A high CD8 to FOXP3 ratio in the tumor stroma and expression of PTEN in tumor cells are associated with improved survival in non-metastatic triple-negative breast carcinoma

Background

Triple-negative mammary carcinoma (TNBC) is an aggressive breast cancer subtype associated with dismal prognosis. The interaction between the immune system and the cancer cells plays a crucial role in tumor development and progression. However, it is still unclear how each diverse cell of the immune system contributes to the prognosis of patients with breast cancer. In this study, we investigated how the cell composition of the immune cell infiltrated modifies the survival of patients with resected TNBC.

Methods

Retrospectively, we collected data from 76 patients diagnosed with non-metastatic TNBC with available tissue blocks for tissue micro-array (TMA) construction. The TMA was constructed using two cores from each tumor block. The expression of CD4, CD8, FOXP3, CD20, CD68, CD163, PD-1, PD-L1, PTEN and phospho-STAT1 was determined by immunohistochemistry.

Results

We observed that the inflammatory infiltrate in TNBC is enriched for M2 macrophages and T lymphocytes (CD4+, CD8+). PD-L1 expression in the stroma was associated with the percentage of TILs (p = 0.018) as, PD-L1 expression in the tumor was associated with the percentage of TILs (p = 0.049). We found a correlation between TILs and PD-L1 expression in stroma cells (p = 0.020) and in tumor cells (p = 0.027). In our cohort, we observed a trend for improved survival associated with higher CD8+ (p = 0.054) and CD4 +  (p = 0.082) cell counts, but the results were not statistically significant. Conversely, the expression of PTEN in tumor cells and a low number of FOXP3+ cells in tumor stroma were both associated with improved OS. The CD8 to FOXP3 ratio and the CD4 to FOXP3 ratio were associated with better OS as well, however, only the CD8 to FOXP3 ratio had its prognostic impact confirmed in the METABRIC TNBC cohort. There was no association between PD-L1 expression and OS.

Conclusion

TNBC tumor microenvironment is enriched for lymphocytes and macrophages. FOXP3 expression and the CD8 to FOXP3 ratio in the tumor stroma as well as the loss of PTEN expression in tumor cells are prognostic factors in non-metastatic TNBC.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12885-021-08636-4.

Abstract 2439: Transcriptome-wide polysome profiling of glioblastomas identifies molecular subgroups with impact in survival and treatment

Glioblastoma (GBM) is the most common primary brain malignancy in adults and one of the most aggressive cancers. While the genetic landscape of glioblastomas has been characterized, the identified molecular subgroups have so far had limited impact on prognosis and clinical practice. Translation of mRNA into proteins is a key mechanism governing gene expression and a node for convergence of signaling pathways frequently dysregulated in cancer. For example, in vitro, mTORC1 activity has been linked to selective translation of a subset of mRNAs including those encoding pro-proliferative and pro-survival proteins, commonly referred to mTORC1 sensitive translation. Thus, cancer may be associated with altered mRNA translation, leading to differences between the transcriptome and the proteome, which could underlie tumor-associated properties. Transcriptome-wide quantification of efficiently translated mRNAs, or the translatome can, in addition to increasing the knowledge on post-transcriptional dysregulation of gene expression, provide a better approximation of the tumor proteome, as compared to studies of transcriptomes, and identify patient subsets defined by altered mRNA translation. Herein, we used a recently developed transcriptome-wide polysome profiling for small samples approach to quantify efficiently translated mRNA from 37 human GBM samples. The resulting translatomes allowed classification into three molecular subgroups differing in survival. Group 1, which had a median survival of 5 months, was characterized by increased translation of mRNAs encoding components of the mTORC2 pathway, mitochondria and cilia. Group 2, with a median survival of 6.3 months, was characterized by augmented mTORC1 dependent translation despite low translation of mRNAs encoding mitochondria associated proteins together with increased translation of mRNAs encoding angiogenesis related proteins. In contrast, group 3 showed a relatively longer median survival of 21.1 months and was characterized by high translation of mRNAs encoding mitochondria associated proteins despite low mTORC1 dependent translation, as well as low translation of mRNAs encoding cilia and mTORC2 pathway associated proteins. Strikingly, these groups could not be defined using corresponding data originating from total RNA and thus do not match previous molecular classifications. These translation profiles suggest that distinct treatment regimens employing e.g. mitochondria inhibitors, mTOR inhibitors or anti-angiogenic agents may be effective in patient subsets defined by translation. In conclusion, although this study is limited in terms of the number of studied patients, our data support that that translatomes may define molecular subgroups of GBMs amendable to distinct therapeutic approaches. Funding support: FAPESP 2018/17796-6

Citation Format: Glaucia N. Hajj, Fernanda C. Lupinacci, Martin Roffe, Hermano M. Bellaro, Tiago G. Santos, Victor P. Andrade, Paulo Sanematsu, Rui M. Reis, Christian Oertlin, Laia M. Sanz, Vilma R. Martins, Ola Larsson. Transcriptome-wide polysome profiling of glioblastomas identifies molecular subgroups with impact in survival and treatment [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2439.

Abstract PS6-61: Survivin immunoexpression: An independent prognostic marker of recurrence in early-stage breast cancer

Survivin is a small protein member of the inhibitor of apoptosis protein family. Its expression occurs in G2/M phase of cell cycle, acting inhibiting apoptosis blocking caspases cascade directly or indirectly, and also controlling cell division. Survivin was found to be overexpressed in breast cancer, and its expression have been associated mostly with poor outcome. The aim of this case-control study was to evaluate the prognostic value of Survivin immunoexpression in early stage (pT1pN0 or pT2pN0) breast cancer. The study was conducted collecting data from 170 women with invasive breast carcinoma. The case group (n=57) and control group (n=113) consisted of patients with and without tumor recurrence, respectively. Immunohistochemical Tissue Microarray analyses were conducted to detect Survivin expression. In addition, molecular classification was done based on immunohistochemistry, and classic clinical and histological breast cancer variables were collected. The findings were submitted to the chi-square test and Fisher’s exact test, followed by multivariate analysis with multinomial logistic regression. The level of statistical significance was set at 5% (p<0.05). Median follow-up time was 6 years, ranging from 4 to 13 years. In the univariate analysis, patients with recurrence presented a higher histologic grade (p=0.005), percentage of tumor cells expressing survivin (p=0.006) and stronger immunostaining for this protein (p=0.021). In the multivariate analysis, stronger immunostaining for survivin (OR 1.850; p=0.023) and greater percentage of survivin expression (OR 2.290; p=0.016) persisted independently associated which higher rates of recurrence. Higher immunoexpression of survivin was independently associated with recurrence in early stage invasive breast tumors.

Multinomial logistic regression model. In the first model, variables with p <0.200 were used in order to highlight the first order factors independently associated with disease-free survival. In the second model, variables with a significant association in model 1 were excluded in order to highlight second order factors independently associated with disease-free survival. In the third model, there were no factors independently associated with disease-free survival.

Table 1 - Clinical-pathological characterization of the 170 cases of early stage breast cancer patients with and without recurrence.RecurrenceTotalNoYespAge≤ 55 years8658280,78650,6%51,3%49,1%> 55 years84552949,4%48,7%50,9%Histological subtypeDuctal158104540,24492,9%92,0%94,7%Lobular5502,9%4,4%,0%Others7434,1%3,5%5,3%StagespT1a7520,9024,1%4,4%3,5%pT1b2113812,4%11,5%14,0%pT1c65452038,2%39,8%35,1%pT277502745,3%44,2%47,4%Histological gradeI332850,00519,4%24,8%8,8%II75492644,1%43,4%45,6%III41192224,1%16,8%38,6%Ignored2117412,4%15,1%7,0%Breast surgeryMastectomy8557281,00050,0%50,4%49,1%Conservative85562950,0%49,6%50,9%Sentinel lymph node biopsyNo3220120,35318,82%17,7%18,2%Yes137934481,5%82,3%80,0%Ignored1010,6%0,0%1,8%ChemotherapyNo5135160,69730,0%31,0%28,1%Yes119784170,0%69,0%71,9%TrastuzumabNo156105510,76192,3%92,9%91,1%Yes13857,7%7,1%8,9%Hormone therapyNo2918110,58117,1%15,9%19,3%Yes141954682,9%84,1%80,7%

Table 2 - Patterns of Survivin expression in tumors of patients with breast cancer with and without recurrence.RecurrenceTotal**NoYespSubcellular localizationAbsent4220,9422,7%2,1%3,8%Cytoplasmic89573260,1%60,0%60,4%Nuclear2315815,5%15,8%15,1%Cytoplasmic and Nuclear32211121,6%22,1%20,8%IntensityAbsent4220,0212,7%2,1%3,8%Weak7353*2049,3%55,8%37,7%Moderate62382441,9%40,0%45,3%Strong927*6,1%2,1%13,2%Percentage of expression≤ 50%10977320,00673,6%81,1%60,4%> 50%39182126,4%18,9%39,6%*p<0,05** 22 patients (12,9%) of sample loss in tissue microarray.

Table 3 - Cox survival regression model of patients diagnosed and treated for invasive breast carcinoma.p-ValorAdjusted ORModel 1Histological grade*0,0072,108Survivin - intensity*0,0231,850Survivin - percentage of expression0,1001,876Breast cancer subtype classified by immunohistochemistry0,2631,126Model 2Survivin - percentage of expression*0,0162,290Breast cancer subtype classified by immunohistochemistry0,0931,170Model 3Breast cancer subtype classified by immunohistochemistry0,2411,107

Citation Format: Heloisa OM Belchior, Victor P Andrade, Marcos VA Lima, Maria do PSS Cunha, Monique BC Lemos, Paulo GB Silva, Isabelle JL Silva-Fernandes. Survivin immunoexpression: An independent prognostic marker of recurrence in early-stage 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 PS6-61.

Polysome-profiling in small tissue samples

Polysome-profiling is commonly used to study translatomes and applies laborious extraction of efficiently translated mRNA (associated with >3 ribosomes) from a large volume across many fractions. This property makes polysome-profiling inconvenient for larger experimental designs or samples with low RNA amounts. To address this, we optimized a non-linear sucrose gradient which reproducibly enriches for efficiently translated mRNA in only one or two fractions, thereby reducing sample handling 5-10-fold. The technique generates polysome-associated RNA with a quality reflecting the starting material and, when coupled with smart-seq2 single-cell RNA sequencing, translatomes in small tissues from biobanks can be obtained. Translatomes acquired using optimized non-linear gradients resemble those obtained with the standard approach employing linear gradients. Polysome-profiling using optimized non-linear gradients in serum starved HCT-116 cells with or without p53 showed that p53 status associates with changes in mRNA abundance and translational efficiency leading to changes in protein levels. Moreover, p53 status also induced translational buffering whereby changes in mRNA levels are buffered at the level of mRNA translation. Thus, here we present a polysome-profiling technique applicable to large study designs, primary cells and frozen tissue samples such as those collected in biobanks.

New Insights into the Role of Polybromo-1 in Prostate Cancer

The human protein Polybromo-1 (PBMR1/BAF180) is a component of the SWI/SNF chromatin-remodeling complex that has been reported to be deregulated in tumors. However, its role in prostate cancer (PCa) is largely unknown. In this study, we described the PBRM1 transcriptional levels and the protein expression/localization in tissues of PCa patients and in prostatic cell lines. Increased PBRM1 mRNA levels were found in PCa samples, when compared to benign disease, and were correlated with higher Gleason score. We also verified that only the nuclear localization of PBRM1 protein is correlated with a more aggressive disease and high Prostate-Specific Antigen (PSA) levels in tissue microarrays. Intriguing expression patterns of mRNA and protein were identified in the cell lines. Although PBRM1 protein was restricted to the nuclei, in tumor cell lines in non-neoplastic cells, it was also present in vesicular-like structures that were dispersed within the cytoplasm. We knocked-down PBRM1 in the castration-resistant PCa (CRPC) cell line PC-3 and we verified that PBRM1 promotes the expression of several markers of aggressiveness, including EpCAM, TGF-β, and N-Cadherin. Therefore, our data supported the hypothesis that PBRM1 displays a pivotal role in the promotion and maintenance of the malignant behavior of PCa, especially in CRPC.

Abstract A49: BRCA1 deficiency is a recurrent event in early onset triple-negative breast cancer (TNBC): A comprehensive analysis of germline mutations and somatic promoter methylation

Background: Triple-negative breast cancer (TNBC) is a breast cancer subtype that accounts for 15-20% of all breast cancer cases. TNBC treatment is challenging because it does not respond to conventional hormonal and available target therapies, which are effective in other subtypes, making systemic chemotherapy the mainstay treatment. Moreover, TNBC displays higher aggressiveness and distinct metastatic pattern compared to other breast tumors, resulting in worse prognosis and survival. We and others have identified high prevalence of BRCA1 germline mutation in TNBC. However, BRCA1 deficiency may also be caused by somatic gene promoter methylation among other mechanisms. BRCA1/2 deficiency may lead to impairment of DNA repair and tumor development. Hence, understanding the mechanisms of BRCA deficiency in driving this tumor subtype, in both hereditary and sporadic scenery, is of great clinical and biologic interest.

Methods: We included in this study TNBC samples unselected for age or family history and attending A. C. Camargo Cancer Center. Tumor tissues were screened for point mutation in BRCA1/2 using next-generation sequencing (NGS). Sanger sequencing was performed in both tumor and normal tissue/leucocyte for categorizing the pathogenic mutations in germline or somatic. Multiplex Ligation-dependent Probe Amplification (MLPA) was used to investigate BRCA1 copy number alterations (CNA) resulting from large rearrangements in tumor and leucocyte. Additionally, for BRCA1 gene silencing investigation a customized bisulfite NGS approach was performed to assess the BRCA1 promoter methylation in tumor tissue.

Results: Point mutations were screened in 131 TNBC tumor samples, detecting a total of 18 pathogenic mutations (13.7%)---16 (88.8%) in BRCA1 and 2 (11.2%) in BRCA2. No large rearrangement was detected by MLPA in tumor tissue or leucocyte. Mutations classified as germline accounted for the majority of the pathogenic mutations detected in tumor tissue (93.75% - 15/16)---81.25% (13/16) in BRCA1 and 12.5% (2/16) in BRCA2. Only one somatic mutation was detected (6.25% - 1/16) in BRCA1 gene. Considering early onset TNBC (≤40 year of age) the germline mutation rate increased to 25% (8/32), mainly in BRCA1 gene (22% - 7/32). BRCA1 promoter hypermethylation in tumor was detected in 20.6%, all in sporadic TNBC, with a slight increase to 28% in early onset cases. Ultimately, BRCA impairment by either constitutive or somatic events was identified in 34% (45/131) of the cases and was significantly more frequent in young women (56% in ≤40; 33% in 41-50; 23% in >50 year of age; p=0.007) and associated with better overall and disease-free survival rates in this group of patients.

Conclusions: We observed that a high number of the TNBC cases are hereditary and BRCA1-related, especially in young women. For the sporadic cases, BRCA1 gene silencing was also a recurrent event. Taken together, our data showed that BRCA1 impairment (either by germline mutation or somatic promoter hypermethylation) was present at high frequency in the early-onset cases and was associated with better survival for these patients. With the new treatment modalities including Poly (ADP-ribose) polymerase (PARP) inhibitors being investigated, our results shed light that a significant proportion of young women with TNBC might benefit from PARP-inhibitor and future investigation in this subject is warranted.

Citation Format: Rafael Canfield Brianese, Kivvi D. M. Nakamura, Fernanda G. S. R. Almeida, Rodrigo F. Ramalho, Elisa N. Ferreira, Bruna D. F. Barros, Maria N. C. Formiga, Victor P. Andrade, Vladmir C. C. Lima, Dirce M. Carraro. BRCA1 deficiency is a recurrent event in early onset triple-negative breast cancer (TNBC): A comprehensive analysis of germline mutations and somatic promoter methylation [abstract]. In: Proceedings of the AACR International Conference held in cooperation with the Latin American Cooperative Oncology Group (LACOG) on Translational Cancer Medicine; May 4-6, 2017; São Paulo, Brazil. Philadelphia (PA): AACR; Clin Cancer Res 2018;24(1_Suppl):Abstract nr A49.

Abstract A22: Stromal cell signature in luminal breast cancer associated with response to neoadjuvant chemotherapy

Background: In locally advanced breast cancer, neoadjuvant chemotherapy may reduce tumor dimension and allow breast-conserving surgeries. However, it is not yet possible to predict which patients will benefit from neoadjuvant chemotherapy, as some patients may not experience tumor reduction, especially in luminal tumor samples. Tumor behavior reflects an intense crosstalk between malignant and stromal cells; however, little importance has been placed on the influence of the stromal cell in tumor response to chemotherapy.

Objective: Our aim was to evaluate whether a stromal cell transcriptional signature might be associated with response to neoadjuvant anthracycline and taxane, in locally advanced luminal breast cancer, using a direct approach of stromal cell selection.

Methodology: Twenty-nine patients diagnosed with locally advanced luminal breast cancer received neoadjuvant chemotherapy (doxorubicin and cyclophosphamide followed by paclitaxel). Breast cancer slices were submitted to laser-capture microdissection (LCM) to select stromal cells. Total RNA from stromal enriched cells were isolated using Arcturus PicoPure RNA isolation (Life technologies) according to the manufacturer's protocol. Linearly amplified two-round RiboAmp HSPlus2-round and Low Input Quick Amp (Agilent Technologies) protocols were adapted to optimize the amplification for the small numbers of cells produced by LCM. The labelled cRNAs were hybridized onto the Sure Print G3 (8×60K, Agilent Technologies). After having washed the slides, the arrays were scanned with the Agilent Bundle Model B Microarray Scanner System (Agilent Technologies). Scanned image files were visually inspected for artifacts, and the fluorescence intensities were extracted and preprocessed with Agilent Feature Extraction software (v10.7.1) and to normalize the results geneSpring GX12.1 software (Agilent Technologies) was used. Expression levels were compared using MultiExperiment Viewer (MeV) software, applying significance analysis of microarrays (SAM). Gene set enrichment analysis (GSEA) was used to identify whether predefined gene sets might associate with gene expression differences between phenotypes (http://software.broadinstitute.org/gsea/index.jsp). This methodology makes it possible to detect situations where all genes, in a predefined set, change in a small but coordinated way.

Results: In estrogen receptor (ER) positive tumors, GSEA (FDR < 0.1) indicated that tumor down-staging was correlated with one KEGG gene set: antigen processing antigen presentation (comprehending CD74, CD8A, CD8B, and 9 molecules of HLA complex, among others) and with four Gene Ontology (GO) gene sets (biologic process), including one related with immune response: regulation of T cell activation (comprehending genes such as ZAP70, LCK, CD24, CD47, CD3E, among others).

Gene sets associated with tumor non-down-staging (GSEA FDR < 0.25) were KEGG gene set: extracellular cell matrix (ECM) receptor interaction (including 5 types of integrins, 6 collagens, 4 laminins, fibronectin 1, and trombospondin 1), as well as seven GO gene sets (biologic process): cell adhesion; cell recognition; embryonic development; (cellular component): cortical cytoskeleton; cell projection part; cell surface; cytosolic part.

Conclusion: A stromal signature associated with immune response in locally advanced luminal breast cancer may be associated with tumor down-staging following neoadjuvant chemotherapy. Financial Support: FAPESP 09/100088-7.

Citation Format: Maria Lucia H. Katayama, Rene A da Costa Vieira, Rosimeire A. Roela, Victor P. Andrade, Luiz Guilherme C. A. de Lima, Giselly Encinas, Ligia M. Kerr, Simone Maistro, M. Mitzi Brentani, Maria A. A. Koike Folgueira. Stromal cell signature in luminal breast cancer associated with response to neoadjuvant chemotherapy [abstract]. In: Proceedings of the AACR International Conference held in cooperation with the Latin American Cooperative Oncology Group (LACOG) on Translational Cancer Medicine; May 4-6, 2017; São Paulo, Brazil. Philadelphia (PA): AACR; Clin Cancer Res 2018;24(1_Suppl):Abstract nr A22.

Pleomorphic lobular carcinoma in situ of the breast: a single institution experience with clinical follow-up and centralized pathology review

PURPOSE

The natural history of pleomorphic lobular carcinoma in situ (PLCIS) remains largely unknown.

METHODS

A pathology database search (1995-2012) was performed to identify patients diagnosed with an LCIS variant. Patients with synchronous breast cancer and/or no evidence of pleomorphism were excluded. Original slides were re-evaluated by three pathologists to identify a consensus cohort of PLCIS. Borderline lesions with focal atypia were classified as LCIS with pleomorphic features (LCIS-PF). Clinical data were obtained from medical records.

RESULTS

From 233 patients, we identified 32 with an LCIS variant diagnosis and no concurrent breast cancer. Following review, 16 cases were excluded due to lack of pleomorphism. The remaining 16 were classified as PLCIS (n = 11) and LCIS-PF (n = 5). 12/16 patients were treated with surgical excision ± chemoprevention. Patients with a prior breast cancer history and those having mastectomy were excluded from outcome analysis. Among the remaining 7 patients with PLCIS/LCIS-PF, 4/7 (57%) developed ipsilateral breast cancer at a median follow-up of 67 months. Median age at the time of breast cancer diagnosis was 56 years old and median time from PLCIS/LCIS-PF to cancer diagnosis was 59 months (range 45-66 months). The four cancers included 1 invasive lobular carcinoma (ILC), 1 microinvasive ILC, 1 invasive ductal carcinoma, and 1 ductal carcinoma in situ.

CONCLUSIONS

We confirm that PLCIS in isolation is indeed a rare entity, further contributing to the difficulty in determining the actual risk conferred by this lesion. Long-term follow-up data on larger cohorts are needed to define standardized management and outcomes for patients with PLCIS.

Abstract B38: Tumor heterogeneity evaluation in glioblastomas using microarray of polysomal mRNAs

Glioblastoma is the most common primary brain malignancy in adults and one of the most aggressive cancers. The overall treatment outcome of this tumor type remains unsatisfactory even though advanced multimodal treatments including surgery, chemotherapy, and radiotherapy have been available for decades. The median survival of patients is typically less than 2 years. Insights into the genetic landscape of glioblastomas have been achieved by high-throughput studies and patterns of gene expression have been able to identify molecular subgroups with putative prognostic or predictive significance. However, this approach provides little information about protein expression levels, since the expression of mRNAs do not necessarily reflect the levels of proteins. In addition, the establishment of molecular subgroups is compounded by the endemic problem of tumor heterogeneity, since subtype classifiers are variably expressed across individual cells within a tumor and the impact of sampling bias has not been addressed. More importantly, the relationships between different sources of intratumoral heterogeneity—genetic, transcriptional and functional—remain obscure. Thus, to evaluate such intratumoral heterogeneity is fundamental to demonstrate potential therapeutic targets, source of tumor recurrences and potential prognostic implications. Herein, we evaluated a specific transcriptomic and translatomic signature of the glioblastoma heterogeneity at the single-patient level. We performed a sampling of 8 pieces from a single glioblastoma tumor. The samples could be histologically classified as high or low grade and total and polysomal mRNA was isolated and identified by microarray. By comparing histologically high vs low grade tumors we were able to identify 42 differentially transcribed and 138 differentially translated genes. Among the differentially translated genes validated by qPCR there are many related to proliferation, development and cancer, such as FOXC1, HOXB5, SNAI2, LOX, WISP1, ITGA11 and COL5A2. Thus, our results demonstrate that the isolation of mRNA engaged in translation can be used to identify biomarkers of tumor progression, leading to new therapeutic approaches. In addition, we reveal previously unappreciated heterogeneity in diverse regulatory programs central to glioblastoma biology, prognosis, and therapy.

Ethical approval: 1775/13. Funding support: FAPESP 2013/03315-2, 2014/15550-9

Citation Format: Fernanda C. S. Lupinacci, Hermano M. Bellato, Martin Roffe, Hellen Kuasne, Tiago G. Santos, Victor P. Andrade, Paulo Sanematsu, Jr., Vilma R. Martins, Silvia R. Rogatto, Glaucia N M Hajj. Tumor heterogeneity evaluation in glioblastomas using microarray of polysomal mRNAs. [abstract]. In: Proceedings of the AACR Special Conference on Translational Control of Cancer: A New Frontier in Cancer Biology and Therapy; 2016 Oct 27-30; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2017;77(6 Suppl):Abstract nr B38.

Abstract 2389: Microarray analysis of polysome-associated mRNAs from different regions of the same human glioblastoma reveals intratumoral heterogeneity

Glioblastoma is among the most aggressive tumor type and less responsive to chemotherapeutic agents, thus a better understanding of the behavior of these tumors may help to develop new treatments for this disease. Currently, many genome-wide projects attempt to define general patterns of gene expression based on deep sequencing or microarray data from total mRNA populations. However, this approach provides little information about the molecular mediators of tumor biology, because the expression levels of mRNAs do not necessarily reflect the levels of proteins. The identification of mRNAs target of translational alterations in tumors can show gene expression profiles that better reflect the population of proteins. In this work we were able to identify mRNAs differentially translated in a human glioblastoma that presented histologically different parts. The sample was divided in 8 pieces that were classified as high or low grade based on histological characteristics. Actively translating ribosomes and their associated mRNAs were isolated biochemically through a polysomal profile. Total and polysomal mRNA was then extracted and submitted to a microarray analysis. By comparing high vs low grade tumor pieces, we were able to identify more differentially translated genes (138 genes) than differentially expressed genes (43 genes). Among the differentially translated mRNAs, there are many related to proliferation, development and cancer. By Integrated Pathway Analysis, we identified the TGF-β pathway among the the most relevant for grade progression. Thus, the technique of isolating mRNAs engaged in translation can be used to identify biomarkers of tumor progression, leading to new therapeutic approaches.

Citation Format: Glaucia N. Hajj, Fernanda S. Lupinacci, Martín Roffé, Hellen Kuasne, Tiago G. Santos, Victor P. Andrade, Paulo Sanematsu, Vilma R. Martins, Silvia R. Rogatto. Microarray analysis of polysome-associated mRNAs from different regions of the same human glioblastoma reveals intratumoral heterogeneity. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 2389.

Clonal relationships between lobular carcinoma in situ and other breast malignancies

Background

Recent evidence suggests that lobular carcinoma in situ (LCIS) can be a clonal precursor of invasive breast cancers of both the ductal and lobular phenotypes. We sought to confirm these findings with an extensive study of fresh frozen breast specimens from women undergoing mastectomy.

Methods

Patients with a history of LCIS presenting for therapeutic mastectomy were identified prospectively. Frozen tissue blocks were collected, screened for lesions of interest, and subjected to microdissection and DNA extraction. Copy number profiling, whole-exome sequencing, or both were performed. Clonal relatedness was assessed using specialized statistical techniques developed for this purpose.

Results

After exclusions for genotyping failure, a total of 84 lesions from 30 patients were evaluated successfully. Strong evidence of clonal relatedness was observed between an LCIS lesion and the invasive cancer for the preponderance of cases with lobular carcinoma. Anatomically distinct in situ lesions of both ductal and lobular histology were also shown to be frequently clonally related.

Conclusions

These data derived from women with LCIS with or without invasive cancer confirm that LCIS is commonly the clonal precursor of invasive lobular carcinoma and that distinct foci of LCIS frequently share a clonal origin, as do foci of LCIS and ductal carcinoma in situ.

Electronic supplementary material

The online version of this article (doi:10.1186/s13058-016-0727-z) contains supplementary material, which is available to authorized users.

ROBO1 deletion as a novel germline alteration in breast and colorectal cancer patients

Despite one third of breast (BC) and colorectal cancer (CRC) cases having a hereditary component, only a small proportion can be explained by germline mutations. The aim of this study was to identify potential genomic alterations related to cancer predisposition. Copy number variations (CNVs) were interrogated in 113 unrelated cases fulfilling the criteria for hereditary BC/CRC and presenting non-pathogenic mutations in BRCA1, BRCA2, MLH1, MSH2, TP53, and CHEK2 genes. An identical germline deep intronic deletion of ROBO1 was identified in three index patients using two microarray platforms (Agilent 4x180K and Affymetrix CytoScan HD). The ROBO1 deletion was confirmed by quantitative PCR (qPCR). Six relatives were also evaluated by CytoScan HD Array. Genomic analysis confirmed a co-segregation of the ROBO1 deletion with the occurrence of cancer in two families. Direct sequencing revealed no pathogenic ROBO1 point mutations. Transcriptomic analysis (HTA 2.0, Affymetrix) in two breast carcinomas from a single patient revealed ROBO1 down-expression with no splicing events near the intronic deletion. Deeper in silico analysis showed several enhancer regions and a histone methylation mark in the deleted region. The ROBO1 deletion in a putative transcriptional regulatory region, its down-expression in tumor samples, and the results of the co-segregation analysis revealing the presence of the alteration in affected individuals suggest a pathogenic effect of the ROBO1 in cancer predisposition.

Targeted capture massively parallel sequencing analysis of LCIS and invasive lobular cancer: Repertoire of somatic genetic alterations and clonal relationships

PURPOSE

Lobular carcinoma in situ (LCIS) has been proposed as a non-obligate precursor of invasive lobular carcinoma (ILC). Here we sought to define the repertoire of somatic genetic alterations in pure LCIS and in synchronous LCIS and ILC using targeted massively parallel sequencing.

METHODS

DNA samples extracted from microdissected LCIS, ILC and matched normal breast tissue or peripheral blood from 30 patients were subjected to massively parallel sequencing targeting all exons of 273 genes, including the genes most frequently mutated in breast cancer and DNA repair-related genes. Single nucleotide variants and insertions and deletions were identified using state-of-the-art bioinformatics approaches.

RESULTS

The constellation of somatic mutations found in LCIS (n = 34) and ILC (n = 21) were similar, with the most frequently mutated genes being CDH1 (56% and 66%, respectively), PIK3CA (41% and 52%, respectively) and CBFB (12% and 19%, respectively). Among 19 LCIS and ILC synchronous pairs, 14 (74%) had at least one identical mutation in common, including identical PIK3CA and CDH1 mutations. Paired analysis of independent foci of LCIS from 3 breasts revealed at least one common mutation in each of the 3 pairs (CDH1, PIK3CA, CBFB and PKHD1L1).

CONCLUSION

LCIS and ILC have a similar repertoire of somatic mutations, with PIK3CA and CDH1 being the most frequently mutated genes. The presence of identical mutations between LCIS-LCIS and LCIS-ILC pairs demonstrates that LCIS is a clonal neoplastic lesion, and provides additional evidence that at least some LCIS are non-obligate precursors of ILC.

Lobular Carcinoma in Situ: A 29-Year Longitudinal Experience Evaluating Clinicopathologic Features and Breast Cancer Risk

PURPOSE

The increased breast cancer risk conferred by a diagnosis of lobular carcinoma in situ (LCIS) is poorly understood. Here, we review our 29-year longitudinal experience with LCIS to evaluate factors associated with breast cancer risk.

PATIENTS AND METHODS

Patients participating in surveillance after an LCIS diagnosis are observed in a prospectively maintained database. Comparisons were made among women choosing surveillance, with or without chemoprevention, and those undergoing bilateral prophylactic mastectomies between 1980 and 2009.

RESULTS

One thousand sixty patients with LCIS without concurrent breast cancer were identified. Median age at LCIS diagnosis was 50 years (range, 27 to 83 years). Fifty-six patients (5%) underwent bilateral prophylactic mastectomy; 1,004 chose surveillance with (n = 173) or without (n = 831) chemoprevention. At a median follow-up of 81 months (range, 6 to 368 months), 150 patients developed 168 breast cancers (63% ipsilateral, 25% contralateral, 12% bilateral), with no dominant histology (ductal carcinoma in situ, 35%; infiltrating ductal carcinoma, 29%; infiltrating lobular carcinoma, 27%; other, 9%). Breast cancer incidence was significantly reduced in women taking chemoprevention (10-year cumulative risk: 7% with chemoprevention; 21% with no chemoprevention; P < .001). In multivariable analysis, chemoprevention was the only clinical factor associated with breast cancer risk (hazard ratio, 0.27; 95% CI, 0.15 to 0.50). In a subgroup nested case-control analysis, volume of disease, which was defined as the ratio of slides with LCIS to total number of slides reviewed, was also associated with breast cancer development (P = .008).

CONCLUSION

We observed a 2% annual incidence of breast cancer among women with LCIS. Common clinical factors used for risk prediction, including age and family history, were not associated with breast cancer risk. The lower breast cancer incidence in women opting for chemoprevention highlights the potential for risk reduction in this population.

Abstract 2971: Whole exome sequencing reveals heterogeneity within lobular carcinoma in situ (LCIS) and clonal selection in the progression to malignant lesions

INTRODUCTION: Lobular carcinoma in situ (LCIS) is considered both a risk factor and non-obligate precursor of low-grade estrogen receptor-positive breast cancer. We sought to define the mutational repertoire, subclone complexity and heterogeneity of LCIS, and whether invasive lobular carcinomas (ILCs) would stem from specific subclones within a LCIS.

METHODS: Patients with a history of LCIS undergoing therapeutic or prophylactic mastectomy were prospectively enrolled in an IRB approved protocol. Frozen tissue blocks were collected, screened for lesions of interest (LCIS, ductal carcinoma in situ (DCIS), ILC, invasive ductal carcinoma (IDC)) and subject to microdissection and DNA extraction. Matched germline DNA was available for all cases. Whole exome sequencing was performed on a HiSeq2000 (Illumina) and data were aligned to the reference human genome hg19 and processed using GATK. SNVs were called using MuTect, and indels were called using a combination of Varscan and Strelka. Purity and ploidy estimates were calculated by ABSOLUTE. Clonal frequencies were estimated using Pyclone.

RESULTS: 30 LCIS, 10 ILCs, 6 IDCs and 7 DCIS from 15 patients qualified for data analysis, resulting in 18 LCIS-ILC pairs, 22 LCIS-LCIS pairs, 12 LCIS-DCIS pairs, and 14 LCIS-IDC pairs for comparison. 9/18 (50%) LCIS-ILC pairs and 8/22 (36%) LCIS-LCIS pairs were clonally related, supported by several shared mutations (median 18, range 7-81 for LCIS-ILC; median 14, range 5-22 for LCIS-LCIS). All related LCIS-ILC pairs and 6/8 related LCIS-LCIS pairs shared a pathogenic CDH1 mutation; 75% of related LCIS-ILC pairs also shared a PIK3CA hotspot mutation. 7/12 (58%) LCIS-DCIS pairs were found to be clonally related but the number of shared mutations was generally lower than that found in LCIS-ILC pairs (median 9, range 2-11). No evidence of a clonal relationship was found in any of the LCIS-IDC pairs tested. Clonal composition analysis revealed that samples of LCIS display intra-lesion genetic heterogeneity in the form of the presence of a minor clone in 70% of cases. In one case, the LCIS minor subclone (∼15%) constituted the major clone in the ILC and in another case the LCIS minor subclone constituted the major clone in the associated DCIS. The majority of the clonally related lesions were located in the same quadrant of the breast, however evidence of clonality was found in 5 LCIS-LCIS and 3 LCIS-DCIS pairs located in separate quadrants of the breast.

CONCLUSIONS: Intra-lesion genetic heterogeneity is a common phenomenon in LCIS. The dominant clone of a LCIS may not always be the clone directly involved in the progression to malignancy. The spatial relationships of clonally related lesions in this study suggest that anatomy does not always infer clonality, as lesions located in separate quadrants of the breast may be clonally related.

Citation Format: Michail Schizas, Rita A. Sakr, Britta Weigelt, Charlotte KY Ng, Jose Victor S. Carniello, Dilip Giri, Salvatore Piscuoglio, Luciano G. Martelotto, Russell Towers, Victor P. Andrade, Raymond Lim, David B. Solit, Jorge S. Reis-Filho, Tari A. King. Whole exome sequencing reveals heterogeneity within lobular carcinoma in situ (LCIS) and clonal selection in the progression to malignant lesions. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 2971. doi:10.1158/1538-7445.AM2015-2971

Gene expression profiling of lobular carcinoma in situ reveals candidate precursor genes for invasion

PURPOSE

Lobular carcinoma in situ (LCIS) is both a risk indicator and non-obligate precursor of invasive lobular carcinoma (ILC). We sought to characterize the transcriptomic features of LCIS and ILC, with a focus on the identification of intrinsic molecular subtypes of LCIS and the changes involved in the progression from normal breast epithelium to LCIS and ILC.

METHODS

Fresh-frozen classic LCIS, classic ILC, and normal breast epithelium (N) from women undergoing prophylactic or therapeutic mastectomy were prospectively collected, laser-capture microdissected, and subjected to gene expression profiling using Affymetrix HG-U133A 2.0 microarrays.

RESULTS

Unsupervised hierarchical clustering of 40 LCIS samples identified 2 clusters of LCIS distinguished by 6431 probe sets (p < 0.001). Genes identifying the clusters included proliferation genes and other genes related to cancer canonical pathways such as TGF beta signaling, p53 signaling, actin cytoskeleton, apoptosis and Wnt-Signaling pathway. A supervised analysis to identify differentially expressed genes (p < 0.001) between normal epithelium, LCIS, and ILC, using 23 patient-matched triplets of N, LCIS, and ILC, identified 169 candidate precursor genes, which likely play a role in LCIS progression, including PIK3R1, GOLM1, and GPR137B. These potential precursor genes map significantly more frequently to 1q and 16q, regions frequently targeted by gene copy number alterations in LCIS and ILC.

CONCLUSION

Here we demonstrate that classic LCIS is a heterogeneous disease at the transcriptomic level and identify potential precursor genes in lobular carcinogenesis. Understanding the molecular heterogeneity of LCIS and the potential role of these potential precursor genes may help personalize the therapy of patients with LCIS.

PI3K pathway activation in high-grade ductal carcinoma in situ--implications for progression to invasive breast carcinoma

PURPOSE

To assess the prevalence of phosphoinositide 3-kinase (PI3K) pathway alterations in pure high-grade ductal carcinoma in situ (DCIS) and DCIS associated with invasive breast cancer (IBC), and to determine whether DCIS and adjacent IBCs harbor distinct PI3K pathway aberrations.

EXPERIMENTAL DESIGN

Eighty-nine cases of pure high-grade DCIS and 119 cases of high-grade DCIS associated with IBC were characterized according to estrogen receptor (ER) and HER2 status, subjected to immunohistochemical analysis of PTEN, INPP4B, phosphorylated (p)AKT and pS6 expression, and to microdissection followed by Sequenom genotyping of PIK3CA and AKT1 hotspot mutations.

RESULTS

Alterations affecting the PI3K pathway were found in a subset of pure DCIS and DCIS adjacent to IBC. A subtype-matched comparison of pure DCIS and DCIS adjacent to IBC revealed that PIK3CA hotspot mutations and pAKT expression were significantly more prevalent in ER-positive/HER2-negative DCIS adjacent to IBC (P values, 0.005 and 0.043, respectively), and that in ER-negative/HER2-positive cases INPP4B loss of expression was more frequently observed in pure DCIS (a P value of 0.013). No differences in the parameters analyzed were observed in a pairwise comparison of the in situ and invasive components of cases of DCIS and adjacent IBC. Analysis of the PIK3CA-mutant allelic frequencies in DCIS and synchronous IBC revealed cases in which PIK3CA mutations were either restricted to the DCIS or to the invasive components.

CONCLUSION

Molecular aberrations affecting the PI3K pathway may play a role in the progression from high-grade DCIS to IBC in a subset of cases (e.g., a subgroup of ER-positive/HER2-negative lesions).

Abstract PD05-02: Novel mutations in lobular carcinoma in situ (LCIS) as uncovered by targeted parallel sequencing

Background: LCIS has traditionally been recognized as a marker of increased risk for the subsequent development of breast cancer, of either the lobular or ductal phenotype, yet due to the incidental nature of LCIS little is known about its underlying biology. Here we describe the first report of novel mutations in LCIS using targeted exome sequencing of fresh frozen tissue samples.

Methods: Fresh frozen tissue samples from patients with a prior history of LCIS undergoing therapeutic or risk-reducing mastectomy from 2003–08 were harvested and systematically reviewed to identify LCIS. Cells from individual LCIS lesions +/− associated cancers were collected by laser capture microdissection. For the purposes of this study, germline DNA (blood) and DNA from 12 unique LCIS lesions were subject to targeted parallel sequencing of exons corresponding to 230 cancer genes using the Illumina HiSeq 2000 platform. DNA from an associated ductal carcinoma in situ (DCIS) and/or an invasive ductal (IDC) or lobular (ILC) lesion was also available for 7 of these cases resulting in 41 samples from 12 pts for mutational analysis. Normalized (RMA) Affymetrix U133A gene expression data were also available.

Results: DNA profiling reliably identified 7 somatic mutations in 5/12 LCIS samples (41.7%). Of these, 4/7 mutations were base substitutions (missense mutations); and the others included: 1 deletion; 1 silent and 1 splice-site mutation. Mutations in LCIS were identified in 5/230 cancer genes analyzed, including: PIK3CA, CDH1, NOTCH4, PREX2 and ARAF. PIK3CA and CDH1 mutations were each identified in two samples, representing 4/7 (57.1%) mutations. Specific mutations found in LCIS and their frequencies are listed (table). Among 3 LCIS-ILC pairs, one shared the G914R mutation in PIK3CA, and 1/3 LCIS-IDC pairs exhibited an identical point mutation (R373W) in the NOTCH4 gene. No shared mutations were observed in 3 LCIS-DCIS pairs. Both CDH1 mutated cases were associated with decreased e-cadherin mRNA levels when compared to non-mutated cases (mean 9.88 vs 11.01), as was the NOTCH4 mutation (mean 6.02 vs 6.47). Mutations in ARAF and PREX2 were associated with increased mRNA levels, mean 7.07 vs 6.52 and 4.82 vs 4.22, respectively. The hotspot PIK3CA mutation (E545K) was also associated with increased gene expression (mean 5.15 vs 4.64) whereas the G914R mutant was associated with decreased expression (mean 4.13 vs 4.64).

Pleomorphic lobular carcinoma in situ: A distinct entity of controversial significance

177

Background: Pleomorphic lobular carcinoma in situ (PLCIS) is an increasingly diagnosed variant of lobular carcinoma in situ. Histologically, it resembles ductal carcinoma in situ (DCIS), leading to controversy over proper management. Yet, the natural history of PLCIS is unknown. Here we describe our experience with PLCIS. Methods: Review of pathology reports (1995–2012) identified 233 cases of LCIS variants. Patients with synchronous ipsilateral DCIS or invasive cancer (IC) were excluded leaving 25 cases for review. Consensus review by 3 pathologists further excluded 7; leaving 18 cases, 12 of which were classified as PLCIS and 6 as LCIS with pleomorphic features (LCIS-PF). (Table) PLCIS was defined by cellular dyshesion, nuclear pleomorphism with a 2-3 fold size variation, conspicuous nucleoli, mitoses and abundant cytoplasm; lesions not meeting all parameters were classified as LCIS-PF. Loss of e-cadherin was confirmed; clinical data were obtained from medical records. Results: Mean patient age at diagnosis of PLCIS/LCIS-PF was 57 yrs (42-67 yrs). All cases presented with imaging abnormalities. A previous history of breast cancer was present in 7/18 (39%) pts (3/7, ipsilateral; 4/7, contralateral). Following PLCIS/LCIS-PF diagnosis, 6/18 (33%) pts underwent mastectomy and 12/18 had excision alone, with (n=3) or without chemoprevention (n=9). Margin status was negative in 4/12 pts; close in 3/12 pts and positive in 5/12 pts undergoing excision. At a median follow-up of 27 mos (2-148 mos), 2/12 pts treated with excision developed ipsilateral breast cancer (1 DCIS; 1 IC). Both had close margins at initial excision; median time to cancer, 54 mos. Conclusions: Pure PLCIS is an uncommon lesion. Synchronous malignancy or prior history of breast cancer are often present in patients with PLCIS, contributing to the difficulty in determining the actual risk conferred by this lesion and appropriate management. Efforts to systematically characterize LCIS variants and prospective documentation of outcomes are needed to clarify the significance of these lesions. [Table: see text]

Clonal relatedness between lobular carcinoma in situ and synchronous malignant lesions

INTRODUCTION

Lobular carcinoma in situ (LCIS) has been accepted as a marker of risk for the development of invasive breast cancer, yet modern models of breast carcinogenesis include LCIS as a precursor of low-grade carcinomas. We provide evidence favoring a clonal origin for LCIS and synchronous estrogen receptor-positive malignant lesions of the ductal and lobular phenotype.

METHODS

Patients with prior LCIS undergoing mastectomy were identified preoperatively from 2003 to 2008. Specimens were widely sampled, and frozen blocks were screened for LCIS and co-existing malignant lesions, and were subject to microdissection. Samples from 65 patients were hybridized to the Affymetrix SNP 6.0 array platform. Cases with both an LCIS sample and an associated ductal carcinoma in situ (DCIS) or invasive tumor sample were evaluated for patterns of somatic copy number changes to assess evidence of clonal relatedness.

RESULTS

LCIS was identified in 44 of the cases, and among these a DCIS and/or invasive lesion was also identified in 21 cases. A total of 17 tumor pairs had adequate DNA/array data for analysis, including nine pairs of LCIS/invasive lobular cancer, four pairs of LCIS/DCIS, and four pairs of LCIS/invasive ductal cancer. Overall, seven pairs (41%) were judged to be clonally related; in five (29%) evidence suggested clonality but was equivocal, and five (29%) were considered independent. Clonal pairs were observed with all matched lesion types and low and high histological grades. We also show anecdotal evidence of clonality between a patient-matched triplet of LCIS, DCIS, and invasive ductal cancer.

CONCLUSION

Our results support the role of LCIS as a precursor in the development of both high-grade and low-grade ductal and lobular cancers.

Abstract 4168: Akt pathway in human breast cancer: A comparison between estrogen positive and estrogen negative tumors using reverse phase protein array

INTRODUCTION: Estrogen receptor status is crucial for breast cancer treatment planning. Some estrogen receptor (ER) negative tumors carry a worse prognosis and lack more specific therapies. The AKT pathway is a promising target in breast cancer and was reported hyper activated in ER- tumors cells using in vitro models. We aimed to compare the level of Akt pathway activation between ER+ and ER- tumors using frozen human breast tumor samples. METHODS: 40 cases of breast cancer (20 ER+, 20 ER-) were identified from the frozen tumor bank. Patients were between 40 and 70 years old, with Stage I or II, node negative disease. About 20.000 cells from each tumor cells were purified by laser capture microdissection (LCM) and the protein lysate applied to the Reverse Phase Protein Array (RPPA). Antibodies tested by RPPA included Src, p-Src, Akt, p-Akt Thr308, p-Akt Ser473, mTOR, p-mTOR, PDGFRα, p-PDGFRα Tyr751. We also compared these results to patient matched non-microdissected samples and to immunohistochemistry (IHQ) using digital quantification. RESULTS: 6 out of 9 antibodies showed higher mean expression in ER- negative tumors but only p-Src had statistically significant different levels (0.043). The coordinated high levels (above median) of p-Src/p-Akt/p-mTOR was observed in 1 (5%) of ER+ and in 8 (40%) of ER- tumors. All 8 cases from the ER- group were triple negative (ER-/PR-/Her2-). Correlation coeficients of LCM-RPPA samples and non-microdissected/RPPA samples varied from 0.02 to 0.47. Only p-Akt Ser473 showed a significant correlation (r=0.47, p=0.003). Correlation coeficients between LCM-RPPA and IHQ for antibodies Akt, p-Akt and mTOR were 0.03, –0.22 and 0.05, respectively. CONCLUSION: Protein quantification using LCM-RPPA in human breast tumors is feasible and can detect significant differences between ER+ and ER- tumors. Triple negative tumors showed a high Akt pathway activation profile compared to ER+ tumors. Triple negative tumors are more likely to benefit from targeted therapies directed against the Akt pathway. LCMed and non-LCMed matching samples analyzed by RPPA showed discrepant results. The same happened to the comparison between LCM-RPPA and IHQ with digital quantification.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 4168. doi:1538-7445.AM2012-4168

Cadherin-catenin complex dissociation in lobular neoplasia of the breast

E-cadherin (E-CD) inactivation with loss of E-CD-mediated cell adhesion is the hallmark of lesions of the lobular phenotype. E-CD is typically absent by immunohistochemistry in both lobular carcinoma in situ (LCIS) and invasive lobular lesions, suggesting it occurs early in the neoplastic process. In laboratory models, downstream post-transcriptional modifiers such as TWIST and SNAIL contribute to the dissociation of the intracellular component of the cadherin-catenin complex (CCC), resulting in tumor progression and invasion. We hypothesized that complete CCC dissociation may play a role in lobular neoplasia progression. Here we explore the relationship between loss of E-CD and dissociation of the CCC in pure LCIS and LCIS associated with invasive cancer. Fresh-frozen tissues were obtained from 36 patients undergoing mastectomy for pure LCIS (n = 11), LCIS with ILC (n = 18) or LCIS with IDC (n = 7). Individual lesions were subject to laser-capture microdissection and gene-expression analysis (Affymetrix HG-U133A 2.0). Immunohistochemistry for ER,PR,HER2, E-CD,N-CD,α-,β-, and phosphoβ-catenin, TWIST, and SNAIL were evaluated in normal, in situ, and invasive components from matched formalin-fixed paraffin-embedded samples (n = 36). CCC-dissociation was defined as negative membranous E-CD, α- and β-catenin expression. E-CD was negative in all LCIS and ILC lesions, and positive in all normal and IDC lesions. Membranous α and β-catenin expressions decreased with the transition from LCIS to ILC (pure LCIS 82%; LCIS w/ILC 28%; ILC 0%), while TWIST expression increased (pure LCIS low; LCIS w/ILC moderate; ILC high). Gene expression paralleled IHC-staining patterns with a stepwise downregulation of E-CD, α and β-catenins from normal to LCIS to invasive lesions, and increasing expression of TWIST from normal to LCIS to ILC. Loss of E-CD expression is an early event in lobular neoplasia. Decreasing membranous catenin expression in tandem with increasing levels of TWIST across the spectrum of lobular lesions suggests that CCC dissociation is a progressive process.

Differentially expressed genes in window trials are influenced by the wound-healing process: lessons learned from a pilot study with anastrozole

BACKGROUND

Perioperative window trials provide an opportunity to obtain intact tumor samples at two different time-points for evaluation of potential surrogate biomarkers. We report results of a pilot trial designed to determine if treatment-mediated changes in gene expression can be detected in formalin-fixed paraffin-embedded (FFPE) samples after 10-d exposure to anastrozole in estrogen receptor (ER)-positive breast cancer compared with untreated controls.

METHODS

Paired tumor samples (biopsy, surgical) were obtained from 26 postmenopausal women with ER-positive breast cancer. Patients were assigned anastrozole (1 mg/d) for 10 d immediately prior to surgery (13 cases) or no treatment (13 controls). Five hundred two cancer-related genes were examined by the Illumina cDNA-mediated annealing, selection, extension, and ligation, FFPE cDNA array (moderated t-test, P ≤ 0.005). Surrogate biomarkers reflecting changes in gene expression were examined by immunohistochemistry (Wilcoxon rank-based test, P < 0.05).

RESULTS

Sufficient RNA was available from 19 paired samples (8 controls, 11 cases). Frozen tissue and FFPE showed good correlation (r = 0.82). Within each group, 18 genes, reflecting roles in proliferation, angiogenesis, and apoptosis, showed differential expression from biopsy to surgery (P < 0.005). Estrogen-related genes were dysregulated in the treated group only. A reduction in Ki-67 was observed in 7 (54%) treated cases and in 1 (7.7%) control patient.

CONCLUSIONS

10-d exposure to anastrozole resulted in dysregulation of 18/502 cancer-related genes, and Ki-67 was reduced in 54% of cases. FFPE samples demonstrated good correlation with frozen samples. However, changes in gene expression and increased Ki-67 in the control group suggest local effects of wound healing may represent a confounding factor in the interpretation of perioperative window trials.

Abstract 3139: Can PI3K/AKT pathway mutations predict for type of recurrence after conservative treatment for DCIS

INTRODUCTION: Although the overall mortality from ductal carcinoma in situ (DCIS) treated with conservative therapy is very low, local recurrence (LR), either as DCIS or invasive carcinoma, remains a significant problem occurring in up to 30% of cases. Young age, positive margins and omission of radiation therapy predict for a higher rate of LR after conservative treatment (BCT) yet cannot predict type of recurrence, DCIS versus invasive breast cancer. Emerging evidence suggests that alterations in the PI3K/AKT pathway may be prognostic in invasive breast cancer; therefore, we examined cases of DCIS that recurred after BCT to determine the relationship between PI3K/AKT mutations and type of recurrence.

METHODS: From a prospectively maintained database of 1873 patients with DCIS undergoing BCT (1991-2006), we identified 190 (10%) patients who recurred. Original DCIS archival blocks were available for 108 (57%) cases. Freshly cut sections were obtained for manual microdissection of pure DCIS lesions and DNA extraction. Genotyping for PIK3CA and AKT1 mutations was performed by Sequenom® MassARRAY® system on prePCR amplified DNA. Fisher's exact test was used to compare cases that recurred as DCIS versus those that recurred as invasive breast cancer.

RESULTS: Among 108 cases, 66 (61%) recurred as DCIS and 42 (39%) recurred as invasive cancer (p=0.002). Type of recurrence in the entire population of 190 patients demonstrated the same pattern. Among studied cases, median time to recurrence was 40 months (range 7-156 mo) and did not differ by type of recurrence. Similarly, patient age, use of radiation and/or tamoxifen therapy or grade of DCIS (low vs high) did not differ by type of recurrence. Sequenom® analysis identified a higher frequency of PIK3CA (n=17) and AKT1 (n=3) mutations among cases that recurred as DCIS compared to those that recurred as invasive cancer, combined mutation rate 16/66 (24%) vs 4/42 (9%), with a trend towards significance (p=0.07). Among the 17 PI3K mutations identified, kinase domain mutations (n=13) were more common than helical domain mutations (n=4). All 4 helical domain mutations were present in cases recurring as DCIS.

CONCLUSIONS: In our population, patients with DCIS who recurred after BCT were more likely recur with DCIS. Standard clinical and pathologic factors did not predict for type of recurrence. PI3K/AKT pathway mutations were more common among cases recurring as DCIS, with a predominance of kinase domain mutations. Further exploration of the significance of PI3K pathway aberrations, in combination with other biomarkers, are warranted to identify predictors for type of recurrence after conservative treatment for DCIS.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 3139. doi:10.1158/1538-7445.AM2011-3139

p21cip/WAF is a key regulator of long-term radiation damage in mesenchyme-derived tissues

This study aimed to determine the mechanisms responsible for long-term tissue damage following radiation injury. We irradiated p21-knockout (p21(-/-)) and wild-type (WT) mice and determined the long-term deleterious effects of this intervention on mesenchyme-derived tissues. In addition, we explored the mechanisms of radiation-induced mesenchymal stem cell (MSC) dysfunction in isolated bone marrow-derived cells. p21 expression was chronically elevated >200-fold in irradiated tissues. Loss of p21 function resulted in a >4-fold increase in the number of skin MSCs remaining after radiation. p21(-/-) mice had significantly less radiation damage, including 6-fold less scarring, 40% increased growth potential, and 4-fold more hypertrophic chondrocytes in the epiphyseal plate (P<0.01). Irradiated p21(-/-) MSCs had 4-fold increased potential for bone or fat differentiation, 4-fold greater proliferation rate, and nearly 7-fold lower senescence as compared to WT MSCs (P<0.01). Ectopic expression of p21 in knockout cells decreased proliferation and differentiation potential and recapitulated the WT phenotype. Loss of p21 function markedly decreases the deleterious effects of radiation injury in mesenchyme-derived tissues and preserves tissue-derived MSCs. In addition, p21 is a critical regulator of MSC proliferation, differentiation, and senescence both at baseline and in response to radiation.

Abstract 785: Gene expression profiling identifies two stable clusters of lobular carcinoma in situ

INTRODUCTION: Historical data suggests that lobular carcinoma in situ (LCIS) is not a precursor to invasive cancer but rather is a marker of increased risk, conferred equally to both breasts. Emerging evidence of genomic similarities between some LCIS and invasive cancers suggests that as subset of LCIS may exhibit precursor potential. The aim of this study was to look for evidence of distinct molecular subtypes of LCIS using cDNA microarray gene expression analysis.

METHODS: Mastectomy specimens from 9 patients with classical LCIS only, 74 patients with classical LCIS & synchronous invasive cancer (51 ILC, 16 IDC, 7 mixed) and 5 patients with LCIS + DCIS were selectively sampled using laser capture microdissection. Representative patient matched normal (NL), LCIS and invasive cells were microdissected from fresh frozen (FF) tissue samples. RNA was extracted and hybridized to Affy. HG-U133A 2.0 oligonucleotide arrays. Unsupervised hierarchical clustering of all LCIS samples and matched paired analysis of NL vs LCIS and LCIS vs ILC were performed using the R software (bioconductor package) and data were analyzed with Ingenuity Pathway Analysis filtered for human genes; p 2.

RESULTS: Suitable RNA was obtained from 48 FF LCIS samples. Patient matched NL and ILC samples were available for 42 and 17 cases, respectively. Hierarchical cluster analysis of all LCIS (n=48) demonstrated two stable clusters with median co-cluster frequency of 79% and 83%. The NL vs LCIS paired comparison (n=42) showed 306 differentially expressed genes (DEG) in Cluster 1 (FC &gt;2: 3.9% DEG) and 2012 DEG in Cluster 2 (FC &gt;2: 2.5% DEG). There were no common DEGs with FC &gt; 2 between clusters 1 and 2 for the NL vs LCIS comparison. The LCIS vs ILC paired comparison (n=17) showed 87 DEG in Cluster 1 (FC &gt;2: 58.6%) and 339 DEG in Cluster 2 (FC &gt;2: 27.7% DEG). There were 18/87 (21%) shared DEG between Cluster 1 and Cluster 2 for the LCIS vs ILC comparison. The functions of these 18 genes include biologically relevant genes involved in cell adhesion, cell-matrix interaction, cell movement, subcellular organization and cell proliferation.

CONCLUSION: Unsupervised hierarchical analysis demonstrated two stable distinct clusters of LCIS. Matched paired analysis of NL vs LCIS suggests that LCIS in cluster 1 is more similar to NL epithelium than LCIS in cluster 2. The absence of overlap in DEG with FC &gt; 2 for this comparison suggests that the initiation of lobular neoplasia may be driven by alternate genes in these two clusters. Matched paired analysis of LCIS vs ILC demonstrates 3.89 times more DEG in cluster 2 than 1, however the proportion of genes with FC &gt;2 was 2.2 times higher in cluster 1, suggesting both quantitative and qualitative differences in these groups. These preliminary analyses support the hypothesis that LCIS is a heterogeneous lesion, further analysis to determine if there is a subtype of LCIS with true precursor potential is underway.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 785.

Diagnosis of suspicious thyroid nodules using four protein biomarkers

PURPOSE

Fine-needle aspiration (FNA) cytology, a standard method for thyroid nodule diagnosis, cannot distinguish between benign follicular thyroid adenoma (FTA) and malignant follicular thyroid carcinoma (FTC). Previously, using expression profiling, we found that a combination of transcript expression levels from DDIT3, ARG2, C1orf24, and ITM1 distinguished between FTA and FTC. The goal of this study was to determine if antibody markers used alone or in combination could accurately distinguish between a wider variety of benign and malignant thyroid lesions in fixed sections and FNA samples.

EXPERIMENTAL DESIGN

Immunohistochemistry was done on 27 FTA, 25 FTC, and 75 other benign and malignant thyroid tissue sections using custom antibodies for chromosome 1 open reading frame 24 (C1orf24) and integral membrane protein 1 (ITM1) and commercial antibodies for DNA damage-inducible transcript 3 (DDIT3) and arginase II (ARG2). FNA samples were also tested using the same antibodies. RNA expression was measured by quantitative PCR in 33 thyroid lesions.

RESULTS

C1orf24 and ITM1 antibodies had an estimated sensitivity of 1.00 for distinguishing FTA from FTC. For the expanded analysis of all lesions studied, ITM1 had an estimated sensitivity of 1.00 for detecting malignancy. Because all four cancer biomarkers did well, producing overlapping confidence intervals, not one best marker was distinguished. Transcript levels also reliably predicted malignancy, but immunohistochemistry had a higher sensitivity. Malignant cells were easily detected in FNA samples using these markers.

CONCLUSIONS

We improved this diagnostic test by adding C1orf24 and ITM1 custom antibodies and showing use on a wider variety of thyroid pathology. We recommend that testing of all four cancer biomarkers now be advanced to larger trials. Use of one or more of these antibodies should improve diagnostic accuracy of suspicious thyroid nodules from both tissue sections and FNA samples.

Motor neuron disease associated with non-fluent rapidly progressive aphasia: case report and review of the literature

The superimposed clinical features of motor neuron disease (MND) and frontotemporal lobar degeneration (FTLD) comprise a rare neurological overlap syndrome that represents a diagnostic challenge to neurologists. Currently, FTLD-MND is considered a distinct entity and its clinicopathological basis has recently been reviewed. Our aim is to present a patient with MND and non-fluent rapidly progressive aphasia with clinical, imaging and histopathological correlation, as well as a brief review of the literature. We demonstrated the selective corticospinal tract (CST) and temporal lobe involvement using T1 spin-echo with an additional magnetization transfer contrast pulse on resonance (T1 SE/MTC) and FLAIR MR sequences in our patient, with further clinical and histopathological correlation. To the best of our knowledge, there is no description about the use of these particular MR sequences in the evaluation of FTLD-MND patients.

Diagnóstico de metástases de carcinoma papilífero de tiróide através da dosagem de tiroglobulina no líquido obtido da lavagem da agulha utilizada na punção aspirativa

Com a introdução da ultra-sonografia cervical (USC) no seguimento dos pacientes com carcinoma papilífero de tiróide (CPT), tornou-se freqüente o encontro de pequenos linfonodos (LNs) cervicais. Porém, apesar de a USC apresentar alta sensibilidade, o estudo citológico obtido por punção aspirativa (PAAF) e, nos últimos anos, a dosagem da tiroglobulina (Tg) no lavado da agulha da PAAF (Tg-PAAF) vêm assumindo papel importante no diagnóstico de LNs cervicais. O objetivo deste estudo é verificar a acurácia da combinação da USC, citologia e Tg-PAAF em LNs suspeitos. Estudamos 32 pacientes que apresentavam 44 LNs à USC, classificados como "inflamatórios" (19) ou "suspeitos" (25). Dos 25 LNs suspeitos, 15 apresentavam Tg-PAAF elevada (13 com citologia compatível com metástases e 2 com citologia não-diagnóstica). Esses 15 LNs (11 pacientes) foram confirmados como metástase de CP pelo exame histopatológico. Os 19 LNs "inflamatórios" e os 10/25 LNs "suspeitos" apresentaram citologia negativa e Tg-PAAF indetectável. Concluímos que a USC apresenta alta sensibilidade na detecção de linfonodos cervicais, porém citologia e dosagem de Tg-PAAF são fundamentais para o diagnóstico. A associação USC, citologia e Tg-PAAF pode ser considerada a abordagem mais sensível e específica na detecção de LNs metastáticos em pacientes com CPT.

Erdheim?Chester disease of the breast associated with Langerhans-cell histiocytosis of the hard palate

We report a patient with Langerhans-cell histiocytosis (LCH) localized to the hard palate that was later proven to be associated with Erdheim-Chester disease (ECD), involving the right breast, skeleton, retroperitoneum and left orbit. The diagnosis was based on the symmetric osteosclerosis of the long bones diaphyses (tibias and fibulas), breast lump histopathological/immunohistochemical findings and retroperitoneum and left orbit images in magnetic resonance. Mammary involvement by ECD is an extremely rare condition, which should be differentiated from some benign and malignant mimickers, especially the histiocytoid type of breast carcinoma. Characteristic histological features plus clinical and radiographic information are needed to achieve a correct diagnosis. The ECD, its relation to the LCH and details of the breast lesion are discussed.