC-cluster-specific signature in predicting breast cancer metastasis. Cancer Res 2019. [DOI: 10.1158/1538-7445.am2019-2783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Circulating tumor cell clusters (CTCcl) have been shown to have a significantly higher metastatic potential compared to single CTCs and to predict long-term outcomes in breast cancer patients. A characterization of primary tumors that give rise to CTCcl hold significant promises for better diagnosis and may uncover targets for prevention and treatment of metastatic breast cancer. In our study, we utilized the available transcriptomic and proteomic data (RNA-Seq and RPPA) of 10 triple-negative breast cancer patient-derived xenograft (TNBC-PDX) transplantable models. The sample set consisted of 6 CTCcl-negative (-) and 4 CTCcl-positive (+) models. Genome-wide transcriptomic analysis revealed 549 differentially expressed genes in CTCcl+ TNBC-PDX models vs. CTCcl- models (316 up-regulated and 233 down-regulated, p<0.05). Gene set enrichment analysis (GSEA) terms significantly enriched (FDR<0.05) in CTCcl+ TNBC-PDXs included Cytoplasmic Ribosomal Proteins (NES=2.53), Angiogenesis (NES=1.95), Type II Interferon signaling (NES=-2.52), Antigen processing and presentation (NES=-2.38), TNF signaling pathway (NES=-2.04), Jak-STAT signaling pathway (NES=-1.91), and apoptosis (NES=-1.69). The proteomic analysis revealed elevated levels of Bcl2 expression in PDX tumors associated with CTCcl positivity, which substantiated the inhibited apoptosis pathway as seen in GSEA analysis. The increase in Bcl2 was also validated independently by IHC staining in primary PDX tumors that were CTCcl+. The distribution of EMT score based on the inferential EMT metric using canonical epithelial and mesenchymal markers was not significantly different between CTCcl+ and CTCcl- TNBC-PDX tumors suggesting no differential regulation of EMT in tumors that give rise to clusters versus only single cells. In summary, our results suggest that primary tumors with active anti-apoptotic and/or survival pathways may promote CTC clusters formation and increase the risk of distant metastasis.
Citation Format: Hariprasad Thangavel, Carmine De Angelis, Suhas Vasaikar, Raksha Bhat, Mohit Kumar Jolly, Lacey Elizabeth Dobrolecki, Jason T. George, Mario Giuliano, Michael Lewis, Herbert Levine, Bing Zhang, Rachel Schiff, Meghana V. Trivedi. OMICS analysis of breast cancer PDX tumors to determine CTC-cluster-specific signature in predicting breast cancer metastasis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2783.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Bing Zhang
- 3Baylor College of Medicine, Houston, TX
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24
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Joseph R, Soundararajan R, Vasaikar S, Yang F, Isgandarova S, Tian L, Haemmerle M, Mino B, Zhou T, Raja GV, Pena ER, Hollander PD, Bhangre N, Shin C, Martinez M, Canales JR, Chang J, Sood A, Wistuba II, Gibbons DL, Rosen JM, Acharya G, Varadarajan N, Zhang XH, Mani SA. Abstract 3761: Regulation of metastasis by CD8 T lymphocytes. Cancer Res 2019. [DOI: 10.1158/1538-7445.am2019-3761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Metastatic breast cancer is the most dreadful malignant disease that accounts for the majority of cancer-related deaths worldwide among women. A number of studies have shown that the tumor microenvironment (TME) plays a crucial role in regulating metastasis. It is therefore imperative to understand the dynamic interactions between cancer cells and their microenvironment to examine the molecular interaction and to effectively target cancer cells. TME comprises a variety of cells including immune cells which can influence tumor survival, growth and metastasis. Tumor-infiltrating lymphocytes (TILs), in particular, the CD8 T lymphocytes, has emerged as a promising prognostic marker for immunotherapy in a variety of cancers. However, the key molecular factors that regulate the cross-talk between tumor cells and CD8 T lymphocytes and its impact on metastatic traits in breast cancer is still inconclusive. Platelets are crucial components of the tumor microenvironment that are known to modulate tumor promotion and metastasis. The contribution of platelets and platelet secreted molecules are also carefully examined in metastasis of various cancers. The primary objective of this study is to investigate the role of CD8 T lymphocytes and platelets in breast tumor progression using isogenic tumor lines that form identical primary tumors but differ in their ability to develop metastasis.
Citation Format: Robiya Joseph, Rama Soundararajan, Suhas Vasaikar, Fei Yang, Sevinj Isgandarova, Lin Tian, Monika Haemmerle, Barbara Mino, Tieling Zhou, Geraldine Vidhya Raja, Esmeralda Ramirez Pena, Petra Den Hollander, Neeraja Bhangre, Crystal Shin, Melisa Martinez, Jaime Rodriguez Canales, Jeffrey Chang, Anil Sood, Ignacio Ivan Wistuba, Don L. Gibbons, Jeffrey M. Rosen, Ghanashyam Acharya, Navin Varadarajan, Xiang H. Zhang, Sendurai A. Mani. Regulation of metastasis by CD8 T lymphocytes [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3761.
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Affiliation(s)
| | | | | | - Fei Yang
- 1MD Anderson Cancer Center, Houston, TX
| | | | - Lin Tian
- 3Baylor College of Medicine, Houston, TX
| | | | | | | | | | | | | | | | | | | | | | | | - Anil Sood
- 1MD Anderson Cancer Center, Houston, TX
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Vasaikar S, Huang C, Wang X, Petyuk VA, Savage SR, Wen B, Dou Y, Zhang Y, Shi Z, Arshad OA, Gritsenko MA, Zimmerman LJ, McDermott JE, Clauss TR, Moore RJ, Zhao R, Monroe ME, Wang YT, Chambers MC, Slebos RJC, Lau KS, Mo Q, Ding L, Ellis M, Thiagarajan M, Kinsinger CR, Rodriguez H, Smith RD, Rodland KD, Liebler DC, Liu T, Zhang B. Proteogenomic Analysis of Human Colon Cancer Reveals New Therapeutic Opportunities. Cell 2019; 177:1035-1049.e19. [PMID: 31031003 DOI: 10.1016/j.cell.2019.03.030] [Citation(s) in RCA: 407] [Impact Index Per Article: 81.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2018] [Revised: 11/22/2018] [Accepted: 03/12/2019] [Indexed: 12/12/2022]
Abstract
We performed the first proteogenomic study on a prospectively collected colon cancer cohort. Comparative proteomic and phosphoproteomic analysis of paired tumor and normal adjacent tissues produced a catalog of colon cancer-associated proteins and phosphosites, including known and putative new biomarkers, drug targets, and cancer/testis antigens. Proteogenomic integration not only prioritized genomically inferred targets, such as copy-number drivers and mutation-derived neoantigens, but also yielded novel findings. Phosphoproteomics data associated Rb phosphorylation with increased proliferation and decreased apoptosis in colon cancer, which explains why this classical tumor suppressor is amplified in colon tumors and suggests a rationale for targeting Rb phosphorylation in colon cancer. Proteomics identified an association between decreased CD8 T cell infiltration and increased glycolysis in microsatellite instability-high (MSI-H) tumors, suggesting glycolysis as a potential target to overcome the resistance of MSI-H tumors to immune checkpoint blockade. Proteogenomics presents new avenues for biological discoveries and therapeutic development.
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Affiliation(s)
- Suhas Vasaikar
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Chen Huang
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Xiaojing Wang
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Vladislav A Petyuk
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Sara R Savage
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Bo Wen
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yongchao Dou
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yun Zhang
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Zhiao Shi
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Osama A Arshad
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Marina A Gritsenko
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Lisa J Zimmerman
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA
| | - Jason E McDermott
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Therese R Clauss
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Ronald J Moore
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Rui Zhao
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Matthew E Monroe
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Yi-Ting Wang
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Matthew C Chambers
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA
| | - Robbert J C Slebos
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA
| | - Ken S Lau
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Qianxing Mo
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Li Ding
- The McDonnell Genome Institute, Washington University in St. Louis, Forest Park Avenue, Campus Box 8501, St. Louis, MO 63108, USA
| | - Matthew Ellis
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Mathangi Thiagarajan
- Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Christopher R Kinsinger
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Henry Rodriguez
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Richard D Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Karin D Rodland
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA; Department of Cell, Developmental, and Cancer Biology, Oregon Health & Science University, Portland, OR 97221, USA.
| | - Daniel C Liebler
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA.
| | - Tao Liu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA.
| | - Bing Zhang
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA.
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Bhat R, Qin L, De Angelis C, Sahay D, Bhargava D, Creighton C, Yadav P, Yazdanfard S, Alrawi A, Yadav V, Vasaikar S, Nanda S, Sethunath V, Fu X, Zhang B, Narkar V, Schiff R, Trivedi M. Abstract P6-20-10: Role of GPR110 in breast cancer. Cancer Res 2019. [DOI: 10.1158/1538-7445.sabcs18-p6-20-10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Our long-term goal is to discover adhesion GPCR targets in breast cancer. Our previous studies have found GPR110 to be overexpressed in tumorigenic cell population as well as in anti-HER2 drug-resistant derivatives of HER2+ breast cancer cells. In subsequent studies, we found that GPR110 knockdown inhibited anchorage-independent cell growth, mammosphere formation, and invasion/migration of HER2+ breast cancer cells. Conversely, overexpression of GPR110 by lentiviral delivery of cDNA enhanced anchorage-independent cell growth, mammosphere formation, and invasion/migration in HER2+ breast cancer cells. In addition, GPR110 overexpression led to increase in the % of Aldefluor-positive tumorigenic cell population, further emphasizing the role of GPR110 as a mediator of tumorigenesis in addition to the metastatic processes in HER2+ breast cancer. Among various subtypes of breast cancer, GPR110 expression was higher in HER2+ and basal subtypes, most of which are triple-negative (negative for ER, PR, and HER2), compared to luminal A and B subtypes. GPR110 was either gene amplified or upregulated in 4% of all breast cancers based on the publicly available TCGA dataset. GPR110 overexpression predicted poorer recurrence-free survival in triple-negative breast cancer. Furthermore, GPR110 was overexpressed in brain metastatic lesions compared to mammary tumors in patient-derived xenograft models of triple-negative breast cancer (WHIM2 and WHIM30). Knocking down GPR110 reduced anchorage-dependent and -independent cell growth, mammosphere formation, and invasion/migration of triple-negative breast cancer cells. Overall, our results suggest that GPR110 may be a potential drug target in HER2+ and triple-negative breast cancer. Drug discovery efforts to identify GPR110 antagonists will provide useful pharmacological tools for validating GPR110 as a drug target in breast cancer. Since GPR110 is also overexpressed in various other types of cancer, understanding the mechanism of GPR110 upregulation and signaling in cancer is an important future direction.
This work was supported by the Department of Defense Grants W81XWH-14-1-0340 and W81XWH-14-1-0341 to Drs. Trivedi and Schiff, respectively.
Citation Format: Bhat R, Qin L, De Angelis C, Sahay D, Bhargava D, Creighton C, Yadav P, Yazdanfard S, Alrawi A, Yadav V, Vasaikar S, Nanda S, Sethunath V, Fu X, Zhang B, Narkar V, Schiff R, Trivedi M. Role of GPR110 in breast cancer [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P6-20-10.
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Affiliation(s)
- R Bhat
- University of Houston College of Pharmacy, Houston; Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston; University of Texas MCGovern Medical School, Houston
| | - L Qin
- University of Houston College of Pharmacy, Houston; Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston; University of Texas MCGovern Medical School, Houston
| | - C De Angelis
- University of Houston College of Pharmacy, Houston; Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston; University of Texas MCGovern Medical School, Houston
| | - D Sahay
- University of Houston College of Pharmacy, Houston; Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston; University of Texas MCGovern Medical School, Houston
| | - D Bhargava
- University of Houston College of Pharmacy, Houston; Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston; University of Texas MCGovern Medical School, Houston
| | - C Creighton
- University of Houston College of Pharmacy, Houston; Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston; University of Texas MCGovern Medical School, Houston
| | - P Yadav
- University of Houston College of Pharmacy, Houston; Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston; University of Texas MCGovern Medical School, Houston
| | - S Yazdanfard
- University of Houston College of Pharmacy, Houston; Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston; University of Texas MCGovern Medical School, Houston
| | - A Alrawi
- University of Houston College of Pharmacy, Houston; Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston; University of Texas MCGovern Medical School, Houston
| | - V Yadav
- University of Houston College of Pharmacy, Houston; Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston; University of Texas MCGovern Medical School, Houston
| | - S Vasaikar
- University of Houston College of Pharmacy, Houston; Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston; University of Texas MCGovern Medical School, Houston
| | - S Nanda
- University of Houston College of Pharmacy, Houston; Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston; University of Texas MCGovern Medical School, Houston
| | - V Sethunath
- University of Houston College of Pharmacy, Houston; Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston; University of Texas MCGovern Medical School, Houston
| | - X Fu
- University of Houston College of Pharmacy, Houston; Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston; University of Texas MCGovern Medical School, Houston
| | - B Zhang
- University of Houston College of Pharmacy, Houston; Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston; University of Texas MCGovern Medical School, Houston
| | - V Narkar
- University of Houston College of Pharmacy, Houston; Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston; University of Texas MCGovern Medical School, Houston
| | - R Schiff
- University of Houston College of Pharmacy, Houston; Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston; University of Texas MCGovern Medical School, Houston
| | - M Trivedi
- University of Houston College of Pharmacy, Houston; Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston; University of Texas MCGovern Medical School, Houston
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Anurag M, Vasaikar S, Zhang X, Zhang B, Ellis MJ. Abstract PD7-08: Immune checkpoint upregulation and T-cell exhaustion in aggressive hormone-receptor positive breast cancer patients. Cancer Res 2019. [DOI: 10.1158/1538-7445.sabcs18-pd7-08] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Early reports from studies focused on assessing the clinical efficacy for immune-checkpoint (IC) inhibitors in breast cancer suggest lower activity than in cancers caused by exogenous mutagens such as melanoma and smoking-related lung cancer. Nonetheless, triple negative breast cancer is under active investigation. In contrast, estrogen receptor positive disease has been considered “immunologically silent” with very few IC studies focused on this disease subset. We therefore undertook an analysis of ER+ breast cancer to determine if there are subsets of patients with poor prognosis ER+ disease that exhibit IC pathway upregulation hence potential candidates for IC-based clinical trials.
Methods: In an unbiased integrative analysis of patient samples, mRNA expression data for ˜15500 genes across 66 Luminal B patient set was used to identify genes for which the expression correlated positively with proliferation marker Ki67 (in aromatase-inhibitor treated tumors) and were upregulated (>2 fold) in endocrine-therapy (ET) resistant samples as compared against the sensitive counterparts. Resulting genes were queried to identify underlying activated pathways and prioritize genes for further analysis. Validation of shortlisted genes was performed on independent patient cohorts (TCGA and METABRIC) using Kaplain-Meier disease-specific survival analysis. Amplification and methylation data for TCGA samples were obtained from CBioportal and Wanderer respectively. Proteomics data for TCGA samples was extracted using LikedOmics server. T-cell activation (TCA) and exhaustion (TCE) scores were devised using mean of standardized expression of genes reported to contribute in these two T cell states.
Result: Approximately 30 genes were found to be deferentially upregulated in ET-resistant aggressive ER+ breast cancer. This gene set was enriched in immune-tolerance biological processes (p<0.005). The three immune-checkpoints constituting these processes are IDO1, LAG3 and PDCD1 (PD1). Upregulation of IDO1 was a confirmed poor prognosis factor across independent patient cohorts. Furthermore, comparative analysis of TCA and TCE scores between ET-resistant and sensitive tumors revealed that resistant tumors have high TCE, despite having high TCA, hence circumventing immunogenic apoptosis.
Conclusion: To date, no substantial study showing prognostic relevance of mRNA levels of ICs in context of ER+ breast cancer patients has been reported. Higher IDO1 and T-cell exhaustion levels in ET-resistant ER+ disease provides clinical evidence for a role for immune-checkpoints in evading immune-driven cell death. These results suggest a potential for IC targeted immunotherapy for ˜ 80% of endocrine therapy resistant clinically aggressive ER+ breast cancers.
Citation Format: Anurag M, Vasaikar S, Zhang X, Zhang B, Ellis MJ. Immune checkpoint upregulation and T-cell exhaustion in aggressive hormone-receptor positive breast cancer patients [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr PD7-08.
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Affiliation(s)
- M Anurag
- Baylor College of Medicine, Houston; Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston
| | - S Vasaikar
- Baylor College of Medicine, Houston; Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston
| | - X Zhang
- Baylor College of Medicine, Houston; Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston
| | - B Zhang
- Baylor College of Medicine, Houston; Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston
| | - MJ Ellis
- Baylor College of Medicine, Houston; Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston
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Abstract
Background Due to recent technology advancements, disease related knowledge is growing rapidly. It becomes nontrivial to go through all published literature to identify associations between human diseases and genetic, environmental, and life style factors, disease symptoms, and treatment strategies. Here we report DLAD4U (Disease List Automatically Derived For You), an efficient, accurate and easy-to-use disease search engine based on PubMed literature. Results DLAD4U uses the eSearch and eFetch APIs from the National Center for Biotechnology Information (NCBI) to find publications related to a query and to identify diseases from the retrieved publications. The hypergeometric test was used to prioritize identified diseases for displaying to users. DLAD4U accepts any valid queries for PubMed, and the output results include a ranked disease list, information associated with each disease, chronologically-ordered supporting publications, a summary of the run, and links for file export. DLAD4U outperformed other disease search engines in our comparative evaluation using selected genes and drugs as query terms and manually curated data as “gold standard”. For 100 genes that are associated with only one disease in the gold standard, the Mean Average Precision (MAP) measure from DLAD4U was 0.77, which clearly outperformed other tools. For 10 genes that are associated with multiple diseases in the gold standard, the mean precision, recall and F-measure scores from DLAD4U were always higher than those from other tools. The superior performance of DLAD4U was further confirmed using 100 drugs as queries, with an MAP of 0.90. Conclusions DLAD4U is a new, intuitive disease search engine that takes advantage of existing resources at NCBI to provide computational efficiency and uses statistical analyses to ensure accuracy. DLAD4U is publicly available at http://dlad4u.zhang-lab.org. Electronic supplementary material The online version of this article (10.1186/s12859-018-2463-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Junhui Shen
- Information Center, Beijing University of Chinese Medicine, Beijing, China
| | - Suhas Vasaikar
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Mail Stop BCM600, Houston, TX, 77030, USA
| | - Bing Zhang
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, USA. .,Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Mail Stop BCM600, Houston, TX, 77030, USA.
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Abstract
Abstract
Background: The Cancer Genome Atlas (TCGA) project has performed molecular profiling of human tumors using genomic, epigenomic, transcriptomic, and proteomic platforms, and each tumor is comprehensively characterized by around 100,000 molecular attributes in addition to typical clinical attributes. To make these data directly available to the entire cancer research community, several data portals have been developed. However, none of the existing data portals allow systematic exploration and interpretation of the complex relationships between the vast amount of clinical and molecular attributes.
Methods: We developed LinkedOmics (http://www.linkedomics.org), a web platform that focuses on the discovery and interpretation of associations between clinical and molecular attributes. LinkedOmics includes three data analysis modules. The LinkFinder module allows flexible exploration of associations between a molecular or clinical attribute of interest and all other attributes, providing the opportunity to analyze and visualize associations between billions of attribute pairs for each cancer cohort. The LinkCompare module enables easy comparison of the associations identified by LinkFinder, which is particularly useful in multi-omics and pan-cancer analyses. The LinkInterpreter module transforms identified associations into biological understanding through pathway and network analysis. All modules provide user-friendly data visualization.
Results: The current version of LinkedOmics contains multi-omics data and clinical data for 32 cancer types and a total of 11,158 patients from the TCGA project. It is also the first multi-omics database that integrates mass spectrometry (MS)-based global proteomics data generated by the Clinical Proteomic Tumor Analysis Consortium (CPTAC) on selected TCGA tumor samples. In total, LinkedOmics has more than a billion data points. We used several case studies to demonstrate the utility of LinkedOmics in revealing functional impact of somatic mutation or copy number alteration on mRNA or protein expression, in deriving multi-omics based protein signature for poor prognosis, in performing pan-cancer analysis to identify survival-associated gene expression signature, and in connecting novel pan-cancer poor prognosis markers to tumor invasiveness and aggressiveness.
Conclusions: LinkedOmics provides a unique platform for biologists and clinicians to access, analyze and compare cancer multi-omics data within and across tumor types. With 5 case studies we demonstrated the power of LinkedOmics in cancer research. Although the current version of LinkedOmics includes only TCGA and CPTAC data, it can be easily extended to support other cohort-based or user provided multi-omics studies.
Citation Format: Suhas Vasaikar, Pater Straub, Jing Wang, Bing Zhang. LinkedOmics: Analyzing multi-omics data within and across 32 cancer types [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2295.
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Affiliation(s)
| | - Pater Straub
- 2Vanderbilt University School of Medicine, Nashville, TN
| | - Jing Wang
- 1Baylor College of Medicine, Houston, TX
| | - Bing Zhang
- 1Baylor College of Medicine, Houston, TX
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Bhat R, Vasaikar S, Bae L, Carmine DA, Cataldo ML, Nanda S, Zhang B, Schiff R, Trivedi MV. Abstract 1926: Npy1r as a prognostic marker and a novel drug target in estrogen receptor-positive breast cancer. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-1926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Despite the crucial role of some G protein-coupled receptors (GPCRs) in cancer progression and metastases reported in recent studies, the function of majority of GPCRs, as a class, remains largely unexplored in breast cancer. In this study, we evaluated transcriptome, proteome and phosphoproteome data for 398 non-sensory GPCRs (IUPHAR v1.0) using the landmark TCGA breast cancer proteogenomics dataset and Illumina HiSeq dataset. Neuropeptide Y Receptor Y1 (NPY1R) was the top most hypo-phosphorylated (at S368) GPCR in 92 out of 99 evaluable samples. Furthermore, NPY1R gene expression was found to be significantly lower in tumor samples than tumor-matched normal (n=112). Among tumor samples, the LumA subtype had significantly higher NPY1R expression than LumB, Basal and Her2 subtype (p<0.05, One-way ANOVA, Tukey test). Interestingly, the trend of NPY1R gene expression, protein expression and phosphosite expression was decreasing in the order of LumA, LumB, Basal and Her2 subtype (p<0.01, Jonckheere trend test). Using publicly available dataset of 22,277 genes on survival in 2,422 patients, we found that higher NPY1R expression predicted better overall survival and recurrence-free survival in estrogen receptor-positive (ER+) breast cancer patients. In light of this, we interrogated NPY1R gene expression in endocrine sensitive and resistant cell line models and the impact of NPY1R antagonist in ER+ breast cancer cell lines. NPY1R expression was increased in response to estradiol in various ER+ breast cancer cell line models (MCF7, T47D, and BT474) in publicly available datasets. Conversely, we found that tamoxifen or estrogen deprivation (ED) treatment reduced NPY1R expression in MCF7 and T47D cells. In our endocrine-resistant (tamoxifen-resistant, estrogen deprivation-resistant, and fulvestrant-resistant) cell line models, NPY1R expression remained significantly lower compared to the parental cells in vitro and in vivo (p<0.05, One-way ANOVA, Tukey test). Treatment of MCF7 parental cells with 100 nM NPY significantly reduced estrogen-stimulated cell growth (p<0.05, One-way ANOVA, Tukey test). Chronic treatment of cells with 1 μM BIBP3226, an NPY1R antagonist, for 2 weeks reversed the effect of NPY on the estradiol-stimulated cell growth. Estradiol-stimulated cell growth was modest (~40%) in ED-resistant MCF7 cells compared to that (~250%) in parental MCF7 cells. While 100 nM NPY treatment did not affect the estrogen-stimulated growth in ED-resistant MCF7 cells, which can be explained by the undetectable expression of NPY1R, it caused significant inhibition of the estrogen-stimulated growth in the same cells treated chronically with BIBP3226. Molecular mechanisms to explain these effects of chronic NPY1R antagonism are underway. Our ongoing studies will further elucidate the role of NPY1R as a novel drug target in ER+ breast cancer.
Citation Format: Raksha Bhat, Suhas Vasaikar, Leon Bae, De Angelis Carmine, Maria Letizia Cataldo, Sarmistha Nanda, Bing Zhang, Rachel Schiff, Meghana V. Trivedi. Npy1r as a prognostic marker and a novel drug target in estrogen receptor-positive breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1926.
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Affiliation(s)
- Raksha Bhat
- 1Univ. of Houston College of Pharmacy, Houston, TX
| | | | - Leon Bae
- 1Univ. of Houston College of Pharmacy, Houston, TX
| | | | | | | | - Bing Zhang
- 2Baylor College of Medicine, Houston, TX
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Costa H, Xu X, Overbeek G, Vasaikar S, Patro CPK, Kostopoulou ON, Jung M, Shafi G, Ananthaseshan S, Tsipras G, Davoudi B, Mohammad AA, Lam H, Strååt K, Wilhelmi V, Shang M, Tegner J, Tong JC, Wong KT, Söderberg-Naucler C, Yaiw KC. Human cytomegalovirus may promote tumour progression by upregulating arginase-2. Oncotarget 2018; 7:47221-47231. [PMID: 27363017 PMCID: PMC5216936 DOI: 10.18632/oncotarget.9722] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 05/14/2016] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Both arginase (ARG2) and human cytomegalovirus (HCMV) have been implicated in tumorigenesis. However, the role of ARG2 in the pathogenesis of glioblastoma (GBM) and the HCMV effects on ARG2 are unknown. We hypothesize that HCMV may contribute to tumorigenesis by increasing ARG2 expression. RESULTS ARG2 promotes tumorigenesis by increasing cellular proliferation, migration, invasion and vasculogenic mimicry in GBM cells, at least in part due to overexpression of MMP2/9. The nor-NOHA significantly reduced migration and tube formation of ARG2-overexpressing cells. HCMV immediate-early proteins (IE1/2) or its downstream pathways upregulated the expression of ARG2 in U-251 MG cells. Immunostaining of GBM tissue sections confirmed the overexpression of ARG2, consistent with data from subsets of Gene Expression Omnibus. Moreover, higher levels of ARG2 expression tended to be associated with poorer survival in GBM patient by analyzing data from TCGA. METHODS The role of ARG2 in tumorigenesis was examined by proliferation-, migration-, invasion-, wound healing- and tube formation assays using an ARG2-overexpressing cell line and ARG inhibitor, N (omega)-hydroxy-nor-L-arginine (nor-NOHA) and siRNA against ARG2 coupled with functional assays measuring MMP2/9 activity, VEGF levels and nitric oxide synthase activity. Association between HCMV and ARG2 were examined in vitro with 3 different GBM cell lines, and ex vivo with immunostaining on GBM tissue sections. The viral mechanism mediating ARG2 induction was examined by siRNA approach. Correlation between ARG2 expression and patient survival was extrapolated from bioinformatics analysis on data from The Cancer Genome Atlas (TCGA). CONCLUSIONS ARG2 promotes tumorigenesis, and HCMV may contribute to GBM pathogenesis by upregulating ARG2.
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Affiliation(s)
- Helena Costa
- Cell and Molecular Immunology, Department of Medicine, Center for Molecular Medicine, Unit for Experimental Cardiovascular Research and Department of Neurology, Karolinska Institutet, Stockholm, Sweden
| | - Xinling Xu
- Cell and Molecular Immunology, Department of Medicine, Center for Molecular Medicine, Unit for Experimental Cardiovascular Research and Department of Neurology, Karolinska Institutet, Stockholm, Sweden
| | - Gitta Overbeek
- Cell and Molecular Immunology, Department of Medicine, Center for Molecular Medicine, Unit for Experimental Cardiovascular Research and Department of Neurology, Karolinska Institutet, Stockholm, Sweden
| | - Suhas Vasaikar
- Unit of Computational Medicine, Department of Medicine, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - C Pawan K Patro
- Social & Cognitive Computing Department, Institute of High Performance Computing, Agency for Science, Technology and Research, Singapore
| | - Ourania N Kostopoulou
- Cell and Molecular Immunology, Department of Medicine, Center for Molecular Medicine, Unit for Experimental Cardiovascular Research and Department of Neurology, Karolinska Institutet, Stockholm, Sweden
| | - Masany Jung
- Cell and Molecular Immunology, Department of Medicine, Center for Molecular Medicine, Unit for Experimental Cardiovascular Research and Department of Neurology, Karolinska Institutet, Stockholm, Sweden
| | - Gowhar Shafi
- Department of Genomics and Bioinformatics, Positive Bioscience, Mumbai, India
| | - Sharan Ananthaseshan
- Cell and Molecular Immunology, Department of Medicine, Center for Molecular Medicine, Unit for Experimental Cardiovascular Research and Department of Neurology, Karolinska Institutet, Stockholm, Sweden
| | - Giorgos Tsipras
- Unit of Computational Medicine, Department of Medicine, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Belghis Davoudi
- Cell and Molecular Immunology, Department of Medicine, Center for Molecular Medicine, Unit for Experimental Cardiovascular Research and Department of Neurology, Karolinska Institutet, Stockholm, Sweden
| | - Abdul-Aleem Mohammad
- Cell and Molecular Immunology, Department of Medicine, Center for Molecular Medicine, Unit for Experimental Cardiovascular Research and Department of Neurology, Karolinska Institutet, Stockholm, Sweden
| | - Hoyin Lam
- Cell and Molecular Immunology, Department of Medicine, Center for Molecular Medicine, Unit for Experimental Cardiovascular Research and Department of Neurology, Karolinska Institutet, Stockholm, Sweden.,Present affiliation: Division of Cancer Studies, King's College London, London, UK
| | - Klas Strååt
- Cell and Molecular Immunology, Department of Medicine, Center for Molecular Medicine, Unit for Experimental Cardiovascular Research and Department of Neurology, Karolinska Institutet, Stockholm, Sweden.,Division of Gene Technology, School of Biotechnology, Science for Life Laboratory, Royal Institute of Technology (KTH), Solna, Sweden
| | - Vanessa Wilhelmi
- Cell and Molecular Immunology, Department of Medicine, Center for Molecular Medicine, Unit for Experimental Cardiovascular Research and Department of Neurology, Karolinska Institutet, Stockholm, Sweden
| | - Mingmei Shang
- Unit of Computational Medicine, Department of Medicine, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Jesper Tegner
- Unit of Computational Medicine, Department of Medicine, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Joo Chuan Tong
- Social & Cognitive Computing Department, Institute of High Performance Computing, Agency for Science, Technology and Research, Singapore
| | - Kum Thong Wong
- Department of Pathology, Faculty of Medicine, University of Malaya, Malaysia
| | - Cecilia Söderberg-Naucler
- Cell and Molecular Immunology, Department of Medicine, Center for Molecular Medicine, Unit for Experimental Cardiovascular Research and Department of Neurology, Karolinska Institutet, Stockholm, Sweden
| | - Koon-Chu Yaiw
- Cell and Molecular Immunology, Department of Medicine, Center for Molecular Medicine, Unit for Experimental Cardiovascular Research and Department of Neurology, Karolinska Institutet, Stockholm, Sweden
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Vasaikar S, Tsipras G, Landázuri N, Costa H, Wilhelmi V, Scicluna P, Cui HL, Mohammad AA, Davoudi B, Shang M, Ananthaseshan S, Strååt K, Stragliotto G, Rahbar A, Wong KT, Tegner J, Yaiw KC, Söderberg-Naucler C. Overexpression of endothelin B receptor in glioblastoma: a prognostic marker and therapeutic target? BMC Cancer 2018; 18:154. [PMID: 29409474 PMCID: PMC5801893 DOI: 10.1186/s12885-018-4012-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Accepted: 01/22/2018] [Indexed: 01/07/2023] Open
Abstract
Background Glioblastoma (GBM) is the most common malignant brain tumor with median survival of 12-15 months. Owing to uncertainty in clinical outcome, additional prognostic marker(s) apart from existing markers are needed. Since overexpression of endothelin B receptor (ETBR) has been demonstrated in gliomas, we aimed to test whether ETBR is a useful prognostic marker in GBM and examine if the clinically available endothelin receptor antagonists (ERA) could be useful in the disease treatment. Methods Data from The Cancer Genome Atlas and the Gene Expression Omnibus database were analyzed to assess ETBR expression. For survival analysis, glioblastoma samples from 25 Swedish patients were immunostained for ETBR, and the findings were correlated with clinical history. The druggability of ETBR was assessed by protein-protein interaction network analysis. ERAs were analyzed for toxicity in in vitro assays with GBM and breast cancer cells. Results By bioinformatics analysis, ETBR was found to be upregulated in glioblastoma patients, and its expression levels were correlated with reduced survival. ETBR interacts with key proteins involved in cancer pathogenesis, suggesting it as a druggable target. In vitro viability assays showed that ERAs may hold promise to treat glioblastoma and breast cancer. Conclusions ETBR is overexpressed in glioblastoma and other cancers and may be a prognostic marker in glioblastoma. ERAs may be useful for treating cancer patients. Electronic supplementary material The online version of this article (10.1186/s12885-018-4012-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Suhas Vasaikar
- Unit of Computational Medicine, Center for Molecular Medicine, Department of Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Giorgos Tsipras
- Unit of Computational Medicine, Center for Molecular Medicine, Department of Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Natalia Landázuri
- Unit of Computational Medicine, Center for Molecular Medicine, Department of Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Helena Costa
- Cell and Molecular Immunology, Experimental Cardiovascular Unit, Departments of Medicine and Neurology, Center for Molecular Medicine, Karolinska Institutet, SE-171 76, Stockholm, Sweden
| | - Vanessa Wilhelmi
- Cell and Molecular Immunology, Experimental Cardiovascular Unit, Departments of Medicine and Neurology, Center for Molecular Medicine, Karolinska Institutet, SE-171 76, Stockholm, Sweden
| | - Patrick Scicluna
- Cell and Molecular Immunology, Experimental Cardiovascular Unit, Departments of Medicine and Neurology, Center for Molecular Medicine, Karolinska Institutet, SE-171 76, Stockholm, Sweden
| | - Huanhuan L Cui
- Cell and Molecular Immunology, Experimental Cardiovascular Unit, Departments of Medicine and Neurology, Center for Molecular Medicine, Karolinska Institutet, SE-171 76, Stockholm, Sweden
| | - Abdul-Aleem Mohammad
- Cell and Molecular Immunology, Experimental Cardiovascular Unit, Departments of Medicine and Neurology, Center for Molecular Medicine, Karolinska Institutet, SE-171 76, Stockholm, Sweden
| | - Belghis Davoudi
- Cell and Molecular Immunology, Experimental Cardiovascular Unit, Departments of Medicine and Neurology, Center for Molecular Medicine, Karolinska Institutet, SE-171 76, Stockholm, Sweden
| | - Mingmei Shang
- Unit of Computational Medicine, Center for Molecular Medicine, Department of Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Sharan Ananthaseshan
- Cell and Molecular Immunology, Experimental Cardiovascular Unit, Departments of Medicine and Neurology, Center for Molecular Medicine, Karolinska Institutet, SE-171 76, Stockholm, Sweden
| | - Klas Strååt
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | | | - Afsar Rahbar
- Cell and Molecular Immunology, Experimental Cardiovascular Unit, Departments of Medicine and Neurology, Center for Molecular Medicine, Karolinska Institutet, SE-171 76, Stockholm, Sweden
| | - Kum Thong Wong
- Department of Pathology, University of Malaya, Kuala Lumpur, Malaysia
| | - Jesper Tegner
- Unit of Computational Medicine, Center for Molecular Medicine, Department of Medicine, Karolinska Institutet, Stockholm, Sweden.,Biological and Environmental Sciences and Engineering Division (BESE), Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Koon-Chu Yaiw
- Cell and Molecular Immunology, Experimental Cardiovascular Unit, Departments of Medicine and Neurology, Center for Molecular Medicine, Karolinska Institutet, SE-171 76, Stockholm, Sweden.
| | - Cecilia Söderberg-Naucler
- Cell and Molecular Immunology, Experimental Cardiovascular Unit, Departments of Medicine and Neurology, Center for Molecular Medicine, Karolinska Institutet, SE-171 76, Stockholm, Sweden.
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Wang J, Mouradov D, Wang X, Jorissen RN, Chambers MC, Zimmerman LJ, Vasaikar S, Love CG, Li S, Lowes K, Leuchowius KJ, Jousset H, Weinstock J, Yau C, Mariadason J, Shi Z, Ban Y, Chen X, Coffey RJC, Slebos RJ, Burgess AW, Liebler DC, Zhang B, Sieber OM. Colorectal Cancer Cell Line Proteomes Are Representative of Primary Tumors and Predict Drug Sensitivity. Gastroenterology 2017; 153. [PMID: 28625833 PMCID: PMC5623120 DOI: 10.1053/j.gastro.2017.06.008] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
BACKGROUND AND AIMS Proteomics holds promise for individualizing cancer treatment. We analyzed to what extent the proteomic landscape of human colorectal cancer (CRC) is maintained in established CRC cell lines and the utility of proteomics for predicting therapeutic responses. METHODS Proteomic and transcriptomic analyses were performed on 44 CRC cell lines, compared against primary CRCs (n=95) and normal tissues (n=60), and integrated with genomic and drug sensitivity data. RESULTS Cell lines mirrored the proteomic aberrations of primary tumors, in particular for intrinsic programs. Tumor relationships of protein expression with DNA copy number aberrations and signatures of post-transcriptional regulation were recapitulated in cell lines. The 5 proteomic subtypes previously identified in tumors were represented among cell lines. Nonetheless, systematic differences between cell line and tumor proteomes were apparent, attributable to stroma, extrinsic signaling, and growth conditions. Contribution of tumor stroma obscured signatures of DNA mismatch repair identified in cell lines with a hypermutation phenotype. Global proteomic data showed improved utility for predicting both known drug-target relationships and overall drug sensitivity as compared with genomic or transcriptomic measurements. Inhibition of targetable proteins associated with drug responses further identified corresponding synergistic or antagonistic drug combinations. Our data provide evidence for CRC proteomic subtype-specific drug responses. CONCLUSIONS Proteomes of established CRC cell line are representative of primary tumors. Proteomic data tend to exhibit improved prediction of drug sensitivity as compared with genomic and transcriptomic profiles. Our integrative proteogenomic analysis highlights the potential of proteome profiling to inform personalized cancer medicine.
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Affiliation(s)
- Jing Wang
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA,CORRESPONDING AUTHORS: Oliver Sieber, Systems Biology and Personalised Medicine Division, The Walter and Eliza Hall Institute of Medial Research, 1G Royal Parade, Parkville, VIC 3052, Australia. . Bing Zhang, Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Dmitri Mouradov
- Systems Biology and Personalised Medicine Division, The Walter and Eliza Hall Institute of Medial Research, Parkville, VIC 3052, Australia,Department of Medical Biology, The University of Melbourne, Parkville, VIC 3052, Australia,CORRESPONDING AUTHORS: Oliver Sieber, Systems Biology and Personalised Medicine Division, The Walter and Eliza Hall Institute of Medial Research, 1G Royal Parade, Parkville, VIC 3052, Australia. . Bing Zhang, Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Xiaojing Wang
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA,CORRESPONDING AUTHORS: Oliver Sieber, Systems Biology and Personalised Medicine Division, The Walter and Eliza Hall Institute of Medial Research, 1G Royal Parade, Parkville, VIC 3052, Australia. . Bing Zhang, Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Robert N. Jorissen
- Systems Biology and Personalised Medicine Division, The Walter and Eliza Hall Institute of Medial Research, Parkville, VIC 3052, Australia,Department of Medical Biology, The University of Melbourne, Parkville, VIC 3052, Australia
| | | | - Lisa J. Zimmerman
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA
| | - Suhas Vasaikar
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Christopher G. Love
- Systems Biology and Personalised Medicine Division, The Walter and Eliza Hall Institute of Medial Research, Parkville, VIC 3052, Australia,Department of Medical Biology, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Shan Li
- Systems Biology and Personalised Medicine Division, The Walter and Eliza Hall Institute of Medial Research, Parkville, VIC 3052, Australia
| | - Kym Lowes
- Systems Biology and Personalised Medicine Division, The Walter and Eliza Hall Institute of Medial Research, Parkville, VIC 3052, Australia
| | - Karl-Johan Leuchowius
- Systems Biology and Personalised Medicine Division, The Walter and Eliza Hall Institute of Medial Research, Parkville, VIC 3052, Australia
| | - Helene Jousset
- Systems Biology and Personalised Medicine Division, The Walter and Eliza Hall Institute of Medial Research, Parkville, VIC 3052, Australia
| | - Janet Weinstock
- Structural Biology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Christopher Yau
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, United Kingdom,Department of Statistics, University of Oxford, Oxford, OX1 3LB, United Kingdom
| | - John Mariadason
- Olivia Newton-John Cancer Research Institute, Heidelberg, VIC 3084, Australia,La Trobe University School of Cancer Medicine, Melbourne, VIC 3086, Australia
| | - Zhiao Shi
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yuguang Ban
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Xi Chen
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA,Department of Public Health Sciences, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Robert J. C. Coffey
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN 37232, USA,Veterans Affairs Medical Center, Nashville, TN 37212, USA
| | | | - Antony W. Burgess
- Department of Medical Biology, The University of Melbourne, Parkville, VIC 3052, Australia,Structural Biology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia,Department of Surgery, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Daniel C. Liebler
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA
| | - Bing Zhang
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.
| | - Oliver M. Sieber
- Systems Biology and Personalised Medicine Division, The Walter and Eliza Hall Institute of Medial Research, Parkville, VIC 3052, Australia,Department of Medical Biology, The University of Melbourne, Parkville, VIC 3052, Australia,Department of Surgery, The University of Melbourne, Parkville, VIC 3052, Australia,School of Biomedical Sciences, Monash University, Clayton, VIC 3800, Australia,CORRESPONDING AUTHORS: Oliver Sieber, Systems Biology and Personalised Medicine Division, The Walter and Eliza Hall Institute of Medial Research, 1G Royal Parade, Parkville, VIC 3052, Australia. . Bing Zhang, Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA.
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Vasaikar S, Bhatia P, Bhatia PG, Chu Yaiw K. Complementary Approaches to Existing Target Based Drug Discovery for Identifying Novel Drug Targets. Biomedicines 2016; 4:E27. [PMID: 28536394 PMCID: PMC5344266 DOI: 10.3390/biomedicines4040027] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Revised: 11/16/2016] [Accepted: 11/17/2016] [Indexed: 02/07/2023] Open
Abstract
In the past decade, it was observed that the relationship between the emerging New Molecular Entities and the quantum of R&D investment has not been favorable. There might be numerous reasons but few studies stress the introduction of target based drug discovery approach as one of the factors. Although a number of drugs have been developed with an emphasis on a single protein target, yet identification of valid target is complex. The approach focuses on an in vitro single target, which overlooks the complexity of cell and makes process of validation drug targets uncertain. Thus, it is imperative to search for alternatives rather than looking at success stories of target-based drug discovery. It would be beneficial if the drugs were developed to target multiple components. New approaches like reverse engineering and translational research need to take into account both system and target-based approach. This review evaluates the strengths and limitations of known drug discovery approaches and proposes alternative approaches for increasing efficiency against treatment.
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Affiliation(s)
- Suhas Vasaikar
- Integrative Biology, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Pooja Bhatia
- School of Biological Sciences, Indian Institute of Technology, Delhi 110016, India.
| | - Partap G Bhatia
- Department of Pharmaceutics and Pharmaceutical Microbiology, Usmanu Danfodiyo University, Sokoto 840231, Nigeria.
| | - Koon Chu Yaiw
- Experimental Cardiovascular Research Unit, Department of Medicine-Solna, Center for Molecular Medicine, Karolinska Institute, Stockholm 17177, Sweden.
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Vasaikar S, Saraswathi K, De A, Varaiya A, Gogate A. Aeromonas species isolated from cases of acute gastroenteritis. Indian J Med Microbiol 2002; 20:107-9. [PMID: 17657045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
A total of 67 Aeromonas strains were isolated as the sole bacterial pathogen from 1485 patients with acute gastroenteritis. A. hydrophila (64.2%) was the predominant isolate followed by A. sobria (28.4%) and A.caviae (7.4%). Majority of the isolates were sensitive to gentamicin, nalidixic acid but were resistant to ampicillin. Minimum inhibitory concentration (MIC) of resistant strains of Aeromonas to ampicillin ranged from 80-1280 microg/mL.
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Affiliation(s)
- S Vasaikar
- Dept. of Microbiology, Seth GS Medical College and KEM Hospital Parel, Mumbai - 400 012, India
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