CD4+ T cell activation distinguishes response to anti-PD-L1+anti-CTLA4 therapy from anti-PD-L1 monotherapy

Cancer patients often receive a combination of antibodies targeting programmed death-ligand 1 (PD-L1) and cytotoxic T lymphocyte antigen-4 (CTLA4). We conducted a window-of-opportunity study in head and neck squamous cell carcinoma (HNSCC) to examine the contribution of anti-CTLA4 to anti-PD-L1 therapy. Single-cell profiling of on- versus pre-treatment biopsies identified T cell expansion as an early response marker. In tumors, anti-PD-L1 triggered the expansion of mostly CD8+ T cells, whereas combination therapy expanded both CD4+ and CD8+ T cells. Such CD4+ T cells exhibited an activated T helper 1 (Th1) phenotype. CD4+ and CD8+ T cells co-localized with and were surrounded by dendritic cells expressing T cell homing factors or antibody-producing plasma cells. T cell receptor tracing suggests that anti-CTLA4, but not anti-PD-L1, triggers the trafficking of CD4+ naive/central-memory T cells from tumor-draining lymph nodes (tdLNs), via blood, to the tumor wherein T cells acquire a Th1 phenotype. Thus, CD4+ T cell activation and recruitment from tdLNs are hallmarks of early response to anti-PD-L1 plus anti-CTLA4 in HNSCC.

Pan-Cancer Detection and Typing by Mining Patterns in Large Genome-Wide Cell-Free DNA Sequencing Datasets

BACKGROUND

Cell-free DNA (cfDNA) analysis holds great promise for non-invasive cancer screening, diagnosis, and monitoring. We hypothesized that mining the patterns of cfDNA shallow whole-genome sequencing datasets from patients with cancer could improve cancer detection.

METHODS

By applying unsupervised clustering and supervised machine learning on large cfDNA shallow whole-genome sequencing datasets from healthy individuals (n = 367) and patients with different hematological (n = 238) and solid malignancies (n = 320), we identified cfDNA signatures that enabled cancer detection and typing.

RESULTS

Unsupervised clustering revealed cancer type-specific sub-grouping. Classification using a supervised machine learning model yielded accuracies of 96% and 65% in discriminating hematological and solid malignancies from healthy controls, respectively. The accuracy of disease type prediction was 85% and 70% for the hematological and solid cancers, respectively. The potential utility of managing a specific cancer was demonstrated by classifying benign from invasive and borderline adnexal masses with an area under the curve of 0.87 and 0.74, respectively.

CONCLUSIONS

This approach provides a generic analytical strategy for non-invasive pan-cancer detection and cancer type prediction.

Abstract 4281: Overcoming preanalytical variabilities for peripheral blood mononuclear cells and exosome profiling in the IMMUcan multicentre study

IMMUcan is a joint public-private partnership to advance our understanding of how tumors and the immune system interact and the effect of therapeutic interventions. The project will collect tumor biopsies and peripheral blood from up to 3,000 patients across 13 European countries for multi-omic analyses.

Here, we assessed the impact of sample collection and processing conditions on the quality of peripheral blood mononuclear cells (PBMCs). We also compared circulating exosomes obtained from plasma and serum to determine the ideal source for the study.

We collected peripheral blood from 9 healthy donors across 3 centers in different countries. PBMC isolation and freezing were either performed locally at 3, 8, 24, 48 and 72 hours delays or alternatively shipped to a designated biobank for central processing at 8, 24, 48 and 72 hours delays. PBMCs were assessed for yield, viability and frequencies of immune cell populations by flow cytometry. Serum vs plasma derived exosomes were compared using nanoparticle tracking analysis for size distribution and immuno-dotblot for protein levels of HER1, HER2, HER3, cMET, P4HA1, S1000A9, PD-L1, and ALIX.

Centralized processing yielded more consistent results with an overall improvement in PBMC numbers and viability. The delay between blood withdrawal and PBMC isolation had a noticeable impact on PBMC quality when it exceeded 24 hours. Between 24 and 48 hours, we observed a significant and donor dependent decrease in viability and a major increase in granulocytic contamination. Relative frequencies of NK cells were the most sensitive to processing delays during the first 24 hours. Despite a slight global decrease in viability at 24 hours, the relative proportions of other major immune subsets remained stable. Regarding exosomes, plasma-exosomes had a significantly higher modal size compared to serum-derived. Particle abundance was minimally higher in the serum-exosomes. There were no significant differences in the levels of most proteins except for HER3 and c-MET, which were significantly upregulated in plasma exosomes.

We opted to centralize PBMC processing to one biobank to minimize variability. As it was logistically impossible to ensure shipments and processing within 24 hours for all recruitment sites, we limited sample inclusion up to 48 hours. This will be accounted for by tracking the number of granulocytes in future CyTOF measurements and including the delay durations in subsequent multi-variate analyses. Exosomes from serum and plasma will be included in the study as the data showed that both sources produced exosomes of adequate quality yet were different enough in protein levels to merit further investigation.

Funding: IMI2 JU grant agreement 821558, supported by EU's Horizon 2020 and EFPIA.

Citation Format: Rami Mustapha, Valentina Pomella, Jose Vicencio, Silvia Lopez-Lastra, Christelle Bahlawane, Wim Ammerlaan, Henoch S. Hong, Marie Morfouace, Caoimhe Vallely-Gilroy, Vassili Soumelis, Emanuela Romano, Sabine Tejpar, Tony Ng, Fay Betsou, IMMUcan consortium. Overcoming preanalytical variabilities for peripheral blood mononuclear cells and exosome profiling in the IMMUcan multicentre study [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 4281.

A pan-cancer blueprint of the heterogeneous tumor microenvironment revealed by single-cell profiling

The stromal compartment of the tumor microenvironment consists of a heterogeneous set of tissue-resident and tumor-infiltrating cells, which are profoundly moulded by cancer cells. An outstanding question is to what extent this heterogeneity is similar between cancers affecting different organs. Here, we profile 233,591 single cells from patients with lung, colorectal, ovary and breast cancer (n = 36) and construct a pan-cancer blueprint of stromal cell heterogeneity using different single-cell RNA and protein-based technologies. We identify 68 stromal cell populations, of which 46 are shared between cancer types and 22 are unique. We also characterise each population phenotypically by highlighting its marker genes, transcription factors, metabolic activities and tissue-specific expression differences. Resident cell types are characterised by substantial tissue specificity, while tumor-infiltrating cell types are largely shared across cancer types. Finally, by applying the blueprint to melanoma tumors treated with checkpoint immunotherapy and identifying a naïve CD4⁺ T-cell phenotype predictive of response to checkpoint immunotherapy, we illustrate how it can serve as a guide to interpret scRNA-seq data. In conclusion, by providing a comprehensive blueprint through an interactive web server, we generate the first panoramic view on the shared complexity of stromal cells in different cancers.

Lineage-dependent gene expression programs influence the immune landscape of colorectal cancer

Immunotherapy for metastatic colorectal cancer is effective only for mismatch repair-deficient tumors with high microsatellite instability that demonstrate immune infiltration, suggesting that tumor cells can determine their immune microenvironment. To understand this cross-talk, we analyzed the transcriptome of 91,103 unsorted single cells from 23 Korean and 6 Belgian patients. Cancer cells displayed transcriptional features reminiscent of normal differentiation programs, and genetic alterations that apparently fostered immunosuppressive microenvironments directed by regulatory T cells, myofibroblasts and myeloid cells. Intercellular network reconstruction supported the association between cancer cell signatures and specific stromal or immune cell populations. Our collective view of the cellular landscape and intercellular interactions in colorectal cancer provide mechanistic information for the design of efficient immuno-oncology treatment strategies.

Abstract 940: Analytical and clinical validation of the Idylla™ ctKRAS and ctNRAS-BRAF liquid biopsy tests identifies mCRC patient groups with high and low ctDNA shedding

Background: Ras mutation analysis is required for the administration of anti-EGFR therapies to mCRC patients. Incorporating ctDNA testing in routine diagnostics allows rapid detection of baseline RAS mutation status from a single blood draw. We validated ctDNA analysis of 21 KRAS, 18 NRAS and 4 BRAF ctDNA mutations using 2 ml of plasma on the Idylla™ platform. The tests were performed using the Idylla™ ctKRAS and ctNRAS-BRAF Mutation Tests, comprising all required reagents for fully automated and integrated ctDNA analysis from plasma with a turnaround time of approximately 2hrs.

Methods: Analytical validation was performed using EDTA plasma samples containing fragmented DNA containing mutant sequences of interest. For both assays the LOD was calculated using regression models. Reproducibility studies were conducted using the Acrometrix™ Idylla™ ctRAS Verification Panel consisting of 4 KRAS mutations, 4 NRAS mutations and 1 BRAF mutation. During between-laboratory reproducibility studies, the panel of reference samples was tested at three different sites using two different Idylla™ instruments. Between-lot reproducibility was assessed on three different lots. For clinical validation, pre-treatment plasma samples from 203 mCRC patients enrolled in the prospective multicenter RASANC study (NCT02502656) were retrospectively assessed. Proper informed consent and statistical analysis were included. As a comparator test, NGS analysis was performed on ctDNA according to Pécuchet et al. (2016). In addition, tissue RAS/BRAF results were available from standard of care testing.

Results: The between-lab reproducibility for the 4 mutations evaluated with the Idylla™ ctKRAS Mutation Test is with 95% confidence at least 98.7% Idylla™ and is with 95% confidence above 98.7% for the 5 mutations evaluated with the Idylla™ ctNRAS-BRAF Mutation Test. The between-lot reproducibility for the evaluated mutations is with 95% confidence at least 98.9% for the ctKRAS Test and 98.5% for the ctNRAS-BRAF Test. In the clinical study, overall RAS agreement between Idylla™ and NGS on plasma was 90.0% with a sensitivity of 89.5% and specificity of 90.4%. RAS concordance between FFPE tissue and plasma was 78.9% in the whole study population. Low amounts of cfDNA in the sample, absence of liver metastases and primary tumor resection were associated with discordant results. In the population with liver metastases showing sufficient cfDNA, overall RAS agreement between plasma and tissue RAS status was 92.5% with a sensitivity of 93.2% and specificity of 90.9%.

Conclusions: The Idylla™ ctKRAS and ctNRAS-BRAF Mutation Tests provide a sensitive, reliable and fast solution for RAS-BRAF ctDNA testing. Results confirm that RAS-BRAF mutation status can be adequately determined using plasma from metastatic colorectal cancer patients with liver metastases.

Citation Format: Bart Jacobs, Bart Claes, Valentina Pomella, Sabine Tejpar, Jean-Baptiste Bachet, Pierre Laurent-Puig, Geert Maertens, Erwin Sablon. Analytical and clinical validation of the Idylla™ ctKRAS and ctNRAS-BRAF liquid biopsy tests identifies mCRC patient groups with high and low ctDNA shedding [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 940.

Velour trial biomarkers update: Impact of RAS, BRAF, and sidedness on aflibercept activity

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Background: Addition of (ziv)-aflibercept (A) to FOLFIRI in second-line therapy for metastatic colorectal cancer (CRC) has been shown to be beneficial in phase III VELOUR trial (NCT00561470). A follow-up study (NCT01754272) was undertaken to acquire tumor samples for biomarker analyses and identify subgroups of patients with differential treatment effects. The primary results assessing efficacy according to well-established CRC subgroups defined by RAS, BRAF status and sidedness are reported here. Methods: Tissue specimens were collected for 666 patients from 1226 ITT pts. Suitable specimens were assayed for somatic mutation using NGS targeting extended RAS and BRAF genes. NGS assays with no missing values were obtained for 482 pts. Affymetrix gene chip technology was used for whole-transcriptome profiling; sidedness was extracted from available pathological reports. Differences between subgroups were assessed by interaction analysis. Results: The treatment effects on overall survival (OS) for the 482 pts is still significant HR=0.80 (CI 0.65-0.99), and similar to the ITT (n=1226) results (HR=0.82, CI 0.71-0.93). Two established ways of defining mutations (traditional KRAS exon 2 and extended RAS using NGS) show a trend for a differential effect across mutation groups.(see table for OS). Interestingly, BRAF mutants (which are all RAS wild type) show a trend for better outcome Same is seen for PFS and RR. Sidedness did not affect efficacy (HR: 0.83 (0.63- 1.1) for left and HR: 0.83 (0.54-1.3) for right. Conclusions: None of the mutations subgroup results shows significant interaction, although the ratios of treatment HR favor RAS wild types. Similar trends were observed in published trials with bevacizumab or ramucirumab. Sanofi supported this ISS. Clinical trial information: NCT01754272. [Table: see text]

Feedback activation of HER3 attenuates response to EGFR inhibitors in colon cancer cells

The EGFR inhibitor cetuximab is approved for the treatment of colorectal cancer. However, both innate and acquired resistance mechanisms, including compensatory feedback loops, limit its efficacy. Nevertheless, the emergence of these feedback loops has remained largely unexplored to date. Here, we showed feedback upregulation of HER3 and induction of HER3 phosphorylation after cetuximab treatment in colon cancer cells. We also showed that this upregulation occurs, at least partly, through AKT inhibition. Together with this, we observed increased HER2:HER3 dimerization upon cetuximab treatment. Interestingly, lapatinib, a dual EGFR and HER2 tyrosine kinase inhibitor, blocked the increase of cetuximab-induced HER3 phosphorylation. Additionally, we showed that upon HER3 knockdown, cetuximab combined with lapatinib was able to decrease cell viability compared to HER3 expressing cells. These results suggest the existence of a cetuximab-induced feedback HER3 activation that could potentially result in reduced cetuximab efficacy in colorectal cancer patients. Taken together, we provide evidence of the limited effectiveness of cetuximab monotherapy compared to rational combinations.