Background

In solid tumors, both actionable gene fusions and MSI-H were rare but associated with better prognosis due to the promising treatments of tyrosine kinase inhibitors (TKIs) and immune checkpoint inhibitors (ICIs). Limited by the low incidence rates of fusions and MSI-H, the association between these two biomarkers remains largely unknown. Here we aimed at characterizing the distribution of fusions and MSI-H in 20296 solid tumors.

Methods

Hybrid capture-based next-generation sequencing (NGS) were performed in 20296 samples of solid tumors and matched normal pairs in a CAP/CLIA-approved laboratory (3DMed). NGS testing for germline and somatic mutations, copy number variation, fusion, and MSI were implemented.

Results

Of the 20296 tumor samples, MSI-H and fusion of ALK/RET/ROS1/FGFR/NTRK were observed in 620 (3.05%) and 410 samples (2.02%), respectively. MSI-H was relatively more prevalent in tumors of uterus (11.03%), intestine (7.85%), and stomach (4.98%), while 78.5% of fusion events were observed in lung cancers. In total, the incidence rate of fusion was higher in the MSI-H samples, compared to the MSS samples (3.06% vs. 1.99%, OR=1.56, P=0.079). This positive correlation was remarkably significant in cancers of intestine (OR=21.73, P=1.64*10^-12), where merely 9 fusions (6 of RET, 2 of NTRK, and 1 of ALK) were observed in 4507 MSS samples (0.20%), while 16 fusions (4 of RET, 8 of NTRK, and 4 of ALK) were detected in 384 MSI-H samples (7.85%). Table: 83MO

Association between gene fusion and MSI-H in the 20296 solid tumors

Conclusions

Our results revealed the positive correlation between actionable gene fusion and MSI-H in solid tumors, especially cancers of intestine. In the rare patients with both actionable gene fusion and MSI-H, observation and comparison of the anti-tumor activities of TKI and ICI are warranted.

Legal entity responsible for the study

Peking University Cancer Hospital.

Funding

Has not received any funding.

Disclosure

All authors have declared no conflicts of interest.

Background

Immune checkpoint inhibitors (ICIs) have dramatically improved the survival of cancer patients. Since the auto-immune toxicities with ICIs can be fatal, it is critical to optimize patient selection criteria. The current use of PD-L1 level and mismatch-repair/microsatellite-instability status has limitations. Recently tumor mutational burden (TMB) has emerged as a promising biomarker for ICI response. Accurate TMB estimation requires patient germline sequencing to filter out non-somatic variants; however, TMB is often calculated from tumor-only sequencing, relying on public databases (DB) to filter out non-somatic polymorphisms. We previously reported that filtering based on public DB significantly inflated TMBs. In this study, we investigated the impact of under-representation of minority ethnic groups in these DB and hypothesized that the inflation of TMBs will be racially disparate with falsely higher TMB in Black vs. White individuals.

Methods

Variants were identified in individual tumor and germline exomes of 157 Black and 713 White patients sequenced by Multiple Myeloma Research Foundation (MMRF). TMBs for each patient were calculated using 4 filtering criteria: (1) excluding variants in paired germline exomes; (2) excluding variants with minor allele frequency (MAF) ≥ 1% in 1000G/ExAc DB; (3) excluding variants with MAF ≥ 0.1% in 1000G/ExAc; and (4) excluding all variants in 1000G/ExAc.

Results

Compared to the gold standard of filtering germline variants by patient-paired germline sequencing data, TMBs were significantly higher in both Black and White patients using public DB for filtering regardless of the MAF thresholds. Furthermore, the TMBs were more significantly overestimated in Blacks compared to Whites (Table). Table: 84MO

Conclusions

TMB as a biomarker for selecting patients to receive ICIs without patient-paired germline sequencing may introduce racial bias.

Legal entity responsible for the study

The authors.

Funding

Has not received any funding.

Disclosure

M. Borad: Research grant/Funding (institution): Senhwa Pharmaceuticals, Adaptimmune, Agios Pharmaceuticals, Celgene Pharmaceuticals, EMD Merck Serono, Toray, Dicerna, Taiho Pharmaceuticals, Sun Biopharma, Isis Pharmaceuticals, Boston Biomed, Basilea, Incyte Pharmaceuticals, Mirna Phamraceuticals, Medim; Advisory/Consultancy, To self: ADC Therapeutics, G1 Therapeutics, Immunovative Therapies, OncBioMune Pharmaceuticals, Western Oncolytics, Lynx, Genentech, Merck, Huya, ; Travel/Accommodation/Expenses: AstraZeneca. A.S. Mansfield: Research grant/Funding (institution): Novartis & Verily; Honoraria (institution), Advisory Boards: AbbVie, AstraZeneca, BMS & Genentech; Travel/Accommodation/Expenses: Roche; Non-remunerated activity/ies, Director: Mesothelioma Applied Research Foundation. All other authors have declared no conflicts of interest.

Background

Alts in certain HR genes are associated with response to chemotherapy and PARP inhibitors. A comprehensive assessment of the distribution of alts in HR genes in a large pan-cancer data set could guide clinical management and trial design.

Methods

Genomic profiling on up to 465 genes, including core and peripheral HR genes BRCA1, BRCA2, PALB2, ATR, ATRX, ATM, BAP1, RAD51B, RAD51C, RAD51D, BRIP1, NBN, CHEK1, CHEK2, FANCA, FANCC and MRE11 was performed in a pan-cancer cohort of ∼150,000 tumour samples (Foundation Medicine, Inc.). Zygosity predictions, gLOH and biallelic status were calculated as described (PMID: 29415044; 27908594).

Results

HR alts were identified in 18.5% of samples (Table). In BRCA-associated (BA) cancers (ovarian, breast, pancreas, prostate), most HR alts were predicted biallelic (75.0%), with a lower rate in non-BA (NBA) cancers (45.7%). Biallelic HR alts had elevated gLOH relative to HR wildtype (HR-WT) (BA: median [med] gLOH 19.2 v 9.7, p <1e-100; NBA: med gLOH 11.0 v 7.1, p <1e-100). Monoallelic alts were not associated with elevated gLOH (p = 1.0). The strength of association between biallelic HR alts and gLOH was strongest in BRCA1, RAD51D, PALB2, RAD51C and BRCA2 (med gLOH 25.5, 21.6, 19.8, 19.3, 19.0 v 7.8 in HR-WT, all p <1e-25). Other genes exhibited weak or no association with gLOH (all med gLOH <15). Additional analyses will be presented examining variant somatic/germline status. Table: 85MO

Conclusions

This study identified five genes where biallelic alterations were strongly associated with high gLOH and found no associations for heterozygous alts. These results highlight the need to incorporate both gene and biallelic status when assessing HR deficiency for personalised treatment and clinical trials.

Editorial acknowledgement

Support for third-party editorial assistance for this abstract, furnished by Susannah Thornhill, PhD, of Health Interactions, was provided by F. Hoffmann-La Roche Ltd, Basel, Switzerland.

Legal entity responsible for the study

F. Hoffmann-La Roche Ltd, Basel, Switzerland.

Funding

F. Hoffmann-La Roche Ltd, Basel, Switzerland.

Disclosure

C. Benedikt Westphalen: Honoraria (self): Bayer, Celgene, Ipsen, Roche, Servier, Taiho; Advisory/Consultancy: Celgene, Shire/Baxalta, Rafael Pharmaceuticals, RedHill, F. Hoffmann-La Roche; Travel/Accommodation/Expenses: Bayer, Celgene, RedHill, Roche, Servier, Taiho; Non-remunerated activity/ies, Third-party editorial assistance: F. Hoffmann-La Roche Ltd, Basel, Switzerland. F. André: Research grant/Funding (institution): Roche, Pfizer, Lilly, Novartis, AstraZeneca, Daiichi Sankyo; Non-remunerated activity/ies, Third-party editorial assistance: F. Hoffmann-La Roche Ltd. S. Ganesan: Advisory/Consultancy: Merck, Novartis, Foundation Medicine, Roche, Foghorn Therapeutics, Inspirata; Shareholder/Stockholder/Stock options, Has equity in Inspirata: Inspirata; Spouse/Financial dependant, Spouse is an employee of Merck and has equity in Merck: Merck; Non-remunerated activity/ies, Third-party editorial assistance: F. Hoffmann-La Roche Ltd. V. Heinemann: Honoraria (self): Merck, Roche, Celgene, Amgen, Sanofi, Lilly, Sirtex, Boehringer-Ingelheim, Taiho, Servier; Advisory/Consultancy: Merck, Roche, Amgen, Sanofi, Sirtex, Servier, Celgene, Boehringer-Ingelheim, Halozyme, MSD, BMS; Research grant/Funding (institution): Merck, Roche, Amgen, Sirtex, Servier, Celgene, Boehringer-Ingelheim, Shire; Travel/Accommodation/Expenses: Merck, Roche, Amgen, Sirtex, Servier, Shire, MSD, BMS; Non-remunerated activity/ies, Third-party editorial assistance: F. Hoffmann-La Roche Ltd. E. Rouleau: Advisory/Consultancy: AstraZeneca, Roche Diagnostic, BMS; Travel/Accommodation/Expenses: AstraZeneca, BMS; Non-remunerated activity/ies, Third-party editorial assistance: F. Hoffmann-La Roche Ltd. A. Fine: Full/Part-time employment: Foundation Medicine; Shareholder/Stockholder/Stock options, Non-remunerated activity/ies, Third-party editorial assistance: F. Hoffmann-La Roche Ltd. L. Garcia Palacios: Full/Part-time employment, Non-remunerated activity/ies, Third-party editorial assistance: F. Hoffmann-La Roche Ltd. E.S. Sokol: Full/Part-time employment: Foundation Medicine ; Shareholder/Stockholder/Stock options, Non-remunerated activity/ies, Third-party editorial assistance: F. Hoffmann-La Roche Ltd. M. Thomas: Shareholder/Stockholder/Stock options, Full/Part-time employment, Non-remunerated activity/ies, Third-party editorial assistance: F. Hoffmann-La Roche Ltd. J. Mateo: Advisory/Consultancy: AstraZeneca, Amgen, MSD, Clovis Oncology, Janssen, Roche; Speaker Bureau/Expert testimony: Astellas; Research grant/Funding (institution): AstraZeneca, Pfizer Oncology; Travel/Accommodation/Expenses: AstraZeneca, Janssen, Astellas; Spouse/Financial dependant, Research grant to institution: AstraZeneca ; Non-remunerated activity/ies, Third-party editorial assistance: F. Hoffmann-La Roche Ltd; Spouse/Financial dependant, Advisory board: F. Hoffmann-La Roche Ltd.

Background

Carcinoma of unknown primary (CUP) is a rare cancer diagnosis of exclusion. Because of the paucity of CUP cases and the ill-defined treatment guidelines, patients have poor prognoses. In efforts to improve patient outcomes, the efficacy of a personalized genomic matched N-of-One approach including tailored combination therapies was investigated.

Methods

Overall, 97 tumors had next-generation sequencing (NGS) of tissue (N=74) and/or cell-free DNA (cfDNA) (N=72). Immune biomarkers including PD-L1 immunohistochemistry, microsatellite instability (MSI) status, and tumor mutation burden (TMB) were also evaluated. Matching Score (MS) (the number of targeted deleterious genomic alterations divided by the total number of deleterious alterations) was assessed for patients.

Results

Overall, 59 of 97 patients (60.8%) were women; median age at diagnosis was 63 years (range, 21-95). The median number of alterations for 74 patients with tissue NGS was 4 (range, 0-25); most commonly altered genes were TP53, 55.4% (41/74); CDKN2A, 24.3%; and KRAS, 20.3%. The median number of alterations for 72 patients with cfDNA was 2 (range, 0-9); most common altered genes were TP53, 61.1% (44/72); KRAS, 22.2%; and PIK3CA, 16.7%. Overall, 30.9% of 55 patients tested for PD-L1 were positive (defined as ≥1% on tumor [n = 16] or tumor-infiltrating lymphocytes [n = 1]); 9.4% (6/64) of tumors had high TMB (≥20 mutations/mb), while 3.6% (2/55) were MSI-High. Clinical outcomes for 62 patients were evaluable. Comparing patients with high degrees of matching of alterations to therapies (MS≥50%; n=15) versus low MS (<50%;n=47, including 25 with no matched therapy), median progression-free survival was 10.4 vs. 2.8 months (95% CI 0.11-0.64; HR 0.27; P=0.002); median overall survival, 15.8 vs. 6.9 months (95% CI 0.17-1.16; HR 0.45; P=0.09). The disease control rate (stable disease ≥6 months plus partial or complete response) was significantly higher in the high vs. low MS group (71% vs. 24%; P=0.003).

Conclusions

Among patients with CUP, personalized combination treatments with high degrees of molecular matching to genomic alterations (MS≥50%) were associated with improved outcomes.

Legal entity responsible for the study

The authors.

Funding

Joan and Irwin Jacobs Fund and NIH P30 CA023100.

Disclosure

S. Kato: Advisory/Consultancy: Foundation Medicine. J. Sicklick: Research grant/Funding (institution): Novartis Pharmaceuticals; Research grant/Funding (institution): Amgen Pharmaceuticals; Research grant/Funding (institution): Foundation Medicine; Advisory/Consultancy: Grand Rounds; Advisory/Consultancy: Loxo Oncology; Advisory/Consultancy: Deciphera; Advisory/Consultancy: Roche. R. Kurzrock: Research grant/Funding (institution): Genentech; Research grant/Funding (institution): Incyte; Research grant/Funding (institution): Merck; Research grant/Funding (institution): Serono; Research grant/Funding (institution): Pfizer; Research grant/Funding (institution): Sequenom; Research grant/Funding (institution): Foundation Medicine; Research grant/Funding (institution): Grifols; Research grant/Funding (institution): Guardant; Advisory/Consultancy: Loxo; Advisory/Consultancy: X Biotech; Advisory/Consultancy: NeoMed; Advisory/Consultancy: Actuate Therapeutics; Speaker Bureau/Expert testimony: Roche; Leadership role, Shareholder/Stockholder/Stock options: IDby DNA; Leadership role, Shareholder/Stockholder/Stock options: Curematch Inc. All other authors have declared no conflicts of interest.

Background

CSF cytology is the gold standard diagnostic test for leptomeningeal metastasis, but has a low sensitivity often requiring multiple repeats. Ultra low pass whole genome sequencing (ulpWGS) allows estimation of the tumour-derived fraction in cell-free DNA (cfDNA) without prior sequencing of primary tumour, and could improve BCLM diagnosis when CSF cytology is equivocal.

Methods

cfDNA was extracted from CSF collected at the time of diagnostic lumbar puncture in patients with breast cancer undergoing investigation for BCLM (n = 25). ulpWGS (0.1X) and estimation of tumour-derived cfDNA fraction (CSF TF) was performed. Serial CSF TF were also measured from patients subsequently undergoing intrathecal therapy for confirmed BCLM.

Results

In 32% (8/25) multiple CSF sampling was performed due to initial negative or equivocal cytology. 20/25 cases had confirmed BCLM: positive MRI and CSF cytology (14/25, 56%); MRI only (3/25, 12%), or cytology only (3/25, 12%). The remaining 5/25 had suspected but non-confirmed BCLM, with negative CSF cytology (5/25) and normal (4/25) or borderline (1/25) MRI findings. At median 20 months follow up, these patients had no evidence of BCLM. CSF TF in confirmed cases was significantly higher (median 61.2%) than non-confirmed BCLM (median 5.0%) (p <0.0001). In those with confirmed BCLM, CSF TF was similar regardless of variable final cytology status (Table). Serial sampling showed that CSF TF changed in response to intrathecal therapy, while CSF cytology and MRI were often unchanged or equivocal. Relapse of BCLM during intrathecal chemotherapy was detected up to 4 weeks before clinical deterioration. Table: 87MO

Conclusions

Measuring CSF TF by ulpWGS appears to better identify confirmed vs non-confirmed BCLM than CSF cytology, and could remove the need for repeat lumbar punctures. Serial CSF TF measurement during intrathecal chemotherapy also provides a quantitative response biomarker to help guide clinical management.

Legal entity responsible for the study

The authors.

Funding

Medical Research Council.

Disclosure

All authors have declared no conflicts of interest.

Background

While the function of myeloid cells in cancer progression is widely studied, clinical data on their role during immune checkpoint blockade (ICB) response are limited. Better understanding of mechanisms contributing to response to ICB will provide a rationale for future combination treatments. By combining unbiased profiling of circulating immune cells in patients treated with ICB with mechanistic studies in mouse models, we aimed to study the role of myeloid cells in ICB response.

Methods

Multiparameter flow cytometry was performed on fresh blood from metastatic triple-negative breast cancer (TNBC) patients in the phase 2 TONIC trial (n=111) before start and after 3 cycles of anti-PD1. In addition, we used genetically engineered mouse models of primary and metastatic breast cancer for mechanistic studies. Finally, we validated our findings in 5 cancer types: metastatic non-small cell lung cancer (NSCLC; n=55), metastatic bladder cancer (n=34), metastatic mismatch repair deficient (dMMR) cancer (n=11) and early-stage dMMR (n=21) or MMR-proficient (pMMR) colon cancer (CC; n=17). RNA-sequencing was available for the TNBC and CC trials.

Results

A significant increase in circulating eosinophils during ICB was observed in patients with TNBC responding to ICB (p=0.002), but not in non-responders. In breast cancer mouse models that respond to dual ICB and cisplatin, we found that ICB response was lost upon depletion of eosinophils. Importantly, we found that an increase in eosinophils was also associated with response in NSCLC (p=0.03), early-stage pMMR CC (p=0.04) and in bladder cancer (p=0.05), but not in early-stage or metastatic dMMR tumors. Furthermore, we observed increased expression of eosinophil-related genes upon ICB in tumors of responders with metastatic TNBC and early-stage CC.

Conclusions

An increase in eosinophils is associated with ICB response in multiple tumor types and studies in mouse models uncovered a functional role for eosinophils during ICB response. These data indicate that eosinophils are mechanistically involved in response to ICB. Future combination strategies should consider engaging eosinophils to increase ICB efficacy.

Legal entity responsible for the study

The authors.

Funding

Dutch Cancer Society.

Disclosure

M. Chalabi: Advisory/Consultancy, Research grant/Funding (institution): Bristol-Myers-Squib; Research grant/Funding (institution): Roche/Genentech. M.S. van der Heijden: Advisory/Consultancy, Research grant/Funding (institution): Roche/Genentech; Advisory/Consultancy, Research grant/Funding (institution): Astellas; Advisory/Consultancy, Research grant/Funding (institution): AstraZeneca; Advisory/Consultancy, Research grant/Funding (institution): Bristol-Myers-Squib. W.S.M.E. Theelen: Research grant/Funding (institution): MSD; Research grant/Funding (institution): AstraZeneca. E.E. Voest: Research grant/Funding (institution): Bristol-Myers-Squib. K.E. de Visser: Research grant/Funding (institution): Roche; Advisory/Consultancy: Third Rock Ventures. M. Kok: Advisory/Consultancy, Research grant/Funding (institution): Bristol-Myers-Squib; Research grant/Funding (institution): Roche/Genentech; Research grant/Funding (institution): AstraZeneca; Advisory/Consultancy: Daiichi Sankyo. All other authors have declared no conflicts of interest.

Background

Triple negative breast cancer (TNBC) presents with an aggressive clinical phenotype lacking expression of conventional drug targets. Overall survival in early- and advanced-stage disease is poor.

Methods

TNBC-MERIT is a phase I trial (NCT02316457) assessing the feasibility, safety and immunogenicity of a liposome-formulated intravenous RNA vaccine encoding different tumor antigen categories in TNBC patients after surgery and (neo-)adjuvant chemotherapy. Patients in two arms of this trial received a personalized set of pre-manufactured non-mutated shared tumor-associated antigens with or without universal T helper epitopes. In a third arm, patients were vaccinated with IVAC_M_uID, an on-demand manufactured Individualized NeoAntigen Specific Immunotherapy (iNeST) encoding neoepitopes derived from up to 20 cancer mutations determined by NGS. This report provides a preliminary data analysis of immune responses in IVAC_M_uID-vaccinated patients as analyzed by IFNγ-ELISpot, multimer staining, TCR repertoire profiling and single cell TCR sequencing (data final mid-2020).

Results

Immunogenicity data was generated from all 14 IVAC_M_uID-treated patients. All analyzed patients had vaccine-induced CD4⁺ and/or CD8⁺ T-cell responses against 1 to 10 of the vaccine neoepitopes detected by IFNγ ELISpot, ex vivo or after in vitro stimulation. A substantial number of T-cell responses against individual neoepitopes were induced de novo and of high magnitude (up to 10.3% of peripheral CD8 T cells). One of the index patients characterized in more detail mounted CD4⁺ and/or CD8⁺ T-cell responses against 10 of 20 vaccine neoepitopes. The highly poly-epitopic TCR-clonotype diversified CD8⁺ T-cell response comprised in aggregate about 30% of total peripheral CD8⁺ T cells and was sustained at high levels for at least 6 months after the last vaccination. Vaccine-induced CD8⁺ T cells were of effector/memory, PD1⁺ phenotype, with a high fraction IFNγ/TNFα/Mip-1a&b triple-positive.

Conclusions

This preliminary data suggests that the iNeST IVAC_M_uID is highly efficient in inducing strong poly-epitopic T-cell responses in patients with TNBC in the post-(neo) adjuvant setting.

Clinical trial identification

NCT02316457.

Legal entity responsible for the study

BioNTech SE.

Funding

BioNTech SE.

Disclosure

M. Schmidt: Honoraria (self), Advisory/Consultancy, Travel/Accommodation/Expenses: Roche; Research grant/Funding (self): BioNTech SE; Research grant/Funding (self): Genentech. I. Vogler: Full/Part-time employment: BioNTech RNA Pharmaceuticals GmbH. E. Derhovanessian: Full/Part-time employment: BioNTech SE. T. Omokoko: Full/Part-time employment: BioNTech Cell & Gene Therapies GmbH. E. Godehardt: Full/Part-time employment: BioNTech RNA Pharmaceuticals GmbH. A. Cortini: Full/Part-time employment: BioNTech Cell & Gene Therapies GmbH. S. Newrzela: Full/Part-time employment: BioNTech Cell & Gene Therapies GmbH. J. Grützner: Full/Part-time employment: BioNTech SE. S. Bolte: Full/Part-time employment: BioNTech SE. D. Langer: Full/Part-time employment: BioNTech SE. T. Sjöblom: Shareholder/Stockholder/Stock options, Officer/Board of Directors: Exscale Biospecimen Solution A. Ö. Türeci: Leadership role, Officer/Board of Directors: BioNTech SE. U. Sahin: Leadership role, Officer/Board of Directors: BioNTech SE. All other authors have declared no conflicts of interest.

Background

The majority of HER2+ breast cancer patients develop resistance to HER2 inhibitors and there is a pressing need for more efficacious therapies. Phosphatases are druggable targets but their role in HER2 therapy resistance is poorly understood. Dual specificity phosphatase (DUSP) 1 & 6 have key roles in tumor cell growth and apoptosis and their blockade augments chemosensitivity in human neoplasms. Here, we investigated the contribution of DUSP1 & 6 to resistance to HER2 inhibitors in breast cancer.

Methods

Genome editing; cell viability; Western blotting; RNA-seq; synergy analysis; xenograft, intracranial inoculation.

Results

DUSPs inhibition by RNAi and CRISPR procedures reduced cell viability and increased sensitivity to HER2 inhibitors in drug resistant cells and DUSPs overexpression promoted drug resistance in senstive cells. In an acquired resistant model with long-term exposure to Lapatinib, DUSP6 was highly expressed in the early stages of drug treatment and combination of Lapatinib or Neratinib with BCI, a DUSP1 & 6 inhibitor, prevented development of resistant clones. The AKT inhibitor MK2206 in combination with HER2-directed therapies is in clinical trials for the resistant disease. We found that compared to MK2206, BCI in combination with Lapatinib induced apoptosis in resistant cells. While MK2206 increased the expression of HER2 & HER3, BCI alone or in combination with Lapatinib reduced both HER2 and HER3. Consistently, RNAi-mediated depletion of DUSP6 reduced HER2 & HER3, implying for DUSP6-mediated regulation of HER2 & HER3. Moreover, mice injected intracranially with DUSP6 knockout cells had longer survival, compared with CAS9. Microenvironmental-mediated resistance to HER2 inhibitors occurs by the HER3 ligand heregulin (HRG). We found that BCI, but not MK2206, abrogates HRG-induced rescue in sensitive cells. Ultimately, a BCI+Lapatinib combination therapy reduced tumor growth in a xenograft model of resistant cells.

Conclusions

DUSP1 & 6 promote both inherent & acquired resistance to HER2 inhibitors and their inhibition provides important advantages over AKT blockade. Further investigation of the expression of DUSP1 & 6 in followed-up patients is warranted to further validate their role in resistance to HER2 inhibitors.

Legal entity responsible for the study

Prof. Jukka Westermarck.

Funding

A K. Albin Johansson Cancer Researcher grant from the Finnish Cancer Institute.

Disclosure

All authors have declared no conflicts of interest.

Background

Preclinical studies indicate that alterations of PIK3/AKT/mTOR pathway may be correlated with resistance to CDK4/6 inhibitors (CDK4/6i) in breast cancer (BC) cells and that PI3K inhibitors could prevent resistance to CDK4/6i [Abreu H MT, et al. Cancer Res 2016;76:2301]. For these compelling evidences the present study evaluated the impact of PI3K mutations on treatment outcome in metastatic BC (mBC) patients (pts) receiving CDK4/6i in association with hormonal therapy as per approved indication.

Methods

Thirty pts treated with palbociclib (n=26) or ribociclib (n=4) plus hormonal therapy were enrolled. Plasma samples were obtained prior to CDK4/6i treatment and circulating free DNA (cfDNA) extraction was performed using the QIAamp Circulating Nucleic Acid Kit (Qiagen). PI3K mutations (C420R, E542K, E545A, E545D, E545G, E545K, Q546E, Q546R, H1047L, H1047R, H1047Y) were analysed on cfDNA using a QX100 ddPCR (Bio-Rad).

Results

In pts with (n=12) vs. without (n=18) PI3K mutations, PFS was significantly shorter (5.9 vs 11.6 months, p=0.01, respectively). The univariate and multivariate analysis comparing PFS and clinically relevant data (i.e., age, metastasis, previous lines of hormonal or chemotherapy), confirmed PI3K as the only biomarker significantly associated to PFS (p=0.01). A significant correlation was observed between Ki67 expression in primary lesions and PI3K status. Higher Ki67 levels were associated with PI3K mutations vs. none (Ki67%, 25.36±11.02 vs. 13.17±10.14; p=0.006). The significance was maintained when PI3K mutant pts were stratified as low (<14%), intermediate (14–20%) and high (>20%) Ki67 levels (p=0.009). Despite the strong correlation, Ki67 did not appear significantly associated with median PFS to CDK4/6i, and the presence of PI3K mutations remained an independent predictor of clinical outcome to CDK4/6i.

Conclusions

In conclusion, PI3K status should be considered a potential predictive biomarker of CDK4/6i and, based on these data, the sequence of treatments (CDK4/6 vs. PI3Ki) may be reconsidered.

Clinical trial identification

Circus study - ID 5694.

Legal entity responsible for the study

The authors.

Funding

Has not received any funding.

Disclosure

All authors have declared no conflicts of interest.

Background

PARSIFAL was a randomized phase II trial aimed at evaluating the efficacy of palbociclib (P) plus either fulvestrant (F) or letrozole (L) in Estrogen Receptor[+]/Human Epidermal Growth Factor Receptor 2[-] metastatic breast cancer. The present study focused on establishing luminal breast cancer PDX models from a cohort of enrolled patients in an effort to develop preclinical models that recapitulate the disease before and after treatment with P and endocrine therapy (ET).

Methods

14 pre- and 18 post-treatment tumors were transplanted into immunocompromised mice. Xenografts were profiled using a capture-based exome sequencing panel and analyzed by immunohistochemistry as well as for the in vivo antiproliferative activity of P plus the patient-matched ET. Models of acquired resistance were generated from responder models and characterized. Predictive markers of response were analyzed and, in the case of non-responder models, additional treatments were tested in vivo and/or ex vivo.

Results

Successful engraftments were established in 3 of the 32 tumors (take rate 9%, 95% CI 1.8% -23.1%). Of those, PDX426 and PDX446 derived from pre-treatment tumors of patients receiving P+L and P+F, respectively, and PDX450 from a post-treatment tumor of a patient treated with P+L. PDX426 harbored an FGFR1 amplification and PDX446 harbored concomitant PIK3CA and PTEN mutations. Both PDXs expressed normal levels of pRb and cyclin E1. PDX446 showed sensitivity to P+F or P+L for >95 days, resembling the patient’s clinical response. Of note, PDX446 was also sensitive to single-agent F or L. The model of acquired resistance to P+F exhibited lower expression of pRb than the sensitive model. PDX450 harbored concomitant ESR1, PIK3CA, and PTEN mutations and expressed low pRb. Despite an initial response, all tumors progressed to P+L after 80 days, matching the clinical disease progression. The P+L-resistant tumors were also resistant to P+F in vivo but sensitive to the PI3K-α inhibitor alpelisib plus F ex vivo.

Conclusions

PDX models showed comparable treatment responses to those observed clinically, providing information about the additional benefit of P to ET alone as well as effective treatment options in the post-P setting.

Clinical trial identification

NCT02491983.

Legal entity responsible for the study

MedSIR.

Funding

Pfizer.

Disclosure

M. Scaltriti: Leadership role: medendi.org; Research grant/Funding (institution): Menarini Richerche, AstraZeneca, Daiichi Sankyo, Regeneron, BD Therapeutics, Puma Biotechnology, Immunomedics, Targimmune ; Advisory/Consultancy: Lilly, Menarini Richerche, AstraZeneca, Daiichi Sankyo. C. Saura: Advisory/Consultancy: AstraZeneca, Celgene, Daiichi Sankyo, F. Hoffmann - La Roche Ltd, Genomic Health, Merck, Sharp and Dhome España S.A., Novartis, Odonate Therapeutics, Pfizer, Philips Healthwork, Pierre Fabre, prIME Oncology, Puma, Synthon and Sanofi Aventis; Honoraria (institution): AstraZeneca, Daiichi Sankyo, Eli Lilly and Company, Genentech, Immunomedics, Macrogenics, Merck, Sharp and Dhome España S.A., Novartis, Pfizer, Piqur Therapeutics, Puma, Roche, Synthon and Zenith Pharma. M. Capelán: Non-remunerated activity/ies, Participation in the video shooting organised by Novartis: Novartis. M. Gil-Gil: Honoraria (self): Novartis, Pfizer. A. Llombart Cussac: Leadership role: Eisai, Celgene, Lilly, Pfizer, Roche, Novartis, MSD; Shareholder/Stockholder/Stock options: MedSIR, Initia-Research; Advisory/Consultancy: Lilly, Roche, Pfizer, Novartis, Pierre-Fabre, GenomicHealth, GSK; Speaker Bureau/Expert testimony: Lilly, AstraZeneca, MSD; Research grant/Funding (self): Roche, Foundation Medicine, Pierre-Fabre, Agendia; Travel/Accommodation/Expenses: Roche, Lilly, Novartis, Pfizer, AstraZeneca. J. Cortés: Advisory/Consultancy: Roche, Celgene, Cellestia, AstraZeneca, Biothera Pharmaceutical, Merus, Seattle Genetics, Daiichi Sankyo, Erytech, Athenex, Polyphor, Lilly, Servier, Merck Sharp&Dohme, GSK, Leuko, Bioasis, Clovis Oncology; Honoraria (self): Roche, Novartis, Celgene, Eisai, Pfizer, Samsung Bioepis, Lilly, Merck Sharp&Dohme, Daiichi Sankyo; Research grant/Funding (institution): Roche, Ariad pharmaceuticals, AstraZeneca, Baxalta GMBH/Servier Affaires, Bayer healthcare, Eisai, F.Hoffman-La Roche, Guardanth health, Merck Sharp&Dohme, Pfizer, Piqur Therapeutics, Puma C, Queen Mary University of London; Shareholder/Stockholder/Stock options: MedSIR. J.M. Perez Garcia: Advisory/Consultancy: Roche, Lilly; Travel/Accommodation/Expenses: Roche. M. Del Campo: Advisory/Consultancy: Pfizer. M. Bellet Ezquerra: Advisory/Consultancy: Novartis, Pfizer, Lilly; Speaker Bureau/Expert testimony, Non-remunerated activity/ies: Novartis, Pfizer, Lilly; Non-remunerated activity/ies, Contracted Research. Site PI clinical trials: Novartis, Pfizer, Lilly, Genentech. V. Serra: Non-remunerated activity/ies, Support for non-commercial research: Novartis, Genetech and AstraZeneca. All other authors have declared no conflicts of interest.