A pan-cancer clinical platform to predict immunotherapy outcomes and prioritize immuno-oncology combinations in early-phase trials

BACKGROUND

Immunotherapy is effective, but current biomarkers for patient selection have proven modest sensitivity. Here, we developed VIGex, an optimized gene signature based on the expression level of 12 genes involved in immune response with RNA sequencing.

METHODS

We implemented VIGex using the nCounter platform (Nanostring) on a large clinical cohort encompassing 909 tumor samples across 45 tumor types. VIGex was developed as a continuous variable, with cutoffs selected to detect three main categories (hot, intermediate-cold and cold) based on the different inflammatory status of the tumor microenvironment.

FINDINGS

Hot tumors had the highest VIGex scores and exhibited an increased abundance of tumor-infiltrating lymphocytes as compared with the intermediate-cold and cold. VIGex scores varied depending on tumor origin and anatomic site of metastases, with liver metastases showing an immunosuppressive tumor microenvironment. The predictive power of VIGex-Hot was observed in a cohort of 98 refractory solid tumor from patients treated in early-phase immunotherapy trials and its clinical performance was confirmed through an extensive metanalysis across 13 clinically annotated gene expression datasets from 877 patients treated with immunotherapy agents. Last, we generated a pan-cancer biomarker platform that integrates VIGex categories with the expression levels of immunotherapy targets under development in early-phase clinical trials.

CONCLUSIONS

Our results support the clinical utility of VIGex as a tool to aid clinicians for patient selection and personalized immunotherapy interventions.

FUNDING

BBVA Foundation; 202-2021 Division of Medical Oncology and Hematology Fellowship award; Princess Margaret Cancer Center.

RAGE/SNAIL1 signaling drives epithelial-mesenchymal plasticity in metastatic triple-negative breast cancer

Epithelial/Mesenchymal (E/M) plasticity plays a fundamental role both in embryogenesis and during tumorigenesis. The receptor for advanced glycation end products (RAGE) is a driver of cell plasticity in fibrotic diseases; however, its role and molecular mechanism in triple-negative breast cancer (TNBC) remains unclear. Here, we demonstrate that RAGE signaling maintains the mesenchymal phenotype of aggressive TNBC cells by enforcing the expression of SNAIL1. Besides, we uncover a crosstalk mechanism between the TGF-β and RAGE pathways that is required for the acquisition of mesenchymal traits in TNBC cells. Consistently, RAGE inhibition elicits epithelial features that block migration and invasion capacities. Next, since RAGE is a sensor of the tumor microenvironment, we modeled acute acidosis in TNBC cells and showed it promotes enhanced production of RAGE ligands and the activation of RAGE-dependent invasive properties. Furthermore, acute acidosis increases SNAIL1 levels and tumor cell invasion in a RAGE-dependent manner. Finally, we demonstrate that in vivo inhibition of RAGE reduces metastasis incidence and expands survival, consistent with molecular effects that support the relevance of RAGE signaling in E/M plasticity. These results uncover new molecular insights on the regulation of E/M phenotypes in cancer metastasis and provide rationale for pharmacological intervention of this signaling axis.

Expression of TILs and Patterns of Gene Expression from Paired Samples of Malignant Pleural Mesothelioma (MPM) Patients

MPM is an aggressive disease with an immunosuppressive tumor microenvironment, and interest in exploring immunotherapy in this disease has been increasing. In the first line of treatment, the combination of nivolumab and ipilimumab demonstrated an improvement in survival over chemotherapy. The presence of TILs has been recognized as a marker of antitumor immune response to chemotherapy in solid tumors. The aim of our study is to identify the effect of treatment on immune cells and the immune gene profile in MPM. We investigated the changes in expression of TILs in 10 human MPM paired tumor tissues using immunohistochemistry and gene expression analysis from paired untreated and treated samples. In this small series, we demonstrated that during the evolution of disease without any treatment there was an increase in the inflammatory component in tumor samples. After systemic treatment there was a decrease in the number of TILs. We observed that after systemic treatment or disease progression immune gene signatures were suppressed. Our integrated analysis of paired samples with immune profile and genomic changes on MPM suggested that during the evolution of the disease the immune system tends to switch, turning off with treatment.

Establishment of patient-derived tumor organoids to functionally inform treatment decisions in metastatic colorectal cancer

BACKGROUND

Metastatic colorectal cancer (mCRC) patients tend to have modest benefits from molecularly driven therapeutics. Patient-derived tumor organoids (PDTOs) represent an unmatched model to elucidate tumor resistance to therapy, due to their high capacity to resemble tumor characteristics.

MATERIALS AND METHODS

We used viable tumor tissue from two cohorts of patients with mCRC, naïve or refractory to treatment, respectively, for generating PDTOs. The derived models were subjected to a 6-day drug screening assay (DSA) with a comprehensive pipeline of chemotherapy and targeted drugs against almost all the actionable mCRC molecular drivers. For the second cohort DSA data were matched with those from PDTO genotyping.

RESULTS

A total of 40 PDTOs included in the two cohorts were derived from mCRC primary tumors or metastases. The first cohort included 31 PDTOs derived from patients treated in front line. For this cohort, DSA results were matched with patient responses. Moreover, RAS/BRAF mutational status was matched with DSA cetuximab response. Ten out of 12 (83.3%) RAS wild-type PDTOs responded to cetuximab, while all the mutant PDTOs, 8 out of 8 (100%), were resistant. For the second cohort (chemorefractory patients), we used part of tumor tissue for genotyping. Four out of nine DSA/genotyping data resulted applicable in the clinic. Two RAS-mutant mCRC patients have been treated with FOLFOX-bevacizumab and mitomycin-capecitabine in third line, respectively, based on DSA results, obtaining disease control. One patient was treated with nivolumab-second mitochondrial-derived activator of caspases mimetic (phase I trial) due to high tumor mutational burden at genotyping, experiencing stable disease. In one case, the presence of BRCA2 mutation correlated with DSA sensitivity to olaparib; however, the patient could not receive the therapy.

CONCLUSIONS

Using CRC as a model, we have designed and validated a clinically applicable methodology to potentially inform clinical decisions with functional data. Undoubtedly, further larger analyses are needed to improve methodology success rates and propose suitable treatment strategies for mCRC patients.

A Comprehensive Biomarker Analysis of Microsatellite Unstable/Mismatch Repair Deficient Colorectal Cancer Cohort Treated with Immunotherapy

The search for immunotherapy biomarkers in Microsatellite Instability High/Deficient Mismatch Repair system (MSI-H/dMMR) metastatic colorectal cancer (mCRC) is an unmet need. Sixteen patients with mCRC and MSI-H/dMMR (determined by either immunohistochemistry or polymerase chain reaction) treated with PD-1/PD-L1 inhibitors at our institution were included. According to whether the progression-free survival with PD-1/PD-L1 inhibitors was longer than 6 months or shorter, patients were clustered into the IT-responder group (n: 9 patients) or IT-resistant group (n: 7 patients), respectively. In order to evaluate determinants of benefit with PD-1/PD-L1 inhibitors, we performed multimodal analysis including genomics (through NGS panel tumour-only with 431 genes) and the immune microenvironment (using CD3, CD8, FOXP3 and PD-L1 antibodies). The following mutations were more frequent in IT-resistant compared with IT-responder groups: B2M (4/7 versus 2/9), CTNNB1 (2/7 versus 0/9), and biallelic PTEN (3/7 versus 1/9). Biallelic ARID1A mutations were found exclusively in the IT-responder group (4/9 patients). Tumour mutational burden did not correlate with immunotherapy benefit, neither the rate of indels in homopolymeric regions. Of note, biallelic ARID1A mutated tumours had the highest immune infiltration and PD-L1 scores, contrary to tumours with CTNNB1 mutation. Immune microenvironment analysis showed higher densities of different T cell subpopulations and PD-L1 expression in IT-responders. Misdiagnosis of MSI-H/dMMR inferred by discordances between immunohistochemistry and polymerase chain reaction was only found in the IT-resistant population (3/7 patients). Biallelic ARID1A mutations and Wnt signalling activation through CTNNB1 mutation were associated with high and low T cell immune infiltrates, respectively, and deserve special attention as determinants of response to PD-1/PD-L1 inhibitors. The non-MSI-H phenotype in dMMR is associated with poor benefit to immunotherapy. Our results suggest that mechanisms of resistance to immunotherapy are multi-factorial.

RNF43 mutations predict response to anti-BRAF/EGFR combinatory therapies in BRAFV600E metastatic colorectal cancer

Anti-BRAF/EGFR therapy was recently approved for the treatment of metastatic BRAF^V600E colorectal cancer (mCRC^BRAF-V600E). However, a large fraction of patients do not respond, underscoring the need to identify molecular determinants of treatment response. Using whole-exome sequencing in a discovery cohort of patients with mCRC^BRAF-V600E treated with anti-BRAF/EGFR therapy, we found that inactivating mutations in RNF43, a negative regulator of WNT, predict improved response rates and survival outcomes in patients with microsatellite-stable (MSS) tumors. Analysis of an independent validation cohort confirmed the relevance of RNF43 mutations to predicting clinical benefit (72.7% versus 30.8%; P = 0.03), as well as longer progression-free survival (hazard ratio (HR), 0.30; 95% confidence interval (CI), 0.12–0.75; P = 0.01) and overall survival (HR, 0.26; 95% CI, 0.10–0.71; P = 0.008), in patients with MSS-RNF43^mutated versus MSS-RNF43^wild-type tumors. Microsatellite-instable tumors invariably carried a wild-type-like RNF43 genotype encoding p.G659fs and presented an intermediate response profile. We found no association of RNF43 mutations with patient outcomes in a control cohort of patients with MSS-mCRC^BRAF-V600E tumors not exposed to anti-BRAF targeted therapies. Overall, our findings suggest a cross-talk between the MAPK and WNT pathways that may modulate the antitumor activity of anti-BRAF/EGFR therapy and uncover predictive biomarkers to optimize the clinical management of these patients.

The presence of inactivating mutations in RNF43, a negative regulator of WNT, in tumor cells predicts improved response rates and survival outcomes in patients with metastatic BRAF^V600E colorectal cancer treated with anti-BRAF/EGFR therapy.

Utility of liquid biopsy for identifying emerging mutations (mut) and novel treatment options in luminal metastatic breast cancer (LMBC)

1061

Background: Molecular characterization of LMBC for the choice of therapy and inclusion in clinical trials is frequently performed in archival biopsies procured several years before. Emerging mut secondary to therapeutic pressure are hence frequently missed but could be detected by real-time analysis of circulating tumor DNA. Aim: 1) To assess the emergence of ERBB2 and other mut upon therapeutic pressure; 2) To compare the concordance of mut in tumor and plasma samples between patients (pts) with metachronous and synchronous sample acquisition. Methods: Pts with LMBC and available tumor biopsy and plasma samples were identified and divided in two groups: 1) Cohort 1 (metachronous) if the time between tissue and plasma acquisition was > 3 months and systemic treatment was given between the sampling; 2) Cohort 2 (synchronous) if sampling occurred with < 3 months interval in the absence of systemic treatment. Tumor and plasma were analyzed using MiSeq Amplicon-based NGS (custom panel of 60 cancer-related genes). The emergent mut in plasma in Cohort 1 and the concordance of ESCAT Tier I and II mut ( PIK3CA, AKT1, ERBB2, ESR1, PTEN) in both Cohorts were determined and correlated with clinical features. Results: 176 pts were included, 112 in Cohort 1 and 64 in Cohort 2. In Cohort 1, emerging mut in PIK3CA were identified in 5 cases (14% of total cases with PIK3CA mut), ESR1 in 22 cases (85% of cases with ESR1 mut) and PTEN in 3 cases (43% of cases with PTEN mut). No emerging ERBB2 or AKT1 mut were seen in plasma. In Cohort 1 ERBB2 mut were identified in 10 pts (8.9%), 5 both in plasma and tissue and 5 only in tissue. Concordance between tumor and plasma was 53% in Cohort 1 and 66% in Cohort 2 (95% CI of the difference -2% to 38%, P =.09). In Cohort 1, concordance was not associated with (neo)adjuvant treatment, number of lines for MBC, presence of visceral metastasis, location of biopsy (primary tumor or metastasis), interval between sampling (range 3.6 – 288 months) or type of systemic treatment before plasma sampling. In Cohort 2, higher concordance associated with shorter interval between primary diagnosis and sampling (p = 0.02). PI3KCA and ESR1 were the two genes most frequently altered in both cohorts. PI3KCA mut had the highest degree of concordance in both groups (70% in Cohort 1 and 76% in Cohort 2). Concordance for ESR1 mut was low in both cohorts (20% and 48%, respectively). Conclusions: A significant number of ESR1 mut emerged upon therapeutic pressure in LMBC. Plasma analysis could also detect the emergence of PIK3CA and PTEN, but not ERBB2 mut. The trend towards lower concordance between metachronous and synchronous tumor and plasma sampling is probably due to increased tumor heterogeneity and clonal diversity secondary to systemic treatment. Our findings confirm that liquid biopsies provide complementary information respect to tumor tissue that may be potentially useful for clinical decisions.

Shedding of ctDNA, radiomics assessment of tumor disease volume (TDV), and concordance of mutations (mut) in synchronous liquid and tumor biopsies in metastatic breast cancer (MBC)

1086

Background: Genomic alterations driving MBC progression may be better captured by ctDNA reflecting clonal evolution, but it is currently unknow whether ctDNA analysis can replace tumor sequencing for clinical decision purposes. Aim: to study the concordance between mut in synchronous plasma and tumor samples prospectively collected from patients (pts) with MBC progressing on their last systemic therapy. Methods: MiSeq Amplicon-based NGS (custom panel of 60 cancer-related genes; BRCA1/2 and PALB2 not included) was performed in both tumor biopsy and plasma. The concordance of ESCAT Tier I and II mut ( PIK3CA, AKT1, ERBB2, ESR1, PTEN) was determined and correlated with mutant allele fraction (MAF), TDV, and clinical features. Findings from liquid biopsies were classified as true positive (TP-ctDNA) if a given mut was detected in both tumor and plasma and false negative (FN-ctDNA) if only in the tumor. TDV: all metastasis volume assessed by CT scan (excluding sclerotic bone metastasis), and analyzed by an experienced radiologist using the 3DSlicer semiautomatic segmentation tool (TDV = pixel size x number of pixels). Non-shedding cases were those where any mut was detected in tumor but none in plasma. Results: 88 cases were collected (luminal 64, HER2+ 17, triple negative 7). Median age at diagnosis 49 years (range 28-80). Radiomics assessment could be performed in 78/88 cases. The plasma/tissue concordance at case level was 74%. Discordance came from 23 cases; in 15 cases mut was only found in tissue and in 8 cases it was only detected in plasma. At gene level, PIK3CA had the highest concordance (79%); in ESR1 it was 52%. Higher concordance associated with non-luminal subtype (OR 0.08, 95%CI 0.002 – 0.59) and shorter interval between primary diagnosis and metastatic relapse (20.3 vs 51 months; p =.02), but not with MAF. FN-ctDNA occurred in 15/49 cases (31%) and associated with luminal subtype (p =.02), but not with other clinical variables. Non-shedding cases associated with older age (p =.03), luminal subtype (p =.007), low TDV (p =.0006) and < 3 metastatic sites (p =.05). In patients with visceral metastasis (n = 45), higher TDV associated with lower probability of FN-ctDNA (p =.03). All non-luminal subtypes were shedders and all but one were TP-ctDNA. In multivariate analysis, higher probability of TP-ctDNA in luminal tumors associated with tumor sampling from a progressing lesion (OR 10.8; 95% 1.5 – 122; p =.03) and shorter interval between diagnosis of metastatic disease and biopsy (OR 0.96, 95% CI 0.92 – 0.99; p =.03). Conclusions: Our results suggest that ctDNA can detect a significant proportion of clinically relevant mut in MBC. Patients’ characteristics, tumor subtype, type of gene, and tumor volume should be integrated with ctDNA results to better inform clinical decisions.

T-cell infiltration in matched samples from malignant pleural mesothelioma (MPM) during evolution of disease

e20595

Background: MPM is an aggressive cancer associated with asbestos exposure. Chemotherapy has been a mainstay of therapy and recently immunotherapy has been associated with survival improvements. Chemotherapy and immunotherapy influence the tumor microenvironment and some reports have shown increased of TIL after chemotherapy in MPM. The purpose of this study was to determine dynamic changes in the tumor immune environment during mesothelioma evolution and after systemic therapies in paired samples. Methods: We examined 20 matched formalin-fixed paraffin embedded tissue samples from 10 patients (p) with MPM taken at diagnosis and at disease progression (follow-up), including untreated and treated with chemotherapy or immunotherapy. Tissue densities (number of cells/mm2) of key immune effector cells such as total lymphocytes (CD3), cytotoxic T cells (CD8), regulatory T cells (FOXP3) and monocytes/macrophages (CD163) were quantified by image analysis using multiplexed immunohistochemistry (IHC). PD-L1 expression in both tumor cells and immune cells was analysed by singleplex IHC and quantified using the CPS score. Results: Median age was 62 years (range 53-84), 7 p were male and all p presented epithelioid histology. Three matched samples belong to patients that did not receive any systemic treatment between biopsies and the other 7 pair of samples belong to patients treated with chemotherapy +/- immunotherapy. The median interval between paired biopsies was 12 m (3-33 m). Median overall survival was 27.8 months (1 m-NR). Median densities of T cells and macrophages in diagnostic and matched follow-up samples were: CD3+:982 vs 712; CD8+:422 vs 334, FOXP3+: 22 vs 25 and CD163+: 2086 vs 1706. Median PD-L1 CPS was 2.5 and 4 in diagnostic and follow-up samples, respectively. In p receiving treatment between sample pairs, the median densities in diagnostic and follow-up matched samples were: CD3+:979 vs 407; CD8+:467 vs 225, FOXP3+: 25 vs 15, CD163+: 1583 vs 1508, and PD-L1: 2 and 1. In p without any systemic treatment between sample pairs, the median densities were CD3+:1645 vs 2397; CD8+:376 vs 1605, FOXP3+: 19 vs 121, CD163+: 2102 vs 2377, and PD-L1: 3 vs 25. Conclusions: In our small series with paired samples from MPM p, we observed immune cells infiltration changes during MPM evolution with a trend towards a decrease after systemic therapy. Further investigation in tumor microenvironment in MPM to define the most appropriate time for immunotherapy is needed.

Performance of 16S Metagenomic Profiling in Formalin-Fixed Paraffin-Embedded versus Fresh-Frozen Colorectal Cancer Tissues

Formalin-fixed, paraffin-embedded (FFPE) tissues represent the most widely available clinical material to study colorectal cancer (CRC). However, the accuracy and clinical validity of FFPE microbiome profiling in CRC is uncertain. Here, we compared the microbial composition of 10 paired fresh-frozen (FF) and FFPE CRC tissues using 16S rRNA sequencing and RNA-ISH. Both sample types showed different microbial diversity and composition. FF samples were enriched in archaea and representative CRC-associated bacteria, such as Firmicutes, Bacteroidetes and Fusobacteria. Conversely, FFPE samples were mainly enriched in typical contaminants, such as Sphingomonadales and Rhodobacterales. RNA-ISH in FFPE tissues confirmed the presence of CRC-associated bacteria, such as Fusobacterium and Bacteroides, as well as Propionibacterium allowing discrimination between tumor-associated and contaminant taxa. An internal quality index showed that the degree of similarity within sample pairs inversely correlated with the dominance of contaminant taxa. Given the importance of FFPE specimens for larger studies in human cancer genomics, our findings may provide useful indications on potential confounding factors to consider for accurate and reproducible metagenomics analyses.

Abstract CT161: A homologous recombination repair (HRR) functional assay to stratify patients with metastatic prostate cancer for PARP inhibitor treatment in the TOPARP-B clinical trial

Background: PARP inhibitors (PARPi) are approved for the treatment of metastatic prostate cancer (mPC) associated to various DNA damage repair (DDR) gene mutations; but clinical benefit differs among patients. Biomarkers of homologous recombination repair (HRR) deficiency may help refine patient stratification for a more precise therapy selection. We report an exploratory analysis from the TOPARP-B phase II clinical trial of olaparib in mPC (NCT01682772), investigating the predictive value of an HRR function assay detecting RAD51 foci by immunofluorescence in tumor biopsies. Design: We analyzed formalin-fixed paraffin-embedded (FFPE) primary or metastatic biopsies from mPC patients treated with olaparib in the clinical trial. We evaluated baseline HRR function based on detection of RAD51 and γH2AX foci in geminin-positive tumor cells by immunofluorescence (IF). All samples were scored by two trained readers blinded to genomic and clinical data. Samples were considered HRR deficient (HRD) when RAD51 scores were low, pre-defined as &lt;10% tumor cells presenting ≥5 RAD51 foci/cell. The association of the RAD51 score, response to olaparib and survival (radiographic progression-free survival, rPFS, and overall survival, OS) was analyzed by Chi-Square and log-rank tests. Results: RAD51 and γH2AX were successfully scored in 52 cases, in the same biopsies previously used for NGS in the clinical trial. All tumors showed abundant DNA damage (γH2AX scores &gt;40%). The intra-class correlation score (ICC) between the two blinded readers was 0.88. Overall, 22 of 52 (42%) cases were considered as HRD based on low RAD51 scores. Response rate (based on the composite RECIST/PSA/CTC trial criteria) was 15/22 (68%) vs 7/30 (23%) for patients with low vs high RAD51 scores (p=0.001). Patients with low RAD51 scores also had longer rPFS (median 9.3 vs 2.9 months p=0.002) and overall survival (median 17.4 vs 9.5 months, p=0.05) from initiation of olaparib. All 16/16 cases with BRCA1/2 alterations were identified as RAD51 low. For patients with PALB2 mutations, 2/2 patients with biallelic loss showed RAD51 low scores and responded to olaparib, whereas 2/2 patients with monoallelic PALB2 mutations showed RAD51 high scores and did not respond to olaparib. Mutations in ATM and CDK12 did not associate with low RAD51. Indeed, 10/11 ATM-mutated and 8/10 CDK12-mutated tumors presented high RAD51 scores; RECIST/PSA responses were observed in two patients with ATM mutations and high RAD51 scores. Conclusion: A RAD51-based IF assay performed on FFPE biopsies can detect prostate cancers with deficient HRR function, including BRCA1/2 and biallelic PALB2 mutated cases, and may be useful for patient stratification for PARP inhibitor treatment in prostate cancer. Further validation of the assay in larger cohorts is warranted.

Citation Format: Sara Arce-Gallego, Alba Llop-Guevara, Suzanne Carreira, Nuria Porta, Roberta Fasani, Diletta Bianchini, George Seed, Pasquale Rescigno, Alec Paschalis, Claudia Bertan, Chloe Baker, Jane Goodall, Susana Miranda, Ruth Riisnaes, Ines Figueiredo, Ana Ferreira, Rita Pereira, Bora Gurel, Daniel Nava Rodrigues, Wei Yuan, Jan Rekowski, Emma Hall, Violeta Serra, Johann S. de Bono, Joaquin Mateo. A homologous recombination repair (HRR) functional assay to stratify patients with metastatic prostate cancer for PARP inhibitor treatment in the TOPARP-B clinical trial [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 CT161.

The temporal mutational and immune tumour microenvironment remodelling of HER2-negative primary breast cancers

The biology of breast cancer response to neoadjuvant therapy is underrepresented in the literature and provides a window-of-opportunity to explore the genomic and microenvironment modulation of tumours exposed to therapy. Here, we characterised the mutational, gene expression, pathway enrichment and tumour-infiltrating lymphocytes (TILs) dynamics across different timepoints of 35 HER2-negative primary breast cancer patients receiving neoadjuvant eribulin therapy (SOLTI-1007 NEOERIBULIN-NCT01669252). Whole-exome data (N = 88 samples) generated mutational profiles and candidate neoantigens and were analysed along with RNA-Nanostring 545-gene expression (N = 96 samples) and stromal TILs (N = 105 samples). Tumour mutation burden varied across patients at baseline but not across the sampling timepoints for each patient. Mutational signatures were not always conserved across tumours. There was a trend towards higher odds of response and less hazard to relapse when the percentage of subclonal mutations was low, suggesting that more homogenous tumours might have better responses to neoadjuvant therapy. Few driver mutations (5.1%) generated putative neoantigens. Mutation and neoantigen load were positively correlated (R2 = 0.94, p = <0.001); neoantigen load was weakly correlated with stromal TILs (R2 = 0.16, p = 0.02). An enrichment in pathways linked to immune infiltration and reduced programmed cell death expression were seen after 12 weeks of eribulin in good responders. VEGF was downregulated over time in the good responder group and FABP5, an inductor of epithelial mesenchymal transition (EMT), was upregulated in cases that recurred (p < 0.05). Mutational heterogeneity, subclonal architecture and the improvement of immune microenvironment along with remodelling of hypoxia and EMT may influence the response to neoadjuvant treatment.

Immune microenvironment characterisation and dynamics during anti-HER2-based neoadjuvant treatment in HER2-positive breast cancer

Despite their recognised role in HER2-positive (HER2+) breast cancer (BC), the composition, localisation and functional orientation of immune cells within tumour microenvironment, as well as its dynamics during anti-HER2 treatment, is largely unknown. We here investigate changes in tumour-immune contexture, as assessed by stromal tumour-infiltrating lymphocytes (sTILs) and by multiplexed spatial cellular phenotyping, during treatment with lapatinib-trastuzumab in HER2+ BC patients (PAMELA trial). Moreover, we evaluate the relationship of tumour-immune contexture with hormone receptor status, intrinsic subtype and immune-related gene expression. sTIL levels increase after 2 weeks of HER2 blockade in HR-negative disease and HER2-enriched subtype. This is linked to a concomitant increase in cell density of all four immune subpopulations (CD3+, CD4+, CD8+, Foxp3+). Moreover, immune contexture analysis showed that immune cells spatially interacting with tumour cells have the strongest association with response to anti-HER2 treatment. Subsequently, sTILs consistently decrease at the surgery in patients achieving pathologic complete response, whereas most residual tumours at surgery remain inflamed, possibly reflecting a progressive loss of function of T cells. Understanding the features of the resulting tumour immunosuppressive microenvironment has crucial implications for the design of new strategies to de-escalate or escalate systemic therapy in early-stage HER2+ BC.

A CT-based Radiomics Signature Is Associated with Response to Immune Checkpoint Inhibitors in Advanced Solid Tumors

Background Reliable predictive imaging markers of response to immune checkpoint inhibitors are needed. Purpose To develop and validate a pretreatment CT-based radiomics signature to predict response to immune checkpoint inhibitors in advanced solid tumors. Materials and Methods In this retrospective study, a radiomics signature was developed in patients with advanced solid tumors (including breast, cervix, gastrointestinal) treated with anti-programmed cell death-1 or programmed cell death ligand-1 monotherapy from August 2012 to May 2018 (cohort 1). This was tested in patients with bladder and lung cancer (cohorts 2 and 3). Radiomics variables were extracted from all metastases delineated at pretreatment CT and selected by using an elastic-net model. A regression model combined radiomics and clinical variables with response as the end point. Biologic validation of the radiomics score with RNA profiling of cytotoxic cells (cohort 4) was assessed with Mann-Whitney analysis. Results The radiomics signature was developed in 85 patients (cohort 1: mean age, 58 years ± 13 [standard deviation]; 43 men) and tested on 46 patients (cohort 2: mean age, 70 years ± 12; 37 men) and 47 patients (cohort 3: mean age, 64 years ± 11; 40 men). Biologic validation was performed in a further cohort of 20 patients (cohort 4: mean age, 60 years ± 13; 14 men). The radiomics signature was associated with clinical response to immune checkpoint inhibitors (area under the curve [AUC], 0.70; 95% CI: 0.64, 0.77; P < .001). In cohorts 2 and 3, the AUC was 0.67 (95% CI: 0.58, 0.76) and 0.67 (95% CI: 0.56, 0.77; P < .001), respectively. A radiomics-clinical signature (including baseline albumin level and lymphocyte count) improved on radiomics-only performance (AUC, 0.74 [95% CI: 0.63, 0.84; P < .001]; Akaike information criterion, 107.00 and 109.90, respectively). Conclusion A pretreatment CT-based radiomics signature is associated with response to immune checkpoint inhibitors, likely reflecting the tumor immunophenotype. © RSNA, 2021 Online supplemental material is available for this article. See also the editorial by Summers in this issue.

Fusobacterium nucleatum persistence and risk of recurrence after preoperative treatment in locally advanced rectal cancer

BACKGROUND

Accumulating evidence has identified Fusobacterium as an important pathogenic gut bacterium associated with colorectal cancer. Nevertheless, only limited data exist about the role of this bacterium in locally advanced rectal cancer (LARC). In this study, we quantified Fusobacterium nucleatum in untreated and post-neoadjuvant chemoradiotherapy (nCRT) samples from LARC patients and investigated its association with therapy response and survival.

PATIENTS AND METHODS

A total of 254 samples from 143 patients with rectal adenocarcinomas were analyzed for the presence and abundance of F. nucleatum using RNA in situ hybridization and digital image analysis. Assay accuracy was determined using infected cell lines and tumor samples with available quantitative PCR data. We studied the impact of F. nucleatum load on pathologic complete response and relapse-free survival. Treatment-induced changes were evaluated in paired pre- and post-nCRT samples (n = 71). Finally, tumor microenvironment changes during nCRT were assessed in paired samples (n = 45) by immune contexture analysis.

RESULTS

F. nucleatum tissue levels by RNA in situ hybridization strongly correlated with quantitative PCR (r = 0.804, P < 0.001). F. nucleatum abundance was higher in untreated [median, 7.4; 95% confidence interval (3.7-16.2)] compared with treated [median, 1.6; 95% confidence interval (1.3-2.4)] tumors (P <0.001) with 58% (73/126) and 26% (22/85) positive tumors, respectively (P < 0.001). Baseline F. nucleatum levels were not associated with pathologic complete response. F. nucleatum positivity after nCRT, but not baseline status, significantly increased risk of relapse [hazard ratio = 7.5, 95% confidence interval (3.0-19.0); P < 0.001]. Tumors that turned F. nucleatum-negative after nCRT had a strong increase in CD8+ T cells post-nCRT (P < 0.001), while those that persisted F. nucleatum-positive after nCRT lacked CD8+ T cells induction in post-nCRT samples compared with baseline (P = 0.69).

CONCLUSION

F. nucleatum persistence post-nCRT is associated with high relapse rates in LARC, potentially linked to suppression of immune cytotoxicity.

Evolving Landscape of Molecular Prescreening Strategies for Oncology Early Clinical Trials

Most academic precision oncology programs have been designed to facilitate enrollment of patients in early clinical trials with matched targeted agents. Over the last decade, major changes were seen both in the targetable molecular alteration landscape and in drug development trends. In this article, we describe how the Vall d’Hebron Institute of Oncology molecular prescreening program adapted to a dynamic model of biomarker-drug codevelopment. We started with a tumor-agnostic hotspot mutation panel plus in situ hybridization and immunohistochemistry of selected markers and subsequently transitioned to tumor-specific amplicon-based next-generation sequencing (NGS) tests together with custom copy number, fusion, and outlier gene expression panels. All assays are optimized for archived formalin-fixed paraffin-embedded tumor tissues without matched germline sequencing. In parallel, biomarker-matched trials evolved from a scenario of few targets and large populations (such as PI3K inhibitors in PIK3CA mutants) to a complex situation with many targets and small populations (such as multiple targetable fusion events). Recruitment rates in clinical trials with mandatory biomarkers decreased over the last 3 years. Molecular tumor board meetings proved critical to guide oncologists on emerging biomarkers for clinical testing and interpretation of NGS results. The substantial increase of immunotherapy trials had a major impact in target prioritization and guided clinical implementation of new markers, such as tumor mutational burden, with larger exon-based NGS assays and gene expression signatures to capture microenvironment infiltration patterns. This new multiomics era of precision oncology is expected to increase the opportunities for early clinical trial matching.

Sequential immunohistochemistry and virtual image reconstruction using a single slide for quantitative KI67 measurement in breast cancer

Objective

Ki67 is a prognostic and predictive marker in breast cancer (BC). However, manual scoring (MS) by visual assessment suffers from high inter-observer variability which limits its clinical use. Here, we developed a new digital image analysis (DIA) workflow, named KiQuant for automated scoring of Ki67 and investigated its equivalence with standard pathologist's assessment.

Methods

Sequential immunohistochemistry of Ki67 and cytokeratin, for precise tumor cell recognition, were performed in the same section of 5 tissue microarrays containing 329 tumor cores from different breast cancer subtypes. Slides were digitalized and subjected to DIA and MS for Ki67 assessment. The intraclass correlation coefficient (ICC) and Bland-Altman plot were used to evaluate inter-observer reproducibility. The Kaplan-Meier analysis was used to determine the prognostic potential.

Results

KiQuant showed an excellent correlation with MS (ICC:0.905,95%CI:0.878–0.926) with satisfactory inter-run (ICC:0.917,95%CI:0.884–0.942) and inter-antibody reproducibilities (ICC:0.886,95%CI:0.820–0.929). The distance between KiQuant and MS increased with the magnitude of Ki67 measurement and positively correlated with analyzed tumor area and breast cancer subtype. Agreement rates between KiQuant and MS within the clinically relevant 14% and 30% cut-off points ranged from 33% to 44% with modest interobserver reproducibility below the 20% cut-off (0.606, 95%CI:0.467–0.727). High Ki67 by KiQuant correlated with worse outcome in all BC and in the luminal subtype (P = 0.028 and P = 0.043, respectively). For MS, the association with survival was significant only in 1 out of 3 observers.

Conclusions

KiQuant represents an easy and accurate methodology for Ki67 measurement providing a step toward utilizing Ki67 in the clinical setting.

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Automated Ki67 scoring workflow improved reproducibility.

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Sequential immunohistochemistry in the same section for precise cell recognition.

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Use of a tumor mask for automatic tumor region selection.

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Outperform pathologist-based Ki67 scoring in prognostic prediction.

HER2-Enriched Subtype and ERBB2 Expression in HER2-Positive Breast Cancer Treated with Dual HER2 Blockade

BACKGROUND

Identification of HER2-positive breast cancers with high anti-HER2 sensitivity could help de-escalate chemotherapy. Here, we tested a clinically applicable RNA-based assay that combines ERBB2 and the HER2-enriched (HER2-E) intrinsic subtype in HER2-positive disease treated with dual HER2-blockade without chemotherapy.

METHODS

A research-based PAM50 assay was applied in 422 HER2-positive tumors from five II-III clinical trials (SOLTI-PAMELA, TBCRC023, TBCRC006, PER-ELISA, EGF104090). In SOLTI-PAMELA, TBCRC023, TBCRC006, and PER-ELISA, all patients had early disease and were treated with neoadjuvant lapatinib or pertuzumab plus trastuzumab for 12-24 weeks. Primary outcome was pathological complete response (pCR). In EGF104900, 296 women with advanced disease were randomized to receive either lapatinib alone or lapatinib plus trastuzumab. Progression-free survival (PFS), overall response rate (ORR), and overall survival (OS) were evaluated.

RESULTS

A total of 305 patients with early and 117 patients with advanced HER2-positive disease were analyzed. In early disease, HER2-E represented 83.8% and 44.7% of ERBB2-high and ERBB2-low tumors, respectively. Following lapatinib and trastuzumab, the HER2-E and ERBB2 (HER2-E/ERBB2)-high group showed a higher pCR rate compared to the rest (44.5%, 95% confidence interval [CI] = 35.4% to 53.9% vs 11.6%, 95% CI = 6.9% to 18.0%; adjusted odds ratio [OR] = 6.05, 95% CI = 3.10 to 11.80, P < .001). Similar findings were observed with neoadjuvant trastuzumab and pertuzumab (pCR rate of 66.7% in HER2-E/ERBB2-high, 95% CI = 22.3% to 95.7% vs 14.7% in others, 95% CI = 4.9% to 31.1%; adjusted OR = 11.60, 95% CI = 1.66 to 81.10, P = .01). In the advanced setting, the HER2-E/ERBB2-high group was independently associated with longer PFS (hazard ratio [HR] = 0.52, 95% CI = 0.35 to 0.79, P < .001); higher ORR (16.3%, 95% CI = 8.9% to 26.2% vs 3.7%, 95% CI = 0.8% to 10.3%, P = .02); and longer OS (HR = 0.66, 95% CI = 0.44 to 0.97, P = .01).

CONCLUSIONS

Combining HER2-E subtype and ERBB2 mRNA into a single assay identifies tumors with high responsiveness to HER2-targeted therapy. This biomarker could help de-escalate chemotherapy in approximately 40% of patients with HER2-positive breast cancer.

Targeted multiplex proteomics for molecular prescreening and biomarker discovery in metastatic colorectal cancer

Protein biomarkers are widely used in cancer diagnosis, prognosis, and prediction of treatment response. Here we introduce the use of targeted multiplex proteomics (TMP) as a tool to simultaneously measure a panel of 54 proteins involved in oncogenic, tumour suppression, drug metabolism and resistance, in patients with metastatic colorectal cancer (mCRC). TMP provided valuable diagnostic information by unmasking an occult neuroendocrine differentiation and identifying a misclassified case based on abnormal proteins phenotype. No significant differences in protein levels between unpaired primary and metastatic samples were observed. Four proteins were found differentially expressed in KRAS-mutant as compared to wild-type tumours (overexpressed in mutant: KRAS, EGFR; overexpressed in wild-type: TOPO1, TOP2A). Survival analyses revealed the association between mesothelin expression and poor overall survival, whereas lack of PTEN protein expression associated with lower progression-free survival with anti-EGFR-based therapy in the first-line setting for patients with RAS wild-type tumour. Finally, outlier analysis identified putative targetable proteins in 65% of patients lacking a targetable genomic alteration. Our data show that TMP constitutes a promising, novel molecular prescreening tool in mCRC to identify protein expression alterations that may impact on patient outcomes and more precisely guide patient eligibility to clinical trials with novel targeted experimental therapies.

Exploratory analysis of the effect of taselisib on downstream pathway modulation and correlation with tumor response in ER-positive/HER2-negative early-stage breast cancer from the LORELEI trial

1050

Background: Taselisib (T) is an oral, potent, selective inhibitor of Class I PI3-kinase with enhanced activity against PIK3CA mutant cancer cells. Results from the LORELEI trial have demonstrated a significant improvement in ORR (objective response rate) by centrally assessed magnetic resonance imaging in all randomized patients as well as in the PIK3CA mutant (MT) cohort treated with neoadjuvant T plus letrozole (L) compared to placebo (P) plus L. Here we present the results of exploratory analyses of selected pathway-related phosphoproteins. Methods: Baseline (BL) and week3 (W3) tumor biopsies were obtained from 334 patients enrolled in the trial. Phosphoproteins (pAKT, pPRAS40 and pS6) were analyzed by IHC. BL levels as well as changes from BL to W3 were correlated with response assessed either by ORR or cell cycle arrest (Ki67 at W3 < 2.7%). Results: In the overall population, BL phosphoproteins levels were similar between the T and P arms. Higher pAKT (p < 0.001) and pPRAS40 (p = 0.004) levels were observed in MT vs wild-type (WT), whereas the opposite result was found for pS6 (p = 0.03). Treatment-induced absolute changes of phosphoproteins adjusted for BL levels were not significantly different between the T and P arms in the overall population, except for pPRAS40 with higher decrease in the T arm (p = 0.014). After stratification for PIK3CA genotype, a significantly greater decrease in expression levels was observed for pPRAS40 (p < 0.001) and pS6 (p = 0.020) in MT tumors treated with T. The treatment effects were not significantly different in the WT population. A trend for an association between decrease in pS6 levels at W3 and improved ORR was observed in the MT (p = 0.08) and T (p = 0.09) subgroups. The magnitude of pS6 suppression at W3 was higher in tumors achieving a cell cycle arrest in the MT/T subgroup (biserial correlation = -0.473). Conclusions: Exploratory analyses of phosphoproteins showed bioactivity of taselisib as indicated by downstream pathway suppression. Translational research aiming to integrate these results with additional exploratory biomarkers data is currently ongoing. Clinical trial information: NCT02273973.

On-treatment changes in tumor-infiltrating lymphocytes (TIL) during neoadjuvant HER2 therapy (NAT) and clinical outcome

574

Background: Higher quantity of pretreatment TIL (PT) is associated with improved pCR and EFS in HER2+ early breast cancer (BC). The value of on-treatment TIL is unknown. Methods: The NeoALTTO trial randomized 455 women with HER2+ BC to 12 weeks NAT with trastuzumab, lapatinib or combination with paclitaxel, followed by FEC after surgery. In the PAMELA trial 151 women received 18 weeks NAT with lapatinib and trastuzumab (±hormonal therapy). TIL were quantified on PT and on-treatment (W2) biopsies using the published method on H&E slides, and tested for associations with pCR (logistic regression), EFS and OS (Cox models) in univariate (UV) and multivariate (MV) analyses. The likelihood ratio test assessed added prognostic value to clinicopathological (CP) variables. pCR associations were validated in PAMELA. We investigated enrichment of immune cell subsets using previously published RNAseq data from NeoALTTO. Results: In NeoALTTO, PT and W2 TIL were evaluable in 277/455 (61%). We defined two groups: immune-poor (L+F) and immune-enriched (II+P), see Table. Immune-enriched (41%; 134) vs poor (59%; 164) patients had significantly higher pCR rates (40% vs 21%; UV OR 2.24; 95%CI 1.31-3.85; P = .003; MV P = .009), and added significant value to CP + PT TIL for prediction of pCR (P = .003). This was further confirmed in PAMELA (N = 94/151) (26% vs 6%; UV P = .021; MV P = .028). In NeoALTTO, the immune-enriched vs poor patients had significantly improved EFS (5 yr est 85% vs 60%; UV HR 0.31; 95%CI 0.18-0.54; P < .001; MV P < .001) and OS (5 yr est 91% vs 77%; UV HR 0.40; 95%CI 0.20-0.82; P = .012; MV P = 0.026), and provided significant added prognostic value beyond CP + pCR + PT TIL (EFS P < .001) In NeoALTTO PT samples, II vs F patients had enrichment of DCs, NKs and CD8+ including tissue resident memory cells (P = .009) suggesting requirement of key immune subsets. Further validation by IHC is ongoing. Conclusions: On-treatment TIL identifies patients more likely to achieve pCR and have improved EFS in early-stage HER2+ BC, beyond CP + PT TIL. This information could aid future trial design. Clinical trial information: NCT00553358, NCT01973660. [Table: see text]

A predictive model of pathologic response based on tumor cellularity and tumor-infiltrating lymphocytes (CelTIL) in HER2-positive breast cancer treated with chemo-free dual HER2 blockade

Background

The presence of stromal tumor-infiltrating lymphocytes (TILs) is associated with increased pathologic complete response (pCR) and improved outcomes in HER2-positive early-breast cancer (BC) treated with anti-HER2-based chemotherapy. In the absence of chemotherapy, the association of TILs with pCR following anti-HER2 therapy-only is largely unknown.

Patients and methods

The PAMELA neoadjuvant trial treated 151 women with HER2-positive BC with lapatinib and trastuzumab [and hormonal therapy if hormone receptor (HR)-positive] for 18 weeks. Percentage of TILs and tumor cellularity were determined at baseline (N = 148) and at day 15 (D15) of treatment (N = 134). Associations of TILs and tumor cellularity with pCR in the breast were evaluated. A combined score based on tumor cellularity and TILs (CelTIL) measured at D15 was derived in PAMELA, and validated in D15 samples from 65 patients with HER2-positive disease recruited in the LPT109096 neoadjuvant trial, where anti-HER2 therapy-only was administer for 2 weeks, then standard chemotherapy was added for 24 weeks.

Results

In PAMELA, baseline and D15 TILs were significantly associated with pCR in univariate analysis. In multivariable analysis, D15 TILs, but not baseline TILs, were significantly associated with pCR. At D15, TILs and tumor cellularity were found independently associated with pCR. A combined score (CelTIL) taking into account both variables was derived. CelTIL at D15 as a continuous variable was significantly associated with pCR, and patients with CelTIL-low and CelTIL-high scores had a pCR rate of 0% and 33%, respectively. In LPT109096, CelTIL at D15 was found associated with pCR both as a continuous variable and as group categories using a pre-defined cut-off (75.0% versus 33.3%).

Conclusions

On-treatment TILs, but not baseline TILs, are independently associated with response following anti-HER2 therapy-only. A combined score of TILs and tumor cellularity measured at D15 provides independent predictive information upon completion of neoadjuvant anti-HER2-based therapy.

Clinical trial number

NCT01973660.

Abstract P6-17-08: Dynamics of tumor-infiltrating lymphocytes (TILs) during neoadjuvant dual HER2 blockade in HER2-positive (HER2+) breast cancer in the absence of chemotherapy

Background: TILs in HER2+ breast cancer (BC) predict 1) prognosis in early setting, 2) complete pathological response (pCR) following neoadjuvant antiHER2-based therapy and 3) response to trastuzumab and pembrolizumab in the metastatic setting. However, less is known regarding changes in TILs during antiHER2-based treatment.

Methods: Stromal TILs where evaluated centrally using H/E slides in tumor samples from the PAMELA (NCT01973660) neoadjuvant phase II trial. Briefly, 151 women with HER2+ BC were treated with lapatinib and trastuzumab, and hormonal therapy if HR positive, for 18 weeks. TIL levels were determined at baseline (n=148), after 2 weeks of treatment (n=134) and at surgery (n=137). Expression of 560 genes, including immune-related genes (e.g. CD8A, CD4, PD1 and PDL1) was measured at the same timepoints (baseline n=151, 2-weeks n=144, surgery n=144) using the nCounter platform. Intrinsic subtyping at baseline was determined using the PAM50 gene expression predictor. Changes in TILs between 2 time-points were determined by paired t-tests. Correlation of TILs with gene expression was assessed by quantitative SAM analysis using a False Discovery Rate &lt;1%. All statistical tests were two-sided and considered significant when p&lt;0.05. All statistical analyses were carried out using the R software.

Results: Compared to baseline, a significant increase in TILs was observed at week 2 in HR- (p&lt;0.001) and HER2-enriched (HER2-E) tumors (p=0.001), but not in HR+ (p=0.133) and non-HER2-E tumors (p=0.067). Within HR- and HER2-E tumors, increase in TILs at week 2 from baseline was observed regardless of pathological response at surgery (pCR and HR- [p=0.008]; RD and HR- [p=0.037]; pCR and HER2-E [p=0.010]; RD and HER2-E [p=0.056]). Compared to week 2, a significant decrease in TILs at surgery was observed in HR- (p=0.002) and HER2-E (p=0.003) tumors, but not in HR+ (p=0.616) and non-HER2-E tumors (p=0.578). Within HR- and HER2-E tumors, a significant decrease in TILs between week 2 and surgery was observed in tumors achieving pCR (p=0.004 and p=0.005), while, in tumors not achieving pCR, no significant tendency was observed (26.4% and 33.0% of tumors showed an increase and a decrease of TILs between week 2 and surgery). Nonetheless, the vast majority of residual tumors (non-pCR) at surgery had TILs above ≥5%: 34.3% 5-10%, 21.0% 10-20%, 15.2% 20-40% and 11.4% ≥40%. Finally, TILs scoring was found highly enriched (FDR&lt;1%) for immune-related genes tracking activated CD8 T-cells (i.e. CD8A, CD3G, LAG3 and PD1). Expression of these immune genes consistently correlated with TIL levels across the 3 time-points.

Conclusions: In early HER2+ BC, a general increase in TILs is observed following 2 weeks of dual HER2 blockade. This observation is mostly observed in HR- and HER2-E subtype, but regardless of pathological response at surgery. After 2 weeks of treatment, TILs consistently decrease in patients achieving a pCR, whereas two main patterns of TILs expression are observed in patients with residual disease at surgery. Nonetheless, most residual tumors at surgery are inflamed (i.e. TILs ≥5%) and might be good candidates for clinical trials evaluating adjuvant immune checkpoint inhibitors.

Citation Format: Griguolo G, Holgado E, Cortés J, Fasani R, Pascual T, Paré L, Bermejo B, Oliveira M, Morales S, Martinez N, Vidal M, Pernas S, Lopez R, Muñoz M, Galvan P, Garau I, Manso L, Alarcón J, Martínez E, Villagrasa P, LLombart-Cussac A, Prat A, Nuciforo P. Dynamics of tumor-infiltrating lymphocytes (TILs) during neoadjuvant dual HER2 blockade in HER2-positive (HER2+) breast cancer in the absence of chemotherapy [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P6-17-08.

p95HER2-T cell bispecific antibody for breast cancer treatment

T cell bispecific antibodies (TCBs) are engineered molecules that include, within a single entity, binding sites to the T cell receptor and to tumor-associated or tumor-specific antigens. The receptor tyrosine kinase HER2 is a tumor-associated antigen in ~25% of breast cancers. TCBs targeting HER2 may result in severe toxicities, likely due to the expression of HER2 in normal epithelia. About 40% of HER2-positive tumors express p95HER2, a carboxyl-terminal fragment of HER2. Using specific antibodies, here, we show that p95HER2 is not expressed in normal tissues. We describe the development of p95HER2-TCB and show that it has a potent antitumor effect on p95HER2-expressing breast primary cancers and brain lesions. In contrast with a TCB targeting HER2, p95HER2-TCB has no effect on nontransformed cells that do not overexpress HER2. These data pave the way for the safe treatment of a subgroup of HER2-positive tumors by targeting a tumor-specific antigen.

Abstract LB-292: p95HER2-T cell bispecific antibody for breast cancer treatment

T cell bispecific antibodies (TCBs) are engineered molecules that include, within a single entity, binding sites to the T cell receptor and to a tumor-specific or a tumor-associated antigen. The receptor tyrosine kinase HER2 is a tumor-associated antigen in ~25% of breast cancers. Clinical evidence shows that TCBs targeting HER2 may result in severe toxicities, likely due to the physiologic levels of HER2 in normal epithelia. Approximately 40% of HER2-positive tumors express detectable levels of p95HER2, a carboxy-terminal fragment of HER2. We previously developed different antibodies that specifically recognize p95HER2 but not full-length HER2 and hypothesized that a TCB antibody recognizing p95HER2 would be exquisitely specific for tumor cells. Here, we describe the development of such p95HER2-TCB and show that it has a potent anti-tumor effect on p95HER2-expressing breast cancers. Since p95HER2 is not expressed in normal tissues, in contrast with HER2-TCB, it has no effect on non-transformed cells expressing physiological levels of HER2. These data paves the way for the safe targeting of a subtype of HER2-positive tumors with a novel tumor-specific TCB.

Citation Format: Rocío Vicario, Irene Rius Ruiz, Beatriz Morancho, Cristina Bernadó Morales, Sylvia Herter, Anne Freimoser-Grundscholber, Jitka Somandin, Johannes Sam, Oliver Ast, Águeda Martinez Barriocanal, Antonio Luque, Marta Escorihuela, Ismael Varela, Paolo Nuciforo, Roberta Fasani, Vicente Peg, Isabel Rubio, Javier Cortés, Violeta Serra, Santiago Escrivá, Jeff Sperinde, Ahmed Chenna, Weidong Huang, John Winslow, Maurizio Scaltriti, Josep Baselga, Josep Tabernero, Pablo Umaña, Marina Bacac, Cristina Saura, Christian Klein, Joaquín Arribas. p95HER2-T cell bispecific antibody for breast cancer treatment [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr LB-292.

Dual MET and ERBB inhibition overcomes intratumor plasticity in osimertinib-resistant-advanced non-small-cell lung cancer (NSCLC)

Background

Third-generation epidermal growth factor receptor tyrosine kinase inhibitors (EGFR-TKIs) such as osimertinib are the last line of targeted treatment of metastatic non-small-cell lung cancer (NSCLC) EGFR-mutant harboring T790M. Different mechanisms of acquired resistance to third-generation EGFR-TKIs have been proposed. It is therefore crucial to identify new and effective strategies to overcome successive acquired mechanisms of resistance.

Methods

For Amplicon-seq analysis, samples from the index patient (primary and metastasis lesions at different timepoints) as well as the patient-derived orthotopic xenograft tumors corresponding to the different treatment arms were used. All samples were formalin-fixed paraffin-embedded, selected and evaluated by a pathologist. For droplet digital PCR, 20 patients diagnosed with NSCLC at baseline or progression to different lines of TKI therapies were selected. Formalin-fixed paraffin-embedded blocks corresponding to either primary tumor or metastasis specimens were used for analysis. For single-cell analysis, orthotopically grown metastases were dissected from the brain of an athymic nu/nu mouse and cryopreserved at -80°C.

Results

In a brain metastasis lesion from a NSCLC patient presenting an EGFR T790M mutation, we detected MET gene amplification after prolonged treatment with osimertinib. Importantly, the combination of capmatinib (c-MET inhibitor) and afatinib (ErbB-1/2/4 inhibitor) completely suppressed tumor growth in mice orthotopically injected with cells derived from this brain metastasis. In those mice treated with capmatinib or afatinib as monotherapy, we observed the emergence of KRAS G12C clones. Single-cell gene expression analyses also revealed intratumor heterogeneity, indicating the presence of a KRAS-driven subclone. We also detected low-frequent KRAS G12C alleles in patients treated with various EGFR-TKIs.

Conclusion

Acquired resistance to subsequent EGFR-TKI treatment lines in EGFR-mutant lung cancer patients may induce genetic plasticity. We assess the biological insights of tumor heterogeneity in an osimertinib-resistant tumor with acquired MET-amplification and propose new treatment strategies in this situation.

RAD51 foci as a functional biomarker of homologous recombination repair and PARP inhibitor resistance in germline BRCA-mutated breast cancer

Background

BRCA1 and BRCA2 (BRCA1/2)-deficient tumors display impaired homologous recombination repair (HRR) and enhanced sensitivity to DNA damaging agents or to poly(ADP-ribose) polymerase (PARP) inhibitors (PARPi). Their efficacy in germline BRCA1/2 (gBRCA1/2)-mutated metastatic breast cancers has been recently confirmed in clinical trials. Numerous mechanisms of PARPi resistance have been described, whose clinical relevance in gBRCA-mutated breast cancer is unknown. This highlights the need to identify functional biomarkers to better predict PARPi sensitivity.

Patients and methods

We investigated the in vivo mechanisms of PARPi resistance in gBRCA1 patient-derived tumor xenografts (PDXs) exhibiting differential response to PARPi. Analysis included exome sequencing and immunostaining of DNA damage response proteins to functionally evaluate HRR. Findings were validated in a retrospective sample set from gBRCA1/2-cancer patients treated with PARPi.

Results

RAD51 nuclear foci, a surrogate marker of HRR functionality, were the only common feature in PDX and patient samples with primary or acquired PARPi resistance. Consistently, low RAD51 was associated with objective response to PARPi. Evaluation of the RAD51 biomarker in untreated tumors was feasible due to endogenous DNA damage. In PARPi-resistant gBRCA1 PDXs, genetic analysis found no in-frame secondary mutations, but BRCA1 hypomorphic proteins in 60% of the models, TP53BP1-loss in 20% and RAD51-amplification in one sample, none mutually exclusive. Conversely, one of three PARPi-resistant gBRCA2 tumors displayed BRCA2 restoration by exome sequencing. In PDXs, PARPi resistance could be reverted upon combination of a PARPi with an ataxia-telangiectasia mutated (ATM) inhibitor.

Conclusion

Detection of RAD51 foci in gBRCA tumors correlates with PARPi resistance regardless of the underlying mechanism restoring HRR function. This is a promising biomarker to be used in the clinic to better select patients for PARPi therapy. Our study also supports the clinical development of PARPi combinations such as those with ATM inhibitors.

Abstract P2-09-14: A predictive model of pathological response following dual HER2 blockade-only based on tumor cellularity and tumor-infiltrating lymphocytes (CelTIL) in HER2-positive breast cancer

Background: Increased number of tumor-infiltrating lymphocytes (TILs) at baseline is associated with pathological complete response (pCR) and improved outcomes in HER2-positive early breast cancer treated with anti-HER2-based chemotherapy. In the absence of chemotherapy, the association of TILs with pCR following anti-HER2 therapy-only is currently unknown.

Methods: The PAMELA (NCT01973660)neoadjuvant trial treated 151 women with HER2-positive breast cancer with lapatinib and trastuzumab (and hormonal therapy if hormone receptor-positive) for 18 weeks. Percentage of TILs and tumor cellularity were determined at baseline (n=148) and after 2 weeks of treatment (n=134). Associations of TILs and tumor cellularity with pCR in the breast were evaluated using univariate and multivariable logistic regression models. The regression coefficients were used to derive a score based on TILs and tumor cellularity measured at week 2 (CelTIL) was derived in PAMELA,and tested in week 2 samples from 65 patients with HER2+ disease recruited in the LPT109096 (NCT00524303) phase 2 neoadjuvant trial, where anti-HER2 therapy-only (trastuzumab, lapatinib or the combination) was administered for 2 weeks, followed by the addition of standard multi-agent chemotherapy for 24 weeks.

Results: In PAMELA, at baseline, TILs were significantly associated with pCR in univariate analysis but not in multivariable analysis (adjusted odds ratio [OR]=1.01, 0.98-1.03; p-value=0.620). A statistically significant increase in TILs was observed at week 2 compared to baseline (mean difference +6.9%; p-value&lt;0.001). At week 2, TILs were significantly associated with pCR in univariate and multivariable analyses (adjusted OR=1.04, 1.01-1.06; p-value=0.009). TILs and tumor cellularity at week 2 were independently associated with pCR and a combined score (from 0 to 100) taking into account both variables was derived. CelTIL as a continuous variable was significantly associated with pCR, and patients with CelTIL-low and CelTIL-high scores (cutoff &lt; 33.59) had a pCR rate of 0% and 33%, respectively. Independent validation of CelTIL in week 2 samples from 65 patients with HER2+ disease recruited in the LPT109096 phase 2 neoadjuvant trial will be presented at the conference.

Conclusions: A combined score of TILs and tumor cellularity at week 2 following anti-HER2 therapy-only is associated with pCR upon completion of neoadjuvant anti-HER2-based therapy.

Citation Format: Nuciforo P, Holgado E, Llombart A, Fasani R, Paré L, Pascual T, Oliveira M, Martínez N, Bermejo B, Vidal M, Pernas S, López R, Muñoz M, Garau I, Manso L, Alarcón J, Martínez E, Villagrasa P, Cortés J, Prat A. A predictive model of pathological response following dual HER2 blockade-only based on tumor cellularity and tumor-infiltrating lymphocytes (CelTIL) in HER2-positive breast cancer [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P2-09-14.

Concordance of blood- and tumor-based detection of RAS mutations to guide anti-EGFR therapy in metastatic colorectal cancer

Background

Circulating tumor DNA (ctDNA) is a potential source for tumor genome analysis. We explored the concordance between the mutational status of RAS in tumor tissue and ctDNA in metastatic colorectal cancer (mCRC) patients to establish eligibility for anti-epidermal growth factor receptor (EGFR) therapy.

Patients and methods

A prospective-retrospective cohort study was carried out. Tumor tissue from 146 mCRC patients was tested for RAS status with standard of care (SoC) PCR techniques, and Digital PCR (BEAMing) was used both in plasma and tumor tissue.

Results

ctDNA BEAMing RAS testing showed 89.7% agreement with SoC (Kappa index 0.80; 95% CI 0.71 − 0.90) and BEAMing in tissue showed 90.9% agreement with SoC (Kappa index 0.83; 95% CI 0.74 − 0.92). Fifteen cases (10.3%) showed discordant tissue-plasma results. ctDNA analysis identified nine cases of low frequency RAS mutations that were not detected in tissue, possibly due to technical sensitivity or heterogeneity. In six cases, RAS mutations were not detected in plasma, potentially explained by low tumor burden or ctDNA shedding. Prediction of treatment benefit in patients receiving anti-EGFR plus irinotecan in second- or third-line was equivalent if tested with SoC PCR and ctDNA. Forty-eight percent of the patients showed mutant allele fractions in plasma below 1%.

Conclusions

Plasma RAS determination showed high overall agreement and captured a mCRC population responsive to anti-EGFR therapy with the same predictive level as SoC tissue testing. The feasibility and practicality of ctDNA analysis may translate into an alternative tool for anti-EGFR treatment selection.

MRI Features of Cotyledonoid Dissecting Leiomyoma of the Uterus

Imaging evaluation of uterine masses is important to assess the type of lesion and to target surgery, if surgical excision is necessary. This can be decisive in fertile women with benign masses resembling malignancies, in order to avoid overtreatment. In this study, the magnetic resonance imaging (MRI) appearance of cotyledonoid dissecting leiomyoma of the uterus, a rare benign variant of leiomyoma mimicking malignancy, is presented.

Analysis of Fusobacterium persistence and antibiotic response in colorectal cancer

Colorectal cancers comprise a complex mixture of malignant cells, nontransformed cells, and microorganisms. Fusobacterium nucleatum is among the most prevalent bacterial species in colorectal cancer tissues. Here we show that colonization of human colorectal cancers with Fusobacterium and its associated microbiome-including Bacteroides, Selenomonas, and Prevotella species-is maintained in distal metastases, demonstrating microbiome stability between paired primary and metastatic tumors. In situ hybridization analysis revealed that Fusobacterium is predominantly associated with cancer cells in the metastatic lesions. Mouse xenografts of human primary colorectal adenocarcinomas were found to retain viable Fusobacterium and its associated microbiome through successive passages. Treatment of mice bearing a colon cancer xenograft with the antibiotic metronidazole reduced Fusobacterium load, cancer cell proliferation, and overall tumor growth. These observations argue for further investigation of antimicrobial interventions as a potential treatment for patients with Fusobacterium-associated colorectal cancer.

Abstract P6-07-16: Quantitative proteomic analysis of FGFR by mass spectrometry may improve identification of FGFR amplified tumors sensitive to inhibitor therapy

Background: The fibroblast growth factor receptors 1 and 2 (FGFR1 and FGFR2) have been reported as amplified in multiple solid tumors, including lung, breast and gastric cancers. The FGFR family of proteins is an attractive target for therapy due to the importance of FGFR signaling in the pathogenesis of diverse tumor types. However, pan-FGFR inhibitor have shown only modest efficacy in patients with FGFR1 or FGFR2 gene amplification as determined by fluorescence in situ hybridization (FISH). Gene copy number alterations may not be the optimal predictive biomarker since the targets of these drugs are FGFR proteins; recent findings suggest that direct measurement of the protein targets of FGFR inhibitor therapies may be necessary to assess their treatment efficacy. We therefore developed quantitative FGFR protein assays using selected reaction monitoring mass spectrometry (SRM-MS). We sought to correlate levels of FGFR1, FGFR2 and pan-FGFR (FGFR1-4) proteins as measured by SRM-MS with FGFR gene amplification status as determined by FISH.

Methods: Formalin-fixed, paraffin-embedded (FFPE) tissue sections from breast (n=18), esophageal (n=1), gastric (n=1), lung (n=2), and endometrial (n=1) tumors were obtained. A board-certified pathologist marked the tumor area for laser microdissection. Tumor cell proteins were extracted using the Liquid Tissue® process and subjected to SRM-MS for analysis of protein expression levels of FGFR1, FGFR2 and FGFR1-4, as well as other targetable proteins including MET, EGFR, and PD-L1. We compared FGFR protein levels with FGFR amplification defined as FGFR to CEP FISH ratio &gt;2.2.

Results: Of 23 tumor samples analyzed, the pan-FGFR1-4 proteomic assay detected FGFR protein in 11 cases (protein expression range: 217.8-3199.5 amol/ug). Ten of these 11 samples (91%) showed FGFR gene amplification. Only a single non-amplified case showed protein expression (235.6 amol/ug). FGFR protein (of 1, 2, and 1-4) was undetectable in 12 samples, of which 5 (42%) harbored FGFR1 amplification. Two of 2 (100%) of FGFR2-amplified cases (average copy number=38) showed high FGFR2 protein expression (3063.0 and 3199.5 amol/ug). Sensitivity of the pan-FGFR1-4 assay was superior to single FGFR assays.

Conclusion: A subset of FGFR-amplified tumors does not express FGFR protein when assessed by highly-sensitive SRM-MS. Patients whose tumors do not express FGFR protein are not likely to respond to FGFR inhibitor therapy, as supported by previous findings in squamous cell lung tumors, in which FGFR1 mRNA and/or protein expression levels greatly outperformed FGFR1 gene copy number in predicting sensitivity to a pan-FGFR inhibitors. An approach combining quantitative proteomics and FISH analyses may accurately identify patients most likely to respond to anti-FGFR protein agents.

Citation Format: Schwartz S, Tian Y, Fasani R, Diaz Delgado M, Hierro C, Rodon J, Sellappan S, Cecchi F, Hembrough T, Nuciforo P. Quantitative proteomic analysis of FGFR by mass spectrometry may improve identification of FGFR amplified tumors sensitive to inhibitor therapy [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P6-07-16.

Abstract S3-03: PAM50 intrinsic subtype as a predictor of pathological complete response following neoadjuvant dual HER2 blockade without chemotherapy in HER2-positive breast cancer: First results of the PAMELA clinical trial

Background: Prior neoadjuvant studies in HER2+ breast cancer have shown that dual HER2 blockade without chemotherapy achieves pathological complete responses (pCR) rates of 6-36% (TBCRC006/TBCRC023/NeoSphere). However, a major challenge today is how to select prospectively patients who will derive the maximum benefit from dual anti-HER2 therapies without chemotherapy. In this context, we and others have previously shown that HER2+ disease is biologically heterogeneous and composed of all the intrinsic molecular subtypes (Luminal A, Luminal B, HER2-enriched [HER2-E] and Basal-like). Among them, the HER2-E subtype shows the highest activation of the EGFR/HER2 pathway.

Methods: PAMELA (NCT01973660) is a non-randomized, open-label, multicentric, prospective translational research study in stage I-IIIA HER2+ breast cancer designed to evaluate the ability of the PAM50 intrinsic subtypes to predict pCR in the breast (pCRB; in situ allowed) following 18 weeks of neoadjuvant lapatinib and trastuzumab). Patients with HR+ disease received letrozole (if postmenopausal) or tamoxifen (if pre-menopausal). The primary objective was to compare the pCRB rates of the HER2-E versus the non-HER2-E subtypes in the intent-to-treat population. The study was planned with a power of 95% at a significance level of 0.05 to detect an absolute relative difference in pCRB rates between the two groups of 27% (i.e. 35% in HER2E and 8% in non-HER2-E). Day-15 formalin-fixed, paraffin-embedded tissue samples were prospectively collected and gene expression profiled using the nCounter platform. The intrinsic subtypes were identified using the research-based PAM50 predictor (Parker JCO 2009).

Results: A total of 151 patients were recruited (n=77 HR+ and n=74 HR-). Patient characteristics were: mean age (55 years), mean tumor size (2.84 cm), negative axilla (63.5%) and postmenopausal (60.2%). At baseline, intrinsic subtype distribution was: HER2-E (n=101, 66.9%), Luminal A (n=22; 14.6%), Luminal B (n=16; 10.6%), Basal-like (n=9; 6%) and Normal-Like (n=3; 2%). The overall pCRB was 30.5% (46/151), 18.2% in HR+ disease and 43.2% in HR- disease. Five patients (3.3%) presented progressive disease. Rates of pCRB in HER2-E and non-HER2-E subtypes were 40.6% and 10.0% (p&lt;0.0001), respectively. HER2-E subtype predicted pCRB independently of HR status. Within HR+ disease, pCRB rates were 31.6% in HER2-E subtype and 5.3% in non-HER2-E subtype (p=0.006). Within HR- disease, pCRB rates were 46.0% in HER2-E subtype and 27.3% in non-HER2-E subtypes (p=0.331). At Day-15, the majority of tumors became Normal-like (48.9%) or Luminal A (27.5%). Rates of pCRB were 46.9% in Normal-like tumors and 11.9% in non-Normal-like tumors when evaluated at day-15 (p&lt;0.0001).

Conclusions: The PAMELA trial met its primary endpoint. PAM50 HER2-E subtype identifies patients with HER2+ disease likely to derive a large benefit from dual anti-HER2 therapies +/- endocrine therapy, especially in HER2+/HR+ disease. In addition, early changes in gene expression indicative of a reduction of tumor cellularity are predictive of pathological complete response at surgery.

Citation Format: Prat Aparicio A, Cortes Castan J, Pare L, Galvan P, Bermejo B, Martínez N, Vidal M, Pernas S, López R, Muñoz M, Nuciforo P, Fasani R, Morales S, Oliveira M, de La Peña L, Peláez A, Llombart A. PAM50 intrinsic subtype as a predictor of pathological complete response following neoadjuvant dual HER2 blockade without chemotherapy in HER2-positive breast cancer: First results of the PAMELA clinical trial [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr S3-03.

Single dose bioavailability and pharmacokinetic study of a innovative formulation of α-lipoic acid (ALA600) in healthy volunteers

AIM

α-Lipoic acid is an important micronutrient with several pharmacological as well as antioxidant properties. The present study was aimed to examine the human bioavailability, pharmacokinetics (PK) and tolerability of an innovative oral formulation (ALA600) containing racemic α-lipoic acid 600 mg.

METHODS

After a single 600-mg oral administration in healthy volunteers, blood samples were collected up to 8 hours post dosing, and plasma α-lipoic acid concentrations were determined by Liquid Chromatography-Mass Spectrometry (LC-MS) detection.

RESULTS

The PK data revealed a short time to reach plasma peak oncentrations (50.8± 4.2 min) with a C(max) of 6.86±1.29 µg/mL. The C(max) implying that the new pharmaceutical form positively influences absorption and absorption time. The AUC value of 5.65±0.79 µg/mL*h is the more reliable measure of new formulation bioavailability. The half-life and MRT values further show that new formulation is absorbed consistently and rapidly and is eliminated efficiently. These PK data appear to promote further refinement of present formulation. Should the authors compare the obtained data with the recent published data, the new formulation of α-lipoic acid tends to show an improvement of C(max) value (2.5-5.4 times) and AUC (1.8 times).

CONCLUSION

ALA600 formulation is characterized by rapid absorption, high bioavailability, brief half-life and low toxicity. These PK parameters could significantly increase clinical use of lipoic acid with improvement of the therapeutic effects at the cellular level and might also prove to be the most suitable formulation for chronic administration such as peripheral neuropathies.

Sebaceous lymphadenoma of salivary gland: a case report and a review of the literature

The unusual case is described of a benign parotid gland neoplasm with intermingled sebaceous and lymphoid tissue, synchronous to breast cancer. In the past, the patient had undergone a simple surgical procedure for a cystic parotid gland lesion in that same gland. Secondary neoplasms have only occasionally been reported, since there are few cases for corroborating the strong correlation between salivary neoplasms and other carcinomas as in Muir-Torre syndrome; the previous cystic lesion showed the origin of the neoplasm from a sebaceous inclusion in the lymph node as a postulate of Warthin tumour.