Understanding the Impact of Population and Cancer Type on Tumor Mutation Burden Scores: A Comprehensive Whole-Exome Study in Cancer Patients From India

PURPOSE

The purpose of this study was to understand the impact of population diversity and geographic variation on tumor mutation burden (TMB) scores across cancers and its implication on stratification of patients for immune checkpoint inhibitor (ICI) therapy.

MATERIALS AND METHODS

This retrospective study used whole-exome sequencing (WES) to profile 1,233 Indian patients with cancer across 30 different cancer types and to estimate their TMB scores. A WES-based pipeline was adopted, along with an indigenously developed strategy for arriving at true somatic mutations. A robust unsupervised machine learning approach was used to understand the distribution of TMB scores across different populations and within the population.

RESULTS

The results of the study showed a biphasic distribution of TMB scores in most cancers, with different threshold scores across cancer types. Patients with cancer in India had higher TMB scores compared with the Caucasian patients. We also observed that the TMB score value at 90th percentile (predicting high efficacy to ICI) was high in four different cancer types (sarcoma, ovary, head and neck, and breast) in the Indian cohort as compared with The Cancer Genome Atlas or public cohort. However, in lung and colorectal cancers, the TMB score distribution was similar between the two population cohorts.

CONCLUSION

The findings of this study indicate that it is crucial to benchmark both cancer-specific and population-specific TMB distributions to establish a TMB threshold for each cancer in various populations. Additional prospective studies on much larger population across different cancers are warranted to validate this observation to become the standard of care.

Abstract P2-21-10: Tumour associated macrophages in Breast Cancer - Are they critical players in response to Neo Adjuvant Chemotherapy?

Background Breast Cancer (BC) patients who do not obtain pathologic complete response (pCR) after neoadjuvant chemotherapy (NACT) present higher rate of relapse and worse overall survival. Recent evidence suggests that chemotherapy (CT) efficacy relies on the capacity of chemotherapeutic agents to interact with the immune system. BC features a unique tumor microenvironment (TME) comprising of multiple immune cell types including Macrophages that share a double-edged relationship with cancer as they get polarised from M1 (anti-tumour) to M2 (Pro-tumour). Pro-tumour M2 macrophages are referred to as tumor-associated macrophages (TAMs) and are implicated extensively in angiogenesis, metastasis and therapy resistance. Establishing role of TAMs, facilitates the emergence of novel strategies that exploit them as theranostic targets/tools of interest for treating cancer. Utility of using Drugs like Zoledronic Acid, Trabectedin, Rebastinib in combination with 5-fu have shown promising anti-TAM activity and improved response to CT in clinical trials. In this study, we have characterized presence of M2-TAM and its correlation to NACT response in matched primary and residual tumours by examining expression of several biomarkers. Methods Treatment naïve primary and their matched residual tumour specimens from 45 women treated at a single center were accessed through IERB approved protocols. The study included locally advanced HR+HER2-ve and TNBC tumours treated with standard NACT regimes between 2018 to 2020. To determine the association of TAM population with response to NACT, expression levels of CD68 (pan macrophage marker) & CD163 (marker of М2 macrophages), were detected by immunohistochemistry (IHC) and represented as combined H score. We also performed gene expression of chemokines, inflammatory cytokines and interleukins involved in M1-M2 polarization by q-RT-PCR. Residual Cancer Burden Scoring was used to assess response and patients were divided into three groups (complete responders, partial responders and non-responders). Univariate and multi variate analysis were performed between gene expression groups and IHC groups with clinicopathological parameters. Findings from this study was validated on public data bases like TCGA, METABRIC and GEO. Results: 20% of all patients included in the study were complete responders. We arrived at a Macrophage Polarisation Score (MPS) by Gene expression and also a combined H score by IHC. MPS and H-score had a positive correlation (p=0.083) overall. Interestingly, Combined analysis of H-Score and MPS with response to treatment showed a greater and statistically significant correlation with residual tumours as compared to treatment naïve tumours (p=0.009). We also observed that high MPS and high combined H score in residual tumours were associated with increased tumour size and LVI (p=0.055 and p=0.03). Other clinicopathological parameters like receptor status, grade and stage at diagnosis were not significantly associated with H score or MPS. Taken together we found that 11% of patients who exhibited high TAM score by both H sascore and MPS fell into the non-responders category. We therefore report TAMs in residual tumours being more indicative for response to therapy compared to primary tumours. Conclusion Although primary tumours are useful for building predictive models to therapy response, we have demonstrated that there is utility in examining residual tumours as well for choice to adjuvant chemotherapy, since the tumour is constantly evolving through the NACT period. More work to arrive at a “TAM score” that could aid in choice of additional adjuvant treatment strategies is underway. We believe our work is helping us to move one step closer to Precision Medicine in a low and middle income country like India that has a higher burden of locally advanced disease. Our analysis also lends itself to becoming a clinical test since it is performed on an FFPE specimen

Citation Format: Lohita Krishna, Aruna Korlimarla, B S Srinath, Anugnya Ranjolkar, Sudipta Nascar, Hari PS, Durga Devi, Nidhi l, Rekha V Kumar. Tumour associated macrophages in Breast Cancer - Are they critical players in response to Neo Adjuvant Chemotherapy? [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 P2-21-10.

Comprehensive characterization of immune landscape of Indian and Western triple negative breast cancers

PURPOSE

Triple-negative breast cancer (TNBC) is a heterogeneous disease with a significant challenge to effectively manage in the clinic worldwide. Immunotherapy may be beneficial to TNBC patients if responders can be effectively identified. Here we sought to elucidate the immune landscape of TNBCs by stratifying patients into immune-specific subtypes (immunotypes) to decipher the molecular and cellular presentations and signaling events of this heterogeneous disease and associating them with their clinical outcomes and potential treatment options.

EXPERIMENTAL DESIGN

We profiled 730 immune genes in 88 retrospective Indian TNBC samples using the NanoString platform, established immunotypes using non-negative matrix factorization-based machine learning approach, and validated them using Western TNBCs (n=422; public datasets). Immunotype-specific gene signatures were associated with clinicopathological features, immune cell types, biological pathways, acute/chronic inflammatory responses, and immunogenic cell death processes. Responses to different immunotherapies associated with TNBC immunotypes were assessed using cross-cancer comparison to melanoma (n=504). Tumor-infiltrating lymphocytes (TILs) and pan-macrophage spatial marker expression were evaluated.

RESULTS

We identified three robust transcriptome-based immunotypes in both Indian and Western TNBCs in similar proportions. Immunotype-1 tumors, mainly representing well-known claudin-low and immunomodulatory subgroups, harbored dense TIL infiltrates and T-helper-1 (Th1) response profiles associated with smaller tumors, pre-menopausal status, and a better prognosis. They displayed a cascade of events, including acute inflammation, damage-associated molecular patterns, T-cell receptor-related and chemokine-specific signaling, antigen presentation, and viral-mimicry pathways. On the other hand, immunotype-2 was enriched for Th2/Th17 responses, CD4⁺ regulatory cells, basal-like/mesenchymal immunotypes, and an intermediate prognosis. In contrast to the two T-cell enriched immunotypes, immunotype-3 patients expressed innate immune genes/proteins, including those representing myeloid infiltrations (validated by spatial immunohistochemistry), and had poor survival. Remarkably, a cross-cancer comparison analysis revealed the association of immunotype-1 with responses to anti-PD-L1 and MAGEA3 immunotherapies.

CONCLUSION

Overall, the TNBC immunotypes identified in TNBCs reveal different prognoses, immune infiltrations, signaling, acute/chronic inflammation leading to immunogenic cell death of cancer cells, and potentially distinct responses to immunotherapies. The overlap in immune characteristics in Indian and Western TNBCs suggests similar efficiency of immunotherapy in both populations if strategies to select patients according to immunotypes can be further optimized and implemented.

Abstract P5-06-14: A novel combination of a 2 gene score & TIL as a predictive Biomarker for responders to novel therapies in Indian TNBC - A population with greater proportion of TNBCs

Introduction: Triple-Negative Breast Cancer (TNBC) comprises approximately 30% of all breast cancers in Indian women. Given their aggressive nature, TNBCs have high rates of systemic metastasis and mortality with only chemotherapy available for treatment. Compelling evidence has demonstrated the prognostic value of tumor-infiltrating lymphocytes (TILs), in many cancers especially in Breast Cancer and play a critical role in tumour progression, response to therapeutics and prognosis. They are typically measured by H&E staining and immunohistochemistry for research purpose and degree of infiltrate is also known to differ among subtypes. Nonetheless, the literature regarding the types of immune cells characterizing TILs and their prognostic utility in TNBC has been conflicting for lack of accurate “functional” TIL assessments. Herein we have used a combination signature of TILs and a 2 gene immune function expression based signature to develop an unique classifier, to identify a subgroup within TNBC that has better clinical outcome, such as survival and response to treatment. Our findings also suggest a possible use of the score as a predictive biomarker for response to immune checkpoint therapy Patients and Methods: Surgically excised TNBC tumor specimens from 44 women from a single treating hospital in Bangalore, India were accessed under IERB approved protocols and assayed on nCounter® PanCancer Immune Profiling Panel which comprised of 740 genes and characterises 14 different immune cell types. Analysis using Non-negative Matrix factorization (NMF) based unsupervised clustering was done to arrive at stable subtypes characterized by different tumor microenvironments within TNBC. SSGSEA analysis was done to identify immune cell types. TILs were characterised by a pathologist on H&E sections according to guidelines from TIL working group. The Immune classifier was validated on Breast Cancer data sets from TCGA. Results: NMF followed by SAM and PAM analysis yielded 2 stable subtypes (ST1 and ST2) of proportions 59% and 41% respectively. TIL groups also were divided into Dense and Mild groups which were 52% and 48% respectively. Despite similar distributions of the groups, ST1 and ST2 had distinct survival with ST2 having poorer outcome (p=0.023) while the dense and mild TIL groups did not separate as distinct groups. On a closer examination using SSGSEA analysis with Rooney et al signature, ST1 was enriched with T-cells, Dendritic cells, MHC-class 1 and very significantly high cytolytic score (CYT), which was defined by Granzyme A and Perforin expressions, proteins secreted by cytotoxic T cells (p=0.0074). The CYT Score ranged from -35 to 170 and cutoff was based on 75th percentile. We next hypothesized that a combined score of TIL and CYT would represent a functional TIL group with high immune activity. We arrived at a CYT+TIL score based on 75th percentile cut off of CYT and 2 groups of TIL. Of the resultant four groups, TIL High-CYT high that constituted about 20% of all TNBCs indicated an elevated immune response because of their microenvironment constitution and this can be identified using our simple immune classifier. On the other hand, in the TIL-high and CYT-low group, despite lymphocyte migration, outcome was not favorable. The classifier was applied to TNBC from TCGA (n=96) and similar results seen, with ST1 and ST2 which had distinctly separate survival and had similar patterns on CYT high groups. Conclusion: We developed a simple immune classifier with 2 gene signature c and H&E slide TIL assessment for identifying a group with TNBC that can be better targeted with therapies. Our signature is predictive for selecting TNBCs which are potential responders to Immune therapies and has the potential for quick clinical adoption though it requires validation on a larger set.

Citation Format: Aruna Korlimarla, Hari PS, Jyothi S Prabhu, Chantirika Ragulan, Ravi B Diwakar, Sandhya Apachu, Maggie Cheang, Rekha V Kumar, BS Srinath, TS Sridhar, Savitha Rajarajan, Annie Alexander, Anguraj Sadanandam. A novel combination of a 2 gene score & TIL as a predictive Biomarker for responders to novel therapies in Indian TNBC - A population with greater proportion of TNBCs [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr P5-06-14.

Abstract P3-10-06: High levels of miR-18a is associated with increased proliferation but suppression of EMT phenotype in ER negative breast cancer

Introduction: miRNA-based regulation has been implicated in tumor evolution and progression. miR-18a belonging to the miR-17-92 polycistronic cluster has also been reported to have oncogenic effects across multiple cancer types including breast cancer. We have previously demonstrated the epigenetic regulation of ER by miR-18a and its high levels as a poor prognostic marker in ER-positive breast tumors (Nair et al, Cancer Med. 2016). Here, we have examined the effects of high expression of miR-18a in the ER-negative subtype of breast cancer. Methods: 275 surgically excised specimens of primary breast cancers were analyzed. Samples were segregated into ER-positive and ER-negative tumors based on ER positivity as determined by Immunohistochemistry. Relative abundance of hsa-miR-18a-5p in these samples was assessed using a TaqMan qRT-PCR and used to correlate with a probability distribution of proliferation that was derived by fitting a binomial logistic regression model using 4 genes - FOXM1, UBE2C, BIRC5 & ANLN. miR-18a was inhibited using synthetic inhibitors in ER-negative breast cancer cell lines - MDA-MB-468 AND MDA-MB-231. Migratory ability was assessed using wound-healing assays. The expression of miR-18a was further analyzed in ER-negative breast cancer samples from the TCGA (n= 116) and the METABRIC cohort (n=107). ER-negative tumors with higher than the third quartile and lower than the first quartile expression of miR-18a were segregated into tumors with high and low expression, respectively. Functional enrichment of differentially expressed genes (DEGs) between these groups was performed using the G: profiler to identify the deregulated pathways. Result: Evaluation of the levels of miR-18a in 275 breast tumor samples showed that the microRNA was highly expressed (p<0.0001) in the ER-negative tumors (n=105) when compared to ER-positive samples (n=170). The ER-negative tumors were further stratified based on the 3rd quartile expression of miR-18a into high (n=27) and low miR-18a (n=78) expressing tumors. The high miR-18a expressing tumors were associated with a higher proliferation score (p=0.005). Inhibition of miR-18a levels in ER-negative breast cancer increased migration ability up to 33 % in MDA-MB-468 (p=0.009) and up to 26 % in MDA-MB-231 (p=0.0003). Analysis of ER-negative tumors of TCGA and METABRIC cohort revealed that the high miR-18a expressing tumors expressed low levels of EMT master regulators-ZEB1 and ZEB2 and low levels of Matrix metalloproteinases -MMP2, MMP3, MMP10, MMP11, MMP13, and MMP17 (p<0.01). Functional enrichment of differentially expressed genes (DEGs) demonstrated suppression of pathways related to cell motility and migration, ECM activation, Wnt signaling, and Focal adhesion-PI3K-Akt signaling pathways (p<0.01). Conclusion: In ER-positive tumors, high levels of miR-18a are associated with activated EMT, increased migratory ability, and poor prognosis. On the contrary, in ER-negative breast tumors, high levels of miR-18a is associated with a higher rate of proliferation but lower migratory ability and suppression of signaling pathways necessary for an epithelial to mesenchymal transition.

Citation Format: Madhumathy G Nair, Chandrakala M, Apoorva D, Snijesh VP, Jyothi S Prabhu, Savitha Rajarajan, Aruna Korlimarla, Rakesh S Ramesh, Srinath BS, Sridhar TS. High levels of miR-18a is associated with increased proliferation but suppression of EMT phenotype in ER negative breast cancer [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr P3-10-06.

NGS-based profiling of key cancer genes in Indian triple-negative breast cancer patients reinforces molecular heterogeneity of the disease

Triple-negative breast cancers (TNBC) are one of the most aggressive forms of breast cancers. With poor patient outcomes, it presents a great burden on the healthcare systems. There have been some efforts to explore the genomic changes that occur in TNBCs. However, there is not enough data on Indian TNBCs. We sought to understand the mutational landscape of key cancer-associated genes in Indian TNBC patients using TruSeq Cancer Amplicon Panel. We sequenced 51 TNBC patient samples and found great heterogeneity amongst samples with respect to the genomic variants. Several previously reported including alterations in PI3K-AKT pathway genes were also identified. Likewise, we identified several novel high-frequency variants, for example, GNAQ F341S (17%), the functional role of which remains unclear. Our study lays the foundation of larger efforts needed to understand the genomic landscape of Indian TNBCs which can aid in classification and better therapeutic management of patients.

Abstract PS6-55: The prognostic utility of AR/ER ratio in young women with breast cancer

Background

World over, less than a quarter of breast cancer diagnoses are in premenopausal women. However, in India premenopausal women constitute half of all women with breast cancer in most hospital case series. Most of these women present at advanced stages with aggressive subtypes of disease and hence the high mortality.The role and utility of detecting androgen receptor (AR) expression in the different sub-types of breast cancer, especially the ones without hormone receptor expression is yet to be firmly established. Evidence from previous studies is suggestive of its beneficial role in hormone receptor positive (HR+) breast cancer. The biological function of AR on the mammary epithelium is determined by the Estrogen receptor (ER) context, in that, it is found to be anti-proliferative in ER positive tumors while it is thought to promote growth in the absence of ER activity. An interesting approach to representing this interplay is as a ratio between AR/ER expressions. As expected, the ratio has been shown to be positively correlated with better outcomes in hormone receptor cancers, mostly in postmenopausal women. The effect of a high ratio in ER negative tumors seems more complicated. In this study, we have evaluated the AR/ER ratio specifically in patients younger than 50 years in whom the estrogenic influence is dominant due to their premenopausal status.

Materials and Methods

Tumor samples from patients 50 years or younger were chosen from a larger cohort of 275 patients with median follow up of 72 months. Expression of ER and AR proteins were detected by immunohistochemistry (IHC), and the transcript levels of ESR1 and AR were determined by quantitative PCR. Relative normalized units of their gene expression were used to calculate the AR/ER ratio. A cut-off at the 3^rd quartile was used to divide tumors into categories of high and low ratios. Clinical characteristics were compared between the low and high ratio groups along with IHC subtype distribution (HR+, HER2+ and Triple negative (TNBC)). Kaplan Meier curves was used for survival analysis and Cox proportional hazard analysis model was used to calculate the hazard ratio (HR). The results were validated in METABRIC dataset.

Results

Eighty-eight (32%) patients were <50 years with a mean age of 43 years. AR/ER ratio ranged between 0.6 to 3.5 with a mean of 1.5. Sixty-six tumors were categorized as low and 22 were high based on the 3Q cut off (1.7). Clinical characters such as age, tumor size, grade, stage of disease was not different between the high and low ratio categories. Distribution of IHC subtypes among each group showed high ratio category had 64% TNBC tumors (p<0.0001). Tumors with high ratio had poor disease-free survival, (HR-2.6(95% CI-1-6.9) p-0.03). Trends in the METABRIC dataset was similar with 411(21%) patients <50 years. Ninety-seven patients with high ratio had significantly poor disease-free survival (HR-1.95 (95% CI-1.3-2.7) p-0.000).

Conclusion

Interaction between AR and ER is known to influence the AR activity and our results reiterate prognostic ability of AR/ER ratio even in young patients of breast cancer. Our results suggest androgenic influences on clinical progression of breast cancer in this age group mediated through AR, has to be examined by its level in relation to the activity of ER, particularly in hormone receptor negative breast cancers. Even more importantly, examining these influences in the context of the menopausal status might help identify subgroups of patients most likely to benefit from interventions targeted at AR.

Pre-Menopausal Women With Breast Cancers Having High AR/ER Ratios in the Context of Higher Circulating Testosterone Tend to Have Poorer Outcomes

Purpose

Women with breast tumors with higher expression of AR are in general known to have better survival outcomes while a high AR/ER ratio is associated with poor outcomes in hormone receptor positive breast cancers mostly in post menopausal women. We have evaluated the AR/ER ratio in the context of circulating androgens specifically in patients younger than 50 years most of whom are pre-menopausal and hence have a high estrogenic hormonal milieu.

Methods

Tumor samples from patients 50 years or younger at first diagnosis were chosen from a larger cohort of 270 patients with median follow-up of 72 months. Expression levels of ER and AR proteins were detected by immunohistochemistry (IHC) and the transcript levels by quantitative PCR. Ciculating levels of total testosterone were estimated from serum samples. A ratio of AR/ER was derived using the transcript levels, and tumors were dichotomized into high and low ratio groups based on the third quartile value. Survival and the prognostic significance of the ratio was compared between the low and high ratio groups in all tumors and also within ER positive tumors. Results were further validated in external datasets (TCGA and METABRIC).

Results

Eighty-eight (32%) patients were ≤50 years, with 22 having high AR/ER ratio calculated using the transcript levels. Circulating levels of total testosterone were higher in women whose tumors had a high AR/ER ratio (p = 0.02). Tumors with high AR/ER ratio had significantly poorer disease-free survival than those with low AR/ER ratio [HR-2.6 (95% CI-1.02-6.59) p = 0.04]. Evaluation of tumors with high AR/ER ratio within ER positive tumors alone reconfirmed the prognostic relevance of the high AR/ER ratio with a significant hazard ratio of 4.6 (95% CI-1.35-15.37, p = 0.01). Similar trends were observed in the TCGA and METABRIC dataset.

Conclusion

Our data in pre-menopausal women with breast cancer suggest that it is not merely the presence or absence of AR expression but the relative activity of ER, as well as the hormonal milieu of the patient that determine clinical outcomes, indicating that both context and interactions ultimately influence tumor behavior.

Abstract PS4-37: A pro-tumorigenic mechanism of M2 tumor-associated macrophages (TAM) in triple-negative breast cancer

Introduction:Triple-Negative Breast Cancer (TNBC) comprises approximately 30% of all breast cancers in Indian women. Given their aggressive nature, TNBCs have high rates of systemic metastasis and mortality with only chemotherapy available for treatment. The success of immunotherapy in solid tumors has raised the hope for their utility in TNBCs as well. But only a subset of patients have a clinical response to check-point inhibitors. The cellular and molecular mechanisms that mediate the immunological response or tolerance are just beginning to be understood. Compared to ER/PR+ breast cancer, TNBC features a unique tumor microenvironment (TME) characterized by a large number of tumor-infiltrating lymphocytes (TILs) and tumor-associated macrophages (TAMs). The density of TILs in and of themselves do not accurately predict response to neoadjuvant chemotherapy or survival. M2 tumor-associated macrophages (M2-TAMs) have been reported to associate with solid tumors to facilitate epithelial to mesenchymal transition (EMT), tumor invasiveness, metastasis, and resistance to therapy. In this study, we have characterized presence of M2-TAM in the TNBC immune environment by examining expression of several biomarkers. Methods:Surgically excised tumor specimens from 88 Indian women with TNBC were accessed from the longitudinal observational series of SJNAHS tissue bank under IERB approved protocols and assayed on nCounter® PanCancer Immune Profiling Panel which comprised of 740 genes and characterises 14 different immune cell types. Transcriptome analysis using Non-negative Matrix factorization (NMF) based unsupervised clustering was done to arrive at stable subtypes characterized by different tumour microenvironments within TNBC. CIEBERSORT tool was used to analyse for distribution of cell types. Identification of macrophages was done by Immunohistochemistry (IHC) for CD68 and CD163 markers in TNBCs and a control group of ER+HER2-.Results:NMF analysis with an enriched immune gene signature of 111 genes, yielded 3 subtypes (ST) (37%, 27% and 36% with relative proportions of ST1, ST2 and ST3) within the TNBC. The three subtypes had distinct survival patterns with ST1 having the best prognosis with enriched TH1 gene signature and ST3 had poorest (log rank p=0.5). On application of this gene signature to TNBC groups in METABRIC and TCGA data, similar pattern emerged with a significant survival pattern of ST 3 having the poorest outcome (p=0.005). A closer examination of ST 3 revealed a signature enriched for M2 macrophages also known as TAM. Immunohistochemistry for Pan macrophage marker CD68 and an M2 specific marker CD163 between TNBC and ER/PR+ revealed difference in the two groups was significantly different (Mann Whitney p=0.03), with TNBC exhibiting 2.4 fold higher expression of CD163. CD 68, was enriched in ST2 and ST3. CD163 which is an M2 specific marker was highest in ST3 as compared to ST 1& 2 (p=0.04). This group also correlated with signal molecules secreted by macrophages containing growth factors, cytokines and chemokines, such as TGF-β, VEGF, IL-10 and CXCL and interleukins like IL4 and IL6 suggestive of TAM recruitment and polarization. It is likely that the TAM enriched subgroup is likely to be unresponsive to PD1/PDL1 inhibitors but could be targeted by novel therapeutic strategies to directly target M2-TAM. In vitro and In vivo analysis to target M2-TAM to evaluate the response to these therapeutic compounds in cell lines as well as a mouse syngeneic model is underway.Conclusions and future directions: As a cell type within the tumor microenvironment, that promotes invasion, M2-TAMs makes an ideal therapeutic target in TNBC. In addition, this sub-type lends itself to easy identification by a simple IHC assay.

Citation Format: Aruna Korlimarla, Jyothi Prabhu, Chantirika Ragulan, Gnanapriya Shivakumar, Krisha Desai, Maggie Cheang, Srinath BS, Ravi Diwakar, Sandhya Apachu, Rekha Kumar, TS Sridhar, Savitha RajaRajan, Rohini Kaluve, Annie Alexander, Anguraj Sadanandam. A pro-tumorigenic mechanism of M2 tumor-associated macrophages (TAM) in triple-negative breast cancer [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr PS4-37.

Abstract PS19-19: Whole exome sequencing and BRCAness estimation in TNBCs and their correlation with response to platinum

Background: Triple-Negative Breast Cancer (TNBC) comprises approximately 30% of all breast cancers in Indian women. The hallmark of TNBC is genomic instability with very high rates of TP53 mutation. BRCAness has been defined by Ashworth et al (2004 &2014), as the phenocopying of BRCA1&2 mutation by alternate genetic or Epigenetic mechanisms. The consequence of this is DNA damage repair (DDR) deficiency. Though PARP inhibitors have been of utility in treating this subset of TNBC, trials have in general not found an unequivocal support for the use of platinum. We have developed an assay for BRCAness, the BRCA1 deficiency score (BDS) (Korlimarla et al 2016). In this study, we have applied BDS assay in tandem with whole exome sequencing to a small retrospective series of TNBC patients more than half of whom were treated with Platinum. Methods: 40 TNBC primary specimens along with complete clinical data from a retrospective series at the SSCHRC were obtained under all IERB approvals and informed patient consent for BDS assay and mutational analysis. BDS assay is a multianalyte assay involving measurement of BRCA1 (Transcript and protein) as well as additional epigenetic regulators of BRCA1, mir182 and ID4. Whole Exome Sequenced (WES) using the Agilent Sureselect V6 kit on Illumina HiSeq platform. Variant calling analysis was performed using GATK Mutect2 with Hg38 reference genome following the best practice workflow. Variants annotated as protein affecting based on their functional impact prediction and mapped to known cancer related genes (from COSMIC), were selected. Results: Clinical details: Mean age of patient in the series was 49. 37/40 qualified for BDS assay. 21/37 (57%) patients were treated with Carboplatin in combination with Docetaxel in an adjuvant setting. Remaining patients were treated with Cyclophosphamide Adriamycin with or without Docetaxel. 15/37 (45%) were BRCA1 deficient and10/15 were treated with Platinum and 8 (80%) were responders.

39 passed QC and considered for analysis. Spectrum of variants were missense mutations (86.5%), followed by stop gained (5.91%) and frame shift (3.76%). Results were compared to TCGA TNBC set (n=123). The most frequently mutated gene was TP53 (62%) as reported in TCGA. We also report higher frequency of deleterious mutations on DNA damage repair (DDR) genes like ATM and BRCA2 (15%). Response to Platinum therapy in this subset, correlated with Mutations in DNA damage repair genes (p ≤ 0.003). 4/6 samples mutated were also In the BDS deficient group. BRCAness score for predicting Platinum response also correlated significantly (p ≤ 0.05). Other genes which showed significant alterations were KMT2A and KMT2D (15% and 13%) which encode the histone methyl transferase and are responsible in altering the chromatin structure and RECQL4 (10%) which is a helicase involved in DDR Conclusion: Both BRCAness and mutation profile identified a DDR deficient group within TNBC patients. In addition to TP53 which is the most frequently mutated gene, our small sample set has shown higher frequencies of mutations in DDR genes like ATM and BRCA2. This group of patients showed favourable response to platinum therapy. Since very little is known about the molecular heterogeneity of TNBCs in Indian patients, our analysis aids in identification of actionable mutations in TNBCs and may be of use in selection of patients for platinum therapy.

CHARACTERSn%Platinum Treatment - ( n )Treatment response%BDS3721Deficient154513BRCA1 deficient response861Proficient19518BRCA1 Proficient response450Undet34

Citation Format: Aruna Korlimarla, Sabarinathan Radhakrishnan, Snijesh VP, Jyothi S Prabhu, Naveen Luke Demonte, Savitha Rajarajan, Yatish Patil, Ravi Diwakar, Sandhya Apachu, BS Srinath, Sridhar TS, Anguraj Sadanandam. Whole exome sequencing and BRCAness estimation in TNBCs and their correlation with response to platinum [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr PS19-19.

Prognostic role of microRNA 182 and microRNA 18a in locally advanced triple negative breast cancer

Background

The study assessed the epigenetic regulation and the role of microRNA (miR) expression in locally advanced triple negative breast cancers (TNBC) and comparison with the clinico-pathological variables and survival.

Methods

Fifty patients of locally advanced TNBC during the period 2011–2013 were included. Expression level of test microRNA (miR-182 and miR-18a) was determined using Taqman quantitative Real time polymerase chain reaction (qRT-PCR) from formalin fixed paraffin embedded biopsy blocks. Clinical and demographic information and survival data was retrieved from the Hospital medical records.

Results

An improved clinical complete response (cCR) was observed in patients with age ≥ 45 years (80%), premenopausal status (70%), tumor size < 6 cms (80%), nodal status N0-N1 (95%) and grade II-III tumor (80%). A statistically significant correlation was observed on comparison of cCR with menopausal status (p-value 0.020), T category (p-value 0.018) and the clinical nodal status (p-value 0.003). pCR also correlated with clinical nodal status (p-value 0.008). Epigenetically, miR-18a under expression (< 8.84) was most commonly associated with tumor size < 6 cms (76.7%), clinical nodal status N0-N1 (90%), cCR (60%) and pCR (53.3%). A similar trend was observed with miR-182. Statistical significance was observed with T category (p-values 0.003 and 0.004), clinical nodal status (p-values 0.001 and 0.001), clinical response (p-values 0.002 and 0.002) and pathological response (p-values 0.007 and 0.006) with respect to miR-18a and miR-182, respectively. Also, the menopausal status significantly correlated with the miR-182 expression (p-value 0.009). miR-182 overexpression (≥ 6.32) was not observed in any of the postmenopausal patients. A univariate cox proportional hazard regression model also showed statistical interactions (p-values <0.004).

Conclusion

miR-182 and miR-18a overexpression correlates with worse clinical and pathological tumor characteristics in locally advanced TNBC and hence could be used to predict the outcomes and prognosis in these patients.

miR-18a activates Wnt pathway in ER-positive breast cancer and is associated with poor prognosis

Despite the established benefits of long‐term endocrine therapy, women with hormone receptor‐positive breast cancer remain at risk for late relapse. The basis of this is multi‐factorial including genetic, epigenetic, and host factors. In this study we have explored the epigenetic regulation of estrogen receptor (ER)‐dependent molecular and cellular phenotype by hsa‐miR‐18a‐5p using well‐established human ER‐positive (ER+) breast cancer cell lines. miR‐18a was overexpressed in MCF7 and ZR‐75‐1 and this led to an increase in the proliferative ability of the cells and concurrently resulted in decreased expression of luminal markers and higher expression of the basal marker, cytokeratin 14. The cells became more migratory with a significant repression of E‐cadherin and activation of the Wnt noncanonical pathway. We observed an activation of the planar cell polarity (PCP) pathway with increased activation of JNK pathway and eventually change in actin dynamics. There was increased F‐actin polymerization in cells with higher expression of miR‐18a. Examination of miR‐18a expression in a set of human ER+ breast cancer specimens showed a negative correlation between miR‐18a and ESR1 transcripts as well as ER protein. Kaplan‐Meier survival analysis of the cohort stratified by tumor hsa‐miR‐18a‐5p levels produced significant differences in disease‐free survival (log rank P < .05). This observation was independently validated in the METABRIC cohort. These data provide support for a role of hsa‐miR‐18a‐5p in altering the proliferative and migratory behavior of ER+ cells and its potential utility as a prognostic marker in clinical ER+ breast cancers.

Cystic Neutrophilic Granulomatous Mastitis: A Clinicopathological Study With 16s rRNA Sequencing for the Detection of Corynebacteria in Formalin-Fixed Paraffin-Embedded Tissue

Cystic neutrophilic granulomatous mastitis (CNGM) is a histologically characterized variant of granulomatous lobular mastitis that is associated with lipophilic Corynebacterium species. It remains a largely underrecognized entity in India. Our aim was to study CNGM in the Asian Indian population and explore if 16s rRNA sequencing could be used on formalin-fixed paraffin-embedded (FFPE) tissue to identify the causative organism. We studied 24 cases with histological features of CNGM with hematoxylin and eosin, Gram, Ziehl-Neelsen, and Periodic acid-Schiff stains. Tuberculosis-polymerase chain reaction and 16s rRNA gene sequencing on DNA extracted from FFPE was attempted (N = 23). Gram-positive bacilli were seen in 20/24 cases. Routine culture with prolonged incubation yielded Corynebacterium species in 8 cases; 7 of these cases were evaluated by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) for species identification. C matruchotti was identified in one case by BD Phoenix. MALDI-TOF MS identified the remaining 7 cases as C kroppenstedtii (N = 4) and C tuberculostearicum (N = 2), with no identification in one. Corynebacteria were identified by 16s rRNA sequencing on DNA extracted from FFPE in 12/23 cases using a primer targeting the V5-V6 region that was found to be more conserved in Corynebacterium species. All cases were negative for the diagnosis of tuberculosis. CNGM can be identified by routine stains. Culture using routine media with prolonged incubation is often adequate to isolate the organism. 16s rRNA sequencing on DNA extracted from FFPE tissue can help make an etiological diagnosis in some cases where only paraffin blocks are available.

Abstract P4-10-12: Treatment decision making, and strategies for coping with financial stress in Indian women diagnosed with breast cancer and their families

Introduction: In spite of rapid urbanization and modernization the family remains central in the socio-cultural structure of India. The individuals are enmeshed into this unit and tend to be interlinked financially, emotionally and socially. The head of this family unit tends to be a male more often than not. As is well known, despite recent attempts by the governments at the state and centre at providing health coverage for cancer through regional cancer centres, a majority have to raise the money for cancer care by themselves. We have examined the role of the family in treatment decision making and in the strategies employed to raise the money and cope with the financial stress imposed by a diagnosis of breast cancer.

Method: 378 women with breast cancer were enrolled into a longitudinal study at first diagnosis between the years 2008-2012, at two tertiary care hospitals in Bangalore, India. The median follow up as of May 31st 2017 is 78 months with only 2% loss to follow-up over the past 8 years. Follow-up was maintained by frequent meetings between a counselling psychologist (AA) and the patient and/or a family member. The frequency of meetings was monthly during the initial treatment and then quarterly over the next 5 years. Information on demographics was collected during the treatment phase and information on the psychosocial aspects was collected in non-structured interactions subsequently. This information included details of support structure, decision making, and financial arrangements.

Results: This is a predominantly urban cohort with 80% being urban. The median age of patients at first diagnosis was 55 years. Almost all of our patients (99%) had the support of one or more family members. We analysed the pattern of decision making for treatment and in half of all cases either the husband or the son were the decision makers. In an additional 15% daughters and other relatives were the primary decision makers. Approximately a third of women made the decision concerning treatment themselves, and these women tended to be college educated (51% vs 16%) and employed (53% vs 12%).

30% of the patients met the costs incurred through medical insurance plans purchased by the family. Another quarter of patients were able to meet the costs from their savings. 45% had difficulty in finding the money for treatment and 15% took personal loans while 30% had to sell land/gold ornaments or take loans against assets of these sorts. Only (3%) discontinued the treatment due to financial difficulties. As in the case of decision making those who had the financial resources tended to be more educated (41% vs 11%), and were employed (31% vs 21%).

Conclusion: The data from a predominantly urban cohort of breast cancer enrolled between 2008-2012, supports the general belief that in India the family remains the fulcrum of an individual during crises, and not surprisingly education and employment lead to both psychological and economic emancipation of women.

Citation Format: Alexander A, Kaluve R, Prabhu JS, Korlimarla A, BS S, Manjunath S, Patil S, KS G, Sridhar TS. Treatment decision making, and strategies for coping with financial stress in Indian women diagnosed with breast cancer and their families [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 P4-10-12.

Dissecting the Biological Heterogeneity within Hormone Receptor Positive HER2 Negative Breast Cancer by Gene Expression Markers Identifies Indolent Tumors within Late Stage Disease

Hormone receptor positive (HR+) breast cancers are a heterogeneous class with differential prognosis. Although more than half of Indian women present with advanced disease, many such patients do well. We have attempted identification of biologically indolent tumors within HR+HER2- tumors based on gene expression using histological grade as a guide to tumor aggression. 144 HR+HER2- tumors were divided into subclasses based on scores derived by using transcript levels of multiple genes representing survival, proliferation, and apoptotic pathways and compared to classification by Ki-67 labeling index (LI). Clinical characters and disease free survival were compared between the subclasses. The findings were independently validated in the METABRIC data set. Using the previously established estrogen receptor (ER) down stream activity equation, 20% of the tumors with greater than 10% HR positivity by immunohistochemistry (IHC) were still found to have inadequate ER function. A tumor aggression probability score was used to segregate the remainder of tumors into indolent (22%) and aggressive (58%) classes. Significant difference in disease specific survival was seen between the groups (P = .02). Aggression probability based subclassification had a higher hazard ratio and also independent prognostic value (P < .05). Independent validation of the gene panel in the METABRIC data set showed all 3 classes; indolent (24%), aggressive (68%), and insufficient ER signaling (7%) with differential survival (P = .01). In agreement with other recent reports, biologically indolent tumors can be identified with small sets of gene panels and these tumors exist in a population with predominantly late stage disease.

HR+HER2− breast cancers with growth factor receptor–mediated EMT have a poor prognosis and lapatinib downregulates EMT in MCF-7 cells

Despite an overall good prognosis, a significant proportion of patients with hormone receptor positive human epidermal growth factor receptor 2 negative breast cancers develop distant metastases. The metastatic potential of epithelial cells is known to be regulated by tumor–stromal interaction and mediated by epithelial-to-mesenchymal transition. Hormone receptor positive human epidermal growth factor receptor 2 negative tumors were used to estimate markers of epithelial-to-mesenchymal transition, and the luminal breast cancer cell line MCF-7 was used to examine the interactions between integrins and growth factor receptors in causation of epithelial-to-mesenchymal transition. A total of 140 primary tumors were sub-divided into groups enriched for the markers of epithelial-to-mesenchymal transition (snail family transcriptional repressor 2 and integrin β6) versus those with low levels. Within the epithelial-to-mesenchymal transition+ tumors, there was a positive correlation between the transcripts of integrin β6 and growth factor receptors—human epidermal growth factor receptor 2 and epidermal growth factor receptor. In tumors enriched for epithelial-to-mesenchymal transition markers, patients with tumors with the highest quartile of growth factor receptor transcripts had a shorter disease-free survival compared to patients with low growth factor receptor expression by Kaplan–Meier analysis (log rank, p = 0.03). Epithelial-to-mesenchymal transition was induced in MCF-7 cells by treatment with transforming growth factor beta 1 and confirmed by upregulation of SNAI1 and SNAI2 transcripts, increase of vimentin and integrin β6 protein, and repression of E-cadherin. Treatment of these cells with the dual-specificity tyrosine-kinase inhibitor lapatinib led to downregulation of epithelial-to-mesenchymal transition as indicated by lower levels of SNAI1 and SNAI2 transcripts, integrin αvβ6, and matrix metalloproteinase 9 protein. The results suggest that synergistic interactions between growth factor receptors and integrin β6 could mediate epithelial-to-mesenchymal transition and migration in a subset of luminal breast cancers and lapatinib might be effective in disrupting this interaction.

Abstract P4-07-10: Epithelial mesenchymal transition associated with high miR-221 and integrin β6 leads to poor prognosis in hormone receptor positive HER2 negative breast cancers

Background: MicroRNA mediated molecular alterations are involved in the initiation and progression of cancer. Altered expression of multiple microRNAs is associated with endocrine resistance in hormone receptor positive HER2 negative (HR+/HER2-ve) cancer. The role of miR-221 in inducing epithelial to mesenchymal transition (EMT) is well documented especially in cell line model systems. However, the detailed mechanism of specific microRNAs in intrinsic and acquired resistance to endocrine therapy needs to be worked out. In addition, more needs to be done in the documentation of these mechanisms in human breast cancer specimens with complete clinical documentation and long-term follow-up. In this study, we have evaluated the clinical significance of miR-221 and its mechanistic role in EMT using human specimens and cell line models.

Materials and Methods: Formalin fixed paraffin embedded tumor from 129 HR+/HER2-ve breast cancer patients with a median follow up of 63 months were used for estimation of miR-221 by quantitative real time PCR. Expression levels of genes which are direct targets of miR-221 and related genes in EMT were analysed from these tumors. Survival between miR-221 high and low groups was compared by Kaplan Meier survival curves and prognostic relevance was estimated by Cox proportional hazard model.

Cell line experiments to investigate the role of miR-221 in inducing EMT through integrin β6 are underway in both wild type and tamoxifen resistant MCF-7 cell lines (A gift from Prof Ben Ho Park, Johns Hopkins University School of Medicine).

Results: A significant elevated level of miR-221 was observed in small proportion (14%) of HR+/HER2-ve tumors. miR-221 expression had an inverse correlation with both ER protein and ESR1 mRNA levels within HR+/HER2-ve tumors. Tumors with high levels of miR-221 showed significantly higher expression of integrin β6 which is a robust marker of EMT. Patients with high expression of miR-221 had a poorer survival in Kaplan Meier analysis.

Results of interrogation of EMT mediated through integrin related pathways involving miR-221 in cell line models will be presented.

Discussion: The association between miR-221 and integrin β6 in HR+/HER2-ve breast cancer with endocrine resistance suggests a potential link between an epigenetic regulator and a mediator of tumor-stromal interaction. The other mediators involved in this pathway are being investigated. miR-221 could be potentially used as a marker for identification of a poor prognostic subtype within HR+/HER2-ve breast cancers.

Citation Format: Prabhu JS, Kaul R, Korlimarla A, Desai K, Gangadharan C, Rajarajan S, Nair MG, Alexander A, Kaluve R, Manjunath S, Correa M, Prasad MSN, Patil S, Srinath BS, Sridhar TS. Epithelial mesenchymal transition associated with high miR-221 and integrin β6 leads to poor prognosis in hormone receptor positive HER2 negative breast cancers [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P4-07-10.

Abstract P4-06-11: Differential regulation of microRNAs and integrins influences metastatic potential: Comparison between locally invasive BT-474 and metastatic MDA-MB-231 xenografts

Background: Generation of BT-474 and MDA-MB-231 xenografts in immunocompromised mice provides one means of dissecting the molecular events involved in local invasion versus distant metastasis. Recently, Glunde et al have shown an interdependence of genes involved in cell-cell and cell-matrix adhesion (E-cadherin and integrin β1) and extra-cellular matrix degradation (MMP-2 and 9) in allowing cells to metastasize. Further, Fite el al have identified a set of microRNAs (miRs) up-regulated by E-cadherin (a pre-EMT marker) and down-regulated by Vimentin (post-EMT marker) in acquiring an invasive phenotype. We have performed a detailed analysis of integrins, matrix metallo-proteases and key miRs to better understand the molecular events underlying these disparate behaviours.

Methods: We injected BT-474 (N=5) and MDA-MB-231 (N=5) cells orthotopically into SCID mice. Xenografts were assessed for local growth rate and monitored for distant metastasis. The implanted tumors as well as the distant metastatic foci were harvested. Markers involved in local invasion, distant metastasis and tumor-stroma interactions including miRs were compared between BT-474 and MDA-MB-231 cell lines and their xenografts by q-RT-PCR, immunofluorescence and immunohistochemistry.

Results: As expected BT-474 xenografts showed a higher rate of tumor growth when compared to MDA-MB-231. Histological examination of BT-474 tumors confirmed only locally invasive tumor growth with infiltrated blood capillaries and vessels; no macro and microscopic metastases were observed in the organs collected. On the contrary, MDA-MB-231 xenografts showed highly undifferentiated tumor growth and frank lung metastasis and extra-pulmonary tumor growth in one of the five mice injected despite slow rate of local growth. Expression of matrix metalloproteases – MMP-2 & 9 was more than 30 fold upregulated in MDA-MB-231 xenografts as compared to BT-474. Elevated level of E-cadherin was observed in BT-474 but was absent in MDA-MB-231.

The most interesting differences were seen in the levels of miRs and cell-surface integrins. High levels of miR-18a, miR-93 and miR-182 were observed in BT-474 implants when compared to MDA-MB-231 which had a much lower level of these miRs. On the contrary, higher levels of integrin β3, and β1 were observed in MDA-MB-231 tumors when compared to BT-474. Integrin β6 was absent in both. The reciprocal relationship between these markers is being examined and compared between locally invasive tumors and metastatic triple negative breast cancers from our case series of human specimens (N=250).

Conclusion: miRs and integrins known to be involved in invasion are differentially regulated in tumors that are locally invasive compared to ones with distant metastasis. The level of the key targets of these miRs as well as additional integrins is being examined. Understanding the epigenetic regulations leading to metastasis via tumor-stroma interaction might help in discerning differential tumor behaviour.

Citation Format: Lawrence PV, Desai K, Prabhu JS, Korlimarla A, Nair MG, Sridhar TS. Differential regulation of microRNAs and integrins influences metastatic potential: Comparison between locally invasive BT-474 and metastatic MDA-MB-231 xenografts [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P4-06-11.

High expression of integrin β6 in association with the Rho-Rac pathway identifies a poor prognostic subgroup within HER2 amplified breast cancers

Integrin αvβ6 is involved in the transition from ductal carcinoma in situ (DCIS) to invasive ductal carcinoma (IDC) of the breast. In addition, integrin β6 (ITGB6) is of prognostic value in invasive breast cancers, particularly in HER2+ subtype. However, pathways mediating the activity of integrin αvβ6 in clinical progression of invasive breast cancers need further elucidation. We have examined human breast cancer specimens (N = 460) for the expression of integrin β6 (ITGB6) mRNA by qPCR. In addition, we have examined a subset (N = 147) for the expression of αvβ6 integrin by immunohistochemistry (IHC). The expression levels of members of Rho–Rac pathway including downstream genes (ACTR2,ACTR3) and effector proteinases (MMP9,MMP15) were estimated by qPCR in the HER2+ subset (N = 59). There is a significant increase in the mean expression of ITGB6 in HER2+ tumors compared to HR+HER2‐ and triple negative (TNBC) subtypes (P = 0.00). HER2+ tumors with the highest levels (top quartile) of ITGB6 have significantly elevated levels of all the genes of the Rho–Rac pathway (P‐values from 0.01 to 0.0001). Patients in this group have a significantly shorter disease‐free survival compared to the group with lower ITGB6 levels (HR = 2.9 (0.9–8.9), P = 0.05). The mean level of ITGB6 expression is increased further in lymph node‐positive tumors. The increased regional and distant metastasis observed in HER2+ tumors with high levels of ITGB6 might be mediated by the canonical Rho–Rac pathway through increased expression of MMP9 and MMP15.

A Majority of Low (1-10%) ER Positive Breast Cancers Behave Like Hormone Receptor Negative Tumors

BACKGROUND

The 2010 guidelines by ASCO-CAP have mandated that breast cancer specimens with ≥1% positively staining cells by immunohistochemistry should be considered Estrogen Receptor (ER) positive. This has led to a subclass of low-ER positive (1-10%) breast cancers. We have examined the biology and clinical behavior of these low ER staining tumors.

METHODS

We have developed a probabilistic score of the "ER-positivity" by quantitative estimation of ER related gene transcripts from FFPE specimens. Immunohistochemistry for ER was done on 240 surgically excised tumors of primary breast cancer. Relative transcript abundance of 3 house-keeping genes and 6 ER related genes were determined by q-RT PCR. A logistic regression model using 3 ER associated genes provided the best probability function, and a cut-off value was derived by ROC analysis. 144 high ER (>10%), 75 ER negative and 21 low-ER (1-10%) tumors were evaluated using the probability score and the disease specific survival was compared.

RESULTS

Half of the low-ER positive tumors were assigned to the ER negative group based on the probability score; in contrast 95% of ER negative and 92% of the high ER positive tumors were assigned to the appropriate ER group (p<0.0001). The survival of the low-ER group was intermediate between that of the high ER positive and ER negative groups (p<0.05).

CONCLUSION

Our results suggest that the newly lowered ASCO-CAP criteria for ER positivity, leads to the false categorization of biologically ER negative tumors as ER positive ones. This may have particular relevance to India, where we have a much higher proportion of ER negative tumors in general.

Abstract P4-07-09: An approach to the identification of tumors driven by HER2 using the integrated activity of oncomiR miR-21 along with HER2 enriched genes

Introduction: The initial identification of HER2 as a driver in a subset of breast cancers was at the level of DNA (amplification), and subsequently noted at the level of transcripts and protein as well. However, the clinical selection of patients for treatment with Trastuzumab, has been through either IHC (protein) or FISH (DNA amplification) and not through transcript abundance. Interestingly, in most studies that have estimated transcript abundance in primary tumors, the proportion of patients that demonstrate increased transcript levels (termed HER2 Enriched) have tended to be slightly larger than the clinical HER2+ category.

A more clinically useful measure might be proof of HER2 downstream activity that might help separate tumors being driven significantly by HER2 from ones where its role is supportive. One of the many consequences of HER2 over-expression is activation of the oncomiR, miR-21 via the MAPK pathway. miR-21 in turn is known to epigenetically regulate multiple targets including the tumor suppressors PTEN and PDCD4. While these molecular mechanisms have been demonstrated convincingly in breast cancer cell lines, clinical studies of these alterations in large numbers are yet to be reported. In this study we have examined the relationship between clinical HER2 positivity and miR-21 levels in 124 surgically excised breast cancer specimens.

Methods: We selected 124 surgically excised specimens of primary breast cancers from our cohort that by HER2 immunohistochemistry (IHC) comprised 42 positive, 62 negative and 20 equivocal. Relative abundance of miR-21 was assessed using a TaqMan qRT-PCR, with normalization by RNU48. Relative transcript abundance of a set of 6 genes (HER2, GRB7, MLN64 and 3 reference genes) were evaluated by SYBR Green real time qPCR.

Results: The majority of tumors that were clinically HER2+ over expressed miR-21. A concordance with an AUC of 96% at 100% sensitivity and 85% specificity was noted. There is a highly significant differential expression of miR-21 between HER2 positive, negative and equivocal samples (P &lt; 0.0001).

HER2 enriched score determined by using the expression levels of 3 genes (HER2, GRB7, MLN64) identified 35% (44/124) of the samples to be HER2 enriched. 72% of these (32/44) were also clinical HER2 positive by IHC. As expected, miR-21 was significantly over expressed in these tumors as well (P&lt;0.0001).

To identify all samples which might show HER2 downstream activity, a logistic regression model was built using expression of miR-21, HER2, MLN64 and GRB7 as the determinants of HER2 status. The best fitting model classified 91% (38/42) of HER2 +, 95% (59/62) of the HER2 negative accurately with 94% specificity and an AUC of 0.96. The model helped identify 10% of clinical HER2 negative samples (6/20 equivocal & 3/62 HER-2 negative) to have a high probability of being HER2+.

Conclusion: Identification of HER2+ tumors with evidence of downstream activity may help identify patients with tumors being driven significantly by HER2 from ones where its role is supportive. The possibility of targeting miR-21 raises the tantalizing prospect of effecting change by altering the epigenetic regulation of multiple targets including tumor-suppressors.

Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P4-07-09.

Abstract P6-08-12: Gains in women’s education has not led to commensurate gains in seeking health-care early in breast cancer patients in urban India

Introduction:

Breast cancer is the leading cancer diagnosed in urban Indian women. Historically the proportion of women presenting with advanced disease has been in excess of 50% at most regional cancer centres. The past 20 years has witnessed rapid economic growth and urbanization with significant gains in women's education and access to health. However, it is not clear if this has translated to earlier seeking of care in the educated.

The aim of this study was to examine if higher education (College) was a determinant in the time of seeking first medical consultation, and whether there were significant differences between women under the age of 40 versus women over 60 years old at the time of diagnosis.

Methods:

The data for analysis were obtained from a prospective longitudinal observational study conducted between 2008-2013 at a medical teaching hospital and a tertiary specialized cancer care centre. A total of 460 patients have been enrolled so far. All patients provided informed consent and the study has been reviewed and approved by the institutional ethics committees at these institutions. We have collected from the patients and their medical records information about their age at diagnosis, educational level, stage of disease, histopathology reports and clinical details.

Results:

Data from 194 patients have been used for the analysis. Patients were divided into one group of &lt; = 40Y of age (Group I, N = 58) and the second of &gt; = 60 years of age (Group II, N = 136). Mean age at presentation for the groups was 35 and 68 years respectively. As expected almost 1.5 times as many women under the age of 40 (36%) were college educated compared to the women over 60 (22%) (p = 0.05). The proportion of LABC in the two groups was not different with group I having 27% and group II 25%. The proportion of older women with LABC and a college degree was 20%. However, rather than the expected decrease in proportion of women with high education and LABC, 31% of young women with LABC had a college degree. LABC in the college educated was not different in the group I when compared to group II. (p = 0.39).

Conclusion:

The determinants of seeking health care are complex and influenced by a variety of factors including socio-economic status, access to health care, education, cultural beliefs, and personal preferences. While urban India's steady economic growth has been highlighted by the scholarly as well as the lay press, the data presented here suggest that there is not an automatic and linear transfer between education, economics and healthcare seeking behaviours. We suggest that while a lot of attention has been paid to awareness and screening, we may need to focus on local cultural factors, and perhaps provide support from female counsellors and care providers as critical components of attempting to bring our women to the hospital at the earliest.

Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P6-08-12.

Evaluation of p53 and BCL2 expression, mutation, and aneuploidy status on treatment response in an Indian cohort of primary Ca larynx

e17057

Background: Organ-sparing therapy consisting of cisplatin and 5-fluorouracil, combined with radiation for advanced head and neck squamous cell carcinoma (HNSCC) have been advocated in Ca larynx patients. However, failure of some tumors to respond to treatment or tumor recurrence limits the overall success of these therapies. P53 mutations have been linked to cisplatin resistance in other solid tumors. In this study we evaluate the relationships between P53 overexpression/mutations, BCL2 expression and ploidy status on treatment response in retrospective cohort of Ca Larynx patients. Methods: Samples from 18 patients with histopathologically confirmed Ca Larynx were analysed from our biorepository after consent. Clinical, sociodemographic information and response to treatment were abstracted from case records. P53 and BCL2 over expression were checked by IHC and p53 mutation by PCR and direct sequencing. DNA ploidy and S-phase fractions were also analysed. Bivariate relationships were determined between these variables using Spearmans rank correlation. Independent samples t tests were used to determine changes in P53 over expression, BCL2 expression Ploidy status and S phase fractions in both responders and non responders. Results: There was a trend for increase in P53 over expression and BCL2 expression and decrease in S phase fractions in responders vs non responders. Neither p53 over expression (75% of cases) and BCL2 over expression (17% of cases) correlated significantly with treatment response. However, BCL2 expression correlated negatively with disease stage (r = - 0.57, p = 0.02). Aneuploidy was observed in node positive tumors (p = 0.04). Conclusions: The results suggest poor association of molecular markers with treatment response and should not be relied as a marker for treatment response. Though there is a trend for association a larger sample size is required to demonstrate the findings.

No significant financial relationships to disclose.

Gene-specific methylation: potential markers for colorectal cancer

PURPOSE

Aberrant methylation of the promoter region is associated with silencing of many genes in neoplasia. CpG island methylation is an epigenetic mechanism for transcriptional silencing that occurs at various stages of colon tumorigenesis. In this study, we tested the promoter methylation and expression of seven genes from various pathways of DNA repair, apoptosis and inflammation, i.e., sFRP1, MLH1, RASSF1A, CDA, v-fgr, LYN-B, and TNFR10d.

METHOD

The genes were analyzed by quantitative polymerase chain reaction for the level of gene expression. The promoter methylation status of the genes was studied by methylation-specific polymerase chain reaction.

RESULT

The correlation of promoter methylation status with suppressed gene expression patterns suggested a potential role for the silencing these genes in colon cancer progression.

CONCLUSION

Promoter methylations of the studied genes could be explored as promising biomarkers for new diagnostic, prognostic and therapeutic targets of colorectal cancer.