Abstract P1-05-15: Multi-omics and immuno-oncology profiling reveal distinct molecular signatures of young Asian breast cancers

Breast cancers (BC) in younger, premenopausal patients (YBC) tend to be more aggressive with worse prognosis, higher chance of relapse and poorer response to endocrine therapies compared to breast cancers in older patients. The proportion of YBC (age ≤ 40) among BC in East Asia is estimated to be 16-32%, significantly higher than the 7% reported in Western countries. To characterize the molecular bases of Asian YBC, we have performed whole-exome sequencing (WES) and whole-transcriptome sequencing (WTS) on tumor and matched normal samples from 134 Korean BC patients consisting of 74 YBC cases (age ≤ 40) and 60 OBC cases (age > 40). We then performed comparison analyses and integrative analyses with the TCGA BC cohort consisting of 1,116 tumors from primarily Caucasian patients, also grouped by age into YBC (age ≤ 40), IBC (40 < age ≤ 60) and OBC (age > 60).

Somatic mutation prevalence analysis identified 7 significantly mutated genes and the same top three genes – TP53, GATA3 and PIK3CA – were reported by the TCGA BC study. To identify differentially expressed (DE) genes and pathways in YBCs vs. OBCs, we performed logistic regression analyses while controlling for the confounding effects of tumor purity and stage. We were surprised to see a significant overlap in DE pathways between a comparison of adjacent normal tissues in younger vs. older TCGA cohorts and a comparison of YBC vs. OBC tumors, indicating that normal tissue compartment could contribute to observed differences between bulk tumors. To separately examine molecular signatures from tumor, stroma and normal compartments, we used non-negative matrix factorization (NMF) analyses to virtually dissect bulk tumor expression data and identified 14 factors including 3 factors associated with normal tissues, 1 factor associated with stroma and 1 factor associated with tumor infiltrating lymphocytes (TIL). Integrative analyses of tumor associated factors and DE pathways revealed that estrogen response, endocrine therapy resistance, and oxidative phosphorylation pathways are up-regulated in YBCs compared to OBCs while cell cycle and proliferation pathways are up-regulated in Asian OBCs. Interestingly, many immune and inflammation pathways correlated with the TIL factor were significantly upregulated in OBCs vs. YBCs. Using gene expression signatures representing distinct immune cell types, we classified our cohort into four subtypes of varying TIL activities and observed significant enrichment of the TIL-high subtype in OBCs compared to YBCs. These observations were confirmed by IHC analyses of four TIL markers (CD45, CD4, CD8 and CD163) in 120 tumors.

To our knowledge, this is the first large-scale multi-omics study of Asian breast cancer and would significantly contribute to the compendium of molecular data available for studying young breast cancers. The major landmarks in the molecular landscape looked similar across BCs of different ethnicities and ages, however, we have identified a number of distinguishing molecular characteristics associated with Asian YBC. The sources for some signatures were further traced to non-tumor intrinsic compartments, indicating that tumor microenvironment may play potentially important roles in driving the carcinogenesis of young breast cancers.

Citation Format: Kan Z, Ding Y, Cho S, Lee S-H, Powell E, Jung HH, Chung W, Deng S, Choi Y-l, Kim J, Park W-Y, Vizcarra P, Fernandez-Banet J, Nichols T, Ram S, Lee SK, Kim SW, Lee JE, Ching KA, Kim J-Y, Ahn JS, Im Y-H, Nam SJ, Park YH. Multi-omics and immuno-oncology profiling reveal distinct molecular signatures of young Asian 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 P1-05-15.

Abstract P1-09-19: Tumor RNA disruption index as a tool to predict response to neoadjuvant chemotherapy in breast cancer: Optimizing timing of biopsy

BACKGROUND. Early detection of tumor response to neoadjuvant therapy (NAT) could be used to tailor therapy and lower toxicity from ineffective treatments. The CCTG MA.22 trial has shown that RNA disruption is associated with breast cancer response to NAT when measured by image guided core biopsy mid-treatment. The objectives of this study were: 1) to determine the optimal time to measure the tumor RNA Disruption Index (RDI) after initiation of NAT when assessed by fine needle aspiration (FNA) in an office setting and 2) to determine if RDI could predict response to a second chemotherapy agent in patients that had a suboptimal response.

METHODOLOGY. We performed a prospective pilot study including patients with palpable biopsy-proven breast cancer eligible for NAT. Chemotherapy and surgery were at the discretion of the treating physician. Two FNAs after cycles 1, 2, 3 and after initiation of a new chemotherapy agent were collected in RNA Protect Cell Reagent and sent to Rna Diagnostics Inc. to assess RDI. Prospectively recorded clinical tumor measurements and surgical pathology reports were obtained. Tumor pathological response (pR) after NAT was measured by pathological complete response (pCR: no invasive disease in breast) and residual cancer burden index (RCBI).

RESULTS. 30 patients were accrued to the study. One patient withdrew consent, one patient was found to have metastatic disease and did not undergo surgery, and one patient had bilateral breast cancer (n= 29 evaluable tumors). ER+HER2-: 38% (11/29), ER-Her2-: 28% (8/29) and HER2+: 34% (10/29). 89% (25/28) of patients received taxane and anthracycline containing regimens. All HER2+ received trastuzumab. Our pCR and RCBI 0-1 rates were 24% (7/29) & 38% (11/29) respectively. At cycles 1, 2 and 3, RDI could be evaluated in 72% (21/29), 73% (16/22) and 44% (7/16) of palpable tumors. After the switch to a new agent, RDI could only be evaluated in 30% (3/10) of patients with palpable tumors. Using a tumor RDA cutoff at 5 (non-responder RDI < 5 (NR) and responder RDI ≥ 5 (R)), responder status between cycle 1 and 2 was concordant in 73% (11/15). After 1 cycle, NR vs. R was associated with numerically lower pCR (13% (2/15) vs. 33% (2/6), p=0.54) and RCBI 0-1 at surgery (20% (3/15) vs. 33% (2/6), p=0.60). These findings were similar after cycle 2. Non-analyzable samples (NAS) because of absence of RNA were associated with high pR (pCR: 38% (3/8) and RBCI 0-1: 75% (6/8)). The 3 NR at cycle 1 that achieved a significant pR had either non-palpable tumors or NAS after switching to a new chemotherapy agent.

CONCLUSION. RDI can be measured by FNA in an office setting and could be helpful to identify early non-responders to NAT. The optimal time to perform RDI is after 1 or 2 cycles of treatment, which should be considered in ongoing and future trials. This study was underpowered to detect a statistically significant correlation between RDI and pR. NAS is associated with high pR and could represent responders to treatment. This early data suggests that RDI is unlikely to be helpful in assessing response to a second chemotherapy agent after receiving 4 cycles of standard chemotherapy. The use of RDI to tailor NAT needs to be evaluated in larger prospective trials.

Citation Format: Samkari A, Chung W, Parissenti A, Pritzker L, Trabulsi N, Basik M, Boileau J-F. Tumor RNA disruption index as a tool to predict response to neoadjuvant chemotherapy in breast cancer: Optimizing timing of biopsy [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 P1-09-19.

Health-Related Quality of Life of Kidney Transplantation Patients: Results from the KoreaN Cohort Study for Outcome in Patients With Kidney Transplantation (KNOW-KT) Study

BACKGROUND

As patient and graft survival rates have been improving after kidney transplantation, health-related quality of life (HR-QOL) has become an important indicator of effective treatment. This study aimed to evaluate changes in HR-QOL after kidney transplantation.

MATERIALS AND METHODS

The KoreaN cohort study for Outcome in patients With Kidney Transplantation (KNOW-KT) is a multicenter, observational, 9-year, cohort study. The HR-QOL of patients in the KNOW-KT study was assessed before transplantation and 2 years after transplantation using the Kidney Disease Quality of Life Short Form (KDQOL-SF) including chronic kidney disease targeted area and the Medical Outcome Study 36-item Short Form Health Survey (SF-36). Multivariate linear regression was used to identify significant factors associated with follow-up QOL scores.

RESULTS

A total of 175 patients from 8 centers were analyzed. All QOL scores including the total QOL score, chronic kidney disease targeted score, and SF-36 at the 2-year follow-up were significantly increased compared to baseline values. Both physical and mental scale scores were improved after transplantation.

CONCLUSION

The QOL scores for both the mental and physical scales were improved at 2 years after kidney transplantation. High glomerular filtration rate at 2 years, high baseline QOL score, and low body mass index were associated with good follow-up QOL scores. Kidney transplantation for an Asian population with end-stage renal disease can result in better QOL as well as better patient and graft survival.

Serum CXCR3 ligands as biomarkers for the diagnosis and treatment monitoring of tuberculosis

SETTING

Tertiary care academic medical centre.

OBJECTIVE

To evaluate the clinical utility of CXC chemokine receptor 3 (CXCR3) ligands in the diagnosis and monitoring of tuberculosis (TB).

DESIGN

Presumptive TB patients (active TB, 256; non-TB disease, 52) and 201 healthy controls were enrolled. The serum levels of interferon-gamma (IFN-γ) and CXCR3 ligands (CXCL9, a monokine induced by IFN-γ [MIG] and CXCL11, an IFN-inducible T-cell α chemoattractant [I-TAC]) were measured using enzyme-linked immunosorbent assay. An IFN-γ release assay (IGRA) was also performed. Serial samplings were performed in 19 TB patients at baseline and at 1, 2, 3, 6 and 12 months after treatment initiation.

RESULTS

All marker levels were higher in TB patients than in controls and non-TB patients. The area under the curve (AUC) for differentiating between all TB patients and controls was 0.96 (95%CI 0.94-0.98) for CXCL9, 0.84 (95%CI 0.80-0.87) for CXCL11 and 0.61 (95%CI 0.57-0.66) for IFN-γ. CXCL9 levels afforded particularly high discriminatory power between TB patients and IGRA-positive controls (AUC = 0.95, 95%CI 0.92-0.97). The levels of CXCR3 ligands decreased significantly during follow-up, and these changes were correlated with treatment response.

CONCLUSION

CXCR3 ligands CXCL9 and CXCL11 may be useful surrogate markers for the diagnosis and follow-up of TB.

Abstract P6-04-01: Single cell RNA sequencing reveals key expression signatures of primary breast cancer cells and immune infiltrates

Introduction: Cancers display intratumoral heterogeneity which interferes with the precise analyses of the tumor entity, and which may affect therapeutic outcomes of targeted treatments. The aim of this study was to evaluate the feasibility of single cell RNA sequencing on primary breast cancer cells and to demonstrate the key gene expression signatures and transcriptome heterogeneity of breast cancer subtypes.

Methods: We performed RNA sequencing on 246 individual cells from 4 primary breast tumors and 2 metastatic lymph nodes from 4 patients, using C1™Single-Cell Auto Prep System (Fluidigm, South San Francisco, CA). RNA sequencing reads were aligned to the human genome reference (hg19) using the 2-pass default mode of STAR_2.4.0d, and gene expression was quantified by RSEM v1.2.18 as the sum of isoform expression.

Results: Pathologic characteristics of the 4 patients is summarized in Table 1.

Table 1. Pathologic characteristics of patients BC01BC02BC03BC04pathologic stagepT1N0 (IA)pT2N0 (IIA)pT1N3 (IIIC)pT2N1 (IIB)Immunohistochemistry   estrogen receptorpositivenegativenegativepositiveprogesterone receptornegativenegativenegativepositiveHER2 (FISH)2+/3 (negative)3+/3 (positive)1+/3 (negative)3+/3 (positive)No. of single cells   tumor (lymph node)214947(50)28(51)HER2, human epidermal growth factor receptor 2; FISH, fluorescence in situ hybridization

To distinguish tumor cells, we chose epithelial cell adhesion molecule (EpCAM) as an archetypal epithelial tumor marker and performed gene signature enrichment analysis for the EpCAM-positive cells. A total of 673 genes with enrichment score > |0.5| were selected and used as an "epithelial breast cancer" signature. Consensus clustering with the epithelial breast cancer signature separated 246 cells into 145 epithelial tumor and 101 non-tumor cell groups. Gene expression profiling in the tumor cells revealed many co-regulated genes in the estrogen receptor (ER)-positive tumor at a single cell resolution, which represent previously known ER-associated genes including MYC, BCL-2, and GATA3. Individual tumor cells from the two human epidermal growth factor receptor 2 (HER2)-amplified tumors demonstrated drastically different degree of HER2 signaling pathway activation, indicating the necessity of molecular subtyping for the identification of HER2-activated tumors. TNBC tumor cells showed an overall upregulation of activator protein 1 transcriptional pathway and strong activation of epithelial-mesenchymal transition signatures in a small sub-population. Immune cells comprised all the non-epithelial population, with mostly T lymphocytes in the primary tumor samples and B lymphocytes in the lymph nodes. The tumor-infiltrating T cells expressed an activated phenotype and many cytotoxic components. Altogether, the single cell RNA sequencing revealed the true identity of the tumor cells and the tumor-associated immune cells.

Conclusion: Single cell RNA sequencing of breast cancer was used to reveal the true gene expression characteristics of the tumor cells and tumor-associated non-tumor compartments. The results showed key gene expression signatures of specific tumor subtypes and a wide range of transcriptome heterogeneity which is shaped by the tumor and microenvironments.

Citation Format: Lee H-B, Eum HH, Chung W, Lee H-O, Lee K-M, Kim K-T, Moon H-G, Noh D-Y, Han W, Park W-Y. Single cell RNA sequencing reveals key expression signatures of primary breast cancer cells and immune infiltrates. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P6-04-01.

Initial locomotor sensitivity to cocaine varies widely among inbred mouse strains

Initial sensitivity to psychostimulants can predict subsequent use and abuse in humans. Acute locomotor activation in response to psychostimulants is commonly used as an animal model of initial drug sensitivity and has been shown to have a substantial genetic component. Identifying the specific genetic differences that lead to phenotypic differences in initial drug sensitivity can advance our understanding of the processes that lead to addiction. Phenotyping inbred mouse strain panels are frequently used as a first step for studying the genetic architecture of complex traits. We assessed locomotor activation following a single, acute 20 mg/kg dose of cocaine (COC) in males from 45 inbred mouse strains and observed significant phenotypic variation across strains indicating a substantial genetic component. We also measured levels of COC, the active metabolite, norcocaine and the major inactive metabolite, benzoylecgonine, in plasma and brain in the same set of inbred strains. Pharmacokinetic (PK) and behavioral data were significantly correlated, but at a level that indicates that PK alone does not account for the behavioral differences observed across strains. Phenotypic data from this reference population of inbred strains can be utilized in studies aimed at examining the role of psychostimulant-induced locomotor activation on drug reward and reinforcement and to test theories about addiction processes. Moreover, these data serve as a starting point for identifying genes that alter sensitivity to the locomotor stimulatory effects of COC.

CXCR3 ligands as clinical markers for pulmonary tuberculosis

SETTING

A tertiary care academic medical centre.

OBJECTIVE

To evaluate the clinical usefulness of CXC chemokine receptor 3 (CXCR3) ligands in active pulmonary tuberculosis (TB).

DESIGN

Patients with various pulmonary diseases and healthy controls were recruited into this cross-sectional study. Plasma levels of interferon-gamma (IFN-γ) and the CXCR3 ligands (CXCL9 [monokine induced by IFN-γ, MIG], CXCL10 [IFN-γ-inducible 10-kDa protein, IP-10] and CXCL11 [IFN-inducible T-cell α chemoattractant, I-TAC] were measured using enzyme immunoassays.

RESULTS

The study included 846 subjects: 201 patients with active pulmonary TB, 389 with other pulmonary diseases, and 256 controls. CXCR3 ligand levels were higher in TB patients than in controls and all other disease groups, whereas the IFN-γ levels did not differ. The area under the curve (AUC) for differentiating active TB from all other groups was 0.797 for CXCL9, 0.726 for CXCL10, 0.846 for CXCL11 and 0.534 for IFN-γ. The AUC for differentiating active TB from controls was 0.926 for CXCL9, 0.818 for CXCL10, 0.865 for CXCL11 and 0.575 for IFN-γ. CXCR3 levels correlated with sputum acid-fast bacilli smear grades and the radiographic extent of pulmonary TB.

CONCLUSION

CXCR3 ligands may be useful surrogate markers for diagnosing active TB and for assessing TB patients clinically.