Abstract 3358: PLCRC-PROVENC3: assessing the prognostic value of post-surgery liquid biopsy cell-free circulating tumor DNA in stage III colon cancer patients

Introduction: Surgery followed by adjuvant chemotherapy (ACT) is standard of care in stage III colon cancer. However, 50% of the patients would be cured by surgery alone and are being overtreated, while 30-35% will experience a recurrence despite adjuvant treatment, resulting in only 15-20% of the patients benefitting from ACT. Therefore, there is a need for prognostic biomarkers to better stratify this group of patients for ACT decisions. Recent observational and interventional studies in non-metastatic colon cancer have shown that detection of cell-free circulating tumor DNA (ctDNA) in blood after surgery is highly prognostic for development of recurrence. Hence, ctDNA analysis is a promising approach to guide treatment decisions in stage III colon cancer, but studies with large well-defined patient cohorts are needed to prove clinical utility.

Aim: Determine the prognostic value of ctDNA in stage III colon cancer patients treated with ACT to reduce futile treatment.

Methods: 241 stage III colon cancer patients treated with ACT were included in the prospective observational study “PROVENC3” (PROgnostic Value of Early Notification by Ctdna in Colon Cancer stage 3), a substudy of the Prospective Dutch Colorectal Cancer cohort (PLCRC). The PLCRC infrastructure accrued patients with colorectal cancer in 23 participating hospitals in the Netherlands. After informed consent, blood was collected pre-surgery, post-surgery, post-ACT and every six months up to 3 years. Tumor-informed detection of ctDNA was performed through integrated whole genome sequencing (WGS) analyses of formalin-fixed paraffin-embedded tumor tissue DNA (80x), germline DNA (40x), and plasma cell-free DNA (30x).

Results: Patient accrual was completed in 2021, with a median follow-up of 35.6 months. In total, 1090 blood samples have been collected to date. Analytical studies demonstrated a limit of detection of the test of 0.005% ctDNA utilizing contrived reference models derived from six independent cell lines, with a specificity of 99.6% across 119 noncancerous donor plasma specimens. From the PROVENC3 study, ctDNA analyses are ongoing for pre-surgery (n=68) and post-surgery (n=241 patients) blood samples. Preliminary results demonstrated a ctDNA detection rate of 93.4% pre-surgery and 17.1% post-surgery, which was associated with disease recurrence. Final analysis will enable determination of: 1) the proportion of ctDNA-positive/negative patients after surgery and the corresponding recurrence rates; 2) the prognostic value of post-surgery ctDNA; and 3) the lead time between post-surgery ctDNA detection and recurrence.

Future Perspective: Ultimately, the results of this study will be used to model and design a ctDNA-guided interventional trial in stage III colon cancer patients, to reduce futile ACT and its associated side-effects.

Citation Format: Carmen Rubio-Alarcon, Steven L. Ketelaars, Ingrid A. Franken, Sietske C. van Nassau, Dave E. van der Kruijssen, Suzanna J. Schraa, Theodora C. Linders, Pien Delis-van Diemen, Maartje Alkemade, Anne Bolijn, Marianne Tijssen, Margriet Lemmens, Miranda van Dongen, Mirthe Lanfermeijer, Annegien Broeks, Lana Meiqari, Linda J. Bosch, Victor E. Velculescu, Amy Greer, Samuel V. Angiuoli, Andrew Georgiadis, David Riley, James R. White, Christopher Greco, Liam Cox, Daan van den Broek, Cornelis J. Punt, Veerle M. Coupé, Miriam Koopman, Jeanine Roodhart, Gerrit A. Meijer, Mark Sausen, Geraldine R. Vink, Remond J. Fijneman. PLCRC-PROVENC3: assessing the prognostic value of post-surgery liquid biopsy cell-free circulating tumor DNA in stage III colon cancer patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3358.

Abstract 3366: A machine learning approach to determine the cellular origin of variants in liquid biopsies

Introduction: Targeted next-generation sequencing (NGS) of cell-free DNA in plasma, referred to as liquid biopsy, has become a valuable diagnostic tool in clinical oncology. However, detection of variants related to clonal hematopoiesis (CH) is a major confounder that significantly impairs the clinical utility of liquid biopsies. Here we developed a machine-learning model to determine tumor versus CH origin of variants identified in plasma-only NGS.

Methods: We assembled a training cohort of 352 variants identified by targeted deep plasma sequencing from 199 patients with stage I-IV breast, colorectal, esophageal, lung, and ovarian cancer, coupled with matched white blood cell (WBC) and tumor tissue NGS to allow determination of the reference origin for each plasma variant. We employed Extreme Gradient Boosting (XGBoost) to integrate fragment, variant, gene, and patient level features to predict tumor versus CH plasma variant origin, evaluating the performance of this approach within the training cohort using 10-fold cross-validation. We applied the fixed model to two independent validation cohorts: a small cell lung cancer (SCLC) cohort comprising of 74 variants from targeted plasma NGS from 26 patients and a multi-cancer cohort of 409 variants detected using the MSK-Impact panel from 74 patients with breast, colorectal, and prostate cancer.

Results: Variant allele frequencies (VAF) did not differentiate tumor from CH variants, as the VAFs between tumor (median VAF 0.53%) and CH (median VAF 0.409%) variants in the training cohort were largely overlapping (area under the ROC curve-AUC 0.54, 95% confidence interval-CI 0.48-0.61). Similarly, individual fragmentomic features (mutant fragment length, cut points, and endpoint motifs) had limited ability to distinguish tumor from CH variants (AUC range 0.51-0.76). Using serial plasma samples, we identified stable statistical measures of differences in fragment feature distributions between mutant and wild type fragments; these were subsequently incorporated into an XGBoost machine-learning model along with variant, gene and patient features to predict tumor versus CH variant origin. Our model predicted variant origin with an AUC of 0.95 (95% CI 0.87-1) from 10-fold cross validation in the training cohort. The performance of the model was tested in independent SCLC and multi-cancer validation cohorts; the fixed model predicted plasma variant origin with an AUC of 0.87 (95% CI 0.73-1) and 0.89 (95% CI 0.86-0.92) respectively.

Conclusion: We developed a machine-learning model that integrates patient, gene, variant and fragment features to predict tumor versus CH origin of plasma variants across solid tumors and NGS sequencing platforms. The ability to identify bona fide tumor variants in plasma-only sequencing fills a critical need in the clinical implementation of liquid biopsy-guided cancer therapy by reducing misinterpretation due to CH contamination.

Citation Format: Jenna V. Canzoniero, Archana Balan, Jillian Phallen, Blair V. Landon, Lavanya Sivapalan, Benjamin Green, Zineb Belcaid, Susan C. Scott, Gavin Pereira, Vincent K. Lam, Ali H. Zaidi, Ronan J. Kelly, Christine L. Hann, Wade T. Iams, Christine M. Lovly, Patrick M. Forde, Gerrit A. Meijer, Geraldine R. Vink, Remond J. Fijneman, The MEDOCC Group, Victor E. Velculescu, Robert B. Scharpf, Valsamo Anagnostou. A machine learning approach to determine the cellular origin of variants in liquid biopsies [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3366.

Abstract 519: Clinical impact ofKRASG12, G13, Q61, K117 and A146 mutations in patients with colorectal liver metastases

Introduction: The distribution of KRAS mutation variants across tumor types is not uniform. The KRAS A146 mutation is predominantly seen in colorectal cancer (CRC) patients. Here, we evaluated how clinical features like tumor load and overall survival differ between metastatic CRC (mCRC) patients carrying distinct somatic KRAS G12, G13, Q61, K117 or A146 mutations.

Methods: 419 CRC patients with initially unresectable liver-limited metastases, who participated in the multicenter CAIRO5 prospective clinical trial, were evaluated for tumor tissue KRAS mutation status. For the subgroup of patients who carried a KRAS mutation and were treated with bevacizumab and doublet or triplet chemotherapy (N=156), clinical outcome was evaluated and pretreatment tumor burden was quantified as liquid biopsy circulating tumor DNA (ctDNA) mutant allele fraction (MAF) and as total tumor volume (TTV) on CT imaging. The MAF, TTV and overall survival were compared between patients harboring different KRAS mutation variants.

Results: Of the 156 patients with a KRAS mutated tumor, most carried a KRAS G12 mutation (N=112, 71.8%), followed by mutations in G13 (N=15, 9.6%), A146 (N=12, 7.7%), Q61 (N=9, 5.8%) and K117 (N=5, 3.2%). High plasma ctDNA levels were observed for patients carrying a KRAS A146 mutation versus those with a KRAS G12 mutation, with a median MAF of 48% versus 19%, respectively. Radiological TTV revealed this difference to be associated with a higher tumor load in patients harboring a KRAS A146 mutation (median TTV 672 cm3 (A146) versus 74 cm3 (G12), p=0.036). Moreover, KRAS A146 mutation carriers showed inferior overall survival compared to patients with mutations in KRAS G12 (median 10.7 versus 26.4 months; HR=2.5; p=0.003), and the multivariable Cox regression analysis showed that the KRAS alteration was the only independent prognostic factor for overall survival.

Conclusion and Relevance: This study revealed that within mCRC patients A146 is the third most common KRAS mutation variant, and mCRC patients carrying a KRAS A146 mutation represent a distinct molecular subtype of patients with high tumor burden and poor clinical outcome. This highlights the importance of testing CRC for all KRAS mutations in routine clinical care and shows the opportunity for personalized treatment beyond detecting the presence of a KRAS mutation by taking the specific KRAS mutation variant into account.

Citation Format: Iris van 't Erve, Nina J. Wesdorp, Jamie E. Medina, Leonardo Ferreira, Alessandro Leal, Joost Huiskens, Karen Bolhuis, Jan-Hein T. van Waesberghe, Rutger-Jan Swijnenburg, Daan van den Broek, Victor E. Velculescu, Geert Kazemier, Cornelis J. Punt, Gerrit A. Meijer, Remond J. Fijneman. Clinical impact ofKRASG12, G13, Q61, K117 and A146 mutations in patients with colorectal liver metastases [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 519.

Abstract 2224: DELFI as a real-time treatment response assessment for patients with cancer

Introduction: Measurement of tumor-derived DNA molecules in the plasma (ctDNA) has become a useful tool to determine the overall tumor burden in patients with cancer. The ctDNA burden may change over time, decreasing after treatment response and increasing with development of resistance to therapy. Monitoring the dynamics of ctDNA burden over the course of treatment with a rapid, non-invasive test enables physicians to make timely treatment decisions. Using the DNA evaluation of fragments for early interception (DELFI) approach, we have developed the DELFI Monitoring Score (DMS) to longitudinally assess ctDNA burden during therapy of cancer patients.

Methods: We performed low coverage whole genome sequencing on 302 cfDNA libraries of 76 treatment-naive metastatic colorectal cancer (mCRC) patients with at least one blood draw prior to and after treatment initiation. Mutations in KRAS, NRAS, or BRAF were independently measured by digital droplet PCR (ddPCR) for all timepoints evaluated. We trained a Bayesian regression model with the mutant allele fraction (MAF) of KRAS, NRAS, or BRAF as response and fragmentation-related features as predictors as well as a random intercept. To avoid overfitting and assess generalizability, we used cross-validation, wherein each patient’s samples were held out of the dataset and a model was trained on the samples of all other patients to generate predictions for the held-out samples. Patients with DMS below and above a detectability threshold at the first blood draw post-treatment (between 4-12 weeks) were classified as molecular responders and non-responders, respectively. Progression-free survival outcomes, defined as time to progression by RECIST 1.1 or death, were evaluated using a Kaplan-Meier estimator in these two groups.

Results: Molecular responders based on DMS assessment experienced longer progression-free survival than molecular non-responders (p < 0.01), similar to a MAF-based approach. Additionally, in the 43 patients for whom the MAF of the KRAS, NRAS, or BRAF variants was 0% at the first blood draw post-treatment, we observed further separation on progression-free survival by the DELFI Monitoring Score (p = 0.014).

Conclusions: We developed a novel quantitative measure of ctDNA burden using cell-free DNA fragmentation patterns that is estimable from low coverage whole genome sequencing. The DMS appears to be useful for measuring ctDNA burden and enabling a non-invasive approach to treatment monitoring, as it distinguishes therapeutic responses in a mCRC cohort. Our ability to detect differences in progression-free survival among patients with undetectable ddPCR MAFs suggests that DMS may be more sensitive and predictive than conventional mutation-based approaches for treatment response monitoring.

Citation Format: Keith Lumbard, Laurel A. Keefer, Iris van't erve, Jacob Carey, Bryan Chesnick, Denise Butler, Michael Rongione, Cornelis J. Punt, Nicholas C. Dracopoli, Remond J. Fijneman, Gerrit A. Meijer, Robert B. Scharpf, Victor E. Velculescu, Alessandro Leal. DELFI as a real-time treatment response assessment for patients with cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2224.

Abstract 540: Molecular response evaluation of patients with metastatic colorectal cancer using circulating tumor DNA

Introduction: Patients with colorectal cancer with unresectable and isolated liver metastases (CRLM) are mostly treated with chemotherapy and targeted treatments like anti-epidermal growth factor receptor (EGFR) monoclonal antibody therapy. Clinical response evaluation of systemic treatment is performed by radiological CT imaging, which can detect disease progression. However, CT imaging does not always give information about the viability of the tumor tissue nor does it constitute the genomic changes of the tumor, i.e. development of sub-clones following the pressure of treatment. Cell-free circulating tumor DNA (ctDNA) derived from liquid biopsies is a minimally invasive biomarker that has great potential for tumor detection and is present in relatively high levels in the plasma of patients with CRLM. Liquid biopsy ctDNA allows for longitudinal follow-up and gives the possibility to track intratumor heterogeneity caused by different sub-clones without a repeated tumor biopsy. Here, we aim to assess the use of molecular profiling using serial liquid biopsies as a biomarker for treatment response evaluation.

Methods: Tumor tissue obtained prior to treatment as well as longitudinal liquid biopsies were collected from patients with CRLM who participated in a prospective clinical trial with CRC and were treated with panitumumab and doublet chemotherapy. Liquid biopsy ctDNA was isolated and analyzed by targeted sequencing using a panel of 33-genes, allowing to map dynamic molecular changes during treatment. ctDNA sequencing results were corrected for germline variants and clonal hematopoiesis variants by using targeted sequencing data of patient-matched tumor tissue DNA and white blood cell (WBC) genomic DNA, respectively. ‘Molecular response' was defined as the elimination of more than 95% of ctDNA after treatment compared to the measurement before treatment initiation. Detection of disease progression by ctDNA was compared to CT imaging.

Results: At present, 110 longitudinal plasma samples as well as WBC genomic DNA and tumor tissue DNA are analyzed from a cohort of 33 patients. Currently, we are expanding the number of patients and samples. Molecular responders to treatment showed a significantly longer overall survival than non-responders (median 51 vs 25 months; p=0.033; HR=3.7). In addition, significantly earlier detection of disease progression was observed using ctDNA compared to radiological imaging (median difference of 4.8 months; p=0.006).

Conclusion: Serial plasma ctDNA analyses in patients with mCRC provide a minimally-invasive tool for longitudinal treatment response evaluation of dynamic genomic alterations and creates an opportunity for patient subset selection for possible adaptation of the treatment regimen.

Citation Format: Iris van 't Erve, Jamie E. Medina, Alessandro Leal, Eniko Papp, Karen Bolhuis, John K. Simmons, Samuel Angiuoli, Cornelis J. Punt, Gerrit A. Meijer, Victor E. Velculescu, Remond J. Fijneman. Molecular response evaluation of patients with metastatic colorectal cancer using circulating tumor DNA [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 540.

Abstract CT251: MEDOCC-CrEATE trial in progress: effectiveness of adjuvant chemotherapy in stage II colon cancer patients with positive circulating tumor DNA

Background Accurate detection of patients with minimal residual disease (MRD) after resection of localized colon cancer remains an unmet clinical need as these patients might benefit from adjuvant chemotherapy (ACT). For stage II colon cancer, ACT is only indicated in patients with a pT4 tumor without a deficient mismatch repair system (dMMR), according to Dutch guidelines. However, recurrence rate (RR) in stage II colon cancer is still 15-20%. Circulating tumor DNA (ctDNA), consisting of small fragments of DNA containing tumor-specific mutations, has been shown to be a promising biomarker for MRD and a strong predictor for recurrent disease when detectable after resection. The MEDOCC-CrEATE trial investigates how many stage II colon cancer patients with detectable ctDNA after surgery will accept ACT and whether ACT reduces RR in these patients.

Methods The MEDOCC-CrEATE study follows the ‘trials within cohorts' (TwiCs) design. Patients with colorectal cancer are included in the Prospective Dutch ColoRectal Cancer (PLCRC) cohort study and give informed consent for collection of clinical data and biomaterials, including tissue and blood samples. Additionally, patients are invited to give their consent for future randomization without being informed when allocated to the control group receiving standard of care. In MEDOCC-CrEATE 1320 stage II colon cancer patients without an indication for ACT will be included and randomized 1:1 into an experimental and a control arm. In the experimental arm, tissue and blood samples are analyzed after surgery for tissue-informed detection of plasma ctDNA, using the PGDx elio™ Platform. Patients with detectable ctDNA after surgery will be offered ACT consisting of 8 cycles of capecitabine plus oxaliplatin. Patients in the experimental arm without detectable ctDNA and patients in the control arm receive standard follow-up. The primary endpoint is the proportion of patients accepting ACT when ctDNA is detectable after resection. Most important secondary endpoint is 2-year RR, but also includes 5-year RR, disease free and overall survival, time to recurrence, quality of life and cost-effectiveness of the ctDNA-based treatment strategy. Data will be analyzed by intention to treat. To our knowledge, MEDOCC-CrEATE is the first trial in which a ctDNA guided strategy for adjuvant chemotherapy in colon cancer is investigated. The first patient was enrolled in August 2020. MEDOCC-CrEATE is now open for inclusion in 8 hospitals in the Netherlands. So far, 9 patients have been randomized. The number of participating hospitals will be expanded to 20-25 hospitals to include all 1320 patients within 3 years. MEDOCC-CrEATE has been registered in the Netherlands Trial Register: NL6281/NTR6455.

Citation Format: Suzanna J. Schraa, Karlijn L. Van Rooijen, Dave E. Van Der Kruijssen, Carmen Rubio Alarcón, Jillian Phallen, John Simmons, Sam Angiuoli, Amy E. Greer, Veerle M. Coupé, Helma M. Van Grevenstein, Sjoerd Elias, Helena M. Verkooijen, Miranda M. Van Dongen, Linda J. Bosch, Daan Van Den Broek, Gerrit A. Meijer, Victor E. Velculescu, Remond J. Fijneman, Geraldine R. Vink, Miriam Koopman. MEDOCC-CrEATE trial in progress: effectiveness of adjuvant chemotherapy in stage II colon cancer patients with positive circulating tumor DNA [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr CT251.

Abstract 708: Limited release of circulating tumor DNA into the systemic circulation by peritoneal metastases from colorectal cancer

Introduction: Circulating tumor DNA (ctDNA) from plasma is a promising biomarker. Patients with metastatic colorectal cancer (CRC) often have high ctDNA levels compared to other cancer types. However, it is unclear whether this is also the case for patients with peritoneal metastases from CRC.

Aim: To compare the propensity of ctDNA shedding by isolated liver metastases and isolated peritoneal metastases from CRC.

Methods: Plasma was collected from 100 CRC patients (64% male, mean age of 60 [SD=10] years) with isolated unresectable liver metastasis (CRC-LM). Plasma and ascites were obtained from 20 CRC patients (60% male, mean age of 63 [SD=9.8] years) with isolated unresectable peritoneal metastases (CRC-PM). All liquid biopsies were obtained prior to treatment and cell-free DNA was isolated using the QIAsymphony (Qiagen, Germany) and assessed by droplet digital PCR (ddPCR; Bio-Rad, Hercules, USA). Patients with a KRAS or BRAF tumor tissue mutation were suited for plasma ctDNA ddPCR analysis, and were detected in 57 CRC-LM (57%) and 11 CRC-PM (55%) patients. The ability to shed ctDNA into the circulation was evaluated by comparing KRAS/BRAF mutation status in plasma and ascites with the mutation status based on tumor tissue. Regarding liquid biopsies, mutant allele fraction (MAF) and mutant copies per ml input (MTc/ml) were reported.

Results: Tissue mutations could be confirmed in plasma in 93% of CRC-LM and only 20% of CRC-PM patients, whereas mutations were detected in ascites in 100% of CRC-PM patients. The MAF and MTc/ml were both significantly lower in CRC-PM plasma ctDNA (median MAF=0.28% and MTc/ml=21) compared to CRC-LM plasma ctDNA (median MAF=18.9% and MTc/ml= 1758; P<0.0001). In addition, the MAF and MTc/ml were significantly higher in CRC-PM ascites ctDNA (median MAF=16.4%, MTc/ml=305) compared to plasma ctDNA (median MAF=0.28%, MTc/ml=21; P<0.0001).

Conclusion: To our knowledge, this is the first study showing a comprehensive comparison of tissue, blood and ascites derived genomic information in patients with CRC and extensive isolated peritoneal metastases. This study concludes that isolated peritoneal metastases from CRC is a malignancy with distinct clinical and biological characteristics, which should be taken into account when considering the clinical utility of ctDNA in different metastatic setting of CRC. To detect genomic alterations, the blood circulation is the preferred source of ctDNA in case of CRC liver metastases, whereas ascites offers an alternative to plasma in patients with peritoneal metastases, which might be suitable as diagnostic, prognostic, predictive or disease monitoring biomarker.

Citation Format: Iris van 't Erve, Koen P. Rovers, Alexander Constantinides, Karen Bolhuis, Emma C. Wassenaar, Robin J. Lurvink, Clément J. Huysentruyt, Petur Snaebjornsson, Daan van den Broek, Tineke E. Buffart, Niels F. Kok, Gerrit A. Meijer, Cornelis J. Punt, Onno Kranenburg, Ignace H. de Hingh, Remond J. Fijneman. Limited release of circulating tumor DNA into the systemic circulation by peritoneal metastases from colorectal cancer [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 708.

Abstract 3096: Liquid biopsy cell-free circulating tumor DNA as prognostic biomarker for stage III colon cancer patients

Introduction: Stage III colon cancer patients undergo surgery followed by adjuvant chemotherapy (ACT) according to clinical guidelines. However, 50% would be cured by surgery alone and are being overtreated, while 30-35% will relapse despite adjuvant treatment. This means that only 15-20% of the patients benefit from ACT. Therefore, there is a need for better prognostic biomarkers to stratify patients for ACT. Detection of cell-free circulating tumor DNA (ctDNA) in blood after surgery is indicative of minimal residual disease and highly prognostic for disease recurrence. Hence, detecting liquid biopsy ctDNA is a promising approach to guide treatment decisions in stage III colon cancer.

Aim: Determine prognostic value of ctDNA in stage III colon cancer patients treated with ACT in order to reduce futile treatment.

Methods: 315 stage III colon cancer patients treated with ACT will be included in the prospective observational study “PROVENC3” (PROgnostic Value of Early Notification by Ctdna in Colon Cancer stage 3). The Prospective Dutch Colorectal Cancer Cohort (PLCRC) infrastructure organizes accrual of colorectal cancer patients in more than 50 hospitals in the Netherlands, among which 25 hospitals that accrue patients for PROVENC3. If informed consent is provided, blood is collected at baseline, post-surgery, post-ACT and every six months up to 3 years, and shipped to a central location. Tumor-informed detection of mutations in ctDNA will be performed by combined analysis of targeted sequencing of a panel of >30 genes in cfDNA (PGDx elio plasma test) and a panel of >500 genes in DNA from formalin-fixed paraffin-embedded tumor tissue (PGDx elio tissue complete assay). The clinical, pathological, and molecular data will be handled according to the FAIR (findable, accessible, interoperable and reusable) principles and integrated in cBioPortal.

Results and future directions: Around 125 patients and 400 blood samples included to date. Once sequencing data are obtained we will determine: 1) the proportion of ctDNA-positive and ctDNA-negative patients after surgery and the corresponding recurrence rates; 2) the prognostic value of ctDNA pre-surgery; and 3) the lead time between ctDNA detection and recurrence. Ultimately, the results of this study will be used to model and design an ethically acceptable and cost-effective ctDNA-guided interventional trial, to reduce futile ACT and its associated side-effects in stage III colon cancer patients.

Citation Format: Carmen Rubio Alarcón, Dave E. van der Kruijssen, Lana Meiqari, Linda J. Bosch, John K. Simmons, Victor E. Velculescu, Daan van den Broek, Cornelis J. Punt, Veerle M. Coupé, Miriam Koopman, Gerrit A. Meijer, Geraldine R. Vink, Remond J. Fijneman. Liquid biopsy cell-free circulating tumor DNA as prognostic biomarker for stage III colon cancer patients [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 3096.

Abstract 2276: Performance and cost comparison of circulating tumor DNA detection platforms

Purpose

The field of circulating cell free DNA (cfDNA) testing is quickly developing. Multiple platforms to detect hotspot mutations in ctDNA are available, including Bio-Rad droplet digital PCR (ddPCR), BioCartis Idylla, Roche COBAS z480 and Sysmex BEAMing. These platforms vary in the amount of plasma required, the method of ctDNA isolation, the number of hotspots analyzed, and the costs per sample. These factors can impact the applicability of a specific platform in the analysis of ctDNA.

In this study we compared these platforms in terms of sensitivity and total costs per sample.

Methods

The platform comparison was performed as follows:

1. Plasma from six metastatic colorectal cancer (mCRC) patients with known tissue KRAS mutation status was analyzed according to the manufacturers’ protocols.

2. Sensitivity was tested using six constructed reference samples with seven KRAS hotspot mutations at various total input (10ng, 50ng) and mutant allele frequencies (0%, 0.04%, 0.50%); each in four replicates.

3. Twelve mCRC patients were analyzed using equal amounts of ctDNA for each platform.

4. Total costs per sample were evaluated, including costs for consumables, technician hands-on time, equipment and maintenance.

Results

1. In six mCRC samples BEAMing (3ml plasma) detected 5/6 mutations, ddPCR and Idylla (both 1ml plasma) 4/6 mutations and COBAS z480 (2ml plasma) 3/6 mutations.

2. In constructed reference samples ddPCR (65%) and BEAMing (46%) yielded the highest sensitivity. With 10ng input BEAMing and COBAS z480 produced “Too little DNA” errors in 60% and 100% of cases, respectively.

3. In twelve mCRC samples, eight had more than 10ng ctDNA and four had less. All platforms were fully concordant for samples with more than 10ng input. Detection rate across twelve samples: Idylla detected 7/11 detectable mutations, COBAS z480 and BEAMing both detected 5/11, ddPCR detected 4/10.

4. BEAMing has the highest cost per sample (€486-€821) whereas ddPCR has the lowest cost per sample (€39-€298).

Conclusions

A direct comparison of ctDNA mutation detection platforms is complex and should take into account the differences in input and output specifications of the platforms.

Factors such as complexity of analysis (Idylla is a low complexity platform, whereas BEAMing requires more specialized training), total costs (varying from ddPCR to BEAMing), sensitivity (ddPCR and BEAMing yielded the highest sensitivity) and the number of mutations evaluated vary greatly between the platforms. All these factors influence ctDNA analysis and will have to be considered when choosing a specific platform for a specific (clinical) question, or when comparing results between studies.

Our data provide insight in the comparative performance of four commercial ctDNA analysis platforms, allowing future users to make an informed decision regarding a platform.

Acknowledgement

Powered by Health~Holland, Top Sector Life Sciences & Health, grant LSHM16047-H005.

Citation Format: Daan C. Vessies, Marjolein J. Greuter, Karlijn L. van Rooijen, Theodora C. Linders, Mirthe Lanfermeijer, Kalpana L. Ramkisoensing, Flore E. Grijseels, Boris van Doorn, Gerrit A. Meijer, Miriam Koopman, Veerle M. Coupé, Geraldine R. Vink, Remond J. Fijneman, Daan van den Broek. Performance and cost comparison of circulating tumor DNA detection platforms [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2276.

Abstract 1588: Liquid biopsy analyses of cell-free circulating tumor DNA as predictive and prognostic biomarker for colorectal cancer patients with metastatic disease

Background: Most colorectal cancer (CRC) deaths are caused by metastatic disease (mCRC). Therapeutic approaches include treatment with monoclonal antibodies (mAbs) against EGFR and VEGF. There is an urgent clinical need to stratify mCRC patients for optimal treatment. Cell-free circulating tumor DNA (ctDNA) derived from blood plasma is expected to improve stratification by early detection of therapy resistance and disease progression.

Aim: The general aim of this study is to advance towards clinical implementation of ctDNA-based tests as molecular biomarkers to improve disease management of mCRC patients. We will investigate added value of liquid biopsy ctDNA-based gene mutation analyses compared to: 1) tissue-based tests for RAS mutation status as determined in standard clinical care setting; and 2) monitoring of disease progression by computed tomography (CT) imaging.

Methods: CAIRO5 is a multicenter, randomized, phase 3 clinical trial of the Dutch Colorectal Cancer Group (DCCG) and includes patients with initially unresectable, liver-only mCRC, as confirmed by a central panel of liver surgeons/radiologists based on CT imaging. This study involves nation-wide longitudinal collection of liquid biopsies (blood samples) using cell-save tubes and CT imaging from up to 564 patients. Hotspot mutations in ctDNA will be analyzed by droplet digital PCR (ddPCR), and mutations in a panel of genes by targeted error correction sequencing (TEC-seq). Clinical, imaging, biobanking, and molecular data will be collected using standardized data fields and data formats and integrated for querying and viewing in tranSMART, making use of the national Health-RI research IT infrastructure.

Results: The nation-wide multi-center logistics for longitudinal blood sample collection and plasma processing has been established, with participation of more than 40 Dutch hospitals. At present (Nov 2017), over 220 patients have been included from whom more than 550 blood samples and 330 CT images were obtained. Proof of concept for the validity of this workflow was obtained by successful subjection of 11 plasma samples to ctDNA mutation analysis by TEC-seq (Phallen et al., 2017).

Discussion: Implementation of ctDNA-based tests as molecular biomarkers to improve disease management of mCRC patients requires collection of information from large, well-defined studies with longitudinal patient follow-up. This translational research project will provide the data that are needed to determine cost-effectiveness analysis of ctDNA mutation analyses by health technology assessment, yielding recommendations for clinical implementation of ctDNA applications.

Citation Format: Iris van 't Erve, Jillian Phallen, Karen Bolhuis, Joost Huiskens, Nicole C. van Grieken, Veerle Coupé, Annegien Broeks, Daan van den Broek, Alessandro Leal, Victor E. Velculescu, Cornelis J. Punt, Gerrit A. Meijer, Remond J. Fijneman. Liquid biopsy analyses of cell-free circulating tumor DNA as predictive and prognostic biomarker for colorectal cancer patients with metastatic disease [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 1588.

Abstract 3676: CMS classification of colorectal adenomas

Background Consensus molecular subtyping (CMS) is an RNA-expression-based classification of colorectal cancers (CRC). Genomic alterations, resulting in specific RNA-expression patterns, accumulate during CRC pathogenesis, including the premalignant adenoma stage.

Aim This study aimed to investigate whether differentiation of colorectal neoplasia into CMS classes can already be recognized at the adenoma stage, and whether specific CMS classes could be associated with DNA copy number aberrations that mark adenomas at high-risk of progressing to CRC.

Materials and Methods RNA-sequencing was performed on 62 advanced adenomas and 59 CRCs. DNA copy number analysis in adenomas was performed by low-coverage DNA-sequencing (n=30) or array-Comparative Genomic Hybridization (n=32). Microsatellite instability (MSI) status was determined by PCR methods. Adenomas and CRCs were classified into CMS subtypes together with CRCs (n=556) from The Cancer Genome Atlas, using the Random Forest CMS classifier.

Results The majority of the adenomas were classified as CMS3 (n=45; 72%), the 'metabolic subtype', recognized as least common among CRCs. No adenomas were classified as the 'mesenchymal' CMS4 subtype. One adenoma was classified as the 'MSI immune' CMS1 (2%), and 8 adenomas as the 'canonical' CMS2 (13%) type. The remaining 8 (13%) could not be classified. The CMS3 class was enriched with adenomas at low-risk of progression.

Conclusion Most adenomas were successfully classified. The lack of CMS4 adenomas is consistent with the fact that adenomas lack invasion-associated stroma. Adenomas showing cancer-associated chromosomal instability (CIN) or MSI (24%) were mostly classified as CMS2 and CMS1, respectively. The CMS3 subtype appeared to be the predominant adenoma signature.

Citation Format: Malgorzata A. Komor, Linda J. Bosch, Gergana Bounova, Anne S. Bolijn, Pien Delis-van Diemen, Christian Rausch, Youri Hoogstrate, Andrew Stubbs, Mark de Jong, Guido Jenster, Nicole C. an Grieken, Beatriz Carvalho, Lodewyk Wessels, Connie R. Jimenez, Remond J. Fijneman, Gerrit A. Meijer, NGS-ProToCol Consortium. CMS classification of colorectal adenomas [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 3676.

Abstract 2208: Peptide-mediated 'miniprep' isolation of extracellular vesicles is suitable for high-throughput proteomics; method evaluation and application in colon cancer

Objective:

Extracellular vesicles (EVs) are cell-secreted membrane vesicles enclosed by a lipid bilayer derived from endosomes or from the plasma membrane. Since they are released into body fluids, and their cargo includes tissue-specific and disease-related molecules, EVs represent a rich source for disease biomarkers. However, standard ultracentrifugation methods for EV isolation (UC-EV) are laborious, time-consuming, and require high inputs.

Method:

A recently described isolation method, which can be performed at small ‘miniprep’ scale, utilizes specific Heat Shock Protein (HSP)-binding peptides to aggregate HSP-decorated EVs (Ghosh et al. (2014), PLoS ONE 9:e110443). The authors showed comparable results for their method (abbreviated HSP-EV here) and UC-EV, but a detailed proteomic comparison was lacking. Therefore, we compared both methods using label-free proteomics of replicate EV isolations from HT-29 cancer cell-conditioned medium. Subsequently we applied this technique on secretomes of fresh human colorectal cancer (CRC) (n=17) and colon adenoma (n=4) tissue as well as patient-matched normal colon tissue.

Results:

Despite a 30-fold different input scale (UC-EV: 60 ml versus HSP-EV: 2 ml), both methods yielded comparable numbers of identified proteins (3115 versus 3085), with reproducible identifications (72.5% versus 75.5%) and spectral count-based quantification (average CV 31% versus 27%). EVs obtained by either method contained established EV markers and proteins linked to vesicle-related gene ontologies. In the EV fraction of the tissue secretomes 6390 proteins were identified, of which 471 proteins were significantly 5-fold more present in CRC samples than in normal tissue EVs. Gene ontology analysis revealed enrichment of nuclear proteins involved in DNA damage response, chromosome organization and RNA processing in the CRC EVs.

Conclusions:

The HSP-EV method provides an advantageous, simple and rapid approach for EV isolation from small amounts of biological samples, enabling high-throughput analysis in a biomarker discovery setting.

Citation Format: Meike De Wit, Jaco Knol, Inge de Reus, Tim Tim Schelfhorst, Logan Bishop-Currey, Nicole van Grieken, Sander Piersma, Thang V. Pham, Remond J. Fijneman, Gerrit A. Meijer, Henk Verheul, Connie R. Jimenez. Peptide-mediated 'miniprep' isolation of extracellular vesicles is suitable for high-throughput proteomics; method evaluation and application in colon cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2208. doi:10.1158/1538-7445.AM2017-2208

Abstract 1559: Proteogenomic analysis of alternative splicing in colorectal adenoma-to-carcinoma progression

Background

Early diagnosis of colorectal cancer (CRC) and identification of its precursor lesions (adenomas) is crucial in reducing CRC mortality rates. The fecal immunochemical test (FIT) is a non-invasive CRC screening test that detects human protein hemoglobin. Although FIT is beneficial in its current form with a sensitivity of ~65% for detection of CRC and ~27% for adenomas, its performance is still suboptimal and needs to be further improved. Adenoma-to-carcinoma progression is accompanied by alternative splicing, which results in expression of tumor-specific protein variants. These may yield novel biomarkers suitable for improving detection of progressive adenomas and CRCs.

Aim

We aim to identify novel biomarkers to improve early detection of CRC.

Materials and methods

RNA was isolated from 3D organoid cultures derived from 5 adenomas and 4 CRC tissues. RNA and proteins were isolated from 18 healthy human colon tissues, 30 adenomas and 30 CRCs. Samples were analyzed by RNA sequencing (Illumina) and in-depth tandem mass spectrometry proteomics (QExactive). For both organoid- and tissue-datasets differential splicing analysis was performed on RNA level to enrich the sequence database, against which mass spectra were searched, with predicted protein isoforms.

Results

Comparative splicing analysis between CRC and adenoma organoids revealed ~90 differentially spliced genes, yielding candidate biomarkers from epithelial origin. In the tissues, differential splicing analysis between CRCs and controls and between CRCs and adenomas identified over 1000 of splice variants. These include known alternatively spliced genes involved in cancer such as CD44 and VEGFA and a number of candidates overlapping with the isoforms derived from the organoids. Proteomics analysis revealed that approximately 150 of the splice variants were expressed on protein level.

Conclusion and Discussion

We have confirmed that adenoma-to-carcinoma progression is accompanied by aberrant splicing. Analysis of the organoid cultures allowed us to identify gene isoforms from (neoplastic) epithelial origin. Tissue analysis yielded tumor-specific splice variants that represent novel protein candidate biomarkers for early detection of CRC. The diagnostic performance of these splice variant proteins will be validated in series of stool and FIT samples.

Citation Format: Malgorzata A. Komor, Thang V. Pham, Sander R. Piersma, Anne S. Bolijn, Tim Schelfhorst, Pien M. Delis-van Diemen, Marianne Tijssen, Annemieke C. Hiemstra, Meike de Wit, Beatriz Carvalho, Gerrit A. Meijer, Connie R. Jimenez, Remond J. Fijneman. Proteogenomic analysis of alternative splicing in colorectal adenoma-to-carcinoma progression [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1559. doi:10.1158/1538-7445.AM2017-1559

Abstract 3125: KCNQ1 expression is a strong prognostic biomarker for disease recurrence in stage II and III colon cancer

Background: Colorectal cancer (CRC) is the third most common cancer worldwide. Accurately identifying stage II CRC patients at high risk of recurrence and stage III patients at low risk of recurrence are key unmet clinical needs. We previously identified KCNQ1 as a tumour suppressor gene of which loss of expression was associated with poor survival in patients with CRC liver metastases. The present study aimed to examine the prognostic value of KCNQ1 in stage II and III colon cancer patients.

Methods: KCNQ1 mRNA expression was assessed in 90 stage II colon cancer patients (AMC-AJCCII-90) using microarray gene expression data. KCNQ1 protein expression was evaluated by immuno-histochemistry on tissue microarrays of 386 stage II and III colon cancer patients.

Results: Low KCNQ1 mRNA expression in microsatellite stable (MSS) stage II colon cancers was associated with poor disease free survival (DFS) (HR 3.35; 95% CI 1.16-9.66; p<0.05). Loss of KCNQ1 protein expression from epithelial cells was strongly associated with poor DFS in MSS stage II (HR 3.82; 95% CI 2.04-7.14; p<0.0001), MSS stage III (HR 2.93; 95% CI 1.70-5.02; p = 0.0001) and MSI stage III colon cancers (HR 5.06; 95% CI 1.07-23.89; p<0.05). Multivariate analysis demonstrated KCNQ1 to have independent prognostic value in addition to established clinicopathological parameters such as angioinvasion, nodal stage en MSI-status.

Conclusion: We conclude that KCNQ1 is a strong prognostic biomarker for prediction of disease recurrence (HR∼4) and may aid stratification of patients with stage II MSS colon cancer and stage III MSI CRC for adjuvant chemotherapy. Because KCNQ1 protein expression is determined by immuno-histochemistry, this biomarker can be implemented in standard clinical care using existing workflows.

Citation Format: Sjoerd H. den Uil, Veerle M.H. Coupe, Janneke F. Linnekamp, Evert van den Broek, Jeroen A.C.M. Goos, Pien M. Delis-van Diemen, Eric J.T. Belt, Nicole C.T. van Grieken, Patricia M. Scott, Louis Vermeulen, Jan Paul Medema, Herman Bril, Hein B.A.C. Stockmann, Robert T. Cormier, Gerrit A. Meijer, Remond J. Fijneman. KCNQ1 expression is a strong prognostic biomarker for disease recurrence in stage II and III colon cancer. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 3125.

Abstract 4526: Lumican and Versican predict good outcome in stage II and III colon cancer

Background and Purpose: Tumor stroma plays an important role in the progression and metastasis of colon cancer. The glycoproteins versican and lumican are overexpressed in colon carcinomas and are associated with the formation of tumor stroma. The aim of the present study was to investigate the potential prognostic value of versican and lumican expression in the epithelial and stromal compartment of stage II and III colon cancer. Methods: Clinicopathological data and tissue samples were collected from stage II (n=226) and stage III (n=160) colon cancer patients. Tissue microarrays (TMAs) were constructed with cores taken both from the center and the periphery of the tumor. These were immunohistochemically stained for lumican and versican. Expression levels were scored on digitized slides. Statistical evaluation was performed using SPSS. Results: Versican expression by epithelial cells in the periphery of the tumor, i.e., near the invasive front, was correlated to a longer disease free survival (DFS) for the whole cohort (P=0.01), stage III patients only (P=0.01), stage III patients with microsatellite instable (MSI) tumors (P=0.04) and stage III patients with microsatellite stable (MSS) tumors who did not receive adjuvant chemotherapy (P=0.006). Lumican expression in epithelial cells overall in the tumor was correlated to a longer disease specific survival (DSS) in stage II patients (P=0.05) and to a longer DFS and DSS in MSS stage II patients (P=0.02 and P=0.004). Conclusion: In the present series, protein expression of versican and lumican predicted good clinical outcome for stage III and stage II colon cancer patients, respectively.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 4526. doi:1538-7445.AM2012-4526

Complexity of lung cancer modifiers: mapping of thirty genes and twenty-five interactions in half of the mouse genome

BACKGROUND

Numerous low-penetrance genes control susceptibility to cancer in experimental animals, but the overall genetic information on this group of genes (i.e., number of loci and their mutual interactions) is missing. We performed a systematic search, scanning roughly half of the mouse genome for lung cancer susceptibility (Sluc) genes affecting tumor size or number by using mouse recombinant congenic (RC) strains. In each RC strain (OcB), approximately 12.5% of the genome is derived from the lung cancer-resistant strain B10.O20, whereas the rest is derived from the lung cancer-susceptible strain O20.

METHODS

A total of 730 F2 hybrids from five (OcB x O20) crosses were tested. Pregnant mice were treated on day 18 of gestation with a single dose of N-ethyl-N-nitrosourea. When offspring were 16 weeks old, whole lungs were removed and sectioned semiserially, and the size of all lung tumors (n = 2658) was determined. Analysis of variance was used for detection of linkage, and models (including main effect and two-way interactions) were tested with a statistical program.

RESULTS

We detected a total of 30 Sluc loci (16 new plus 14 previously reported) and 25 two-way interactions. Some of these interactions are counteracting (e.g., Sluc17 and Sluc20), resulting in the partial or total masking of the individual independent effect (main effect) of each involved locus. Seven loci (Sluc1, Sluc5, Sluc12, Sluc16, Sluc18, Sluc20, and Sluc26) and two interactions (Sluc5 x Sluc12 and Sluc5 x Sluc26) were detected in more than one RC strain.

CONCLUSIONS

The extrapolation of our results to the whole genome suggests approximately 60 Sluc loci (90% confidence intervals = 42 to 78). Despite the genetic complexity of lung cancer, use of appropriate mapping strategies can identify a large number of responsible loci and can reveal their interactions. This study provides an insight into the genetic control of lung tumorigenesis and may serve as a paradigm for investigating the genetics of other cancer types.

Low molecular weight group IIA and group V phospholipase A(2) enzymes have different intracellular locations in mouse bone marrow-derived mast cells

The subcellular location of the enzymes of eicosanoid biosynthesis is critical for their co-ordinate action in the generation of leukotrienes and prostaglandins. This activity is thought to occur predominantly at a perinuclear location. Whereas the subcellular locations of cytosolic phospholipase (PL) A(2) and each of the pathway enzymes of eicosanoid generation have been defined, the distribution of the low molecular weight species of PLA(2) has remained elusive because of the lack of antibodies that distinguish among homologous family members. We have prepared affinity-purified rabbit antipeptide IgG antibodies that distinguish mouse group IIA PLA(2) and group V PLA(2). Immunofluorescence staining and immunogold electron microscopy reveal different subcellular locations for the enzymes. Group IIA(2) PLA(2) is present in the secretory granules of mouse bone marrow-derived mast cells, consistent with its putative role in facilitating secretory granule exocytosis and its consequent extracellular action. In contrast, group V PLA(2) is associated with various membranous organelles including the Golgi apparatus, nuclear envelope, and plasma membrane. The perinuclear location of group V PLA(2) is consistent with a putative interaction with translocated cytosolic PLA(2) in supplying arachidonic acid for generation of eicosanoid products, while the location in Golgi cisternae may also reflect its action as a secreted enzyme. The spatial segregation of group IIA PLA(2) and group V PLA(2) implies that these enzymes are not functionally redundant.

High frequency of interactions between lung cancer susceptibility genes in the mouse: mapping of Sluc5 to Sluc14

Although several genes that cause monogenic familial cancer syndromes have been identified, susceptibility to sporadic cancer remains unresolved. Animal experiments have demonstrated multigenic control of tumor susceptibility. Recently, we described four mouse lung cancer susceptibility (Sluc) loci, the main effects of which are masked by their mutual interactions. Because such interactions can considerably affect the strategies for identification of cancer susceptibility genes in humans, it is necessary to establish whether they are common or rare. Here, we report the mapping of 10 additional Sluc loci and show that 13 of the 14 Sluc loci are involved in one or more interactions, demonstrating that interactions of tumor susceptibility genes are frequent and that they probably form complex networks.

Genetics of quantitative and qualitative aspects of lung tumorigenesis in the mouse: multiple interacting Susceptibility to lung cancer (Sluc) genes with large effects

Inbred strains of mice exhibit large differences in their susceptibility to various complex quantitative genetic traits, among which is the susceptibility to lung cancer. These differences are caused by the combined effects of multiple quantitative trait loci (QTLs). Due to their multiplicity, it is relatively difficult and laborious to study the effects of individual QTLs. To dissect complex genetic traits the authors make use of recombinant congenic strains (RCS), a system of mouse inbred strains in which the genetic complexity is reduced. The susceptibility to lung cancer is studied by using the series of O20-congenic-B10.O20 (OcB) RC strains. They are derived from the parental background strain O20 and the parental donor strain B10.O20, two mouse inbred strains that differ from each other in both quantitative and qualitative aspects of lung tumorigenesis. This study describes the segregation of lung tumor number, size, and histology among the OcB RC strains, and indicates that these traits are influenced by multiple interacting QTLs with considerable individual effects. The results suggest that some of the susceptibility loci to lung cancer affect the susceptibility to other types of cancer as well, possibly by functioning systematically.

Complex interactions of new quantitative trait loci, Sluc1, Sluc2, Sluc3, and Sluc4, that influence the susceptibility to lung cancer in the mouse

Many complex traits, including susceptibility to lung cancer, are controlled by multiple genes--quantitative trait loci (QTLs). We facilitated the mapping of QTLs by making use of recombinant congenic strains (RCS), a system of mouse inbred strains in which the genetic complexity is reduced, and by applying MQM-mapping (multiple-QTL models or marker-QTL-marker), a multilocus method with an increased power of detecting of individual QTLs and interacting QTLs (epistasis). The mouse strain O20 develops significantly larger N-ethyl-N-nitrosourea induced lung tumours than mice of the RC strain OcB-9 (ref. 5); the latter share approximately 87.5% of their genes with strain O20 and 12.5% with strain B10.O20 (refs 6,7). QTL analysis of 222 (OcB-9 x O20) F2 mice revealed four new loci that influence susceptibility to lung cancer (Sluc genes). They are involved in two significant, partly counteracting interactions which mask their individual main effects: Sluc1 (on chromosome 19) interacts with Sluc2 (chromosome 2), and Sluc3 (chromosome 6) interacts with Sluc4 (chromosome 11). Together with the data of van Wezel et al. in the accompanying report, our results indicate that interactions between tumour susceptibility genes are a common phenomenon which complicates their mapping.

A gene for susceptibility to small intestinal cancer, ssic1, maps to the distal part of mouse chromosome 4

Mouse inbred strains B10.O20 and O20 were used to study the genetics of susceptibility to small intestinal cancer. Strain B10.O20 is susceptible to tumors of the small intestine induced by a transplacental treatment with the carcinogen N-ethyl-N-nitrosourea on day 18 of gestation, whereas strain O20 is completely resistant. F1 hybrid mice are also completely resistant, indicating that homozygosity of the B10.O20 allele of at least one susceptibility gene is required for the development of tumors of the small intestine. To map this gene, we used backcross 2 (N3) mice. We tested 283 [((B10.O20 x O20)F1 x B10.O20) x B10.020] N3 mice, 67 of which developed tumors of the small intestine. Their genotype was determined with the use of more than 85 simple sequence length polymorphisms (SSLPs) spread over the genome. If a SSLP is linked closely to a susceptibility gene, it is expected that almost none of the N3 mice with small intestinal tumors are heterozygous for this marker. We found that very few tumor-bearing N3 mice were heterozygous for SSLP markers on the distal part of chromosome 4 compared with the N3 mice without small intestinal tumors. This difference is highly significant (chi 2 = 31 for D4Mit158). Therefore, one of the genes that influence susceptibility to small intestinal cancer, ssic1, maps to the distal part of chromosome 4.

A susceptibility gene for alveolar lung tumors in the mouse maps between Hsp70.3 and G7 within the H2 complex

Lung tumor susceptibility (LTS) in the mouse is influenced by multiple loci within the H2 complex. We compared the LTS of two H2 congenic strains with intra H2 recombinations, B10.A(1R) and B10.A(2R), whose genetic difference has been reduced to a region of approximately 50 kilobases within the C4-H2D interval, between Hsp70.3 and G7. After transplacental induction with N-ethyl-N-nitrosourea the load of alveolar lung tumors in strain B10.A(2R) is significantly higher than in strain B10.A(1R) (P < 0.001). For papillary tumors no significant differences were observed. We conclude that the alveolar lung tumor load is influenced by an LTS gene located within the Hsp70.3-G7 interval.

Kras-2 alleles, mutations, and lung tumor susceptibility in the mouse--an evaluation

Lung Tumor Susceptibility (LTS) in the mouse has been shown to be influenced by loci within the Major Histocompatibility Complex (MHC) and the Kras-2 regions. In crosses between susceptible and resistant strains, one allele of Kras-2 has been linked with a high LTS, whereas the other allele has been linked with a low LTS. Furthermore, these Kras-2 alleles affect differently the occurrence of Kras-2 mutations in lung tumors. In this study we evaluated the relationship between LTS, Kras-2 alleles and Kras-2 mutations, using Recombinant Congenic Strains with identical MHC haplotypes. The Kras-2 region indeed influences the frequency of Kras-2 mutations in N-ethyl-N-nitrosourea-induced lung tumors. These mutations are associated with larger tumors. However, Kras-2 affects LTS only marginally. Several strains with identical Kras-2 alleles and mutation frequency differ widely in LTS, while some strains with different alleles and mutation frequency do not. We conclude that a considerable part of the genetic variability in LTS is caused by LTS-loci other than Kras-2 and MHC.