Browsing Over 167 Presentations
5O - Using single cell data to validate the cellular origins of a clonal expression biomarker in lung cancer
- Dhruva Biswas, London, United Kingdom, UCL Cancer Institute/Paul O'Gorman Building
Abstract
Background
Molecular biomarkers aim to stratify cancer patients into disease subtypes predictive of outcome, improving diagnostic precision beyond clinical descriptors such as tumour stage. Transcriptomic intra-tumour heterogeneity (RNA-ITH) has been shown to confound existing expression-based biomarkers across multiple cancer types.
Methods
Here, we analyse multi-region whole-exome and RNA sequencing data for 156 tumour regions from 48 TRACERx patients to explore and control for RNA-ITH in non-small cell lung cancer (NSCLC).
Results
We find that chromosomal instability (CIN) is a major driver of RNA-ITH, and existing prognostic gene expression signatures are vulnerable to tumour sampling bias. To address this, we identify genes expressed homogeneously within individual tumours that encode expression modules of cancer cell proliferation and are often driven by DNA copy-number gains selected early in tumour evolution. Leveraging single-cell data, we examine the origins of the expression signals, and relate our findings to published biological and clinical gene expression signatures.
Conclusions
Clonal transcriptomic biomarkers overcome tumour sampling bias, associate with survival independently of clinicopathological risk factors, and may provide a general strategy to refine biomarker design across cancer types.
Clinical trial identification
NCT0188860.
Legal entity responsible for the study
University College London (UCL/12/0279) and has been approved by an independent Research Ethics Committee (13/LO/1546).
Funding
Francis Crick Institute that receives its core funding from Cancer Research UK (FC001169, FC001202), the UK Medical Research Council (FC001169, FC001202), and the Wellcome Trust (FC001169, FC001202). The research leading to these results has received funding from the European Research Council (ERC) under the European Union’s Seventh Framework Programme (FP7/2007-2013) Consolidator Grant (FP7-THESEUS-617844), European Commission ITN (FP7-PloidyNet 607722), ERC Advanced Grant (PROTEUS) has received funding from the European Research Council under the European Union’s Horizon 2020 research and innovation programme (grant agreement No. 835297), Chromavision – this project has received funding from the European’s Union Horizon 2020 research and innovation programme (grant agreement No. 665233).
Disclosure
D. Biswas: Non-remunerated activity/ies, patent co-inventor: CRUK; Studentship: Jean Shanks Foundation MBPhD; Funding (self): MBPhD programme at University College London; Funding (institution): the NIHR BRC at University College London Hospitals. N.J. Birkbak: Non-remunerated activity/ies, patent co-inventor: CRUK; Fellow: Lundbeck Foundation; Funding (self): the Aarhus University Research Foundation; Funding (institution): Danish Cancer Society. N. McGranahan: Non-remunerated activity/ies, patent co-inventor: CRUK. Fellow: Sir Henry Dale Fellow, jointly funded by the Wellcome Trust and the Royal Society (Grant Number 211179/Z/18/Z); Funding (institution): CRUK, Rosetrees, the NIHR BRC at University College London Hospitals. C. Swanton: Advisory / Consultancy, Research grant / Funding (institution): Pfizer; Advisory / Consultancy, Research grant / Funding (institution): AstraZeneca; Advisory / Consultancy, Research grant / Funding (institution): BMS; Advisory / Consultancy, Research grant / Funding (institution): Roche; Advisory / Consultancy, Research grant / Funding (institution): Ventana; Advisory / Consultancy: Novartis; Advisory / Consultancy: GlaxoSmithKline; Advisory / Consultancy: MSD; Advisory / Consultancy: Celgene; Advisory / Consultancy: Illumina; Advisory / Consultancy: Genentech; Advisory / Consultancy, Shareholder / Stockholder / Stock options: GRAIL; Advisory / Consultancy: Medicxi; Advisory / Consultancy: Sarah Cannon Research Institute; Advisory / Consultancy: Dynamo Therapeutics; Shareholder / Stockholder / Stock options: ApoGen Biotechnologies; Shareholder / Stockholder / Stock options: Epic Bioscience; Shareholder / Stockholder / Stock options: Achilles Therapeutics. Funding (institution) Cancer Research UK (TRACERx and CRUK Cancer Immunotherapy Catalyst Network), the CRUK Lung Cancer Centre of Excellence, Stand Up 2 Cancer (SU2C), the Rosetrees Trust, Butterfield and Stoneygate Trusts, NovoNordisk Foundation (ID16584), the Prostate Cancer Foundation, the Breast Cancer Research Foundation (BCRF), National Institute for Health Research, the University College London Hospitals Biomedical Research Centre, and the Cancer Research UK University College London Experimental Cancer Medicine Centre.
91P - Exploration of biologic significances and mechanisms of combined atorvastatin with PI3K/Akt inhibitor in radiotherapy of colorectal cancer
- Ching Hsueh Cheng, Taipei City, Taiwan, National Taiwan University Hospital
Abstract
Background
Radiotherapy of pelvic or abdominal cancer may cause radiation enteritis or colitis. We have reported previously that atorvastatin which is a cholesterol-lowering drug and attenuate radiation-induced intestine damage including apoptosis, inflammatory, fibrogenesis and oxidative stress through activation of autophagy. Several studies have been demonstrated that statin drugs have effects of inhibiting of tumor cell proliferation. We sought to explore whether atorvastatin can play a role in enhancing the efficiency of radiotherapy combined with BKM120 and decreasing radiation-induced colitis.
Methods
Two colorectal cancer cell lines including HCT116, HT29, and HCT116 xenograft tumors were separated into 3 study groups: (1) untreated, (2) NVP-BKM120 + RT (CCRT), (3) the administration of atorvastatin followed by CCRT. MTT and colony assay was used to determine whether the administration of atorvastatin can increase sensitivity of colorectal cancer cell to CCRT. Moreover, activation of apoptosis (the levels of cleaved-caspase 3), inflammation (the levels of NF-κB p65), and AKT/mTOR signaling pathway was analyzed to clarify the radiosensitizing mechanism induced by atorvastatin. In the HCT116 xenograft tumor model, tumor sizes and body weights of the mice were measured once per week after treatment for evaluation of anti-tumor effect.
Results
In MTT assay and colony formation assay, we observed that the administration of atorvastatin followed by CCRT significantly inhibits cell viability in 2 CRC cells when compared with concurrent BKM120 and RT treatment. Moreover, atorvastatin could significantly sensitize colorectal cancer cell lines to the CCRT by upregulated the level of apoptosis and attenuating CCRT-induced inflammation and AKT/mTOR signaling. Furthermore, the animal experiments also showed similar results that the administration of atorvastatin could significantly increase anti-tumor effect induced by CCRT.
Conclusions
Our data indicated that atorvastatin treatment could attenuate intestinal damage and sensitize colorectal cancer to CCRT. This approach will help us further develop a more efficient modality therapy for patients with colorectal cancer.
Legal entity responsible for the study
National Taiwan University Hospital.
Funding
Has not received any funding.
Disclosure
The author has declared no conflicts of interest.
37P - Plasma ctDNA RAS mutation analysis by digital polymerase chain reaction in patients with inoperable pancreatic cancer
- Stefania Gkoura, Ioannina, Greece, University Hospital of Ioannina
Abstract
Background
Pancreatic ductal adenocarcinoma (PDAC) is associated with poor prognosis and high mortality worldwide. Despite the emergence of new therapeutic approaches for the treatment of inoperable PDAC, reliable prognostic/predictive biomarkers are lacking. PDAC harbours mutations in the KRAS gene in 80-90% of patients. The aim of the present study is the detection and quantification of RAS mutations in the ctDNA of patients with inoperable PDAC by BEAMing digital polymerase chain reaction (PCR), in order to (a) evaluate the correlation with tissue RAS mutation status in the tumour, (b) study the baseline prognostic significance and (c) study the predictive significance of ctDNA RAS mutation kinetics for the prediction of response to systemic/neoadjuvant therapy.
Methods
Plasma samples of patients with locally advanced or metastatic inoperable PDAC were collected at diagnosis and at 4-6 weeks after treatment initiation and were tested for 34 mutations in the KRAS and NRAS genes by BEAMing digital polymerase chain reaction (PCR). This method has a particularly high sensitivity and can accurately quantify mutated DNA as the Mutant Allele Fraction (MAF). To test the efficacy and validity of ctDNA for the detection of RAS mutations, RAS mutations will also be tested for on paired tumour tissue samples of the patients under study by PCR.
Results
So far, 38 plasma samples from 20 patients were available for analysis. At baseline, mutant ctDNA pertaining to exon 2 codon 12 of the KRAS gene was detected in all patients’ samples and, additionally, to exon 3 codon 61 of the NRAS gene in one of them. Comparison of plasma and tissue results revealed a high agreement of the RAS mutational profile in plasma ctDNA and tissue tumour DNA. Kinetics of the RAS mutational load during therapy and its prognostic or predictive value will be analysed with further cohort expansion.
Conclusions
This work highlights the potential role of liquid biopsies in the management of PDAC and, more specifically, will yield preliminary data on the role of RAS ctDNA profiling as a predictive and prognostic marker.
Legal entity responsible for the study
Department of Medical Oncology, University General Hospital of Ioannina.
Funding
Hellenic Society of Medical Oncology (HeSMO) and Society for Study of Clonal Heterogeneity of Neoplasia (EMEKEN).
Disclosure
G. Pentheroudakis: Research grant / Funding (institution), Support material was provided for this project: Sysmex Inostics. All other authors have declared no conflicts of interest.
44P - Association of metastatic pattern and molecular status in metastatic lung non-small cell lung cancer adenocarcinomas
- Alison Dormieux, Villejuif, France, Gustave Roussy - Cancer Campus
Abstract
Background
The recent identification of molecular alterations in some lung adenocarcinomas has led to the emergence of effective targeted therapies thus drastically improving their prognosis.The aim of our study was to investigate the association between driver oncogene alterations and metastatic patterns on imaging assessment, in a large cohort of metastatic lung adenocarcinoma patients.
Methods
From January 2010 to May 2017, 656 patients with stage IV lung adenocarcinoma with molecular analysis were studied retrospectively including 135 EGFR, 81 ALK, 47 BRAF, 141 KRAS, and 146 negative tumors for these 4 mutations (4N). After review of the complete imaging report by two radiologists (junior and senior) to identify metastatic sites, univariate correlation analyzes were performed.
Results
We found differences in metastatic tropism depending on the molecular alteration type when compared to the non-mutated 4N group: in the EGFR group, pleural metastases were more frequent (32% versus 20%; p = 0.021), and adrenal and node metastases less common (6% versus 23%; p < 0.001 and 11% versus 23%; p = 0.011). In the ALK group, there were more brain and lung metastases (respectively 42% versus 29%; p = 0.043 and 37% versus 24%; p = 0.037). In the BRAF group, pleural and pericardial metastases were more common (respectively 47% versus 20%; p < 0.001 and 11% versus 3%; p = 0.04) and bone metastases were rarer (21% versus 42%; p = 0.011). Lymphangitis was more frequent in EGFR, ALK and BRAF groups (respectively 6%, 7% and 15% versus 1%); p = 0,016, p = 0,009 and p < 0,001).
Conclusions
The application of these correlations between molecular status and metastatic tropism in clinical practice may lead to earlier and more accurate identification of patients for targeted therapy, savings in iterative biopsies, as well as improved and personalized imaging interpretation.
Legal entity responsible for the study
Alison Dormieux.
Funding
Has not received any funding.
Disclosure
All authors have declared no conflicts of interest.
Myc and microenvironment
- Gerard Evan, Cambridge, United Kingdom, University of Cambridge
7O - Contrasting the drivers of response to immunotherapy across solid tumour types: Results from analysis of > 1000 cases
- Kevin Litchfield, London, United Kingdom, The Francis Crick Institute
Abstract
Background
Multiple genomic and transciptomic biomarkers have been associated with response to immune checkpoint inhibitor (CPI) therapy. Emerging evidence suggests that each solid tumour type has a unique mix of factors determining CPI response, reflecting the subtle differences in antigen repertoire and immune microenvironment across histologies. Compiling large-scale sequencing datasets of patients treated with CPI therapy, from a range of solid tumour types, allows detailed comparison of the contrasting immune drivers per histology. Understanding these differences enhances our understanding of the pathways influencing CPI response, which may be of utility for therapeutic and biomarker development.
Methods
We compiled data from 13 CPI treated cohorts, across 6 solid tumour types, encompassing 1,453 patients (n = 1,453 with exome data, n = 674 with RNAseq data). All raw data was accessed, and reprocessed through a standardised state of the art bioinformatics pipeline. A comphrehensive range of genomic & transcriptomic biomarker metrics were derived across the cohort. A combined predictive model was constructred encompassing all biomarkers, & the importance weighting was calculated for each biomarker, in each tumour type.
Results
TMB was found to be a universal predictor of response across all tumour types, except for renal cell carcinoma (RCC). Instead CPI response in RCC appears to be strongly driven by expression of human endogeneuos retroviruses (hERV). In malignant melanoma, while TMB (nsSNVs) was associated with CPI response, the number of expressed indel mutations was found to be a stronger predictor. Shared antigen expression also demonstrated tumour specific predictive patterns. A signature of high immune inflitatation was found to be another universal predictor of response across multiple tumour types, however differences in the varying importance of immune cell subsets across histologies was observed. The rate of HLA LOH, and other immune evasion mechanisms also varied dramatically by cancer type.
Conclusions
The determinants of immunotherapy response vary across solid tumour types, offering unique insight into both tumour intrinsic and extrinsic drivers of immunogenicity.
Legal entity responsible for the study
The Francis Crick Institute.
Funding
Has not received any funding.
Disclosure
All authors have declared no conflicts of interest.
116P - Large scale functional characterization of mutations and their susceptibility to targeted therapy
- Zohar Barbash, Jerusalem, Israel, NovellusDx
Abstract
Background
Extensive use of NGS profiling in precision oncology is uncovering a staggering amount of novel alterations in the sequenced genes. Strikingly, the number of variants of uncertain significance (VUS) increases linearly with the addition of sequenced samples. While some of the VUS are inconsequential mutations many other VUS lead to activation of the proteins and are therefore involved in oncogenicity and may cause drugs resistance. These new activating mutations can also serve as novel drug targets.
Methods
We report here a method for functional annotation of these VUS as well as their sensitivity to targeted therapy. The system is based on rapid synthesis of the mutations and expression of the mutated protein together with fluorescently labeled reporters in a cell-based assay. The assay allows the accurate measurement of signaling pathway activation using fluorescence imaging coupled with high content image analysis. This process can also be performed with targeted agents to determine the sensitivity of the mutation. The output of the system is the level of activity of the mutant relative to a mutation with known activity in the same gene.
Results
Our results show that this method is able to accurately identify known driver mutations in 10 different oncogenes spanning 4 major cancer associated signaling pathways as well as over 100 different VUS in these genes. We also extend this analysis and show that the method correctly recapitulates differential sensitivity of EGFR mutations to 2nd and 3rd generation EGFR inhibitors and that different classes of BRAF mutations differ in response to specific inhibitors. Finally, we establish the importance of concurrent mutations in the response to EGFR inhibitors.
Conclusions
Taken together, this system provides crucial information for the development of new targeted agents and establishes an experimental tool both for patient stratification into clinical trials and patient treatment.
Legal entity responsible for the study
The authors.
Funding
NovellusDx.
Disclosure
Z. Barbash: Full / Part-time employment: NovellusDx. G. Tarcic: Full / Part-time employment: NovellusDx. D. Haham: Full / Part-time employment: NovellusDx. L. Hafzadi: Full / Part-time employment: NovellusDx. R. Zipor: Full / Part-time employment: NovellusDx. S. Barth: Full / Part-time employment: NovellusDx. A. Aizenman: Full / Part-time employment: NovellusDx.
117P - Correlation of MRI derived parameters and SUV uptake obtained from FDG- PET-CT with human papillomavirus status in oropharyngeal squamous cell carcinomas
- Sumit Goyal, New Delhi, Uttar Pradesh, India, Rajiv Gandhi Cancer Institute & Research Center
Abstract
Background
A favorable response to (chemo) radiotherapy (CCRT) is seen in human papillomavirus (HPV)-positive OPSCC patients. Apparent diffusion coefficient (ADC) derived from MRI has shown to predict treatment response. We evaluated the correlation between clinico-demographic profile of oropharyngeal squamous cell carcinomas patients (OPSCC patients) HPV status and ADC values, SUV uptake obtained from FDG- PET-CT.
Methods
The study population was obtained from a historical cohort diagnosed with HPV-related OPSCC. A total of 105 OPSCC patients who had undergone molecular testing for HPV status by p16 with Immuno-histochemistry (IHC) were identified. 96 patients had pretreatment imaging (either PET-CT or MRI) and post CCRT imaging was included. Imaging was evaluated by head and neck radiologists to calculate mean ADC and SUV max. Pearson Chi- Square and ANOVA analyses were performed to evaluate the correlation.
Results
26 OPSCC were HPV-positive. HPV-positive HNSCC showed significantly association with smoking, grade & stage of the tumor, T status, Response to CCRT, lymph nodes, and ADC values on follow up imaging.
Conclusions
In OPSCC patient’s positive HPV status correlates with follow up mean apparent diffusion coefficient. The complimentary prognostic value of post treatment apparent diffusion coefficient might be partially ascribed to patients with a positive HPV status. Further studies are reasonable to determine whether PET-CT is a useful imaging biomarker in comparison to ADC to risk-stratify patients with HPV-related OPSCC.
Editorial acknowledgement
Authors would like to acknowledge Dr Nishtha Sachdeva for her significant work in data collection .
Legal entity responsible for the study
The authors.
Funding
Has not received any funding.
Disclosure
All authors have declared no conflicts of interest.
Artificial Intelligence (AI) in radiology
- Hugo Aerts, Boston, United States of America, Harvard Medical School
Bioinformatics and mathematics to analyse single cell data
- Charlotte K. Ng, Bern, Switzerland, University of Bern
96P - Assessments of cancer-free lymph nodes for the prediction of disease progression
- Anita Grigoriadis, London, United Kingdom, King's College London Guy's Hospital
Abstract
Background
Histological changes in the cancer-free lymph nodes (LNs) can add to the risk prediction of developing distant metastasis for LN-positive breast cancer patients. As Whole Slide Images (WSI) demonstrated suitability for detection of LN metastasis with high accuracy based on Convolutional Neural Networks (CNN), we extended the assessments to cancer-free LNs to determine whether early signs of disease progression could be identified.
Methods
Clinico-pathological data, including level of LNs in the axilla, were available for 143 LN-positive breast cancer patients. All resected LNs were digitised (×40 magnification), totalling to 1,054 WSI. CNN models were based on standard ResNet architecture, and trained using 224x224 sized WSI patches, to classify germinal centres (GC), follicles, sinus histiocytosis, and adipose tissue as defined by 2 independent pathologists. To increase the robustness of the CNN, training data was augmented using image rotation and colour perturbation. A weighted cross entropy was used as a training loss function to account for the imbalance in the four types of patches. Confusion matrix and one-vs-all AUC scores were computed on WSIs patches extracted from held-out test patients to assess the discriminative power of the trained CNN models. Multivariate and cross-validated L2-regularised proportional hazard regression analyses were used for outcome prediction.
Results
An increased number and smaller sized GCs in cancer-free LNs, the prevalence of metastatic LNs in the low axilla, the location of GCs in metastatic LNs, and lymphocytic infiltration at the tumour invasive front were all indicative of developing distant metastasis in LN-positive breast patients. Metastatic LNs were found exclusively in the low axilla in 77% of patients. Amongst the 913 H&E WSI of cancer-free LNs, 21% presented with GC. Patch level AUC scores of detecting each type of tissue region ranged between 0.82 to 0.94 on held-out patients quantifying the effectiveness of CNN to be used as topological feature detector.
Conclusions
Addition planned WSI analyses of large breast cancer cohorts will expand on these data, capturing histological features in LNs, with the aim of identifying high-risk and low-risk disease, and aiding in pathological prognostication.
Legal entity responsible for the study
The authors.
Funding
Breast Cancer Research Trust, Breast Cancer Now, CRUK.
Disclosure
All authors have declared no conflicts of interest.
56P - Ibrutinib for relapsed/refractory mantle cell lymphoma: 7-year experience
- Ines T. Grilo, Vila Real, Portugal, Centro Hospitalar Tras-os-Montes e Alto Douro, E.P.E.
Abstract
Background
Mantle cell lymphoma (MLC) is nowadays an aggressive and incurable Non-Hodgkin’s lymphoma, characterized by multiple relapses.The persistent activation of B-cell receptor pathway is critical for pathogenesis. Ibrutinib is a potent covalent inhibitor of Bruton’s tyrosine kinase (BTK) that inhibits B-cell antigen receptor signaling downstream of BTK and changed for better how MCL is treated in relapsed/refractory setting. However, resistance is common and response limited.
Methods
Retrospective analysis and follow-up of all MCL patients treated with Ibrutinib in a Onco-Hematology Department.
Results
Eleven patients were identified, with a median age of 68 years [58-78], the majority of them were males (83.3%). At diagnosis, 9% were in stage III of Ann Arbor while 81.8% were in stage IV. The median MIPI (MCL International Prognostic Index) was 5.5 [4-8]. These patients were exposed to a median of 3 treatments [3-5]. The majority of them performed as 1ºline treatment R-FCM (18.2%) or R-CHOP (54.5%); as 2ºline R-CHOP (45.5%), as 3ºline Ibrutinib (63.6%), as 4ºline PEPC (60%) and as 5ºline Ibrutinib (100%). Ibrutinib therapy was prescribed as a 2ºline in 9.1% of the patients, as a 3ºline in 63.6%, as 4ºline in 40% and as a 5ºline in 100%. Ibrutinib achieved a complete response rate in 9.1%, a partial response in 45.5% (response rate, RR, of 54.5%), disease progression in 36.4%, stable disease in 9,1%. At the end of the study, 5 patients were alive and still doing Ibrutinib (4 of them in full dose 560 mg/day). The median progression free survival (PFS) was 3 months [1-26]. Overall survival was not reached (3 patients died with disease progression).
Conclusions
Although a larger sample and a longer follow-up are needed, these data showed worse results when compared to previous phase 2 trials demonstrating a 68% response rate (RR), including for high-risk patients and heavily pretreated. Most recently, a pooled analysis of the three open-label studies of ibrutinib in MCL, PCYC-1104, SPARK, and RAY revealed an ORR of 68%, 63% and 72%. Ibrutinib may be changing the natural history of MCL as many other agents still under development. Enrollment in clinical trials is crucial not only for discovery of new agents and testing combinations but also to understand the natural history of relapsed MCL.
Legal entity responsible for the study
Onco-Hematology Service of Instituto Português de Oncologia do Porto, F.G., E.P.E.
Funding
Has not received any funding.
Disclosure
All authors have declared no conflicts of interest.