Sotiris Lakis

Tumors with high-density tumor infiltrating lymphocytes constitute a favorable entity in breast cancer: a pooled analysis of four prospective adjuvant trials

Background Tumor infiltrating lymphocytes (TILs) are considered in the prognosis of breast cancer (BC) patients. Here, we investigated the prognostic/predictive effect of TILs in patients treated in the frame of four prospective trials with adjuvant anthracycline-based chemotherapy in the pre- and post-trastuzumab era. Methods TILs density was histologically assessed as percentage of stromal area on whole routine sections of 2613 BC (1563 Luminal A/B; 477 Luminal HER2; 246 HER2-enriched; 327 triple negative [TNBC]) and were evaluated as high/low at three cut-offs (c/o; 50% [lymphocytic predominance, LP], 35% and 25%), in separate training and validation sets. Results High TILs were present in 3.5%, 6.5% and 11.5% of all tumors, using the 50%, 35% and 25% c/o, respectively. TILs status did not interact with BC subtypes or trastuzumab treatment. LPBC patient outcome was not affected by nodal status, while high TILs were favorable in TNBC with unfavorable nodal status. When adjusted for standard clinicopathological parameters and treatment, high TILs independently predicted for favorable outcome, e.g., disease-free survival with the 35% c/o in the entire cohort (HR = 0.44, 95% CI 0.28-0.69, p < 0.001) and in specific subtypes. Conclusions High TILs tumors, especially LPBC seem worthy validating as a separate entity of favorable prognosis in breast cancer.

TP53 mutations and protein immunopositivity may predict for poor outcome but also for trastuzumab benefit in patients with early breast cancer treated in the adjuvant setting

Background We investigated the impact of PIK3CA and TP53 mutations and p53 protein status on the outcome of patients who had been treated with adjuvant anthracycline-taxane chemotherapy within clinical trials in the pre- and post-trastuzumab era. Results TP53 and PIK3CA mutations were found in 380 (21.5%) and 458 (25.9%) cases, respectively, including 104 (5.9%) co-mutated tumors; p53 immunopositivity was observed in 848 tumors (53.5%). TP53 mutations (p < 0.001) and p53 protein positivity (p = 0.001) were more frequent in HER2-positive and triple negative (TNBC) tumors, while PIK3CA mutations were more frequent in Luminal A/B tumors (p < 0.001). TP53 mutation status and p53 protein expression but not PIK3CA mutation status interacted with trastuzumab treatment for disease-free survival; patients with tumors bearing TP53 mutations or immunopositive for p53 protein fared better when treated with trastuzumab, while among patients treated with trastuzumab those with the above characteristics fared best (interaction p = 0.017 for mutations; p = 0.015 for IHC). Upon multivariate analysis the above interactions remained significant in HER2-positive patients; in the entire cohort, TP53 mutations were unfavorable in patients with Luminal A/B (p = 0.003) and TNBC (p = 0.025); p53 immunopositivity was strongly favorable in patients treated with trastuzumab (p = 0.009). Materials and Methods TP53 and PIK3CA mutation status was examined in 1766 paraffin tumor DNA samples with informative semiconductor sequencing results. Among these, 1585 cases were also informative for p53 protein status assessed by immunohistochemistry (IHC; 10% positivity cut-off). Conclusions TP53 mutations confer unfavorable prognosis in patients with Luminal A/B and TNBC tumors, while p53 immunopositivity may predict for trastuzumab benefit in the adjuvant setting.

Genes associated with histopathologic features of triple negative breast tumors predict molecular subtypes

Distinct subtypes of triple negative (TN) breast cancer have been identified by tumor expression profiling. However, little is known about the relationship between histopathologic features of TN tumors, which reflect aspects of both tumor behavior and tumor microenvironment, and molecular TN subtypes. The histopathologic features of TN tumors were assessed by central review and 593 TN tumors were subjected to whole genome expression profiling using the Illumina Whole Genome DASL array. TN molecular subtypes were defined based on gene expression data associated with histopathologic features of TN tumors. Gene expression analysis yielded signatures for four TN subtypes (basal-like, androgen receptor positive, immune, and stromal) consistent with previous studies. Expression analysis also identified genes significantly associated with the 12 histological features of TN tumors. Development of signatures using these markers of histopathological features resulted in six distinct TN subtype signatures, including an additional basal-like and stromal signature. The additional basal-like subtype was distinguished by elevated expression of cell motility and glucose metabolism genes and reduced expression of immune signaling genes, whereas the additional stromal subtype was distinguished by elevated expression of immunomodulatory pathway genes. Histopathologic features that reflect heterogeneity in tumor architecture, cell structure, and tumor microenvironment are related to TN subtype. Accounting for histopathologic features in the development of gene expression signatures, six major subtypes of TN breast cancer were identified.

Evaluation of two highly-multiplexed custom panels for massively parallel semiconductor sequencing on paraffin DNA.

Background—Aim Massively parallel sequencing (MPS) holds promise for expanding cancer translational research and diagnostics. As yet, it has been applied on paraffin DNA (FFPE) with commercially available highly multiplexed gene panels (100s of DNA targets), while custom panels of low multiplexing are used for re-sequencing. Here, we evaluated the performance of two highly multiplexed custom panels on FFPE DNA. Methods Two custom multiplex amplification panels (B, 373 amplicons; T, 286 amplicons) were coupled with semiconductor sequencing on DNA samples from FFPE breast tumors and matched peripheral blood samples (n samples: 316; n libraries: 332). The two panels shared 37% DNA targets (common or shifted amplicons). Panel performance was evaluated in paired sample groups and quartets of libraries, where possible. Results Amplicon read ratios yielded similar patterns per gene with the same panel in FFPE and blood samples; however, performance of common amplicons differed between panels (p<0.001). FFPE genotypes were compared for 1267 coding and non-coding variant replicates, 999 out of which (78.8%) were concordant in different paired sample combinations. Variant frequency was highly reproducible (Spearman’s rho 0.959). Repeatedly discordant variants were of high coverage / low frequency (p<0.001). Genotype concordance was (a) high, for intra-run duplicates with the same panel (mean±SD: 97.2±4.7, 95%CI: 94.8–99.7, p<0.001); (b) modest, when the same DNA was analyzed with different panels (mean±SD: 81.1±20.3, 95%CI: 66.1–95.1, p = 0.004); and (c) low, when different DNA samples from the same tumor were compared with the same panel (mean±SD: 59.9±24.0; 95%CI: 43.3–76.5; p = 0.282). Low coverage / low frequency variants were validated with Sanger sequencing even in samples with unfavourable DNA quality. Conclusions Custom MPS may yield novel information on genomic alterations, provided that data evaluation is adjusted to tumor tissue FFPE DNA. To this scope, eligibility of all amplicons along with variant coverage and frequency need to be assessed.

Efficiency of different decalcification protocols for nasal osseous structures in a rat experimental model of allergic rhinitis, and their effects on epithelial histology: an attempt at standardization.

INTRODUCTION Decalcification of osseous specimens is required for histological analysis; this however may cause tissue damage. In rodent models of allergic rhinitis (AR), epithelial histologic assessment necessitates prior decalcification of the nasal osseous structures. However, respiratory epithelium is highly susceptible to damage, and rat nasal architecture is elaborate and its sectioning is challenging. Nevertheless, decalcification is not standardized in experimental AR. We therefore undertook this task, in order to reduce experimental bias. METHODS Six-to-eight week-old Wistar rats underwent an AR protocol. Subsequently, nasal structures were decalcified in the following mediums: (i) formic acid 10% for 5 and 20 days; (ii) formic acid 15% for 5 and 15 days; (iii) Morse Solution for 5 and 20 days and (iv) EDTA for 20 and 40 days. Decalcification efficiency/speed was evaluated via radiographic analysis. Furthermore, specimens were stained with hematoxylin and eosin and assessed for preservation of epithelial features. RESULTS Specimens were appropriately decalcified in 5 days in the formic acid-based mediums and in 20 days in EDTA with minimal epithelial damage. EDTA for 40 days had no unacceptable adverse effects; conversely, 15 and/or 20 days in acid-based agents provided no extra benefit for decalcification and were detrimental to the epithelium. CONCLUSIONS EDTA treatment for 20 days is appropriate for decalcification of nasal structures in rat models of allergic rhinitis; further incubation preserves epithelial integrity but is not required. When urgency is a factor, formic-acid-based decalcification for 5 days yields acceptable results.

Tumor Infiltrating Lymphocytes Affect the Outcome of Patients with Operable Triple-Negative Breast Cancer in Combination with Mutated Amino Acid Classes

Background Stromal tumor infiltrating lymphocytes (TILs) density is an outcome predictor in triple-negative breast cancer (TNBC). Herein we asked whether TILs are related to coding mutation load and to the chemical class of the resulting mutated amino acids, i.e., charged, polar, and hydrophobic mutations. Methods We examined paraffin tumors from TNBC patients who had been treated with adjuvant chemotherapy mostly within clinical trials (training cohort, N = 133; validation, N = 190) for phenotype concordance; TILs density; mutation load and types. Results Concordance of TNBC phenotypes was 42.1% upon local / central, and 72% upon central / central pathology assessment. TILs were not associated with mutation load, type and class of mutated amino acids. Polar and charged mutation patterns differed between TP53 and PIK3CA (p<0.001). Hydrophobic mutations predicted for early relapse in patients with high nodal burden and <50% TILs tumors (training: HR 3.03, 95%CI 1.11–8.29, p = 0.031; validation: HR 2.90, 95%CI 0.97–8.70, p = 0.057), especially if compared to patients with >50% TILs tumors (training p = 0.003; validation p = 0.015). Conclusions TILs density is unrelated to mutation load in TNBC, which may be regarded as an unstable phenotype. If further validated, hydrophobic mutations along with TILs density may help identifying TNBC patients in higher risk for relapse.

Abstract 3579: Routinely applicable, highly multiplexed triple-negative breast cancer (TNBC) genotyping

Proceedings: AACR Annual Meeting 2014; April 5-9, 2014; San Diego, CA In order to address TNBC diversity, determining the individual clonal genotypes of each tumor is urged as prerequisite. However, the applicability of whole genome approaches on routinely processed paraffin tissue material (FFPE) is still limited. Herein, we used targeted massive parallel sequencing (MPS) for genotyping FFPE tumors from patients with operable TNBC treated with adjuvant chemotherapy. Methods: Centrally assessed FFPE TNBC (n=260) were evaluated for tumor cell content (TCC) and submitted for DNA extraction. A custom panel targeting genomic regions in 43 genes previously implicated in TNBC was submitted for primer design (286 amplicons covering 21216bp). Barcoded FFPE libraries were massively processed on Ion Proton™ Sequencer PI and on Ion PGM™ Sequencer 318 chips (30 samples with both platforms, at least 2 runs each). Variants were called and annotated at higher-than-default-stringency conditions (63% of all detected variants excluded). Amplicons were checked for sequence specificity, blood DNA and FFPE performance prior to accepting results (informative: 280/286). Annotated SNVs (coding and non-coding) were assessed for allelic imbalance (AI) based on allelic frequency and TCC (AI: >0.3 unstable SNVs/tumor). The rate of failed samples was significantly higher with PGM (29.5%) than with Proton (3%). Results: In total, 238 informative TNBC were analyzed. AI was noticed in 169 tumors (71%) for multiple genes, more often TP53 (124 tumors, 52.1%), TERT (39.9%), MDM2 (35.7%), MET (24.4%), BRCA1 (20.2%) and NOTCH1 (18.9%). Coding mutations were identified in 40/43 genes but their number varied extensively per tumor (0-87). SNV functional mutations were observed in 55 tumors (23.1%), more often in PIK3CA (12 tumors, 5%). Non-SNV mutations were observed in 153 tumors (64.2%), more often TP53 (128 tumors, 53.8%), CDH1 (17.2%), MAP3K1 (8%), PTEN (6.3%), and PIK3CA (4.6%). High frequency mutations (>50% tumor cells) were found in TP53, PTEN, PIK3CA. Individually, the presence of AI (unstable tumors) and mutations predicted for worse survival. Importantly though, in comparison to patients with unstable mutated tumors, patients with unstable nonmutated tumors had significantly better outcome (DFS, HR:0.41, 95%CI:0.20-0.84, Wald p=0.014; OS, HR:0.36, 95%CI:0.15-0.86, p=0.021), similar to that observed for the favorable stable tumors, where the presence of mutations did not add any effect on survival. The same survival pattern was observed when evaluating AI and high frequency mutations. Conclusions: Targeted MPS with custom panels is an attractive option for highly multiplexed FFPE tissue genotyping, although differences in the efficiency of available platforms should be considered. With respect to potential clinical implications, identifying tumors with allelic (in)stability and clonal mutations seems important for assessing TNBC patient outcome and merits further validation. Citation Format: Vassiliki Kotoula, Kyriaki Papadopoulou, Elpida Charalambous, Flora Zagouri, Sotiris Lakis, Angeliki Lymperopoulou, Eleftheria Tsolaki, George Pentheroudakis, Kostas Lilakos, Dimitrios Pectasides, George Fountzilas. Routinely applicable, highly multiplexed triple-negative breast cancer (TNBC) genotyping. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 3579. doi:10.1158/1538-7445.AM2014-3579

Abstract P2-07-02: Tumor infiltrating lymphocytes density and coding mutations effects on the outcome of operable triple negative breast cancer patients

Background-Aim: Neoantigens are considered to trigger host immune responses against tumors, which may be reflected by tumor infiltrating lymphocytes (TILs) density within the tumor stroma. High TILs levels have been associated with favorable triple-negative breast cancer (TNBC) patient outcome. Herein we evaluated the presence of coding mutations and TILs density with regard to outcome in a cohort of TNBC patients treated with anthracycline-based adjuvant chemotherapy. Patients and Methods: Paraffin TNBC tissues from 242 patients treated in the context of four prospective clinical trials were histologically reviewed and submitted to massively parallel semiconductor sequencing with a custom panel targeting 57 breast cancer (BC)-related genes. Mutations (mut) were evaluated in 210 informative samples as missense/nonsense amino acid changing variants, with minor allele frequency 50%. Disease-free survival (DFS) was used as the endpoint for the present analysis. Results: 426 Mut were observed for 40 genes in 147 TNBC patients (70%). Among mutated genes, ranging from 1 in 97 tumors up to >10 in 8 tumors, the most frequently affected were TP53 (102 tumors, 69%) and PIK3CA (40 tumors, 27%). Intriguingly, mut rate (p=0.042) and number of mut genes (p=0.018) per tumor were inversely associated with TILs density. Nineteen tumors (10%) were LP-TNBC, carrying TP53 and PIK3CA mut as the only coding alterations in 10 and 3 cases, respectively. LP-TNBC patients did not experience any relapses during a follow-up period of 46-152 months (mean 66 months). For the 90% of non-LP-TNBC, the previously reported outcome benefit for 10% increments of TILs density was only demonstrated for tumors with 31-50% TILs. In non-LP-TNBC, upon adjustment for standard clinicopathological parameters, PIK3CA mut, TP53 mut and TILs density as a continuous variable, TP53 mut and nodal status independently conferred unfavorable DFS (HR=1.89, 95% CI 1.03-3.47, p=0.040 and HR=2.89, 95% CI 1.59-5.24, p=0.001, respectively). When continuous TILs density was added in the multivariate models in the entire cohort, 10% increments significantly predicted favorable DFS (HR=0.73, 95% CI 0.59-0.91, p=0.006), while high nodal status predicted unfavorable DFS (HR=2.75, 95% CI 1.51-4.99, p Conclusions: In the present study, tumors with higher TILs density, including LP-TNBC, were not characterized by multiple mutations or mutated genes with the panel tested. In TNBC, increasing TILs density is a strong favorable and high nodal status a strong unfavorable prognosticator. Importantly, LP-TNBC may be regarded as a distinct subgroup with excellent prognosis concerning 10% of TNBC. In non-LP-TNBC, TP53 mut and nodal status were significant unfavorable prognosticators. These data may suggest that the level of morphologically assessed TILs density does not necessarily correspond to the tumoral mutational load and merit validation in larger cohorts. Citation Format: Kotoula V, Fountzilas E, Chatzopoulos K, Alexopoulou Z, Timotheadou E, Xanthakis I, Gogas H, Skondra M, Christodoulou C, Papadopoulou K, Chrisafi S, Koutras A, Xepapadakis G, Venizelos V, Efstratiou I, Patsea H, Kalogeras KT, Lakis S, Fountzilas G. Tumor infiltrating lymphocytes density and coding mutations effects on the outcome of operable triple negative breast cancer patients. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P2-07-02.

Abstract P3-09-07: Prognostic value of immunophenotypically defined subtypes in patients treated with dose-dense sequential adjuvant chemotherapy in the trastuzumab era. A Hellenic Cooperative Oncology Group study

Background-Aim: The aim of the present study was to explore the efficacy of dose-dense sequential adjuvant chemotherapy followed by trastuzumab in HER2-positive patients according to the immunohistochemically (IHC) defined subtypes. Patients and methods: A total of 771 formalin-fixed paraffin-embedded (FFPE) tumor tissue samples, prospectively collected from 990 eligible patients with high-risk N 0 or N 1 operable breast cancer participating in a phase III trial (HE10/05), were centrally assessed in tissue microarrays by IHC for 6 biological markers, that is, estrogen receptor (ER), progesterone receptor (PgR), HER2, Ki67, cytokeratin 5 (CK5) and EGFR. All cases were further evaluated for HER2 amplification by FISH. Patients were classified as: luminal A (ER/PgR-positive, HER2-negative, Ki67 low , N=382, 49.5%); luminal B (ER/PgR-positive, HER2-negative, Ki67 high , N=136, 17.6%); luminal-HER2 (ER/PgR-positive, HER2-positive, N=125, 16.2%); HER2-enriched (ER-negative, PgR-negative, HER2-positive, N=63, 8.2%); triple-negative (TNBC) (ER-negative, PgR-negative, HER2-negative, N=65, 8.4%); and basal core phenotype (BCP) (TNBC, CK5-positive and/or EGFR-positive, N=53, 6.9%). Results: At a median follow-up of 60.5 months, the 3-year disease-free survival (DFS) and overall survival (OS) rates for the total patient population were 88.3% and 96.0%, respectively. The 3-year DFS rates for luminal A, luminal B, luminal-HER2, HER2-enriched, TNBC and BCP patients were 91.1%, 88.2%, 86.4%, 93.7%, 87.7%, and 89.4%, respectively, while the corresponding 3-year OS rates were 95.8%, 95.6%, 97.6%, 95.2%, 95.4%, and 95.0%, respectively. No significant differences were detected for either 3-year DFS or OS in the immunohistochemically defined subtypes, except a trend for significantly worse DFS in patients with luminal-HER2 tumors compared to patients with HER2-enriched tumors (log-rank, p=0.069). Conclusions: In the post-trastuzumab era, at a relatively short follow-up, the luminal-HER2 patients show a trend for worse DFS compared to patients with HER2-enriched tumors treated with dose-dense sequential adjuvant chemotherapy followed by trastuzumab. No other significant differences were detected, with follow-up however being continued. Citation Format: George Fountzilas, Eleni Timotheadou, Georgia Gourgioti, Petroula Arapantoni-Dadioti, Sotiris Lakis, Anna Batistatou, Triantafyllia Koletsa, Olympia Tzaida, Mattheos Bobos, Alexandra Papoudou-Bai, Eleftheria Tsolaki, Sofia Chrisafi, Elena Fountzilas, Ioannis Efstratiou, Helen Gogas, Flora Zagouri, Dimitrios Pectasides. Prognostic value of immunophenotypically defined subtypes in patients treated with dose-dense sequential adjuvant chemotherapy in the trastuzumab era. A Hellenic Cooperative Oncology Group study [abstract]. In: Proceedings of the Thirty-Seventh Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2014 Dec 9-13; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2015;75(9 Suppl):Abstract nr P3-09-07.

258PDINVESTIGATING THE CLINICAL RELEVANCE OF GENOMIC CHARACTERISTICS IN LUMINAL A AND B BREAST CANCER (BC)

Methods: Histologically reviewed, paraffin tumour DNA samples (N = 1092) from patients who had received anthracycline-based adjuvant chemotherapy in the frame of two randomized trials by HeCOG (HE10/00, pre-trastuzumab; HE10/05, post-trastuzumab era), were investigated with targeted massively parallel sequencing (Ion Torrent systems) for variants in 58 genes implicated in BC. Upon multiple stringent quality filters, pathogenic mutations (mut) and allelic imbalance (AI) were evaluable in 844 cases (77.3%). IHC4 was used for BC subtyping.