Abstract P1-05-02: CRISPR/Cas9-guided editing of spliceosome factors enhances major histocompatibility complex proteins in triple-negative breast cancer

Triple-negative breast cancer (TNBC) exhibits an extraordinary plasticity allowing adaptation to unfamiliar microenvironments and survival despite hindrances imposed by aggressive therapeutic approaches and the immune system. Alternative mRNA splicing (AS), catalyzed by spliceosome factors (SFs), is a major source of transcriptional diversity and phenotypic plasticity for normal and cancer cells. We ascertained that patients with TNBC present up-regulation of specific subsets of SFs mainly involving the epithelial splicing regulatory proteins 1 and 2 (ESRP1/2) and the polypyrimidine tract binding proteins (PTBP1/2). Methods and Results: Through the integration of in-house and publicly-available gene expression profiles (n=890), we evaluated the correlation between the levels of 290 SFs in patients with TNBC. This analysis identified nine subsets of TNBC based on SFs expression profiles with diverse clinical and pathological characteristics. These findings were further validated using data generated by the TCGA-BRCA (n=1,105) and METABRIC projects (n=2,509). Interestingly, up-regulation of PTBP1 was significantly associated with a shorter relapse-free survival interval for patients with TNBC (n=305; HR=1.58 (1.07 − 2.33); p-value=0.02). To systematically identify PTBP1-regulated AS events, we generated and clonally selected CRISPR/Cas9-guided PTBP1 knock-out (KO) TNBC cell lines. Analysis of our RNA-sequencing data at the gene level revealed a significant enrichment of inflammatory response and antigen presentation pathways. Evaluation of potential upstream transcriptional regulators for the enriched molecular pathways and predicted PTBP1 targets identified SMARCA4, a member of the SWI/SNF chromatin remodeling complex, to be significantly activated after PTBP1KO (q-value<0.01). Integration of ENCODE ChIP-sequencing and JASPAR transcription factor binding profile databases revealed clusters of SMARCA4 binding sites upstream of several members of the major histocompatibility (MHC) class I and MHC class II genes. Mechanistically, we identified that PTBP1 induces SMARCA4 exon 30 retention leading to the full length transcript variant 1, which has lower affinity for HLA gene promoter regions. Significant up-regulation of HLA-A, HLA-B, HLA-DPA1, and HLA-DRA genes in CRIPSR-guided PTBP1KO TNBC cells was further demonstrated by either western blot or indirect immunofluorescence. Finally, a negative correlation between PTBP1 and HLA genes expression was also identified in multiple breast cancer gene expression datasets. Conclusions: This study suggests that alterations in the PTBP1-associated splicing programming lead to a reduction of the antigen presentation capability of TNBC cells. Due to the limited therapeutic alternatives for patients with TNBC, beyond chemotherapy, further understanding and modulation of this novel alteration may expand the applications of immunotherapy for patients with TNBC.

Citation Format: Bustos MA, Orozco JIJ, Salomon MP, Hoon DSB, Marzese DM. CRISPR/Cas9-guided editing of spliceosome factors enhances major histocompatibility complex proteins in triple-negative breast cancer [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P1-05-02.

Abstract P1-04-04: DNA methylation landscapes of breast cancer progression to brain metastasis: A pre-clinical study

Due to improvements in overall survival rates, breast cancer brain metastasis (BCBM) is a major life-limiting condition with rising incidence. The molecular mechanisms involved in breast cancer (BC) progression to brain metastasis are still poorly understood. We have demonstrated that DNA methylation, a key epigenetic regulatory mechanism, is involved in BC progression to metastatic disease. Here, we characterized the BCBM DNA methylation landscapes according to their molecular subtypes. Methods: This study included 22 BCBM specimens from 19 patients (ER+/PgR+/HER2-(n=6), HER2+(n=7), and ER-/PgR-/HER2-(TNBC; n=6)) and primary BC specimens with paired molecular subtypes. After microdissection, we generated genome-wide DNA methylomes using HM450K BeadChips. Results: Multidimensional scaling revealed that DNA methylation patterns specifically clustered BCBMs according to their respective molecular subtypes. Additionally, we observed that while ER+/PgR+/HER2- BCBM showed a significant global hypermethylation, HER2+ and TNBC BCBMs presented a significant global hypomethylation compared to the respective primary BC specimens. Hypermethylation on ER+/PgR+/HER2- BCBMs mainly affected CpG islands and was significantly enriched in regions overlapping tumor-related genes, such as APC2, CREB3L1, and GLI3; and a large number of developmental genes, including HOXA9, HOXA10, HOXB13, and PAX6 (Table1). On the other hand, hypomethylation on HER2+ and TNBC BCBMs significantly overlapped with conserved intergenic cis regulatory elements. Two significantly affected regions included enhancer elements associated with NEUROD1, a neurogenic differentiation factor, and MYT1L, a Pan-neural transcription factor associated with neuronal differentiation, suggesting an acquisition of brain-like properties (Table2). Conclusions: Our study suggests a significant role of DNA methylation reprogramming during BC progression to brain metastasis and describes the existence of molecular subtype-specific DNA methylomes. Altogether, this data offers new insight into the complexity of this clinical complication.

Table1: Hypermethylated CpG sites in ER+/PgR+/HER2- BCBMChrStartGeneCpG ContextDiff. MethFDR P-val1746802888HOXB13Island0.824.6E-061656666575MT1MIsland0.813.7E-101685160569IntergenicShelf0.773.7E-17742277807GLI3Island0.738.7E-0567728888BMP6Island0.713.1E-051811149470FAM38BIsland0.703.4E-081146317577CREB3L1Shore0.705.3E-17191467979APC2Island0.693.0E-05727213984HOXA10Island0.697.5E-061131826421PAX6Island0.677.4E-06727205381HOXA9Island0.651.7E-061396204854CLDN10Island0.642.1E-042176956678HOXD13Island0.632.3E-04

Table2: Hypomethylated CpG sites in HER2+ and TNBC BCBMsChrStartGeneCpG ContextDiff. Meth.FDR P-val1746619555IntergenicShore-0.583.2E-042182543233NEUROD1OpenSea-0.566.9E-0312132900938GALNT9Island-0.562.1E-051391827042IntergenicShore-0.558.7E-051746618614IntergenicShore-0.551.4E-0522119853MYT1LOpenSea-0.532.5E-041156623074BCANOpenSea-0.532.1E-0310128275008IntergenicOpenSea-0.521.6E-04480885981ANTXR2Island-0.515.2E-037157280331IntergenicShelf-0.516.9E-032059832924CDH4Shelf-0.512.7E-0241407858IntergenicIsland-0.513.7E-03592925721NR2F1Shore-0.513.1E-08

Citation Format: Orozco JIJ, Bustos MA, Nelson N, Hsu SC, Cheung G, Bostick PJ, Lucci A, DiNome M, Kelly DF, Hoon DSB, Marzese DM. DNA methylation landscapes of breast cancer progression to brain metastasis: A pre-clinical study [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 P1-04-04.

Lentivirus-induced 'Smart' dendritic cells: Pharmacodynamics and GMP-compliant production for immunotherapy against TRP2-positive melanoma

Monocyte-derived conventional dendritic cells (ConvDCs) loaded with melanoma antigens showed modest responses in clinical trials. Efficacy studies were hampered by difficulties in ConvDC manufacturing and low potency. Overcoming these issues, we demonstrated higher potency of lentiviral vector (LV)-programmed DCs. Monocytes were directly induced to self-differentiate into DCs (SmartDC-TRP2) upon transduction with a tricistronic LV encoding for cytokines (granulocyte macrophage colony stimulating factor (GM-CSF) and interleukin-4 (IL-4)) and a melanoma antigen (tyrosinase-related protein 2 (TRP2)). Here, SmartDC-TRP2 generated with monocytes from five advanced melanoma patients were tested in autologous DC:T cell stimulation assays, validating the activation of functional TRP2-specific cytotoxic T lymphocytes (CTLs) for all patients. We described methods compliant to good manufacturing practices (GMP) to produce LV and SmartDC-TRP2. Feasibility of monocyte transduction in a bag system and cryopreservation following a 24-h standard operating procedure were achieved. After thawing, 50% of the initial monocyte input was recovered and SmartDC-TRP2 self-differentiated in vitro, showing uniform expression of DC markers, detectable LV copies and a polyclonal LV integration pattern not biased to oncogenic loci. GMP-grade SmartDC-TRP2 expanded TRP2-specific autologous CTLs in vitro. These results demonstrated a simpler GMP-compliant method of manufacturing an effective individualized DC vaccine. Such DC vaccine, when in combination with checkpoint inhibition therapies, might provide higher specificity against melanoma.

Transcriptional repression of IFNβ1 by ATF2 confers melanoma resistance to therapy

The resistance of melanoma to current treatment modalities represents a major obstacle for durable therapeutic response, and thus, the elucidation of mechanisms of resistance is urgently needed. The crucial functions of Activating Transcription Factor-2 (ATF2) in the development and therapeutic resistance of melanoma have been previously reported, although the precise underlying mechanisms remain unclear. Here, we report a protein kinase C epsilon (PKCε)- and Activating Transcription Factor-2 (ATF2)-mediated mechanism that facilitates resistance by transcriptionally repressing the expression of IFNβ1 and downstream type-I IFN signaling, which is otherwise induced upon exposure to chemotherapy. Treatment of early stage melanomas expressing low levels of PKCε with chemotherapies relieves its transcriptional repression of IFNB1, resulting in impaired S-phase progression, a senescence-like phenotype, and increased cell death. This response is lost in late stage metastatic melanomas expressing high levels of PKCε. Notably, nuclear ATF2 and low expression of IFNβ1 in melanoma tumor samples correlates with poor patient responsiveness to biochemotherapy or neoadjuvant IFN-α2a. Conversely, cytosolic ATF2 and induction of IFNβ1 coincides with therapeutic responsiveness. Collectively, we identify an IFNβ1-dependent, cell autonomous mechanism that contributes to the therapeutic resistance of melanoma via the PKCε-ATF2 regulatory axis.

Epigenetic status of LINE-1 predicts clinical outcome in early-stage rectal cancer

BACKGROUND

We evaluated the clinical prognostic value of methylation of two non-coding repeat sequences, long interspersed element 1 (LINE-1) and Alu, in rectal tumour tissues. In addition to DNA methylation, expression of histone modifications H3K27me3 and H3K9Ac was studied in this patient cohort.

METHODS

LINE-1 and Alu methylation were assessed in DNA extracted from formalin-fixed paraffin-embedded tissues. A pilot (30 tumour and 25 normal tissues) and validation study (189 tumour and 53 normal tissues) were performed. Histone modifications H3K27me3 and H3K9Ac were immunohistochemically stained on tissue microarrays of the study cohort.

RESULTS

In early-stage rectal cancer (stage I-II), hypomethylation of LINE-1 was an independent clinical prognostic factor, showing shorter patient survival (P=0.014; HR: 4.6) and a higher chance of tumour recurrence (P=0.001; HR: 9.6). Alu methylation did not show any significant correlation with clinical parameters, suggesting an active role of LINE-1 in tumour development. Expression of H3K27me3 (silencing gene expression) and H3K9Ac (activating gene expression) in relation to methylation status of LINE-1 and Alu supported this specific role of LINE-1 methylation.

CONCLUSION

The epigenetic status of LINE-1, but not of Alu, is prognostic in rectal cancer, indicating an active role for LINE-1 in determining clinical outcome.

Assessment of DNA methylation status in early stages of breast cancer development

Background:

Molecular pathways determining the malignant potential of premalignant breast lesions remain unknown. In this study, alterations in DNA methylation levels were monitored during benign, premalignant and malignant stages of ductal breast cancer development.

Methods:

To study epigenetic events during breast cancer development, four genomic biomarkers (Methylated-IN-Tumour (MINT)17, MINT31, RARβ2 and RASSF1A) shown to represent DNA hypermethylation in tumours were selected. Laser capture microdissection was employed to isolate DNA from breast lesions, including normal breast epithelia (n=52), ductal hyperplasia (n=23), atypical ductal hyperplasia (n=31), ductal carcinoma in situ (DCIS, n=95) and AJCC stage I invasive ductal carcinoma (IDC, n=34). Methylation Index (MI) for each biomarker was calculated based on methylated and unmethylated copy numbers measured by Absolute Quantitative Assessment Of Methylated Alleles (AQAMA). Trends in MI by developmental stage were analysed.

Results:

Methylation levels increased significantly during the progressive stages of breast cancer development; P-values are 0.0012, 0.0003, 0.012, <0.0001 and <0.0001 for MINT17, MINT31, RARβ2, RASSF1A and combined biomarkers, respectively. In both DCIS and IDC, hypermethylation was associated with unfavourable characteristics.

Conclusion:

DNA hypermethylation of selected biomarkers occurs early in breast cancer development, and may present a predictor of malignant potential.

Aberrant hypermethylation in primary tumours and sentinel lymph node metastases in paediatric patients with cutaneous melanoma

BACKGROUND

Debate on how to manage paediatric patients with cutaneous melanoma continues, particularly in those with sentinel lymph node (SLN) metastases who are at higher risk of poor outcomes. Management is often based on adult algorithms, although differences in clinical outcomes between paediatric and adult patients suggest that melanoma in paediatric patients differs biologically. Yet, there are no molecular prognostic studies identifying these differences.

OBJECTIVES

We investigated the epigenetic (methylation) regulation of several tumour-related genes (TRGs) known to be significant in adult melanoma progression in histopathology(+) SLN metastases (n = 17) and primary tumours (n = 20) of paediatric patients with melanoma to determine their clinical relevance.

METHODS

Paediatric patients (n = 37; ≤ 21 years at diagnosis) with American Joint Committee on Cancer stage I-III cutaneous melanoma were analysed. Gene promoter methylation of the TRGs RASSF1A, RARβ2, WIF1 and APC was evaluated.

RESULTS

Hypermethylation of RASSF1A, RARβ2, WIF1 and APC was found in 29% (5/17), 25% (4/16), 25% (4/16) and 19% (3/16) of histopathology(+) SLNs, respectively. When matched to adult cutaneous melanomas by Breslow thickness and ulceration, hypermethylation of all four TRGs in SLN(+) paediatric patients with melanoma was equivalent to or less than in adults. With a median follow-up of 55 months, SLN(+) paediatric patients with melanoma with hypermethylation of > 1 TRG vs. ≤ 1 TRG had worse disease-free (P = 0·02) and overall survival (P = 0·02).

CONCLUSIONS

Differences in the methylation status of these TRGs in SLN(+) paediatric and adult patients with melanoma may account for why SLN(+) paediatric patients have different clinical outcomes. SLN biopsy should continue to be performed; within SLN(+) paediatric patients with melanoma, hypermethylation of TRGs can be used to identify a subpopulation at highest risk for poor outcomes who warrant vigilant clinical follow-up.

Immunity against breast cancer by TERT DNA vaccine primed with chemokine CCL21

Human telomerase reverse transcriptase (TERT) has been considered a potential tumor-associated antigen for active-specific immunotherapy. However, effective specific tumor antigen-specific immunity has been difficult to induce consistently by various TERT vaccine formulations. New adjuvant strategies have been employed, such as utilizing chemokines to attract T cells and antigen-presenting cells. Chemokine adjuvant strategies may enhance tumor antigen-specific immunity induced by vaccines. Therefore, we utilized chemokine ligand 21 (CCL21) as an adjuvant with a xenogeneic TERT DNA vaccine to induce tumor antigen-specific immunity against TERT-expressing breast cancer. The TERT DNA vaccine consisted of a plasmid containing the COOH terminal end of the TERT (cTERT) gene, encapsulated in multilayered liposomes with hemagglutinating virus of Japan coating. We demonstrated that CCL21 treatment before cTERT DNA vaccine, given intramuscularly, induced significantly higher anti-TERT specific cell-mediated immunity compared to cTERT DNA vaccine alone. Effective tumor antigen-specific immunity was shown both in prophylactic and therapeutic regimens against TS/A murine breast cancer. The study demonstrated that CCL21 administration before cTERT DNA vaccination significantly augmented tumor antigen-specific immunity against breast cancer.

Unfavourable prognosis associated with K-ras gene mutation in pancreatic cancer surgical margins

BACKGROUND

Despite intent to cure surgery with negative resection margins, locoregional recurrence is common in pancreatic cancer.

AIMS

To determine whether detection of K-ras gene mutation in the histologically negative surgical margins of pancreatic cancer reflects unrecognised disease.

PATIENTS

Seventy patients who underwent curative resection for pancreatic ductal adenocarcinoma were evaluated.

METHODS

All patients had surgical resection margins (pancreatic transection and retroperitoneal) that were histologically free of invasive cancer. DNA was extracted from these paraffin embedded surgical margins and assessed by quantitative real time polymerase chain reaction to detect the K-ras gene mutation at codon 12. Detection of K-ras mutation was correlated with standard clinicopathological factors.

RESULTS

K-ras mutation was detected in histologically negative surgical margins of 37 of 70 (53%) patients. A significant difference in overall survival was demonstrated between patients with margins that were K-ras mutation positive compared with negative (median 15 v 55 months, respectively; p = 0.0008). By univariate and multivariate analyses, detection of K-ras mutation in the margins was a significant prognostic factor for poor survival (hazard ratio (HR) 2.8 (95% confidence interval (CI) 1.5-5.3), p = 0.0009; and HR 2.8 (95% CI 1.4-5.5), p = 0.004, respectively).

CONCLUSIONS

Detection of cells harbouring K-ras mutation in histologically negative surgical margins of pancreatic cancer may represent unrecognised disease and correlates with poor disease outcome. The study demonstrates that molecular-genetic evaluation of surgical resection margins can improve pathological staging and prognostic evaluation of patients with pancreatic ductal adenocarcinoma.

Ultrastaging of early colon cancer using lymphatic mapping and molecular analysis

Approximately one-third of node-negative colon cancers will recur, possibly due to understaging and inadequate pathological examination of lymph nodes (LNs). We evaluated the sensitivity, accuracy and feasibility of staging based on lymphatic mapping, focused examination, and molecular analysis of the sentinel node (SN) in patients with primary colorectal carcinoma. Between 1996 and 2000, 100 patients with colon carcinoma (CRC) underwent lymphatic mapping immediately after peritumoral injection of 1.0 cc of isosulphan blue dye. All LNs in the CRC specimen were examined by routine haematoxylin and eosin (H&E) staining. Sentinel nodes were examined by step serial sectioning, cytokeratin immunohistochemistry (CK-IHC) and/or reverse transcriptase-polymerase chain reaction (RT-PCR) analysis in an attempt to identify occult micrometastatic disease. Lymphatic mapping was successful in 97% of the cases. There were 5 false-negative cases, predominately associated with T3/T4 tumours. Aberrant lymphatic drainage was identified in 8 patients (8%) altering the operative approach. 26 patients had H&E-positive LNs. In 74 patients who were node-negative by routine H&E, 18 (24%) had occult nodal micrometastases missed on routine H&E examination, but detected by focused analysis of the SN. RT-PCR analysis of the SN was performed in 40 patients, 26 of which were negative by H&E and CK-IHC. In 12/26 (46%) of these patients, there was additional evidence of micrometastatic disease. In this study, focused examination of the SN in conjunction with RT-PCR analysis identified micrometastatic disease in a significant number of node-negative patients. This may have important implications when selecting patients for adjuvant treatment protocols.

Protective immunization against melanoma by gp100 DNA-HVJ-liposome vaccine

DNA-based vaccine immunization effectively induces both humoral and cell-mediated immunity to antigens and can confer protection against numerous infectious diseases as well as some cancers. Human and mouse melanomas consistently express the tumor-associated antigen interacted with the melanogenesis pathway. Gp100 is immunogenic and has been shown to induce both antibody and cytotoxic T cell (CTL) responses in humans. To explore the potential use of DNA immunization to induce melanoma-specific immune responses, we assessed HVJ-AVE liposome incorporated with plasmid DNA encoding human gp100. The gp100 DNA vaccine was used in a mouse melanoma model to assess immunity against the B16 melanoma of C57BL/6 mice. Intramuscular injection of the DNA-HVJ-AVE liposomes induced both anti-gp100 antibody and CTL responses. Gp100 DNA-HVJ-AVE liposome immunization significantly delayed tumor development in mice challenged with B16 melanoma cells. Mice immunized with gp100 DNA-HVJ-AVE liposomes survived longer compared with control mice immunized with HVJ-AVE liposome alone. These results indicate that immunization with human gp100 DNA by HVJ-AVE liposomes can induce protective immunity against melanoma in this pre-clinical mouse model. This strategy may provide an effective approach for vaccine therapy with tumor-associated antigens against human melanoma.

Modulation of histamine type II receptors on CD8+ T cells by interleukin-2 and cimetidine

CD8+ T cells are known to play a major role in regulating immune functions under normal and disease conditions. In this study a radioligand binding assay was used to quantitate histamine type II (H2) receptors on activated T cells. The objective was to examine the expression of H2 receptors on T cells during activation with interleukin-2 (IL-2) and treatment with cimetidine. Activated suppressor T cells induced by concanavalin A+IL-2 showed a significant (p less than 0.01) increase in H2 receptors compared to the control nonactivated T cells. The T cells expressing the H2 receptors were identified as CD8+ cells; those among them that had an enhanced level of H2 receptors were identified as CD25+. Treatment of activated suppressor cells with the H2 receptor antagonist cimetidine at a concentration of 10(-5) M significantly reduced the number of H2 receptors. Suppressor cells induced by Con A+IL-2 were able to suppress both IgG and IgM production that was reversible with cimetidine. Incubation of lymphocytes with 50 U/ml IL-2 alone in 3-day culture significantly (p less than 0.005) enhanced H2 receptor expression. These studies demonstrate that activated suppressor T cells that are CD8+CD25+ have enhanced levels of H2 receptors and can be modulated by cimetidine.

A 6-thioguanine-resistant variant of the 13762 cell line which is no longer tumorigenic or metastatic

A 6-thioguanine resistant (TGR) variant of the highly tumorigenic and metastatic mammary adenocarcinoma cell line 13762 was obtained. This variant was no longer tumorigenic or metastatic in normal syngeneic rats but did grow as a primary tumor in irradiated animals. Our results suggest that the TGR cell line was rejected by an irradiation-sensitive immunological mechanism. Although the TGR cells produced primary tumors in irradiated animals, there was no evidence of the extensive metastasis seen with the 13762 cells. This apparent inability to metastasize was confirmed by injecting the TGR cells intravenously. Whereas the 13762 cells produced large numbers of metastatic lung foci, there was no evidence of lung metastasis with the TGR cells, even in irradiated animals. Revertant cells for the 6-thioguanine-resistant phenotype were still non-tumorigenic and non-metastatic in normal rats, suggesting that 6-thioguanine resistance is not associated with the altered tumorigenic phenotype. From the TGR variant, cell lines were selected with an increased ability to produce tumors in normal rats. Although some of these revertants were capable of producing limited lung metastases in normal animals, extensive metastases were always seen when the cells were injected into irradiated animals. Differences between the 13762 and the TGR variants were also found in their ability to produce plasminogen activator. The TGR cells released far less plasminogen activator in culture than the 13762 cells. This could be a contributing factor in their different metastatic potentials.