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Acute myeloid leukemia (AML) is a clonal malignancy characterized by genetic heterogeneity due to recurrent gene mutations. Treatment with cytotoxic chemotherapy has been the standard of care for more than half of a century. Although much progress has been made toward improving treatment related mortality rate in the past few decades, long term overall survival has stagnated. Exciting developments of gene mutation-targeted therapeutic agents are now changing the landscape in AML treatment. New agents offer more clinical options for patients and also confer a more promising outcome. Since Midostaurin, a FLT3 inhibitor, was first approved by US FDA in 2017 as the first gene mutation-targeted therapeutic agent, an array of new gene mutation-targeted agents are now available for AML treatment. In this review, we will summarize the recent advances in gene mutation-targeted therapies for patients with AML.

Purpose Age at breast cancer diagnosis not only predicts clinical outcome, but also indicates distinct molecular features thus we can choose the most appropriate treatment strategies. Yet little is known about the molecular profile of young and elderly triple negative breast cancers (TNBCs). Methods Clinical, genomic and transcriptome features of young ( Results In this study, 50, 354 and 69 patients were Conclusions TNBCs of different age had distinct clinical and molecular features. We should pay attention to that nearly half of the TNBCs diagnosed at 65 years-old or later were not basal-like cancers but a special group with positive AR staining. Taking together with the higher fibrosis/MES proportion in elderly TNBC, we should reconsider the benefit of specific treatment strategies (like neoadjuvant chemotherapy) in these patients. The young TNBCs were characterized by activated cell cycle, elevated nucleotide metabolism (especially TYMS expression and corresponding pyrimidine metabolism) and enhanced DNA damage (especially HRD). These molecular features supported the aggressive phenotypes of young TNBC, while also provide us with potential therapeutic strategies. Citation Format: Ma D, Jiang Y-Z, Xie M-D, Xiao Y, Zhao S, Shao Z-M. Multi-omics profiling reveals distinct molecular features in young and elderly triple negative breast cancer [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P3-08-11.

Background: Metastatic regional lymph nodes (LN) is a strong predictor of worse long-term outcome after resection of breast cancer. This study aimed to compare the prognostic performance of American Joint Committee on Cancer (AJCC) N stage relative to lymph node ratio (LNR), log odds of metastatic lymph nodes (LODDS), number of removed lymph nodes (NRLNs), and number of negative lymph nodes (NNLNs) in breast cancer patients. Methods: All of the breast cancer patients who underwent surgery between 2004 and 2012 were identified from the Surveillance, Epidemiology, and End Results database. Restricted cubic spline functions were used to characterize the association between continuous variables and the risk of death and determine the optimal cut-off points. The Cox proportional hazards models were constructed, and the relative discriminative abilities of the different LN staging systems were assessed using the Akaike's Information Criterion (AIC) and the Harrell's concordance index (C-index). Results: A total of 264,096 breast cancer patients were enrolled, and 177,598 (67.2%) had no lymph node metastasis, whereas 86,498 (32.8%) had lymph node metastasis. 187,785 (71.1%) patients had a limited number of LNs harvested (NRLN Conclusions: Although LNR assessed as a continuous variable was the most potent method to stratify patients regardless of LN status, the prognostic superiority of LNR is confounded by a limited LN harvest. LODDS was a better and more powerful predictor of survival when patients were LN positive, especially among those patients with either very low or high LNR. Citation Format: Gong Y, Ji P, Jiang Y-Z, Hu X, Shao Z-M. Comparing prognostic performance of different lymph node staging systems among patients with breast cancer [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P2-08-36.

Background: Estrogen receptor positive/ progesterone receptor negative/ human epidermal growth factor receptor 2 negative (ER+/PR-/HER2-) tumors define a distinct subtype of ER+ breast cancer, characterized by poor response to endocrine therapy and poor prognosis. The genomic landscape of ER+/PR-/HER2- tumor has yet to be systematically studied,and driver events for tumor progression and endocrine resistance with loss of PR expression are yet to be identified. Methods: We assessed 13,410 ER+/PR-/HER2- patients from Surveillance, Epidemiology, and End Results (SEER), the Cancer Genome Atlas (TCGA) and Molecular Taxonomy of Breast Cancer International Consortium (METABRIC) for clinicopathologic characteristics, survival and genomic analyses. Patients were divided into endocrine-resistant and endocrine-sensitive groups using an endocrine therapy sensitivity score [(0.8*ER+1.2*PGR+BCL2+SCUBE2)/4], and we further explored genomic events enriched in the endocrine-resistant group. Results: Clinicopathologic features and survival outcomes of ER+/PR-/HER2- patients were worse than ER+/PR+/HER2- in SEER and METABRIC cohort. The genomic landscape of ER+/PR-/HER2- tumors revealed them to have more aggressive properties, like a higher percentage of luminal B (29-35%) and basal-like (4-16%) subtypes; more intClust subtypes with high genomic instability (intClust1, 6); more TP53 mutation and less PIK3CA mutation; and more copy number variation events. ER+/PR-/HER2- tumors have more focal amplification events, including 8p11.23 (ZNF703) and 17q23.1 (RPS6KB1) and more focal deletion events, such as 17q21.31 (BRCA1) and 14q24.3 (MLH3). Pathifier pathway analyses showed that up-regulated pathways in ER+/PR-/HER2-tumors included those associated with biosynthesis, metabolism, drug resistance and DNA replications (FDR Citation Format: Liu X, Ma D, Jiang Y-Z, Liu Y-R, Yu K-D, Shao Z-M. Clinicopathologic characteristics and genomic essence analyses revealed estrogen receptor positive, progesterone receptor negative and human epidermal growth factor receptor 2 negative breast cancer to be more basal-like and endocrine resistant [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 P2-06-03.

Background The microenvironment phenotypes strongly affect the immunotherapeutic strategies for triple-negative breast cancer (TNBC). Although the multi-omics profile of TNBC has been comprehensively characterized, few studies have focused on the microenvironment phenotypes of TNBC. Methods With multi-omics data for the largest single-center TNBC cohort (n=386), we first established a TNBC-specific microenvironment cell signature. We further used single sample gene set enrichment analysis to calculate the relative number of microenvironment cell subsets in each sample. Then, we performed k-means clustering to classify the TNBC microenvironment phenotypes into heterogeneous clusters. Furthermore, we systematically analyzed the extrinsic and intrinsic immune escape mechanisms of different TNBC microenvironment clusters. In addition, we explored genomic alterations that might decrease immune infiltration in certain TNBC microenvironment clusters. Results We classified the TNBC microenvironment phenotypes into three heterogeneous clusters. Cluster 1 (type 1 “cold tumor”) had low microenvironment cells infiltration. Cluster 2 (type 2 “cold tumor”) was characterized by resting innate immune cells, fibroblasts and endothelial cells infiltration. Cluster 3 (“hot tumor”) was featured by adaptive immune cells infiltration. Analysis of immune escape mechanism revealed that an incapability to attract innate immune cells (resulting in failure of adaptive immunity) led to immune escape of cluster 1. The chemotaxis but inactivation of innate immunity (also leading to failure of adaptive immunity) and low tumor antigen burden resulted in immune escape of cluster 2. High expression of immune checkpoint molecules contributed to immune escape of cluster 3. In addition, we found that tumor infiltrating lymphocytes (TILs) were positively correlated with immune checkpoint molecules expression, while mutation load was negatively correlated with those indicators in triple-negative breast cancer. Analysis of enrichment pathways, mutations and somatic copy number variations between the “cold tumor” and “hot tumor” clusters revealed that amplification of MYC and activation of MYC-related pathways might decrease the immune infiltration of cluster 1. Mutations in PI3K-AKT pathway members and activation of fibroblasts-related pathways might decrease the immune infiltration of cluster 2. Conclusion Utilizing the largest single-center TNBC cohort with multi-omics data, our study first revealed the heterogeneity of the TNBC microenvironment, with translational significance both clinically and biologically. First, we identified a subtype of “hot tumor” in TNBC (cluster 3), for which immune checkpoint blockers (ICBs) might be effective. TILs and immune checkpoint molecules expression but not mutation load might predict the efficacy of ICBs. Second, we presumed some genomic alterations that might drive “cold tumor” formation in TNBC. Our study represents a step toward personalized immunotherapy for TNBC patients. Key Words triple-negative breast cancer, multi-omics, microenvironment heterogeneity, immune escape Citation Format: Xiao Y, Ma D, Zhao S, Jiang Y-Z, Shao Z-M. Microenvironment heterogeneity of triple-negative breast cancer reveals distinct immune escape mechanisms and potential driver events [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 P4-06-24.

Background: Intra-tumor heterogeneity (ITH) plays a pivotal role in driving breast cancer progression and therapeutic resistance. Emerging evidence has indicated that the extent of genetic heterogeneity may serve as a clinically useful biomarker. While several studies have suggested the prognostic value of ITH in several cancer types, the clinical significance of genetic ITH and molecular portraits that correlated with different ITH levels were poorly understood in breast cancer. The establishment of algorithms estimating genetic ITH based on sequencing of bulk tumor DNA offered us an opportunity to explore the clinical implication of ITH in large breast cancer cohorts and, for the first time, to use integrative genomic analyses to reveal molecular portraits related to intra-tumor genetic heterogeneity. Methods: We assessed 916 female breast cancer patients from The Cancer Genome Atlas. Mutant-allele tumor heterogeneity (MATH) values were calculated from whole-exome sequencing data. We used integers nearest to the tertiles of the MATH values as cutoff points to divide the patients into three groups nearly equal in size. The association between MATH value and clinical characteristics was evaluated, followed by survival analyses in these different MATH groups. We then compared the rates of total non-silent somatic mutations among the different MATH groups, and further determined the mutations independently associated with high MATH by logistic regression adjusting for T classification and clinical subtypes. Similar methods, superadding somatic copy number alteration (SCNA) burden in logistic model, were used to evaluate SCNA events that were significantly associated with high MATH level. Gene enrichment between the high and rest MATH groups was analyzed using Gene Set Enrichment Analysis. Results: The patients were divided into low (MATH value lower than 33), intermediate (MATH between 33 and 46) and high (MATH higher than 46) MATH groups. High T stage, African American race, and triple-negative or basal-like subtype were associated with a higher MATH level (all P Conclusion: Our study extended the knowledge concerning the clinical role of ITH in breast cancer, especially the distinct pattern of prognostic values in different clinical subtypes, which may help promote the clinical utilization of genetic ITH. Our attempt at exploring the molecular features related to ITH might provide clues for the source and consequences of ITH, inspiring subsequent experiments investigating the laws underling tumor heterogeneity. Citation Format: Ma D, Jiang Y-Z, Liu X-Y, Liu Y-R, Yu K-D, Shao Z-M. Clinical and molecular relevance of intra-tumor genetic heterogeneity in breast cancer: Integrative analysis of data from The Cancer Genome Atlas [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 P1-06-07.

We investigate the clinical characteristics, prognosis and treatment of relapsed and refractory Hodgkin's lymphoma. Twenty patients with relapsed and refractory Hodgkin lymphoma were treated by chemotherapy or autologous stem cell transplantation in our hospital from April 2006 to August 2012. The retrospective analysis of the records from the 20 patients reflected both 5-year overall survival (OS) and progression-free survival (PFS). The overall effectiveness was 80% for the 20 patients. The 5-year overall survival rate and 5-year progression-free survival rate were 73.5% and 62.7%, respectively. Therefore, comprehensive treatment should be actively utilized in the case of invalid second-line regimen for the refractory HL patients.

Purpose: The aim of this study is to evaluate the role of postmastectomy radiotherapy (PMRT) in clinical stage II and III breast cancer patients who achieved negative node status (pN0) after neoadjuvant chemotherapy (NAC). Material and methods: We retrospectively analyzed the outcomes of 143 patients with pN0 after NAC and mastectomy at Fudan University Shanghai Cancer Center. In total, 103 (72%) patients received PMRT, and 40 (28%) patients did not. Univariate and multivariate survival analyses were performed to evaluate the effect of PMRT on locoregional recurrence-free survival (LRRFS) and overall survival (OS) of the two groups. Results: There were no differences between the two groups with respect to age, nuclear grade, estrogen receptor (ER) status, HER2/neu receptor status, lymphovascular space invasion (LVSI) status or pathological tumor size. However, a significantly higher proportion of patients in the irradiated group (64%) had clinical lymph node involvement than in the nonirradiated group (45%). After a median follow-up time of 49 months, 10 locoregional recurrence events occurred. For the entire cohort of patients, use of radiation therapy improved the 5-year LRRFS rate (94.5% vs. 80.2%; P =0.032) but not the 5-year OS rate (92.2% vs. 88.7%; P =0.617). In the subset of patients who presented with clinically stage II disease, the 5-year LRRFS and 5-year OS did not differ significantly between the PMRT and no-PMRT group (96.3% vs. 91.3%; P = 0.190 and 96.2% vs. 91.3%; P = 0.199, respectively). For patients with stage III disease at diagnosis, a trend was seen toward better local regional control with PMRT (the 5-year LRRFS rate was 92.7% vs. 64.2%; P = 0.063), although the benefit from radiation with respect to OS was not significant (5-year OS rate was 88.1% vs. 85.2%; P = 0.657). On multivariate Cox regression analyses, the clinical tumor size (hazard ratio [HR], 3.27; 95% confidence interval [CI], 1.05-10.18; P = 0.041), pathologic breast tumor response (HR, 1.82; 95% CI, 1,11-3.77; P = 0.046) and delivery of radiation therapy (HR, 1.27; 95% CI, 1.08-9.25; P = 0.047) were independent predictors of locoregional recurrence. Conclusions: For patients who achieved pN0 after NAC, PMRT seemed to provide a clinical benefit for breast cancer patients with stage III disease. Omission of PMRT in patients with stage II disease did not increase the risk of locoregional recurrence and death. Citation Format: He M, Li J, Ni X-J, Chen S, Jiang Y-Z, Di G-H, Shao Z-M. Postmastectomy radiotherapy improves the outcomes of stage III breast cancer patients with negative lymph nodes after neoadjuvant chemotherapy. [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 P1-14-18.

Purpose Luminal breast cancer (estrogen receptor [ER] and/or progesterone receptor [PR] positive) represents approximately two-thirds of all breast cancer. This type of cancer constitutes a group of highly heterogeneous diseases with a sustained high risk of late recurrence. In this study, we aimed to develop comprehensive and practical nomograms for the first time to better estimate the long-term survival of luminal breast cancer. Thus, those patients with high risk of late recurrence and poor prognosis could be screened out and individualized treatments can be applied. Methods Patients with luminal breast cancer diagnosed between 1990 and 2006 were retrieved from the Surveillance, Epidemiology, and End Results (SEER) database, and randomly divided into the training (n=87,867) and validation (n=88,215) cohorts. The inclusion criteria we used to identify eligible patients were as follows: female; aged 18 to 79 years old at diagnosis; known time of diagnosis from January 1, 1990, to December 31, 2006; unilateral breast cancer; breast cancer as the first and only cancer diagnosis; diagnosis not obtained from a death certificate or autopsy; surgical treatment with either mastectomy or breast-conserving surgery; pathologic confirmation of invasive carcinoma; AJCC stages I-III; histological grade I-III and known ER and PR statuses. Patients with inflammatory breast cancer or Paget's disease and lack of data on the above inclusion criteria were also excluded. Univariate and multivariate survival analyses were applied to identify prognostic factors for overall survival (OS). The cumulative incidence function (CIF) and a competing-risks model were used to estimate the probability of breast cancer-specific survival (BCSS) and death from other causes. We integrated significant prognostic factors to build nomograms, and subjected the nomograms to bootstrap internal validation and external validation. Results We screened 176,082 luminal breast cancer cases. The mean age at diagnosis was 57.5 years, and mean survival time was 107.4 months. By the end of the last follow-up, 36,911 (21.0%) patients had died, including 17,855 (10.1%) died from breast cancer and 19,056 (10.8%) from other causes. The 5- and 10-year probabilities of overall death were 0.089 and 0.202, respectively. The 5- and 10-year probabilities of breast cancer specific-mortality (BCSM) were 0.053 and 0.112, respectively. Independent prognostic factors for both OS and BCSS were integrated to construct the nomograms, including age at diagnosis, race, tumor size, histology, grade, positive lymph nodes, ER/PR status and radiation. The calibration curves for the probabilities of 5- and 10-year OS and BCSS showed excellent agreement between the nomogram prediction and actual observation. The C-indexes of the nomograms were high in both internal validation (0.732 for OS and 0.800 for BCSS) and external validation (0.731 for OS and 0.794 for BCSS). Conclusion We established and validated nomograms that accurately predict OS and BCSS of luminal breast cancer based on a large, population-based cohort with long-term follow-up. The nomograms can identify patients with higher risk of late overall mortality and BCSM, helping physicians in facilitating individualized treatment. Citation Format: Sun W, Jiang Y-Z, Liu Y-R, Ma D, Shao Z-M. Nomograms to estimate long-term overall survival and breast cancer-specific survival of patients with luminal breast cancer. [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 P2-07-03.

Background: In developed countries, T1 stage breast cancers have become the most frequently diagnosed invasive breast diseases. Patients with early stage breast cancer with lymph nodes metastasis have been proven to have more aggressive biologically phenotypes. The risk of missing metastases using sentinel lymph node biopsy can range from 1% to 4%, with a false negative rate of 10%. This evidence implies that SLNB might not be sufficient for the diagnosis of lymph node metastasis in T1 breast cancer patients. The aim of this study was to build a nomogram to predict lymph node metastasis in patients with T1 breast cancer. Methods: We identified female patients with T1 breast cancer diagnosed between 2010 and 2014 in the Surveillance, Epidemiology and End Results database. The patients were randomized into training and validation sets. Univariate and multivariate logistic regressions were carried out to assess the relationships between lymph node metastasis and age, race, and tumour size, primary site, pathological grade, histologic type, and molecular subtype. A nomogram was developed in the training set and validated by a calibration curve with the bootstrapping method and receptor operating characteristic curve analysis. Result: A total of 91,364 T1 breast cancer patients were included in the present study. For patients with T1 breast cancer, age, race, tumour size, tumour primary site, pathological grade, oestrogen receptor status, progesterone receptor status and human epidermal growth factor receptor 2 status were independent predictive factors of positive lymph node metastasis (P182). We found a significant difference in the probability of lymph node metastasis between the high and low score groups in univariate analysis in both the training set (OR=4.15, 95% CI:3.77-4.57, P Conclusions: A better understanding of the clinicopathological characteristics of T1 breast cancer patients could be vital for the assessment of their metastatic lymph node status. The nomogram developed here, if further validated in other large T1 patient cohorts, might provide additional information regarding lymph node metastasis. Together with sentinel lymph node biopsy, this nomogram can help comprehensively predict lymph node metastasis. Citation Format: Zhao Y-X, Liu Y-R, Jiang Y-Z, Xie S, Shao Z-M. A nomogram predicting lymph node metastasis in T1 breast cancer based on the surveillance, epidemiology, and end results program [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 P3-03-09.

Purpose A membrane-bound microtubule-associated protein chain 3B(LC3B) is known as one of the most specific biomarker for autophagy. The goal of this study is to investigate the prognostic value of autophagy marker LC3B in patients with residual tumors after neoadjuvant chemotherapy(NCT) for local advanced breast cancer(LABC) Patients and Methods Expression of LC3B in residual breast cancer cells were assessed by immunohistochemistry in surgical specimens from 229 patients who were diagnosed with histological proven invasive breast cancer. All patients had undergone neoadjuvant chemotherapy followed by mastectomy, and were considered as non pathological complete responders(non-pCR)after pathological evaluation. The density of positive staining of LC3B was measured with the use of a computerized image system. Prognostic value of various clinicopathologic factors was combined and evaluated by using Cox regression model. Results LC3B density was similar in the peripheral and central area of tumor(P = 0.328), however, it was siginifcantly lower in the extratumoral area(P Conclusion LC3B is a prognostic marker in non-pCR patient after neoadjuvant chemotherapy for breast cancer, which highlighting the importance of autophagy in the biological behavior of chemo-resistence cancer cells. Evaluating and targeting autophagy in neoadjuvant setting may help in prevention of disease relapse in non-pCR patients. Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P3-14-06.

Background Girdin is identified as a novel modulator of the PI3K-Akt signaling pathway in regulating neurons integration during neurogenesis process. Recently, several studies demonstrated that Girdin and its phosphorylation type (p-Girdin) were also involved in tumor metastasis and angiogenesis. However, the clinical implications of Girdin and p-Girdin in breast cancer remain unclear. In this study, we detected the expression pattern of p-Girdin (Ser1416) and Girdin in breast cancer to uncover the association between p-Girdin/Girdin status and clinicopathological parameters like estrogen receptor (ER), progestogen receptor (PR), and human epidermal growth factor receptor 2 (Her2), etc. Methods This study included 250 patients who were histologically confirmed as invasive ductal breast cancer and underwent mastectomy in the Department of Breast Surgery in Shanghai Cancer Center during 2001 to 2006. We performed immunohistochemistry of p-Girdin/Girdin on tissue microarrays constructed from above specimens. Results We observed that Girdin was mainly located in the cytoplasm of mammary epithelial carcinoma cells (195/248, 78.63%) while p-Girdin was mainly located in the nucleus (160/250, 64.00%). However, Girdin/p-Girdin was also weakly expressed in the nucleus/cytoplasm (77/248, 31.05% for Girdin and 193/250, 77.2% for p-Girdin). By the Chi-square test, we found that Girdin in the nucleus (GN) was positively associated with ER status (P = 0.012); Girdin in the cytoplasm (GC) was positively associated with ER (P = 0.004), PR (P = 0.028), and Her2 status (P = 0.004); p-Girdin in the cytoplasm (pGC) was positively associated with PR status (P = 0.001) and negatively associated with tumor size (P = 0.025). However, no significant association was observed between p-Girdin in the nucleus (pGN) and other parameters. Using Kaplan-Meier method, we disclosed a trend that GN indicated poor disease-free survival (DFS) in ER-positive breast cancer (P = 0.075). After adjusted for histological grade and tumor size, multivariate cox regression analysis confirmed this trend (HR = 3.051, 95% CI: 1.137-8.191, P = 0.027). Furthermore, GC was prone to associating with poor DFS, especially in stage II (P = 0.079) and grade III (P = 0.058) patients. Conclusions Our work reveals, for the first time, that the location and expression pattern of both Girdin and p-Girdin (Ser1416) in breast cancer, suggesting that p-Girdin/Girdin are associated with ER, PR and Her2 status. In addition, Girdin in the nucleus is associated with poor DFS in ER-positive breast cancer. Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P5-11-05.

Background: As a critical factor, age at the time of diagnosis has a significant impact on cancer therapy and outcomes. The purpose of this study is to investigate the overall mortality (OM) and breast cancer-specific mortality (BCSM) in patients with breast cancer corresponding to age at the time of diagnosis, thus constructing an age-related pattern on breast cancer survival. Methods: We analyzed data for 396,978 women aged 20-79 from 1990 to 2008 diagnosed with breast cancer from the population-based Surveillance, Epidemiology, and End Results (SEER) program of the U.S. national cancer institute. Clinicopathological factors and outcomes were compared using a chi-square test, the Kaplan-Meier method, and Cox proportional hazards regression model. Results: In the multivariable analysis, a significant relationship was found between age at the time of diagnosis and OM (p Conclusion: Patients at very young and very old age (20-29 years old and 70-79 years old) have the poorest outcomes while prognosis improves with age towards mean level. The very young age (20-29 years old) may be regarded as a significant hazard factor for BCSM in patients with ER+PR+ breast cancer. Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P2-14-04.

This abstract was not presented at the symposium.

New understanding of the alloresponse following bone marrow transplantation supports the possibility that the graft-versus-host disease (GVHD) response can be separated from a favorable graft-versus-leukemia (GVL) effect. We used chronic myeloid leukemia (CML) cells to generate 122 recipient-reactive T cell clones from a closely HLA-matched sibling responder. Clones were tested for their proliferative response to stimulator CML cells or PHA-transformed (non-leukemic) lymphoblasts. Of 78 clones tested, 32 recognized both leukemia cells and PHA blasts, 19 only CML and four only PHA blasts. The remainder were non-specific responders. This functional specificity corresponded to distinct patterns of T cell receptor (TCR) V beta usage: clones recognizing CML cells preferentially used V beta 5, V beta 6/7 while clones recognizing both CML and PHA blasts or only PHA blasts preferentially used V beta 3 and V beta 8. It may therefore be possible to identify in vitro-generated myeloid leukemia-restricted donor T cells by their pattern of V beta usage. TCR V beta antibodies could thus be used to select and expand leukemia-restricted donor T cells for transfusion after BMT to specifically enhance the GVL response.

We studied patients relapsing with myeloid leukemias following allogeneic bone marrow transplantation (BMT) for evidence of immune escape by clonal evolution of the leukemia. Relapsed cells from four out of five patients had a reduced ability to stimulate proliferation of lymphocytes from an HLA-mismatched responder. There was decreased susceptibility to lysis by CTL in three and reduced susceptibility to NK-mediated lysis in one. Relapsed leukemias had marked alterations in expression of critical surface molecules involved in immune responsiveness. Three had decreased expression of MHC class I and II, with no change or increase in CD54 (ICAM-1) or CD80 (B7.1). None of these responded to treatment with donor lymphocytes. Three patients showed no change, or increased expression of MHC with no change or decrease in ICAM-1 or B7.1. Two achieved remission - one in response to donor lymphocytes and one following withdrawal of cyclosporine. In one patient transplanted with myelodysplastic syndrome in transformation, interferon-gamma upregulated expression of MHC molecules in relapsed cells and increased their stimulatory capacity and target susceptibility to unmatched responder lymphocytes. These results suggest that immune escape through clonal evolution of the leukemia is a common occurrence in patients who relapse with myelogenous leukemias after BMT.

There is good evidence that T lymphocytes play an important role in the graft-versus-leukemia (GVL) effect following allogeneic bone marrow transplantation (BMT) for hematologic malignancies. However, the role of natural killer (NK) cells in GVL is less clear. To further investigate a possible association of NK cells with GVL we studied 15 patients undergoing BMT for chronic myeloid leukemia (CML), correlating T-cell (CD4+ and CD8+) and NK-cell (CD16+ 56+) recovery with relapse and graft-versus-host disease (GVHD). Patients were studied on three occasions up to 9 months after BMT, for lymphocyte surface phenotype and for spontaneous and IL-2-stimulated (LAK cell) cytotoxic function. Circulating CD8+ and NK but not CD4+ cell numbers were significantly lower in five patients who relapsed compared with those remaining in remission after BMT (mean 0.03 vs 0.32 x 10(9)/l, p = 0.002 for CD8+ cells: mean 0.03 vs 0.11 x 10(9)/l, p = 0.002 for NK cells). There was no correlation of CD4+. CD8+, or NK cell numbers and development of grade-II or more acute GVHD. Spontaneous NK cytotoxic function rose to within the normal range in the first month after BMT. LAK function remained low during the study period. These results link NK cell recovery more closely with a GVL than with a GVH effect.

Background: Triple-negative breast cancer (TNBC) is a highly heterogeneous group of cancers with no effective therapeutic targets hitherto. Thus molecular subtyping is necessary to better identify molecular-based therapies. While some classifiers have been established, no one has integrated the expression profiles of long-noncoding RNAs (lncRNAs) into such subtyping criterions. Considering the emerging important role of lncRNAs in gene regulation and other cellular processes, a novel classification integrating the transcriptome profiles of both messenger RNA (mRNA) and lncRNA would help us better understand the heterogeneity of TNBC and treat patients accordingly. Methods: Using human transcriptome microarray, we retrieved the transcriptome profiles of 165 consecutive TNBC samples. We used k-means clustering to classify the samples based on the most differentially expressed genes (standard deviation>0.65). Empirical cumulative distribution function was analyzed to determine the optimal number of subtypes. Then the new classifier was compared with the Lehmann/Pietenpol system, and survival analyses were performed to compare the recurrence-free survival (RFS) in different subtypes. Gene Ontology (GO) and pathway analyses were applied to determine the main function of the subtype-specific genes and pathways. We conducted co-expression network analysis to identify interactions between lncRNAs and mRNAs, and to predict possible functions of subtype specific lncRNAs. Results: All 165 TNBC tumors were classified into four distinct clusters, each displaying unique GOs and pathways. These include an immunomodulatory (IM) subtype, a luminal androgen receptor (LAR) subtype, a mesenchymal-like (MES) subtype and a basal-like and immune suppressed (BLIS) subtype, accounting for 17.0%, 17.6%, 33.3%, and 32.2% of the patients, respectively. The IM subtype had unique GOs and pathways involving immune cell process. The LAR subtype was highly enriched in hormonally regulated pathways. Enriched pathways in the MES subtype included ECM-receptor interaction, focal adhesion, and processes linked to growth factor signaling pathways. The BLIS subtype was characterized by downregulation of immune response gene and activation of cell cycle and DNA repair, and patients in this subtype experienced worse RFS compared to other subtypes (log-rank test,P=0.045), which was in concordance with the highly proliferative and immune-suppressed nature of these tumors. When analyzing the distribution of the Lehmann/Pietenpol subtypes in our classification system, we found that the two classification systems were significantly correlated (P=0.039). However, our novel classification was more concise and significantly connected with survival outcome. Subtype-specific lncRNAs were identified and their possible functions were predicted using co-expression network analysis. Conclusions: We developed a novel TNBC classification system integrating the expression profiles of both mRNAs and lncRNAs, and determined subtype-specific lncRNAs that are potential biomarkers and targets of TNBC. If further validated in larger population, our novel classification system could facilitate patient counseling and individualize treatment of TNBC. Citation Format: Liu Y-R, Jiang Y-Z, Xu X-E, Zuo W-J, Yu K-D, Jin X, Hu X, Wu J, Liu G-Y, Di G-H, Shao Z-M. Comprehensive transcriptome analysis identifies novel molecular subtypes and subtype-specific lncRNAs of triple-negative breast cancer. [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 P6-04-04.

Purpose: The changed gene-expression profiles of breast cancer under neoadjuvant chemotherapy (NCT) have been described. However, it remains unclear whether chemotherapy affects somatic mutation status in breast cancer. We investigated the influence of paclitaxel-based chemotherapy on somatic mutations in tumor tissues from patients with breast cancer. Patients and Methods: Samples were derived from two cohorts: first, 296 patients who underwent paclitaxel-based NCT with matched pre- and post-chemotherapy tumor tissues; second, 81 patients who underwent paclitaxel-based chemotherapy with pre-chemotherapy tumor tissues. First, we performed whole exome sequencing (WES) to examine the exomes (100-fold coverage) of two paired basal-like breast cancer samples (pre-treatment tumor biopsies and post-treatment tumors). Shift in somatic mutation status was validated by Sanger sequencing and analyzed in an extension cohort of 296 patients. Furthermore, we performed microdissection and genetic heterogeneity analysis for samples from 81 patients who underwent paclitaxel-based chemotherapy. Somatic mutation status was determined to reveal potential impact of paclitaxel-based chemotherapy on mutation status. Results: Compared with post-treatment biopsies, the analysis of WES data identified and validated TP53 and PIK3CA — as significantly mutated genes in pre-treatment tumors with a mutation frequency of approximately 10% in an independent extension cohort of 296 paired samples of different molecular subtypes. Somatic mutations of TP53 or PIK3CA were detected in 24.3% of the pre-chemotherapy tumor samples (35 of 296 for TP53, 32 of 296 for PIK3CA, 5 of 296 for both genes, respectively) but in only 12.2% of the post-chemotherapy tumor samples (18 of 296 for TP53, 16 of 296 for PIK3CA, 2 of 296 for both genes, respectively). The decrease in mutation rate was statistically significant (P < 0.001). Patients with TP53/PIK3CA mutations switched from positive to negative after chemotherapy had better partial response than patients with no change or with a reverse change (P = .008). Furthermore, patients with TP53/PIK3CA mutations switched from positive to negative had improved disease-free survival (P = 0.018) and improved overall survival (P = 0.032) relative to patients with no change or with a reverse change. In the second cohort, 18.5% of the tumors (15 of 81) showed intratumoral heterogeneity of TP53 or PIK3CA somatic mutations, whereas 81.5% (66 of 81) were homogeneous, either with mutations of certain genes or not. Conclusion: Our data reveal the novel concept that significant evolution might occur during chemotherapy. Chemotherapy may reduce somatic mutation frequency in patients with breast cancer, likely the result of a preferential response of highly fit sub-clones without mutations of certain genes. In addition, the identification of somatic mutations of TP53 and PIK3CA as biomarkers for prediction of treatment response and prognosis might help us optimize choice for sequential therapy and improve patients’ survival. KEY WORDS: Exome sequencing; TP53; PIK3CA; neoadjuvant chemotherapy; breast cancer. Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr S4-05.

A substantial proportion of patients undergoing allogeneic bone-marrow transplantation (BMT) develop moderate-to-severe acute graft-versus-host disease (GVHD). Anti-recipient helper (interleukin-2-producing) T-lymphocyte precursors (HTLp) have an important role in the control and amplification of the alloreactive immune response that initiates GVH D. We used a limiting dilution assay to measure the frequency of HTLp in the blood of marrow donors for 25 patients undergoing genotypically HLA-identical BMT for chronic myeloid leukaemia (n = 20), acute myeloid leukaemia (4), or thalassaemia (1). HTLp frequencies in donor blood ranged from 1 in 18x10 3 to less than 1 in 500x10 3 ; they were significantly higher (p=0·02) in patients with grade II-IV acute GVHD than in those with grade 0-I GVHD. The HTLp assay seems sufficiently sensitive to detect clinically significant minor histocompatibility antigen differences between the donor and recipient. The assay should prove valuable in selecting the best donor/recipient combination and could indicate the need to intensify GVH D prophylaxis when the only available donor has a high HTLp frequency.

Accumulating evidence indicates that alloreactive donor T cells confer both graft-versus-host (GVH) and graft-versus-leukaemia (GVL) reactivity following allogeneic bone marrow transplantation. We have developed a method to deplete alloreactive donor T cells with an immunotoxin targeting the α chain of the IL-2 receptor. In patients with chronic myeloid leukaemia and their HLA-identical sibling donors, we measured donor helper T-lymphocyte precursor frequencies (HTLPf) against recipient peripheral blood mononuclear cells (PBMNC; donor versus host), recipient leukaemia cells (donor versus leukaemia) and third-party PBMNC, before and after the depletion. In seven pairs there was a 4.3-fold reduction of donor-versus-host HTLPf (P = 0.017), without a significant change in the donor frequencies against third party (P = 0.96). In eight further donor–recipient pairs, immunotoxin-depleted donor versus patient PBMNC HTLPf 4.5-fold (mean 1/155 000 before and 1/839 000 after depletion, P = 0.007). There was a smaller non-significant 1.8-fold reduction in donor-versus-leukaemia HTLPf from 1/192 000 to 1/334 000 (P = 0.19). These results suggest that selective T-cell depletion can significantly deplete donor anti-host reactivity while conserving antileukaemia reactivity in HLA-matched donor–recipient pairs.