Browsing Over 140 Presentations
8P - A Gradient Boosting Decision Tree (GBDT) Approach to Identify Potential Therapeutic Targets
- Ilona Kifer (Jerusalem, Israel)
- Ilona Kifer (Jerusalem, Israel)
- Eden Goldfarb (Ness Ziona, Israel)
- Elinor Dehan (Framingham, AL, United States of America)
- Michael Vidne (Ness Ziona, Israel)
- Gabi Tarcic (Ness Ziona, Israel)
Abstract
Background
Identification of novel therapeutic targets is the first step in the drug development journey, and traditionally relies on deep understanding of the biology, a process which is lengthy and non-scalable. The advent of high-throughput screening and advanced machine learning methods enables rapidly uncovering novel therapeutic targets even where the biology is not yet well understood. This, in turn, allows the expansion of the universe of targets and even the reach of current compounds.
Methods
Using the CancerRx dataset of 987 human cell-lines screened across 346 compounds we train a GBDT to predict the sensitivity (IC50) of each cell-line to each drug. Each cell-line is represented as a vector of binary values (WT/MT) according to the genomic data of 299 cancer related genes. Once high accuracy of predicting the cell-line-drug IC50 is obtained we use SHAP values, which represent the extent of a feature's responsibility for a change in the model output, to obtain the genetic features which influence sensitivity the most. These features, specific mutations and combinations of mutations, represent potential therapeutic targets of each screened drug.
Results
We report here a validation set consisting of 8 drugs with well-known targets and/or biomarkers. In all cases we identify the correct drug-target without any use of the underlying biology or prior mechanistic knowledge. We then report additional genomic features the model predicts to be important for the sensitivity to specific drugs, representing potential targets which to date are unknown. Additionally, we identify specific genetic features that increase the resistance to specific compounds.
Conclusions
Using an unbiased GBDT-based ML algorithm on publicly available high throughput screening data we accurately identify known drug-targets as well as additional previously unknown candidates. These new findings can expand the patient population for whom a certain drug can provide benefit. Furthermore, due to the unbiased nature of the algorithm and the wide array of drugs and drug-targets used in the screen we identify additional potential drugs targets which are not being targeted by the current drugs.
Legal entity responsible for the study
The authors.
Funding
Fore Biotherapeutics.
Disclosure
I.K. Kifer, G. Tarcic: Financial Interests, Personal, Full or part-time Employment: NovellusDx. E. Goldfarb, M. Vidne: Financial Interests, Personal, Stocks/Shares: NovellusDx. All other authors have declared no conflicts of interest.
9P - small-scale ROS1 Aberrations: functional impact and therapeutic potential
- Moritz Glaser (Köln, Germany)
- Moritz Glaser (Köln, Germany)
- Cornelia Von Levetzow (Köln, Germany)
- Sebastian Michels (Köln, Germany)
- Lucia Nogova (Köln, Germany)
- Marianna Katzenmeier (Köln, Germany)
- Claudia Wömpner (Köln, Germany)
- Jaqueline Schmitz (Köln, Germany)
- Elisabeth Bitter (Köln, Germany)
- Inken Terjung (Köln, Germany)
- Elke Passmann (Köln, Germany)
- Diana Schaufler (Köln, Germany)
- Anna Eisert (Köln, Germany)
- Rieke N. Fischer (Köln, Germany)
- Richard Riedel (Köln, Germany)
- Sabine Hahne (Köln, Germany)
- Sabine Merkelbach-Bruse (Köln, Germany)
- Reinhard Büttner (Köln, Germany)
- Jurgen Wolf (Köln, Germany)
- Matthias Scheffler (Köln, Germany)
Abstract
Background
ROS1-directed Tyrosine-Kinase-Inhibitors (TKIs) target activating fusions in the ROS1 proto-oncogene efficiently in non-small cell lung cancer (NSCLC) patients. Besides solvent-front mutations (SFMs) in resistance to targeted therapy, ROS1 aberrations other than fusions remain biologically unexplored. Driving on our thus far clinical investigations, we aimed at determining the functional impact and the potential to act as a drug target.
Methods
Tumor samples from NSCLC patients were screened with two next-generation sequencing (NGS) panels. Patients with activating ROS1 fusions, SFMs and benign Single-Nucleotide Polymorphisms (SNPs) were excluded using the gnomAD database. The Provean and PolyPhen-2 tools predicted the functional impact of the detected aberrations. ChimeraX was used for drug binding analysis.
Results
Of 8072 patients analyzed by NGS between 2018 and 2022, 110 (1.4%) patients harbored small-scale ROS1 aberrations. Our cohort consists of 113 aberrations leading to 95 (84.1%) missense, 12 (10.6%) truncating and 1 (0.1%) in-frame aberrations. In 10% of patients ROS1 aberration was mutually exclusive and most ROS1 aberrations were transitions (55%). Polyphen predicts 75.5% of aberrations to be ‘possibly’ (6.4%), respectively ‘probably damaging’ (68.1%, mean score 0.75, median score 0.999). Provean predicts 50% of aberrations to be ‘deleterious’. Polyphen-2 and Provean coherently predict 46.8% of aberrations to be ‘deleterious’ respectively ‘possibly/probably damaging’. Amid the tyrosine kinase domain almost all aberrations are predicted to be ‘probably damaging’ respectively ‘deleterious’ by both tools coherently and feature a higher-than-average score. Besides, no distinct molecular pattern occurs. The M2029T and R2083T missense mutations interfere with single hydrogen-bonds and Van-Der-Waals forces in the ROS1 drug-binding pocket between the respective residues and the TKIs crizotinib and lorlatinib. However, drug binding analysis revealed that the overall binding of the TKIs is not affected.
Conclusions
This evidence proves a functional and deleterious impact of specific aberrations and indicates a high potential to be targetable. We warrant further studies to elaborate these findings in vitro and in vivo.
Legal entity responsible for the study
M. Scheffler.
Funding
Has not received any funding.
Disclosure
L. Nogova: Financial Interests, Personal, Other, honoraria: Pfizer, Celgene, Novartis, Roche, Boehringer Ingelheim, Janssen Pharmaceuticals, Bristol Myers Squibb. D. Schaufler: Financial Interests, Personal, Other, honoraria: BMS, Boehringer Ingelheim, MSD, Novartis, Roche, Healthcare Consulting Cologne, AbbVie. R.N. Fischer: Financial Interests, Personal, Other, honoraria: BMS, MSD, Roche, Boehringer Ingelheim, AstraZeneca. R. Riedel: Financial Interests, Personal, Other, honoraria: Boehringer Ingelheim, Novartis. R. Büttner: Financial Interests, Personal, Other, consultant: Pfizer, Novartis. J. Wolf: Financial Interests, Personal, Other, honoraria: AbbVie, AstraZeneca, BMS, Boehringer Ingelheim, Chugai, Ignyta, Lilly, MSD, Novartis, Pfizer, Roche; Financial Interests, Personal, Other, consultant: AbbVie, AstraZeneca, BMS, Boehringer Ingelheim, Chugai, Ignyta, Lilly, MSD, Novartis, Pfizer, Roche. M. Scheffler: Financial Interests, Personal, Other, consultant: BMS, Boehringer Ingelheim, Takeda, Roche; Financial Interests, Personal, Other, travel funding: Boehringer Ingelheim, Mediolanum. All other authors have declared no conflicts of interest.
10P - Detection of early-stage lung cancer using 5-hydroxymethylcytosine signatures in circulating cell-free DNA
- Xiaozheng Kang (Beijing, China)
- Xiaozheng Kang (Beijing, China)
- Ruiyao Ma (Beijing, China)
- Xiaoxiao Li (Beijing, China)
- Yingzhu Chen (Beijing, China)
- Hangyu Chen (Beijing, China)
- Zhen Liang (Beijing, China)
- Haitao Zhou (Beijing, China)
- Guobing Xu (Beijing, China)
- Chaoran Dong (Beijing, China)
- Jian Lin (Beijing, China)
Abstract
Background
The goal of lung cancer early detection is to identify the malignancy at the stage where surgical cure is possible, outcomes are superior, and treatment is less morbid. 5-Hydroxymethylcytosine (5hmC) signatures in circulating cell-free DNA (cfDNA) as diagnostic biomarkers have been examined in different types of cancer. However, little is known in the field of early lung cancer detection.
Methods
We utilized well established 5hmC-Seal method (5 ml plasma per patient) to map the 5hmC profiles in cfDNA from a cohort of 100 newly diagnosed early-stage lung adenocarcinoma (LUAD) patients and 90 healthy individuals. The differentially methylated regions (DhMRs) and differentially regulated 5hmC genes were identified, and then the functional enrichment analysis for genes with upregulated and downregulated 5hmC levels was performed. Using multiple deep learning methods, we separated samples into two groups (95 training samples, and 95 validation samples) for classifier model training and evaluation, which was used to assign a methylation score to the withheld samples. This process was repeated with 100 randomly selected training-test sets.
Results
We identfied 1,315 DhMRs including upregulated (n = 99) and downregulated (n = 1,216) regions in LUAD groups by comparing LUAD groups with control groups. Applying the variable selection procedure of the Elastic Net algorithm, we identified a nine-gene model. To evaluate the performance, the model training was repeated 100 times and received an average AUC of 0.969 (95%CI: 0.935-1) on training set and 0.936 (95%CI: 0.890-0.983) on validating set, revealing high sensitivity (86.0%) and specificity (91.1%).
Conclusions
We firstly discovered 5hmC-based biomarkers in circulating cfDNA of early-stage LUAD. It provides a foundation for effective future fluid-biopsy-based lung cancer screening.
Legal entity responsible for the study
Peking University Cancer Hospital and Institute.
Funding
National Key R&D Program of China.
Disclosure
All authors have declared no conflicts of interest.
11P - Mapping the pattern and pace of tumour dissemination using longitudinal imaging and ctDNA in the TRACERx lung study
- Wing Kin Liu (London, United Kingdom)
- Wing Kin Liu (London, United Kingdom)
- Boyue Ding (London, United Kingdom)
- Sonya Hessey (London, United Kingdom)
- Jeanette Kittel (London, United Kingdom)
- Cristina Lombardelli (London, United Kingdom)
- Hyothaek Lee (London, United Kingdom)
- Catarina Veiga (London, United Kingdom)
- Ariana Huebner (London, United Kingdom)
- Allan Hackshaw (London, United Kingdom)
- Christopher Z. Abbosh (London, YO, United Kingdom)
- Alexander M. Frankell (London, United Kingdom)
- Gary Royle (London, United Kingdom)
- Charles Swanton (London, United Kingdom)
- Mariam Jamal-Hanjani (London, United Kingdom)
Abstract
Background
TRACERx is a multicentre, prospective study recruiting patients with early stage non small cell lung cancer. By leveraging longitudinal CT imaging, patterns and timing of metastatic spread and tumour growth rates can be tracked lesion by lesion. Circulating tumour DNA (ctDNA) in longitudinal plasma samples can be mapped to imaging timepoints to assess their role as a biomarker in monitoring cancer progression and the impact of therapy.
Methods
436 imaging scans were reviewed by two clinicians from 50 patients (median 7 scans per patient) with disease relapse post-surgical resection. Volumetric growth dynamics of individual metastatic lesions were tracked on serial images and tumour dimensions contoured using ITK-SNAP. ctDNA levels were detected using patient bespoke multiplex-PCR assay-panels based on tissue exome sequencing tracking 200-600 mutations per patient. For 22 patients we tracked ctDNA in 147 plasma samples (median 8 samples per patient) taken from before primary tumour resection to disease relapse and subsequent progression. Clonal mutations were used to track overall disease burden and subclonal mutation to track lesion-specific metastatic subclones.
Results
56% of patients had intrathoracic only relapse and 44% patients had extrathoracic relapse. Common sites of relapse were lung (30%), lymph node (30%), bone (12%) and brain (5%). ctDNA levels were overlayed with tumour growth rate plots demonstrating that ctDNA fraction does not always track with total volume. For two patients we assessed the subclonal composition of ctDNA, tracking lesions with specific subclones detected at autopsy. Most lesion-specific subclones were absent in ctDNA in both cases, despite encompassing a large fraction of total tumour volume on imaging, suggesting many metastatic lesions do not shed substantial amounts of ctDNA. In contrast subclones from specific sites of disease were overrepresented in ctDNA, suggesting a high rate of shedding.
Conclusions
Large-scale studies with longitudinal imaging, ctDNA tracking and clinical annotation, such as TRACERx, can map the pattern and pace of cancer progression adding further insight into the clinical disease course and mechanisms of spread.
Clinical trial identification
The TRACERx study (NCT01888601) is a prospective observational cohort study and PEACE (NCT03004755) is a national research autopsy programme, both approved by independent research ethics committees (13/LO/1546 and 13/LO/0972/AM05, respectively).
Legal entity responsible for the study
Cancer Research UK.
Funding
Cancer Research UK funded TRACERx, Invitae has funded ctDNA research.
Disclosure
A. Hackshaw: Financial Interests, Institutional, Advisory Board, Received fees as a member of Independent Data Monitoring Committee: Roche. C.Z. Abbosh: Financial Interests, Institutional, Invited Speaker: Novartis, Roche, AstraZeneca, BMS; Financial Interests, Institutional, Full or part-time Employment: AstraZeneca; Non-Financial Interests, Institutional, Other, patents issued to detect tumour recurrence (PCT/GB2017/053289): Patent; Non-Financial Interests, Institutional, Other, methods for lung cancer detection (PCT/US2017/028013): Patent; Non-Financial Interests, Institutional, Other, co-inventor to a patent application methods for tumour monitoring GB2114434.0: Patent. A.M. Frankell: Non-Financial Interests, Institutional, Other, co-inventor on a patent application to determine methods and systems for tumour monitoring (GB2114434.0): Patent. C. Swanton: Financial Interests, Personal, Invited Speaker, Activity took place in 2016: Pfizer, Celgene; Financial Interests, Personal, Invited Speaker, October 26th 2020: Novartis; Financial Interests, Personal, Invited Speaker: Roche/Ventana, BMS, AstraZeneca, MSD, Illumina, GlaxoSmithKline; Financial Interests, Personal, Advisory Board, AdBoard - November 12th, 2020: Amgen; Financial Interests, Personal, Advisory Board: Genentech, Sarah Canon Research Institute, Medicxi; Financial Interests, Personal, Advisory Board, Joined October 2020. Also have stock options: Bicycle Therapeutics; Financial Interests, Personal, Advisory Board, Member of the Science Management Committee. Also have stock options: GRAIL; Financial Interests, Personal, Other, Consultancy agreement: Roche Innovation Centre Shanghai; Financial Interests, Personal, Full or part-time Employment, Chief Clinician since October 2017: Cancer Research UK; Financial Interests, Personal, Ownership Interest, Co-Founder of Achilles Therapeutics. Also, have stock options in this company: Achilles Therapeutics; Financial Interests, Personal, Stocks/Shares, Stocks owned until June 2021: GRAIL, ApoGen Biotechnologies; Financial Interests, Personal, Stocks/Shares: Epic Biosciences, Bicycle Therapeutics; Financial Interests, Institutional, Research Grant, Funded RUBICON grant - October 2018 - April 2021: Bristol Myers Squibb; Financial Interests, Institutional, Research Grant, Collaboration in minimal residual disease sequencing technologies: Archer Dx Inc.; Financial Interests, Institutional, Research Grant: Pfizer, Ono Pharmaceutical, Boehringer Ingelheim; Financial Interests, Institutional, Invited Speaker, Chief Investigator for the MeRmaiD1 clinical trial and chair of the steering committee: AstraZeneca; Financial Interests, Institutional, Research Grant, Research Grants from 2015-2019: Roche-Ventana; Financial Interests, Personal, Other, Co-chief investigator: NHS-Galleri Clinical Trial; Non-Financial Interests, Personal, Principal Investigator, Chief Investigator for MeRmaiD1 clinical trial: AstraZeneca; Non-Financial Interests, Personal, Invited Speaker, From 2019: AACR; Non-Financial Interests, Personal, Other, Board of Directors: AACR; Non-Financial Interests, Personal, Advisory Role, EACR Advisory Council member: EACR. M. Jamal-Hanjani: Financial Interests, Institutional, Funding, CRUK Career Establishment Awardee: CRUK; Financial Interests, Institutional, Funding: IASLC, International Lung Cancer Foundation, Lung Cancer Research Foundation, Rosetrees Trust, UKI NETs, NIHR, NIHR UCLH Biomedical Research Centre; Financial Interests, Institutional, Advisory Board: Achilles Therapeutics; Financial Interests, Institutional, Invited Speaker: Astex Pharmaceuticals, Oslo Cancer Clusters; Non-Financial Interests, Institutional, Other, methods for lung cancer detection (PCT/US2017/028013): Patent. All other authors have declared no conflicts of interest.
12P - The efficacy of EGFR tyrosine kinase inhibitors and its clinical prognostic factors in lung adenocarcinoma patients harboring different types of EGFR mutations: Real World Data
- Marina Vitorino (Amadora, Portugal)
- Marina Vitorino (Amadora, Portugal)
- Ricardo Ferreira (Amadora, Portugal)
- Andreia F. Chaves (Amadora, Portugal)
Abstract
Background
Lung cancer has the highest incidence and mortality among all cancers, with a 5-year survival rate of 15%. Presently, epidermal growth factor receptor (EGFR) mutation is the most common type of gene mutations detected in patients (pts) with advanced non-small-cell lung cancer, and EGFR is identified as the therapeutic target of EGFR tyrosine kinase inhibitors (TKIs). EGFR-TKIs have become the standard treatment. However, the most of the trials were developed in Asian countries, with a lack of data in western population.
Methods
This retrospective study aimed to review the medical records of EGFR- mutant advanced lung adenocarcinoma (LA) undergoing EGFR-TKIs treatment from 2015 to 2021, so as to examine the association of clinical factors with EGFR-TKI efficacy.
Results
Of the 53 stage IV LA pts enrolled in this study, 9 were treated with more than one TKI. The mean age was 74,2 years old, 32 pts were non-smoker females and 38 had ECOG-PS 0-1. The mutations del19 or 21 L861G were the most frequent (23 and 20 pts respectively). The 20 T790M mutation was detected in 6 pts. First-line TKI (Gefitinib, Afatinib, Erlotinib and Osimertinib) were used in 26 pts and prior chemotherapy was preferred in 29 pts. A 24% objective response rate (ORR) and 67% disease control rate were observed for EGFR-TKIs treatment in all lines. Higher ORR was seen in patients with 0/1 ECOG scores than those with 2 or greater scores (p=0.046). The subjects had a progression free survival (PFS) of 17,8 months (p<0,01; 95% CI:12.9-22.84) and an overall survival (OS) of 27,5 months (p<0.01; 95% CI: 18.27-36.823). The median PFS was longer in pts treat with first-line TKI (p=0.029). The multivariate analysis indicated that ECOG-PS (p=0.04) and bone metastasis (p=0.036) were independent prognostic factors for OS.
Conclusions
The EGFR-TKI therapy results in survival benefits for EGFR-mutant advanced LA patients. ECOG-PS and bone metastasis were independent prognostic factors for OS.
Legal entity responsible for the study
Hospital Professor Doutor Fernando Fonseca.
Funding
Has not received any funding.
Disclosure
All authors have declared no conflicts of interest.
13P - Hypermethylation of microRNA gene: potential in the diagnosis of lung cancer
- Irina Pronina (Moscow, Russian Federation)
- Irina Pronina (Moscow, Russian Federation)
- Marina Gubenko (Moscow, Russian Federation)
- Alexey Burdennyy (Moscow, Russian Federation)
- Vitaly Loginov (Moscow, Russian Federation)
Abstract
Background
Non-small cell lung cancer (NSCLC) is one of the most common human cancers. In this regard, the search for new biomarkers for detecting NSCLC at early stages is relevant, and one of these markers may be the methylation of CpG-islands of miRNA genes. The aim of this work was to study the level of methylation of promoter CpG-islands of miRNA genes as promising NSCLC markers.
Methods
A representative set of 80 paired (tumour/normal) NSCLC samples was used in the study. The analysis of methylation was carried out using the method of quantitative methyl-specific PCR. Statistical analysis of methylation levels was performed using a non-parametric Mann-Whitney U-test. The optimal marker systems were selected based on the results of the ROC analysis. Mathematical packages IBM SPSS Statistics 22 are used.
Results
A representative set of 80 paired (tumour/normal) NSCLC samples was used in the study. The analysis of methylation was carried out using the method of quantitative methyl-specific PCR. Statistical analysis of methylation levels was performed using a non-parametric Mann-Whitney U-test. The optimal marker systems were selected based on the results of the ROC analysis. Mathematical packages IBM SPSS Statistics 22 are used. Results. The methylation status of 10 miRNA genes was studied, significant differences were established between methylation levels in tumour samples and histologically normal tissue of NSCLC patients for 8 genes: MIR-124A-1/3, MIR-125B-1, MIR-127, MIR-129-2, MIR-137, MIR-339 and MIR-375 (p‹0.001). Significant correlations were found between the methylation frequency of a number of miRNA genes and NSCLC progression: MIR-125B-1, MIR-137, MIR-124A-3 with cancer stage (p=0.001, 0.004 and 0.001, respectively) and MIR-125B-1 with metastasis (p=0.005). An effective marker system of 4 genes (MIR-125B-1, MIR-137, MIR-129-2, MIR-375) was determined by ROC analysis for the diagnosis of NSCLC at early stages with high clinical sensitivity (90%) and specificity (90 %); AUC value > 0.9.
Conclusions
Thus, new hypermethylated miRNA genes can be used as potential biomarkers for the early diagnosis of NSCLC.
Legal entity responsible for the study
The authors.
Funding
The study was supported by the state assignment of the Ministry of Science and Higher Education of the Russian Federation number FGFU-2022-0007.
Disclosure
All authors have declared no conflicts of interest.
14P - Up-regulated PI3K/mTOR/AKT pathway behind the downregulation of PTEN, FBXW7, genes and miRNA 140-145, ALK mediated chemotherapy resistance in non-small cell lung carcinoma (NSCLC)
- Jawad Aslam (Faisalabad, Pakistan)
- Jawad Aslam (Faisalabad, Pakistan)
- Muhammad N. Faisal (Faisalabad, Pakistan)
- Hamza Nazeer (Faisalabad, Pakistan)
- Jazib Hussain (Copenhagen, Denmark)
- Humaira Muzaffar (Faisalabad, Pakistan)
- Aisha Mahmood (Bahawalpur, Pakistan)
- Hira Javed (Faisalabad, Pakistan)
- Qaiser Tanveer (Edinburgh, United Kingdom)
Abstract
Background
Tumor cells have a tendency to proliferate rapidly and can metastasize to other organs of the body. Respiratory carcinomas are among 3rd predominant causes of cancer-related deaths in both genders around the globe. Type of epithelial lung cancer non-small cell lung carcinoma (NSCLC) constitutes 80% of all lung cancer types. The 5-year survival rate of NSCLC is about 16%. This Study was conducted to understand the chemoresistance through expression of proto-onco genes (AKT1, ALK), onco-suppressive (FBXW7, PTEN) genes and their correlation with miRNA 140-145 in NSCLC.
Methods
Bronchoscopy of lung cancer patients who were on different medications was conducted for collection of samples from regional health care facility under the guidelines of ethical review committee. Samples were subjected to histopathology and for further processing to carry out RNA extraction and gene expression studies through qRT-PCR/ gel-electrophoresis. The data was analyzed statistically through one-way ANOVA for analysis of variance and DMR.
Results
It has been revealed that the expression level of proto-onco ALK and AKT1 genes is significantly higher in lung cancer patients in comparison to normal ones (P<0.05). PTEN and FBXW7 are onco-suppressive genes, so these genes are downregulated after mutational changes in lung parenchyma of cancer patient samples (P<0.05). Correlation of PTEN and AKT1 genes revealed that upregulation of PTEN gene down express the AKT1 gene through PI3K/AKT/mTOR signaling pathway. Relatively higher expression of miRNA 140-145 disrupt the function of c-Myc and Cyclin-E proteins which is the thought to be the reason behind chemoresistance in NSCLC patients (P<0.05). Histopathological examination showed neoplastic cellular proliferation without infiltration into dermal areas in lung cancer tissue but in control, there is uniform cellular structure.
Conclusions
This study concludes that perturbation in miRNA 140-145 mediate post transcriptional activation of proto-onco genes through PI3k/ AKT pathway and hence contribute towards chemoresistance in 2nd-3rd grade NSCLC patients.
Legal entity responsible for the study
The authors.
Funding
Has not received any funding.
Disclosure
All authors have declared no conflicts of interest.
15P - KRAS mutation in metastatic non-small cell lung carcinoma (NSCLC) - the Indian subcontinent experience from a tertiary cancer center!
- Anindya Mukherjee (New Delhi, India)
- Anindya Mukherjee (New Delhi, India)
- Shrinidhi Nathany (New Delhi, India)
- Mansi Sharma (New Delhi, India)
- Amrith B Patel (New Delhi, India)
- Ullas Batra (New Delhi, RO, India)
Abstract
Background
The pathbreaking discovery of sotorasib as KRAS G12C inhibitor has revolutionized the prognostic outcome of KRAS mutated metastatic NSCLC. This is a single centre experience of KRAS mutated NSCLC in an Indian cohort, underscoring the unmet urgent need of sotorasib in this part of the world.
Methods
Among the 3899 NSCLC patients registered between 2016 to 2020, 163 patients were tested for KRAS alterations, of which 50 patients were confirmed to harbor a KRAS variant by molecular testing. Appropriate statistical analysis was done to compare G12C and non-G12C subtypes, including their survival outcomes.
Results
Median age was 63 years (range: 36-81years) with a preponderance of non-G12C mutations in both sexes. Smokers were higher in G12C group (16 vs 4 pts, p=0.09). G12C group showed lesser PDL1 expression (>1%) than non-G12C group (13 vs. 15 pts, p=0.09). Molecular analysis revealed 3 main types of KRAS mutations: G12C, G12V and G12D in 17 (34%), 9(18%) and 6 (12%) pts respectively. None of them had KRAS complex mutations. The co-mutations predominantly detected included TP53 in 7 (14%), STK11 in 3 (6%), FGFR4 in 4 (8%), PIK3CA, EGFR and ALK in 2 cases each, BRAF and CTNNB1 in 1 case each. Co-mutations were significantly more frequent in the non-G12C group (p<0.05). 36 patients received chemotherapy and rest were lost to follow up. The median PFS and OS of the entire cohort on chemotherapy were 5.4 months (mo) and 11.1 mo respectively. The median PFS and OS of G12C vs non-G12C groups were 6.4 mo (95% CI: 2.8-11.8) vs 3.8 mo (95%CI: 2.9-7.7) and 15.2 mo (95% CI: 9.8-17.2) vs 16.1 mo (95% CI: 10.7-19.3) respectively. With a median follow-up of 14.3 mo, both PFS and OS were not statistically significant between the groups, p=0.08 and 0.20 respectively.
Conclusions
This is by far the largest experience from India of KRAS mutated NSCLC, comparing G12C with other KRAS mutants. Despite limitations of retrospective nature, small sample size, heterogeneity in the cohort and missing data points, and limited molecular profiling this study is relevant in the light of approval of targeted therapy, sotorasib, which is currently unavailable in this country.
Legal entity responsible for the study
The authors.
Funding
Has not received any funding.
Disclosure
All authors have declared no conflicts of interest.
16P - KRAS and CTLA-4 expression profiling in circulating tumor cells in patients with colorectal cancers
- Sharmin Aktar (Gold Coast, Australia)
- Sharmin Aktar (Gold Coast, Australia)
- Tracie Cheng (Gold Coast, QL, Australia)
- Sujani Gamage (Gold Coast, Australia)
- Farhadul Islam (Rajshahi, Bangladesh)
- Vinod Gopalan (Gold Coast, QL, Australia)
- Alfred KY Lam (Gold Coast, QL, Australia)
Abstract
Background
Circulating tumour cells (CTCs) could escape the host immune surveillance by altering the expression of immune regulatory molecules (PD-L1, PD-L2, CTLA-4, CD47) in cancer patients. Recent studies suggested that KRAS mutation might promote the immune escape of tumour cells by inducing the upregulation of these molecules. However, the regulatory effects of KRAS on the expression of CTLA-4 in patients with colorectal cancer (CRC) have yet to be explored. This study aimed to investigate KRAS and CTLA-4 mRNA expression profiling in CTCs from patients with CRC.
Methods
Peripheral blood from 50 CRC patients was collected to isolate CTCs using a negative selection (EasySepTM) method. The presence of CTCs was confirmed by immunofluorescence staining using multiple tumor cell surface biomarkers (EpCAM, SNAIL-1, E-cadherin and MMP-9). The mRNA expressions of CTLA-4 and KRAS in CTCs were analysed by RT-qPCR. The association between the presence of CTCs and clinicopathological variables was evaluated.
Results
The cells, which are positive for at least one of the markers (EPCAM, SNAIL-1, E-Cadherin and MMP-9), and enlarged nucleus and cell size >8μm were considered as CTCs. Approximately 66% (n=33/50) of patients with CRC were CTC positive. The majority of patients with zero CTC or low CTC counts (˂10 CTCs) were diagnosed with early stages (stage I or II), while patients with higher CTCs counts (≥10 CTCs) were with advanced stages (stages III or IV) with CRC ((p < 0.0064). The presence of CTC were also significantly correlated with tumour type, size. The expressions of CTLA-4 and KRAS were higher in CTC positive groups compared to CTC negative in patients with CRC. Also, the expression levels of these two molecules were positively correlated to each other (Spearman’s rank test, r = 0. 0.6674; p<0.0001). Additionally, from clinical data analysis, we found that CTLA-4 gene expression weakly correlates with KRAS mutation (p < 0.060).
Conclusions
Our study demonstrated that KRAS gene activation might upregulate CTLA-4 expression in patients with CRC. Thus, understanding the role of the interactions between oncogenes and immune checkpoint molecules is essential to fully uncover the molecular mechanisms involved in immune escape by CTCs in patients with CRC.
Legal entity responsible for the study
The authors.
Funding
School of Medicine and Dentistry, Griffith University.
Disclosure
All authors have declared no conflicts of interest.
17P - Increased expression of POU5F1 in metastatic colorectal cancer is not caused by increased expression of OCT4A and OCT4B isoforms
- Eva Turyova (Martin, Slovak Republic)
- Eva Turyova (Martin, Slovak Republic)
- Peter Mikolajcik (Martin, Slovak Republic)
- Veronika Holubekova (Martin, Slovak Republic)
- Marian Grendar (Martin, Slovak Republic)
- Ludovit Laca (Martin, Slovak Republic)
- Zora Lasabova (Martin, Slovak Republic)
Abstract
Background
The gene POU5F1 (also known as an OCT4) belonging to POU protein family is composed of 5 exons that can create many isoforms by alternative splicing. Most known isoform is OCT4A that is expressed in many types of stem cells. Its nuclear localization and presence of the DNA-binding domain enable it to regulate the expression of genes that are responsible for pluripotency and blocking of the differentiation of the cells. Other splicing products are numerous OCT4B isoforms (OCT4B-OCT4B5) that differ from OCT4A in the cell localization and in absence of the DNA-binding domain. Majority of OCT4 isoforms were discovered only recently and there have not been clear evidences about their role in the cells yet. The role of OCT4A, OCT4B and OCT4B1 in tumorigenesis have already been explored but without definite results. The aim of our research is the analysis of alternative splicing variants of the gene POU5F1 in association with the patient´s prognosis and their occurrence in the metastasis.
Methods
For this analysis we used fresh surgical specimens of the patients with colorectal cancer that were isolated from primary tumours (n=47) and from the metastasis (n=31). Subsequently, the total RNA was isolated and transcribed to cDNA. Through the quantitative PCR method using particular TaqMan assays for specific variants and with ΔΔ Ct method, we separately analyzed the relative gene expression of isoform A, isoforms B, but also all isoforms together.
Results
We found out that in tumour specimens isolated from primary tumours was the expression of all POU5F1 isoforms significantly lower than in adjacent non-tumour tissue. On the other hand, the significantly increased expression in metastatic tumor compared to primary tumours was observed only in experiment with probe specific for all POU5F1 isoforms whereas isoform A, neither isoform B were not reason of increased expression of POU5F1 in metastasis.
Conclusions
Our analysis indicate that alternative splicing play a pivotal role in metastatic colorectal cancer and whereas we exclude isoform A and isoforms B as a cause of increased expression of POU5F1 in metastasis, we consider as an important to identify responsible alternative transcript.
Legal entity responsible for the study
The authors.
Funding
VEGA 1/0269/22.
Disclosure
All authors have declared no conflicts of interest.
18P - Trastuzumab in HER2 Amplified or Overexpressed Gallbladder Cancer: Experience from an Indian Cancer Center
- Debapriya Mondal (Kolkata, India)
- Debapriya Mondal (Kolkata, India)
- Sandip Ganguly (Kolkata, India)
- Joydeep Ghosh (Kolkata, India)
- Prashant Pandey (Kolkata, India)
- Somnath Roy (Kolkata, India)
- Bivas Biswas (Kolkata, WE, India)
Abstract
Background
The prognosis of advanced gall bladder carcinoma (GBC) remains poor despite the addition of newer targeted therapies. HER2 is a potential therapeutic target expressed in up to 20% GBC. We present an analysis of advanced or metastatic HER2-amplified or overexpressed GBC treated with trastuzumab and chemotherapy from an Indian cancer center.
Methods
Patients with advanced or metastatic GBC with immunohistochemical evidence of HER2 overexpression (IHC 3+) or HER2 amplification detected with FISH, treated with trastuzumab and first-line chemotherapy between 2020 and 2021 were included. Outcome measures were objective response rate (ORR), progression-free survival (PFS), and overall survival (OS).
Results
Twenty-six patients (age range, 44-71) with GBC were treated with trastuzumab and chemotherapy. Twenty patients (76.9%) had newly diagnosed advanced disease while six patients (23.1%) had recurred after prior curative treatment. Twenty-four patients (92.3%) received gemcitabine-cisplatin and two received (7.7%) gemcitabine-oxaliplatin as chemotherapy. Partial response was seen in 11 patients (42.3%) while 10 patients (38.5%) had stable disease (objective response rate 42.3%, overall response rate 80.8%). At a median follow-up of 15.7 months, median PFS was 9.7 months (95% CI, 9.3-10) and median OS was 11.9 months (95% CI, 11.2-12.5). Grade 2 ejection fraction drop was seen in 1 patient (3.8%). No adverse events of grade 3 or more were attributable to trastuzumab.
Conclusions
Trastuzumab added to chemotherapy for advanced GBC demonstrated better ORR, and PFS compared to historical control of chemotherapy alone, without any additional toxicities.
Legal entity responsible for the study
The authors.
Funding
Has not received any funding.
Disclosure
All authors have declared no conflicts of interest.
19P - Deciphering the role of precision oncology in the treatment of biliary tract cancer in daily routine practice- retrospective analysis from the cancer center Upper Austria
- Bernhard Doleschal (Linz, Austria)
- Bernhard Doleschal (Linz, Austria)
- Holger Rumpold (Linz, Austria)
Abstract
Background
The routine therapeutic landscape of metastatic CCC is still largely based on cytotoxic chemotherapy. This standard gets increasingly challenged with the advent of next generation sequencing (NGS) in routine practice and evolving trials of targeted therapies in CCC. However the value of comprehensive genetic profiling of CCC in actual routine clinical practice remains poorly characterized.
Methods
We performed a retrospective study at the clinical cancer center of Upper Austria (Tumorzentrum Oberösterreich) in 2018-2021. Tumor samples from 56 patients with advanced CCC underwent comprehensive genetic profiling. TruSight Tumor 170 Assay (Illumina), Archer FusionPlex Panel (ArcherDX), Oncomine Focus Assay (Thermo Fisher Scientific) were used for NGS analysis. Furthermore MSI status was determined by custom made Multiplex PCR-Based Methods. Immunhistochemistry (IHC) collected data on Her2neu and PDL-1expression.
Results
A potentially actionable pathogenic variant was identified in 32 patients (57%). Pathogenic variants were ranked according ESMO Scale for Clinical Actionability of molecular Targets (ESCAT). In 15 patients with ESCAT I-III criteria a molecular informed therapy was established targeting 8 FGFR alterations, 2 MSI high status, 1 Pi3kinase mutation, 2 BRCA1/2 mutations, 2 BRAF V600Emutations. In 13 of the 15 treated patients we could observe a favorable PFS2 (targeted therapy)/PFS1 (previous standard therapy) ratio >1,3, suggesting clinical benefit. Overall survival in patients receiving molecular matched therapy showed a positive trend compared to patients remaining on standard treatment protocol.
Conclusions
We could show that comprehensive molecular characterization of advanced CCC during routine clinical care leads to favorable PFS2/PFS1 ratios and probable positive overall survival. This underscores the recent ESMO recommendations for NGS reflex testing in advanced CCC.
Legal entity responsible for the study
The authors.
Funding
Has not received any funding.
Disclosure
All authors have declared no conflicts of interest.