1
|
Badve SS, Cho S, Gokmen-Polar Y, Zavodszky M, Sui Y, Chadwick C, Tan PH, Gerdes M, Harris AL, Ginty F. Abstract P4-08-17: Expression score (Escore) for the prediction of likelihood of recurrence of DCIS. Cancer Res 2019. [DOI: 10.1158/1538-7445.sabcs18-p4-08-17] [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: Ductal carcinoma in situ (DCIS) accounts for at least 20% of breast cancers. Factors associated with recurrence of DCIS or progression to invasive carcinoma are not well delineated. The goals of the current study were to profile the epithelial cells using the GE Cell DIVE™ immuno-fluorescent based analyses. This was coupled with semi-automated algorithms to characterize the inter-relationships between cell populations and likelihood of recurrence.
Patients and Methods: A TMA-based (total 8 TMAs) cohort of cases of DCIS with and without recurrence was obtained from Oxford University. Recurrence in this cohort was defined as ipsilateral DCIS, ipsilateral invasive, contralateral invasive and metastatic. Analysis for 31 epithelial markers (HER4, CK56, ABCG2, PTEN, S6, CKAE1, PR, ER, NaKATPase, CK19, ALDH1, CK PCK26, cMET, CD44v6, HER2, CDCP1, p53, CK15, COX2, VEGFR2, ABCb1, HTF9C, CD10, MRP4, CEACAM5, EGFR, p21, MRP5, SLC7A5, Ki67, DAPI) was performed on a single FFPE TMA section containing cases of DCIS. Briefly, FFPE sections from TMAs containing DCIS were sequentially (cyclically) stained for the markers. Each cycle entailed staining with 2-3 markers followed by imaging, dye inactivation, and re-staining. DAPI was used for nuclear demarcation and for registration of the images, while S6, pan-cadherin, Na+K+ATPase and pan-cytokeratin were used for epithelial segmentation. K-means clustering followed regression analysis was performed to identify inter-relationships between markers and association with likelihood of recurrence. Log-rank analysis was performed and the relapse-free survival data depicted using Kaplan Meier plots. Escore was developed by logistic regression model, classification model on recurrence
Results: Filtering of the expression analysis by the quality, specificity, compartment localization and fields entirely composed of DCIS, in addition to availability of clinical data resulted final analysis of 31 markers in 67 cases. Correlation analyses were performed on each of the markers to identify markers that were significantly correlated in univariate analysis. K-means cluster analysis was performed using a set of 4 markers (ER, HER2, SLC7A5 and cMET) to identify 6 clusters. High cMET (cluster 1; low HER2 and SLC7A5) and High ER (low cMET, HER2, SLC7A5; Cluster 5) were associated with low risk of recurrence (p values 0.014 and <0.0001). In contrast, Cluster 2 (High HER2, high SLC7A5, low ER) and Cluster 3 (High HER2, low ER, SLC7A5and cMET) were associated with increased risk of recurrence (P values 0.038 and 0.076). A regression analysis based algorithm was developed using these markers to calculate a numerical score which could predict likelihood of recurrence. As depicted in the KM plots, the HR for recurrence increases significantly (P-value 2.4E-05; p=0.02 with LOOCV) with increase in expression score (Escore).
Conclusions: We describe the development of an Escore using expression 4 markers to predict likelihood of recurrence. Additional ongoing studies will seek to validate the utility of the Escore in predicting likelihood of recurrence of DCIS and development of invasive carcinomas and comparison with other scoring systems.
Citation Format: Badve SS, Cho S, Gokmen-Polar Y, Zavodszky M, Sui Y, Chadwick C, Tan PH, Gerdes M, Harris AL, Ginty F. Expression score (Escore) for the prediction of likelihood of recurrence of DCIS [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 P4-08-17.
Collapse
Affiliation(s)
- SS Badve
- Indiana University, Indianapolis, IN; GE Global Research Center, Niskayuna, NY; Singapore General Hospital, Singapore, Singapore; Oxford University, Oxford, United Kingdom
| | - S Cho
- Indiana University, Indianapolis, IN; GE Global Research Center, Niskayuna, NY; Singapore General Hospital, Singapore, Singapore; Oxford University, Oxford, United Kingdom
| | - Y Gokmen-Polar
- Indiana University, Indianapolis, IN; GE Global Research Center, Niskayuna, NY; Singapore General Hospital, Singapore, Singapore; Oxford University, Oxford, United Kingdom
| | - M Zavodszky
- Indiana University, Indianapolis, IN; GE Global Research Center, Niskayuna, NY; Singapore General Hospital, Singapore, Singapore; Oxford University, Oxford, United Kingdom
| | - Y Sui
- Indiana University, Indianapolis, IN; GE Global Research Center, Niskayuna, NY; Singapore General Hospital, Singapore, Singapore; Oxford University, Oxford, United Kingdom
| | - C Chadwick
- Indiana University, Indianapolis, IN; GE Global Research Center, Niskayuna, NY; Singapore General Hospital, Singapore, Singapore; Oxford University, Oxford, United Kingdom
| | - PH Tan
- Indiana University, Indianapolis, IN; GE Global Research Center, Niskayuna, NY; Singapore General Hospital, Singapore, Singapore; Oxford University, Oxford, United Kingdom
| | - M Gerdes
- Indiana University, Indianapolis, IN; GE Global Research Center, Niskayuna, NY; Singapore General Hospital, Singapore, Singapore; Oxford University, Oxford, United Kingdom
| | - AL Harris
- Indiana University, Indianapolis, IN; GE Global Research Center, Niskayuna, NY; Singapore General Hospital, Singapore, Singapore; Oxford University, Oxford, United Kingdom
| | - F Ginty
- Indiana University, Indianapolis, IN; GE Global Research Center, Niskayuna, NY; Singapore General Hospital, Singapore, Singapore; Oxford University, Oxford, United Kingdom
| |
Collapse
|
2
|
Gokmen-Polar Y, Gu Y, Gu X, Badve SS. Abstract P5-04-13: Splicing factor ESRP1 controls ER-positive breast cancer progression by altering metabolic pathway genes. Cancer Res 2019. [DOI: 10.1158/1538-7445.sabcs18-p5-04-13] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [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 Epithelial Splicing Regulatory Protein (ESRP1)is a key splicing factor that regulates Epithelial-to-Mesenchymal Transition (EMT) splicing program. Our previous study demonstrated that high levels of ESRP1 are associated with poor prognosis in human ER-positive (ER+) breast tumors in an independent manner of EMT process. We next explored the potential mechanisms that contribute to the role ESRP1 in endocrine therapy-resistant breast cancer.
Methods Probe based-Human Transcriptome Array 2.0 (HTA; Applied Biosystems/Thermo Fisher) was performed using RNAs from control and ESRP1 knockdown cells (LCC2 versus 2C3 ESRP1 and LCC9 versus 9C2 ESRP1) of endocrine resistant breast cancer. Functional enrichment analyses were performed using the DAVID functional annotation tool (http://david.abcc.ncifcrf.gov/). To confirm the functional importance of ESRP1 on regulation of cellular metabolism, we have performed experiments that analyze the metabolic substrate flux in response to ESRP1 knockdown in resistant cells (The Seahorse XFp Cell Energy Phenotype Assay). Differentially expressed genes were validated using Western blotting assay.
Results Transcriptome profiling of ESRP1in 2C3 and 9C2 knockdown models revealed differentially expressed genesusing HTA 2.0 platform. In LCC2 versus 2C3 ESRP1 knockdown, expression of 1186 genes (1263 transcripts) have been altered significantly, while 413 genes (432 transcripts) have been significantly regulated in LCC9 versus 9C2 ESRP1 knockdown with FDR<0.1 Of these significant genes, 34 downregulated and 68 upregulated (102 genes total) were shared by both 2C3 and 9C2 ESRP1 knockdowns. Using the DAVID Functional Annotation Clustering Tool, we identified the biological processes altered significantly in response to ESRP1 knockdown. The most significant annotation clusters downregulated in ESRP1 knockdown consists of fatty acid metabolism/lipid metabolism (SCD, ACACA, FASN, ACAT2, PLCH1, and HPGD), and oxireductase processes (SCD, PHGDH, FASN, DHTKD1 and HPGD. We confirmed the altered metabolic function using the Seahorse analyzer. These analyses confirmed that ESRP1 knockdown altered the glycolysis rate (extracellular acidification rate; ECAR) in both tamoxifen-resistant and fulvestrant-resistant models. In addition, ESRP1 knockdown decreased the mitochondrial respiration in tamoxifen-resistant cells, but not fulvestrant resistant cells. Using Western blotting, we validated the altered levels of fatty acid synthase (FASN) and Stearoyl-CoA desaturase 1 (SCD1), key enzymes in fatty acid metabolism. Phosphoglycerate Dehydrogenase (PHGDH), a poor prognosis marker in cancers including breast cancer, was also downregulated in response to ESRP1 knockdown. Taken together, we have demonstrated a novel functional impact of ESRP1 on the regulation of tumor growth at the functional and molecular level independent of EMT.
Conclusions For the first time, we show the role of ESRP1 in altering the cellular metabolism thereby contributing to tumor growth. The study provides a molecular evidence for the role of altered metabolism in determining adverse prognosis of ER+ breast cancer via the control of ESRP1, a splicing factor. Further studies to determine the therapeutic value are underway.
Citation Format: Gokmen-Polar Y, Gu Y, Gu X, Badve SS. Splicing factor ESRP1 controls ER-positive breast cancer progression by altering metabolic pathway genes [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 P5-04-13.
Collapse
Affiliation(s)
| | - Y Gu
- Indiana University, Indianapolis, IN
| | - X Gu
- Indiana University, Indianapolis, IN
| | - SS Badve
- Indiana University, Indianapolis, IN
| |
Collapse
|
3
|
Padda S, Gokmen-Polar Y, Badve S, Vasista S, Basu K, Kumar A, Vali S, Abbasi T, Wakelee H. P1.14-17 Identification of Molecular Subtypes of Thymic Epithelial Tumors and Novel Treatments Using a Computational Biological Model. J Thorac Oncol 2018. [DOI: 10.1016/j.jtho.2018.08.919] [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: 11/25/2022]
|
4
|
Badve S, Wang V, Willis S, Leyland-Jones B, Gokmen-Polar Y, Shulman L, Martino S, Sparano J, Davidson N, Goldstein L, Buechler S. Abstract P1-06-08: Independent validation of EarlyR gene signature in E2197: A randomized clinical trial comparing doxorubicin plus docetaxel to doxorubicin plus cyclophosphamide as adjuvant chemotherapy in breast cancer. Cancer Res 2018. [DOI: 10.1158/1538-7445.sabcs17-p1-06-08] [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: EarlyR is a prognostic gene signature score in ER+ breast cancer (BC) computed from the expression values of ESPL1, SPAG5, MKI67, PLK1 and PGR using a nonlinear mathematical formula. EarlyR has been validated in multiple cohorts profiled on Affymetrix and Illumina microarrays and by RNA-seq. This study sought to assess the prognostic features of EarlyR in a cohort of E2197.
Patients and Methods: Illumina DASL assay was used to measure gene expression in FFPE tissue of primary BC from a case-cohort sampling subset of women in E2197 treated with doxorubicin plus docetaxel (AT) or doxorubicin plus cyclophosphamide (AC). ER+ patients received hormone therapy at physician's discretion. After 79.5 months median follow-up, disease-free survival was 85% in both treatment arms. Among patients centrally reviewed with sufficient RNA material for the DASL assay, 319 with ER+ status and assessed for EarlyR are included in the analytic cohort. EarlyR scores and pre-specified risk strata (≤25=low, 26-75=intermediate, >75=high) were computed, while blinded to clinical data. The analysis endpoint was disease-free survival (DFS), defined as the time from randomization to date of invasive BC recurrence or death from any cause within 8 years. Weighted Cox proportional hazards models were used to associate EarlyR score or risk strata with DFS. Variances of the estimated coefficients were adjusted to account for the case-cohort design.
Results: The distribution of the EarlyR risk groups was 59% low, 11% intermediate and 30% high risk in this ER+ cohort. The continuous EarlyR score was significantly prognostic of DFS up to 8 years after randomization (p = 0.02). Patients with low EarlyR score (≤ 25) had significantly lower risk of BC recurrence within 8 years (p = 0.031, univariate HR=0.562, 95%CI: 0.334-0.948) compared to those with high EarlyR score (> 75). Analysis within the AC arm showed that patients with low EarlyR score had significantly lower risk of 8-year BC recurrence (p = 0.023, univariate HR=0.392, 95%CI: 0.175-0.878) compared to those with high EarlyR score. Within the AT arm there was no significant difference in 8-year DFS prognosis between any of the EarlyR risk groups.
Conclusions: This study confirmed the prognostic significance of EarlyR using FFPE tissue in a cohort of patients treated with AC chemotherapy from E2197. Patients with high EarlyR score who were treated with AC had significantly higher risk of recurrence than low EarlyR score patients treated with AC. On the other hand, prognosis of high EarlyR score AT-treated patients was not significantly lower than the prognosis of low EarlyR score AT-treated patients. Further study in a larger cohort is needed to assess the relative benefits of AC versus AT within the EarlyR high risk group and the EarlyR low risk group.
Citation Format: Badve S, Wang V, Willis S, Leyland-Jones B, Gokmen-Polar Y, Shulman L, Martino S, Sparano J, Davidson N, Goldstein L, Buechler S. Independent validation of EarlyR gene signature in E2197: A randomized clinical trial comparing doxorubicin plus docetaxel to doxorubicin plus cyclophosphamide as adjuvant chemotherapy in breast cancer [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P1-06-08.
Collapse
Affiliation(s)
- S Badve
- Indiana University, Indianapolis, IN; ECOG-ACRIN, Boston, MA; Avera Health, Sioux Falls; University of Pennslyvania, Philadelphia, PA; The Angles Clinic, Los Angeles, CA; Montefiore Medical Center, Bronx, NY; Fred Hutchinson Cancer Center, Seattle, WA; Fox Chase Cancer Center, Philadelphia, PA; Notre Dame University, South Bend, IN
| | - V Wang
- Indiana University, Indianapolis, IN; ECOG-ACRIN, Boston, MA; Avera Health, Sioux Falls; University of Pennslyvania, Philadelphia, PA; The Angles Clinic, Los Angeles, CA; Montefiore Medical Center, Bronx, NY; Fred Hutchinson Cancer Center, Seattle, WA; Fox Chase Cancer Center, Philadelphia, PA; Notre Dame University, South Bend, IN
| | - S Willis
- Indiana University, Indianapolis, IN; ECOG-ACRIN, Boston, MA; Avera Health, Sioux Falls; University of Pennslyvania, Philadelphia, PA; The Angles Clinic, Los Angeles, CA; Montefiore Medical Center, Bronx, NY; Fred Hutchinson Cancer Center, Seattle, WA; Fox Chase Cancer Center, Philadelphia, PA; Notre Dame University, South Bend, IN
| | - B Leyland-Jones
- Indiana University, Indianapolis, IN; ECOG-ACRIN, Boston, MA; Avera Health, Sioux Falls; University of Pennslyvania, Philadelphia, PA; The Angles Clinic, Los Angeles, CA; Montefiore Medical Center, Bronx, NY; Fred Hutchinson Cancer Center, Seattle, WA; Fox Chase Cancer Center, Philadelphia, PA; Notre Dame University, South Bend, IN
| | - Y Gokmen-Polar
- Indiana University, Indianapolis, IN; ECOG-ACRIN, Boston, MA; Avera Health, Sioux Falls; University of Pennslyvania, Philadelphia, PA; The Angles Clinic, Los Angeles, CA; Montefiore Medical Center, Bronx, NY; Fred Hutchinson Cancer Center, Seattle, WA; Fox Chase Cancer Center, Philadelphia, PA; Notre Dame University, South Bend, IN
| | - L Shulman
- Indiana University, Indianapolis, IN; ECOG-ACRIN, Boston, MA; Avera Health, Sioux Falls; University of Pennslyvania, Philadelphia, PA; The Angles Clinic, Los Angeles, CA; Montefiore Medical Center, Bronx, NY; Fred Hutchinson Cancer Center, Seattle, WA; Fox Chase Cancer Center, Philadelphia, PA; Notre Dame University, South Bend, IN
| | - S Martino
- Indiana University, Indianapolis, IN; ECOG-ACRIN, Boston, MA; Avera Health, Sioux Falls; University of Pennslyvania, Philadelphia, PA; The Angles Clinic, Los Angeles, CA; Montefiore Medical Center, Bronx, NY; Fred Hutchinson Cancer Center, Seattle, WA; Fox Chase Cancer Center, Philadelphia, PA; Notre Dame University, South Bend, IN
| | - J Sparano
- Indiana University, Indianapolis, IN; ECOG-ACRIN, Boston, MA; Avera Health, Sioux Falls; University of Pennslyvania, Philadelphia, PA; The Angles Clinic, Los Angeles, CA; Montefiore Medical Center, Bronx, NY; Fred Hutchinson Cancer Center, Seattle, WA; Fox Chase Cancer Center, Philadelphia, PA; Notre Dame University, South Bend, IN
| | - N Davidson
- Indiana University, Indianapolis, IN; ECOG-ACRIN, Boston, MA; Avera Health, Sioux Falls; University of Pennslyvania, Philadelphia, PA; The Angles Clinic, Los Angeles, CA; Montefiore Medical Center, Bronx, NY; Fred Hutchinson Cancer Center, Seattle, WA; Fox Chase Cancer Center, Philadelphia, PA; Notre Dame University, South Bend, IN
| | - L Goldstein
- Indiana University, Indianapolis, IN; ECOG-ACRIN, Boston, MA; Avera Health, Sioux Falls; University of Pennslyvania, Philadelphia, PA; The Angles Clinic, Los Angeles, CA; Montefiore Medical Center, Bronx, NY; Fred Hutchinson Cancer Center, Seattle, WA; Fox Chase Cancer Center, Philadelphia, PA; Notre Dame University, South Bend, IN
| | - S Buechler
- Indiana University, Indianapolis, IN; ECOG-ACRIN, Boston, MA; Avera Health, Sioux Falls; University of Pennslyvania, Philadelphia, PA; The Angles Clinic, Los Angeles, CA; Montefiore Medical Center, Bronx, NY; Fred Hutchinson Cancer Center, Seattle, WA; Fox Chase Cancer Center, Philadelphia, PA; Notre Dame University, South Bend, IN
| |
Collapse
|
5
|
Badve SS, Neelamraju Y, Goswami CP, Gu X, Nallamothu G, Gu Y, Vieth E, Janga SC, Ryan M, Gokmen-Polar Y. Abstract P5-04-03: Aggressiveness of epithelial cancers is independent of epithelial-to-mesenchymal transition. Cancer Res 2018. [DOI: 10.1158/1538-7445.sabcs17-p5-04-03] [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: Epithelial-to-Mesenchymal Transition (EMT)is postulated to be an important step in cancer progression and controlled by multiple mechanisms including EMT transcription factors (EMT-TFs) and splicing factors such as Epithelial Splicing Regulatory Proteins (ESRP1 and ESRP2). We previously have shown that the expression of ESRP1 and ESRP2 have significantly elevated in cases with high Oncotype DX scores and in ERα-positive cells with acquired endocrine resistance (SABCS 2013). This study seeks to identify the role of EMT-TFs and ESRP1s in the determination of outcomes of patients with ER+ breast cancer.
Patients and Methods: The expression of EMT-TFs and ESRP1 was analyzed in the Affymetrix microarray and TCGA BRCA databases. Next, we generated genetically engineered knockdown models of ESRP1 to understand its functional role in endocrine resistance. We performed RNA-seq and MATS analysis to identify alternative splicing events (ASEs) between ESRP1 knockdown and control cell lines [(2C3 vs 2-control (LCC2 set) and 9C2 vs 9-control(LCC9 set)]. Validation of the ASEs was performed using a probe-based platform [Human Transcriptome Array 2.0 (HTA)] and TCGA SpliceSeq from breast tumors.
Results: High levels of ESRP1 mRNA, but not EMT-TFs, are associated with poor prognosis in human ER+ breast tumors (Affymetrix; P=2.8e-07 and TCGA; P=0.00011). Knockdown of ESRP1 in ER+ endocrine resistant breast cancer induced glandular differentiation, rather than mesenchymal features. This was associated with significant reduction in cell and tumor growth in mammary fat pad orthotopic xenograft mice models of LCC2 and LCC9. No alterations in EMT-TFs were observed in these cells. Transcriptome profiling of ESRP1 knockdown cells further revealed altered ASEs in EMT splicing gene signature, but not at the gene level. These alterations (SE-skipped exon) were further validated for ARHGEF11, ENAH, FNIP1, SCRIB, and SLK using probe based HTA platform for ESRP1 knockdown cells and TCGA-SpliceSeq ER+ BRCA tumors in ER+ ESRP1low versus ESRP1high breast tumors.
Conclusions: Our data demonstrates for the first time that high ESRP1 is associated with poor prognosis in ER+ breast cancer. Despite its involvement in regulation of EMT splicing signature, low levels (or knockdown) of ESRP1 were not associated with EMT phenotype in tumors or in endocrine-resistant ER+ cells. Taken together, our findings indicate that EMT is not important in determining prognosis in ER+ breast cancer and that ESRP1 exerts a different role in aggressive ER+ breast cancers.
Citation Format: Badve SS, Neelamraju Y, Goswami CP, Gu X, Nallamothu G, Gu Y, Vieth E, Janga SC, Ryan M, Gokmen-Polar Y. Aggressiveness of epithelial cancers is independent of epithelial-to-mesenchymal transition [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P5-04-03.
Collapse
Affiliation(s)
- SS Badve
- Pathology and Lab Medicine, Indiana University, Indianapolis, IN; School of Informatics and Computing, Indiana University, Indianapolis, IN; In Silico Solutions, Falls Church, VA
| | - Y Neelamraju
- Pathology and Lab Medicine, Indiana University, Indianapolis, IN; School of Informatics and Computing, Indiana University, Indianapolis, IN; In Silico Solutions, Falls Church, VA
| | - CP Goswami
- Pathology and Lab Medicine, Indiana University, Indianapolis, IN; School of Informatics and Computing, Indiana University, Indianapolis, IN; In Silico Solutions, Falls Church, VA
| | - X Gu
- Pathology and Lab Medicine, Indiana University, Indianapolis, IN; School of Informatics and Computing, Indiana University, Indianapolis, IN; In Silico Solutions, Falls Church, VA
| | - G Nallamothu
- Pathology and Lab Medicine, Indiana University, Indianapolis, IN; School of Informatics and Computing, Indiana University, Indianapolis, IN; In Silico Solutions, Falls Church, VA
| | - Y Gu
- Pathology and Lab Medicine, Indiana University, Indianapolis, IN; School of Informatics and Computing, Indiana University, Indianapolis, IN; In Silico Solutions, Falls Church, VA
| | - E Vieth
- Pathology and Lab Medicine, Indiana University, Indianapolis, IN; School of Informatics and Computing, Indiana University, Indianapolis, IN; In Silico Solutions, Falls Church, VA
| | - SC Janga
- Pathology and Lab Medicine, Indiana University, Indianapolis, IN; School of Informatics and Computing, Indiana University, Indianapolis, IN; In Silico Solutions, Falls Church, VA
| | - M Ryan
- Pathology and Lab Medicine, Indiana University, Indianapolis, IN; School of Informatics and Computing, Indiana University, Indianapolis, IN; In Silico Solutions, Falls Church, VA
| | - Y Gokmen-Polar
- Pathology and Lab Medicine, Indiana University, Indianapolis, IN; School of Informatics and Computing, Indiana University, Indianapolis, IN; In Silico Solutions, Falls Church, VA
| |
Collapse
|
6
|
Hahn N, Cramer H, Badve S, Cheng L, Gokmen-Polar Y, Miller D, Buechlein A, Rusch D, Fang F, Frankhouser D, Bundschu R, Ganbat J, Foster R, Bihrle R, Masterson T, Gardner T, Koch M, Marchionni L, Pearlly Y, Nephew K. 2648 Novel DNA methylation therapeutic targets in urothelial carcinoma (UC) from patients with paired metachronous primary and metastatic tumors. Eur J Cancer 2015. [DOI: 10.1016/s0959-8049(16)31465-4] [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: 10/22/2022]
|
7
|
Mina LA, Gokmen-Polar Y, Goswami C, Storniolo AM, Li L, Badve S, Sledge GW. P2-13-01: Gene Profiling of Whole Blood May Identify Patients with BRCA Mutations. Cancer Res 2011. [DOI: 10.1158/0008-5472.sabcs11-p2-13-01] [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: 11/16/2022]
Abstract
Abstract
Background:The BRCA1 and the BRCA2 proteins play a role in DNA repair and confer genomic stability to the cell. Identifying BRCA mutation carriers has become an important tool for prevention as well as guiding therapy in cancer patients. We proposed to test the hypothesis that gene expression analysis of peripheral whole blood can reliably detect these mutations.
Materials and methods: Following IRB approval, 10cc of blood was collected from 36 women (BRCA1 (n=8), BRCA2 (n=9), Hereditary breast cancer without BRCA (FAM) (n=7), sporadic breast cancer (SPO) (n=11)). 3 of BRCA1 and 5 of BRCA2 samples were from women without cancer. Following RNA extraction (using the method described by Beekman et al) and quality assessment, Illumina® Whole-Genome DASL™ microarray (Human Ref-8 BeadChips) analysis was performed. The raw data was normalized and analyzed using Partek® Genomic Suite. Differentially expressed genes were identified using ANOVA analysis. Geneset specific supervised analysis was performed to visualize the inherent similarities and differences in the gene expression amongst different groups for 1) DNA repair and 2) Immune-system-related genes. Ingenuity Pathway Analysis (IPA) was performed to interpret the data in the context of biological processes, pathways and networks.
Results: Twenty-nine of the 87 immune-related genes were up-regulated in BRCA1 and BRCA2 groups compared to SPO or FAM groups; these included IL7R, CD53, CD2, CD48 and HLA-DRA. Twenty-five of the 79 DNA repair genes were up-regulated in BRCA1 and BRCA2; these included FANCC, RAD51L3, MSH2, MSH6 and PCNA. In IPA analysis, the comparison of BRCA1 vs. REST (BRCA2 + FAM + SPO) showed a strong immunologic signal, with the top altered biological processes including “Immunologic disease”, “Infection mechanism”, “Immune cell trafficking” and “cell-mediated immune response “. The top 5 canonical pathways also reflected a similar pattern and included “iCOS-iCOSL Signaling in T Helper Cells”, “OX40 Signaling Pathway”, “Calcium-induced T Lymphocyte”, “Apoptosis Regulation of IL-2 Expression in Activated and Anergic T Lymphocytes” and “Protein Ubiquitination Pathway”. When BRCA2 was compared with the REST (BRCA1 + FAM + SPO), a much weaker signal was noted with none of the canonical pathways being significantly altered. PAM analysis showed that a set of 16 genes could differentiate the BRCA patients from the rest with an error rate of 5%. Further validation of this geneset is being performed.
Conclusion: Gene profiling in whole blood may offer an easy, reliable and inexpensive way to identify patients with BRCA mutation. Further studies are currently underway to validate our results in a larger patient population.
Citation Information: Cancer Res 2011;71(24 Suppl):Abstract nr P2-13-01.
Collapse
Affiliation(s)
- LA Mina
- 1Indiana University School of Medicine, Indianapolis, IN
| | - Y Gokmen-Polar
- 1Indiana University School of Medicine, Indianapolis, IN
| | - C Goswami
- 1Indiana University School of Medicine, Indianapolis, IN
| | - AM Storniolo
- 1Indiana University School of Medicine, Indianapolis, IN
| | - L Li
- 1Indiana University School of Medicine, Indianapolis, IN
| | - S Badve
- 1Indiana University School of Medicine, Indianapolis, IN
| | - GW Sledge
- 1Indiana University School of Medicine, Indianapolis, IN
| |
Collapse
|
8
|
Badve SS, Goswami C, Gokmen-Polar Y, Nelson RP, Henley J, Miller N, Jain RK, Mehta RJ, Zaheer NA, Sledge GW, Li L, Kesler K, Loehrer PJ. Molecular predictors of metastases and stage of thymoma. J Clin Oncol 2011. [DOI: 10.1200/jco.2011.29.15_suppl.10599] [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: 11/20/2022] Open
|
9
|
Duchnowska R, Jassem J, Szutowicz E, Biernat W, Jankowski T, Och W, Staszkiewicz R, Chudzik M, Rogowski W, Flores N, Woditschka S, Li L, Goswami C, Thorat MA, Gokmen-Polar Y, Sledge GW, Steeg PS, Palmieri D, Badve SS. RAD51 and brain metastases (BM) in patients (pts) with HER2+ breast cancer. J Clin Oncol 2011. [DOI: 10.1200/jco.2011.29.15_suppl.634] [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: 11/20/2022] Open
|
10
|
Gokmen-Polar Y, Toroni RA, Badve S, Bruckheimer E, Kinch MS, Miller KD. Dual targeting of EphA2 and ER restores tamoxifen sensitivity in ER/EphA2-positive breast cancer. Cancer Res 2009. [DOI: 10.1158/0008-5472.sabcs-3020] [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
Abstract #3020
Background: Overexpression and altered function of EphA2 receptor tyrosine kinase are critical in the progression of breast cancer and provide a novel target for breast cancer therapy. We have previously demonstrated that EphA2 overexpression decreases estrogen dependence and tamoxifen sensitivity both in vitro and in vivo. EA5, a novel monoclonal antibody that mimicks the binding of ephrin A to EphA2, reverses the effect of EphA2 overexpression and restores tamoxifen sensitivity in EphA2-transfected MCF-7 cells (MCF-7EphA2) in vitro. Here we report the impact of EA5 on in vivo tumor growth and its ability to overcome in vivo tamoxifen resistance in MCF-7EphA2 xenografts. Furthermore, we investigated the mechanisms by which EphA2 overexpression decreases the estrogen dependence and contributes to tamoxifen resistance in ER+ breast cancer models.
 Material and Methods: MCF-7 cells transfected with vector (MCF-7neo) or EphA2 (MCF-7EphA2) were implanted in the right and left mammary fat pads of athymic mice. Treatment with EA5 (5 mg/kg/i.p./5 days/week), vehicle, tamoxifen (1 mg/oral gavage/5 days/week), or EA5 and tamoxifen in combination was initiated once tumors were established. To explore the role of EphA2 overexpression on ER-dependent mechanisms, we used two different ER+/EphA2-transfected cell line models (MCF-7neo/ MCF-7EphA2 and T47Dneo/ T47DEphA2). We measured ER activity and expression of ER-dependent proteins in response to 17β-estradiol (E2;10-10 M), 4-hydroxy-tamoxifen (10-6 M, and EA5 antibody (3μg/mL). Interaction of ER and EphA2 was investigated using GST-pulldown and co-immunoprecipitation approaches. Gene array studies suggested that EphA2 may impact ER via noncanonical pathways, leading to an investigation of focal adhesion kinase (FAK) signaling.
 Results: EA5 inhibits primary tumor growth and restores tamoxifen sensitivity in the MCF-7EphA2 in vivo model;EA5 had no impact on in vivo tumor growth in MCF-7neo xenografts. Using T47DEphA2 in vitro model, we verified that EphA2 decreases ER activation in response to E2 stimulation consistent with our earlier results in MCF-7EphA2 model. We found no direct interaction between ER and EphA2 and no difference in expression of canonical ER-dependent proteins, ER coactivators or corepressors. However, E2 stimulation phosphorylates FAKTyr925 in ER+/EphA2+ cell lines but not in ER+/EphA2- cell lines. Treatment of T47DEphA2 cells with EA5 and tamoxifen leads to dephosphorylation of FAKTyr925 in the presence of E2 stimulation.
 Conclusion: Our data demonstrate that dual targeting of EphA2 and ER is a promising approach for delaying resistance to tamoxifen. The data support our hypothesis that EphA2 impacts ER function via a FAK dependent pathway.
Citation Information: Cancer Res 2009;69(2 Suppl):Abstract nr 3020.
Collapse
Affiliation(s)
- Y Gokmen-Polar
- 1 Indiana University Melvin and Bren Simon Cancer Center, Indianapolis, IN
| | - RA Toroni
- 1 Indiana University Melvin and Bren Simon Cancer Center, Indianapolis, IN
| | - S Badve
- 1 Indiana University Melvin and Bren Simon Cancer Center, Indianapolis, IN
| | | | | | - KD Miller
- 1 Indiana University Melvin and Bren Simon Cancer Center, Indianapolis, IN
| |
Collapse
|
11
|
Abstract
Insulin is an important regulator of glucose transport and lipolysis in adipocytes. The present studies compared the effects of insulin in rat adipocytes with the effects of oxytocin and peroxovanadate, which mimic some effects of insulin. The antilipolytic effects of peroxovanadate and oxytocin were unaffected by 500 nmol/L wortmannin, which blocked the antilipolytic action of insulin. However, wortmannin, which is a relatively specific inhibitor of phosphatidylinositol 3-kinase, did block most of the stimulation of glucose metabolism by peroxovanadate while having little effect on that due to oxytocin. Under appropriate conditions, it was also possible to demonstrate a lipolytic action of insulin, especially with low (0.1 to 1 nmol/L) concentrations of insulin after exposure of adipocytes to 50 nmol/L wortmannin. The data provide additional support for the hypothesis that oxytocin and peroxovanadate affect adipose tissue metabolism by mechanisms distinctly different from those involved in insulin action.
Collapse
Affiliation(s)
- J N Fain
- Department of Biochemistry, University of Tennessee, Memphis 38163, USA
| | | | | |
Collapse
|
12
|
Bahouth SW, Gokmen-Polar Y, Coronel EC, Fain JN. Enhanced desensitization and phosphorylation of the beta 1-adrenergic receptor in rat adipocytes by peroxovanadate. Mol Pharmacol 1996; 49:1049-57. [PMID: 8649343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Peroxovanadate (PVN) is an insulin-like agent that inhibits the dephosphorylation of the insulin receptor kinase. PVN inhibited the lipolytic action of 0.1 microM isoproterenol by 88%, which is a relatively specific beta 1 catecholamine agonist at this concentration, but was largely ineffective against beta 3 agonists or forskolin. To determine whether PVN-mediated desensitization of the beta 1 AR was associated with enhanced phosphorylation, we immunoprecipitated the beta 1 AR from rat adipocytes that were metabolically labeled with 32PO4. Isoproterenol enhanced the net phosphorylation of the beta 1 AR by 8 +/- 2-fold over control. PVN increased the net phosphorylation of the beta 1 AR by 5 +/- 0.5-fold, and together with isoproterenol, they enhanced the phosphorylation of the beta 1 AR by 2-fold over isoproterenol alone. Phosphoamino acid analysis of the phosphorylated receptor revealed phosphate incorporation into serine that was proportional to the radioactivity incorporated into the immunoprecipitated receptor. PVN inhibited the serine/threonine phosphatase calcineurin, suggesting that inhibition of receptor dephosphorylation may play a role in the actions of PVN. Cyanogen bromide cleavage of the phosphorylated beta 1 AR generated a phosphoprotein with a molecular mass consistent with carboxyl-terminal phosphorylation. Furthermore, the magnitude of receptor phosphorylation by isoproterenol was 3-fold larger than that due to forskolin, suggesting that beta 1 AR is a substrate for the beta AR kinase that phosphorylates carboxyl-terminal residues in the beta(2) AR. Our findings suggest that PVN may be a powerful new tool with which to study the phosphorylation of other G protein-coupled receptors.
Collapse
Affiliation(s)
- S W Bahouth
- Department of Pharmacology, University of Tennessee, Memphis, 38163, USA
| | | | | | | |
Collapse
|
13
|
Abstract
The present studies examined the effect of NMDA on carbachol-stimulated accumulation of inositol polyphosphates, with emphasis on the accumulation of inositol 1,3,4,5-tetrakisphosphate (Ins 1,3,4,5-P4), at short time periods in rat brain cortical slices. There was a stimulatory effect of NMDA on accumulation of labeled inositol mono-, bis- and trisphosphates but not on labeled inositol tetrakisphosphates. In the presence of carbachol Ins 1,3,4,5-P4 accumulation was preferentially inhibited by NMDA at early time periods (within 30 seconds after NMDA addition). Subsequently, total phosphoinositide breakdown was inhibited by NMDA. NMDA did not stimulate accumulation of total Ins 1,3,4,5-P4 but immediately inhibited carbachol stimulated accumulation of Ins 1,3,4,5-P4. The inhibitory effect of NMDA (1 mM) was not mimicked by increasing K+ in the medium from 10 to 30 mM. However 30 mM K+ reversed the inhibitory effect of 1 mM NMDA on carbachol-stimulated Ins 1,3,4,5-P4. Parallel experiments with veratridine (a sodium channel activator) suggest that the early inhibitory effects of NMDA on Ins 1,3,4,5-P4 accumulation are not due to decreases in ATP availability or elevations in intracellular Na+. These data indicate that NMDA increases inositol mono-, bis- and trisphosphate accumulation while blocking muscarinic cholinergic stimulated accumulation of Ins 1,3,4,5-P4.
Collapse
Affiliation(s)
- M E Myles
- University of Tennessee, Memphis, Department of Biochemistry 38163, USA
| | | | | |
Collapse
|
14
|
Gokmen-Polar Y, Coronel EC, Bahouth SW, Fain JN. Insulin sensitizes beta-agonist and forskolin-stimulated lipolysis to inhibition by 2',5'-dideoxyadenosine. Am J Physiol 1996; 270:C562-9. [PMID: 8779920 DOI: 10.1152/ajpcell.1996.270.2.c562] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
In isolated rat adipocytes incubated in the absence of insulin, 2',5'-dideoxyadenosine blocked the increase in total adenosine 3',5'-cyclic monophosphate (cAMP) accumulation due to beta 1- or beta 3-catecholamine agonists and forskolin without affecting their stimulation of lipolysis. The inhibition of cAMP accumulation by 2',5'-dideoxyadenosine was not reflected in the total cytosolic cAMP-dependent protein kinase A activity, suggesting that the inhibition of cAMP occurred in cellular compartments distinct from those involved in the regulation of bulk protein kinase A activity. However, there was a good correlation between effects of lipolytic agents on cytosolic protein kinase A activity in fat cell extracts and lipolysis. Furthermore, it was possible to see an inhibition of the increase due to beta-agonists in cAMP accumulation, protein kinase A activity, and lipolysis by 2',5'-dideoxyadenosine in the presence of insulin. These data suggest that the readily measurable accumulation of cAMP seen with catecholamines in the absence of insulin is in a compartment separate from that involved in protein kinase A activation.
Collapse
Affiliation(s)
- Y Gokmen-Polar
- Department of Biochemistry, University of Tennessee, Memphis 38163, USA
| | | | | | | |
Collapse
|
15
|
Myles ME, Gokmen-Polar Y, Fain JN. Inhibition by veratridine of carbachol-stimulated inositol tetrakisphosphate accumulation in rat brain cortical slices. Neurochem Res 1995; 20:1057-64. [PMID: 8570010 DOI: 10.1007/bf00995560] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [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] [Indexed: 01/31/2023]
Abstract
The present studies examined the inhibitory effect of veratridine (a Na+ channel activator) on carbachol (a cholinergic agonist) stimulated inositol 1,3,4,5-tetrakisphosphate accumulation in rat brain cortical slices. Veratridine inhibited carbachol stimulation of inositol 1,3,4,5-tetrakisphosphate formation (after a delay of about 30 seconds) at 60 or 120 seconds when there was little inhibition of inositol 1,4,5 trisphosphate accumulation. The inhibitory effect of veratridine on carbachol stimulated inositol 1,3,4,5-tetrakisphosphate accumulation was abolished in the presence of ouabain or tetrodotoxin but was unaffected in low calcium conditions. Veratridine reduced the total ATP content and this effect was abolished by tetrodotoxin. The inhibitory effect of 10 but not 30 microM veratridine on inositol 1,3,4,5-tetrakisphosphate accumulation in the presence of carbachol was reversed by the presence of exogenous 8-bromo cyclic AMP or forskolin which activates adenylyl cyclase. However, the decrease in brain slice ATP seen in the presence of veratridine was unaffected by forskolin. Our results are compatible with the hypothesis that veratridine inhibition of carbachol-stimulated inositol 1,3,4,5-tetrakisphosphate formation is due to depletion of ATP at the site of Ins 1,3,4,5-P4 formation from Ins 1,4,5-P3.
Collapse
Affiliation(s)
- M E Myles
- Department of Biochemistry, University of Tennessee, Memphis 38163, USA
| | | | | |
Collapse
|