Right ventricular assessment of the adolescent footballer's heart

INTRODUCTION

Athletic training can result in electrical and structural changes of the right ventricle that may mimic phenotypical features of arrhythmogenic right ventricular cardiomyopathy (ARVC), such as T-wave inversion and right heart dilatation. An erroneous interpretation may have consequences ranging from false reassurance in an athlete vulnerable to cardiac arrhythmias, to unnecessary sports restriction in a healthy individual. The primary aim of this study was to define normal RV dimension reference ranges for academy adolescent footballers of different ethnicities. Secondary aims include analysis of potential overlap between this adolescent group with ARVC criteria and comparison with normal adult ranges.

RESULTS

Electrocardiographic (ECG) and echocardiographic data of 1087 academy male footballers aged between 13 and 18 years old (mean age 16.0 ± 0.5 years), attending mandatory cardiac screening were analysed. Ethnicity was categorised as white (n = 826), black (African/Caribbean; n = 166) and mixed-race (one parent white and one parent black; n = 95). Arrhythmogenic right ventricular cardiomyopathy major criteria for T-wave inversion was seen in 3.3% of the cohort. This was more prevalent in black footballers (12%) when compared to mixed race footballers (6.3%) or white footballers (1%), P < 0.05. Up to 59% of the cohort exceeded adult reference ranges for some of the right ventricular parameters, although values were similar to those seen in adult footballers. There were no differences in right ventricular dimensions between ethnicities. In particular, the right ventricular outflow tract diameter would fulfil major criteria for ARVC dimension in 12% of footballers. Overall, 0.2% of the cohort would fulfil diagnosis for 'definite' arrhythmogenic right ventricular cardiomyopathy and 2.2% would fulfil diagnosis for 'borderline' arrhythmogenic right ventricular cardiomyopathy for RV dimensions and ECG changes. This was seen more frequently in black footballers (9.9%) than mixed race footballers (3.9%) or white footballer (0.6%), P < 0.05. Among athletes meeting definite or borderline arrhythmogenic right ventricular cardiomyopathy criteria, no cardiomyopathy was identified after comprehensive clinical assessment, including with cardiac magnetic resonance imaging, exercise testing, ambulatory electrocardiograms and familial evaluation.

CONCLUSION

Right heart sizes in excess of accepted adult ranges occurred in as many as one in two adolescent footballers. Structural adaptations in conjunction with anterior T-wave inversion may raise concern for ARVC, highlighting the need for evaluation in expert settings.

Comprehensive Landscape of BRAF Variant Classes, Clonalities, and Co-Mutations in Metastatic Colorectal Cancer Using ctDNA Profiling

Although V600E accounts for the majority of the BRAF mutations in metastatic colorectal cancer (mCRC), non-V600 BRAF variants have been shown in recent years to represent a distinct molecular subtype. This study provides a comprehensive profile of BRAF variants in mCRC using a large genomic database of circulating tumor DNA (ctDNA) and analyzing clinical outcomes in a cohort of patients with atypical (non-V600) BRAF variants (aBRAF; class II, class III, unclassified). Overall, 1733 out of 14,742 mCRC patients in the ctDNA cohort had at least one BRAF variant. Patients with atypical BRAF variants tended to be younger and male. In contrast to BRAFV600E, BRAF class II and III variants and their co-occurrence with KRAS/NRAS mutations were increased at baseline and especially with those patients predicted to have prior anti-EGFR exposure. Our clinical cohort included 38 patients with atypical BRAF mCRC treated at a large academic referral center. While there were no survival differences between atypical BRAF classes, concurrent RAS mutations or liver involvement was associated with poorer prognosis. Notably, patients younger than 50 years of age had extremely poor survival. In these patients, the high-frequency KRAS/NRAS co-mutation and its correlation with poorer prognosis underlines the urgent need for novel therapeutic strategies. This study represents one of the most comprehensive characterizations to date of atypical BRAF variants, utilizing both ctDNA and clinical cohorts.

Impact of KRAS mutations and co-mutations on clinical outcomes in pancreatic ductal adenocarcinoma

The relevance of KRAS mutation alleles to clinical outcome remains inconclusive in pancreatic adenocarcinoma (PDAC). We conducted a retrospective study of 803 patients with PDAC (42% with metastatic disease) at MD Anderson Cancer Center. Overall survival (OS) analysis demonstrated that KRAS mutation status and subtypes were prognostic (p < 0.001). Relative to patients with KRAS wildtype tumors (median OS 38 months), patients with KRASG12R had a similar OS (median 34 months), while patients with KRASQ61 and KRASG12D mutated tumors had shorter OS (median 20 months [HR: 1.9, 95% CI 1.2-3.0, p = 0.006] and 22 months [HR: 1.7, 95% CI 1.3-2.3, p < 0.001], respectively). There was enrichment of KRASG12D mutation in metastatic tumors (34% vs 24%, OR: 1.7, 95% CI 1.2-2.4, p = 0.001) and enrichment of KRASG12R in well and moderately differentiated tumors (14% vs 9%, OR: 1.7, 95% CI 1.05-2.99, p = 0.04). Similar findings were observed in the external validation cohort (PanCAN's Know Your Tumor® dataset, n = 408).

Novel Clinical Tool to Estimate Risk of False-Negative KRAS Mutations in Circulating Tumor DNA Testing

PURPOSE

In metastatic colorectal cancer, the detection of RAS mutations by circulating tumor DNA (ctDNA) has emerged as a valid and noninvasive alternative approach to determining RAS status. However, some RAS mutations may be missed, that is, false negatives can occur, possibly compromising important treatment decisions. We propose a statistical model to assess the probability of false negatives when performing ctDNA testing for RAS.

METHODS

Cohorts of 172 subjects with tissue and multipanel ctDNA testing from MD Anderson Cancer Center and 146 subjects from Massachusetts General Hospital were collected. We developed a Bayesian model that uses observed frequencies of reference mutations (the maximum of APC and TP53) to provide information about the probability of KRAS false negatives. The model was alternatively trained on one cohort and tested on the other. All data were collected on Guardant assays.

RESULTS

The model suggests that negative KRAS findings are believable when the maximum of APC and TP53 frequencies is at least 8% (corresponding posterior probability of false negative <5%). Validation studies demonstrated the ability of our tool to discriminate between false-negative and true-negative subjects. Simulations further confirmed the utility of the proposed approach.

CONCLUSION

We suggest clinicians use the tool to more precisely quantify KRAS false-negative ctDNA results when at least one of the reference mutations (APC, TP53) is observed; usage may be especially important for subjects with a maximum reference frequency of <8%. Extension of the methodology to predict false negatives of other genes is possible. Additional reference genes can also be considered. Use of personal training data sets is supported. An open-source R Shiny application is available for public use.

Impact of KRAS Mutations and Co-mutations on Clinical Outcomes in Pancreatic Ductal Adenocarcinoma

The relevance of KRAS mutation alleles to clinical outcome remains inconclusive in pancreatic adenocarcinoma (PDAC). We conducted a retrospective study of 803 PDAC patients (42% with metastatic disease) at MD Anderson Cancer Center. Overall survival (OS) analysis demonstrated that KRAS mutation status and subtypes were prognostic (p<0.001). Relative to patients with KRAS wildtype tumors (median OS 38 months), patients with KRASG12R had a similar OS (median 34 months), while patients with KRASQ61 and KRASG12D mutated tumors had shorter OS (median 20 months [HR: 1.9, 95% CI 1.2-3.0, p=0.006] and 22 months [HR: 1.7, 95% CI 1.3-2.3, p<0.001], respectively). There was enrichment of KRASG12D mutation in metastatic tumors (34% vs 24%, OR: 1.7, 95% CI 1.2-2.4, p=0.001) and enrichment of KRASG12R in well and moderately differentiated tumors (14% vs 9%, OR: 1.7, 95% CI 1.05-2.99, p=0.04). Similar findings were observed in the external validation cohort (PanCAN's Know Your Tumor® dataset, n=408).

Survival improvement for patients with metastatic colorectal cancer over twenty years

Over the past two decades of successive clinical trials in metastatic colorectal cancer (CRC), the median overall survival of both control and experimental arms has steadily improved. However, the incremental change in survival for metastatic CRC patients not treated on trial has not yet been quantified. We performed a retrospective review of 1420 patients with de novo metastatic CRC who received their primary treatment at the University of Texas M.D. Anderson Cancer Center (UTMDACC) from 2004 through 2019. Median OS was roughly stable for patients diagnosed between 2004 and 2012 (22.6 months) but since has steadily improved for those diagnosed in 2013 to 2015 (28.8 months), and 2016 to 2019 (32.4 months). Likewise, 5-year survival rate has increased from 15.7% for patients diagnosed from 2004 to 2006 to 26% for those diagnosed from 2013 to 2015. Notably, survival improved for patients with BRAFV600E mutant as well as microsatellite unstable (MSI-H) tumors. Multivariate regression analysis identified surgical resection of liver metastasis (HR = 0.26, 95% CI, 0.19-0.37), use of immunotherapy (HR = 0.44, 95% CI, 0.29-0.67) and use of third line chemotherapy (regorafenib or trifluridine/tipiracil, HR = 0.74, 95% CI, 0.58-0.95), but not year of diagnosis (HR = 0.99, 95% CI, 0.98-1), as associated with better survival, suggesting that increased use of these therapies are the drivers of the observed improvement in survival.

Dose-escalated pancreas radiotherapy for unresected pancreatic adenocarcinoma: Patterns of care and survival in the United States

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Background: Randomized trials have not shown an overall survival (OS) benefit to adding radiotherapy (RT) to chemotherapy for patients with locally advanced pancreatic adenocarcinoma (LAPC). However, trials such as LAP07 did not incorporate escalated-dose RT (EDR), which may confer longer survival. The adoption of EDR across the United States and associated outcomes are unknown. Methods: We queried the National Cancer Data Base for non-surgically managed patients with LAPC diagnosed between 2004 and 2019. RT with biologically effective doses (BED10) > 70 and ≤ 200 Gy were labeled EDR and conventional-dose RT (CDR) for 39-70 Gy doses. Associations with receipt of EDR and with OS were identified using multivariate analysis (MVA) logistic and Cox regressions, respectively. Bonferroni corrections were applied. Cochran-Armitage and Mann-Kendall trend tests were performed to assess trends in use of RT. Results: Of 64,303 patients, the most common treatments were chemotherapy alone (CT) (71%), chemoradiation (CRT) (27%), and pancreas RT alone (2%). 18,970 patients received pancreas RT, of which 91% was CDR (median dose 50.4 Gy; median 28 fractions) and 9% was EDR (50 Gy; 5 fractions). Use of pancreas RT increased from 14% in 2004 to a peak of 18% in 2010, decreased to a nadir of 13% in 2016, and subsequently increased to 15% by 2019 ( Ptrend < 0.001). EDR use increased from 7% in 2004 to 22% in 2019 ( Ptrend < 0.0001). Median BED10 increased from 53 to 59 Gy ( Ptrend< 0.001). Of patients receiving pancreas RT, use of intensity-modulated RT (IMRT) and stereotactic body RT (SBRT) respectively increased from 25% and 2% in 2004 to 60% and 27% in 2019, while use of 3-D conformal RT (3D-CRT) decreased from 64% to 9% ( Ptrend < 0.02 for all comparisons). On MVA logistic regression, primary tumor location in the body/tail vs. head (aOR 1.22, 95% CI 1.07-1.40; P = 0.003) associated with greater EDR receipt, whereas T3-4 vs. T2 disease (aOR 0.81, CI 0.71-0.92; P = 0.002) associated with lesser receipt. At a median follow up of 59.1 months (CI 57.5-61.0), median OS estimates for CDR and EDR were 10.2 months (CI 10.1-10.3) and 13.3 months (CI 13.2-13.5; P < 0.0001), respectively. On MVA Cox regression, N1 vs. N0 disease (HR 1.08, CI 1.06-1.10; P < 0.001) correlated with higher risk of death, whereas CRT vs. CT (HR 0.83, CI 0.81-0.85; P < 0.001) correlated with lower risk of death. Subset MVA of 14,634 CRT patients correlated higher RT dose—as both a categorical variable (EDR vs. CDR; HR 0.84, CI 0.79-0.90; P < 0.001) and continuous variable (BED10; HR 0.994, CI 0.992-0.995; P < 0.001)—with lower risk of death. Conclusions: Fewer than 1 in 6 patients with unresected LAPC received pancreas RT, despite a nominal increase in utilization in recent years. Although retrospective, these NCDB data suggest longer OS with the addition of RT for unresected LAPC, suggesting continued unmet need. EDR is associated with longer survival vs. CDR.

ctDNA-based fusion detection for advanced colorectal cancer with a partner-agnostic assay

186

Background: Actionable mutations can predict therapeutic benefit in patients with advanced malignancies, though clinical relevance of fusion testing for advanced colorectal cancer (aCRC) remains undefined. Identification of fusions from circulating tumor DNA (ctDNA) has previously been restricted to defined oncogenic fusion partners. To improve the sensitivity for fusion detection, we evaluated a partner-agnostic fusion analysis from ctDNA of patients with aCRC. Methods: De-identified data from Guardant Health was reviewed for 18,558 patients with aCRC who underwent ctDNA NGS testing by Guardant360 (Redwood City, CA) between 2017-2022. Fusion results were analyzed with a partner-agnostic bioinformatic approach. A fusion was defined as “clonal” if the variant allele frequency (VAF) ratio exceed ≥50% of highest somatic VAF, and “subclonal” if < 50% maxVAF. Microsatellite instability (MSI) status [MSI-high (bMSI-H) or microsatellite stable (bMSS)] and anti-EGFR exposure signature were determined using prior methods. Associations between fusion occurrence and coexisting alterations were performed using Fisher’s exact test. Results: Fusions were detected in 221 (1.2%) of patients with aCRC. 258 activating fusions were detected in 187 patients; FGFR3 (N = 59, 23%), RET N = 55, 21%), BRAF (N = 43, 17%), and ALK (N = 41, 16%) were most frequent. There were 71 previously unreported fusions in 28 additional patients; RET (N = 16; 23%), MET (N = 15, 21%), and BRAF (N = 11; 15%) were most prevalent. Clonal fusions occurred in 7% (18/258) of all activating fusions; RET (5/18, 28%) and FGFR3 (3/18, 17%) were most common and associated with bMSI-H status relative to bMSS (27% vs 4%, OR 8.165, 95% CI 2.332-33.99; p = 0.0076). Clonal fusions occurred less commonly in samples with a prior EGFR signature (OR 0.22, 95% CI 0.05-0.997, p = 0.049). Most detected fusions were subclonal including ALK, FGFR1-3, MET, RET and ROS1. Conclusions: Highly specific partner-agnostic fusion detection is feasible to increase sensitivity of ctDNA assay performance. Oncogenic fusions occurred in ~1% of all patients with aCRC. Clonal fusions as oncogenic drivers were infrequent and associated with bMSI-H status. Subclonal fusions were more common and occur in a setting consistent with prior exposure to anti-EGFR therapies. Reporting fusion partners and clonality from ctDNA may guide oncologists on the appropriate context for consideration of fusion-directed treatments.

Tumor mutations associated with outcomes in colorectal peritoneal metastases

196

Background: The association between tumor mutations beyond KRAS and BRAF for patients with peritoneal metastases (PM) from colorectal cancer (CRC) are poorly understood. Here we describe these associations with survival after diagnosis of PM. Methods: CRC patients with PM with or without synchronous liver or lung metastases treated at a single institution from 2016 to 2020 were retrospectively studied. Standard of care next-generation sequencing was performed on tissue specimens with a targeted panel of genes frequently mutated in cancer. Clinical data, including survival and last contact, were obtained from medical records. Multivariate Cox regression was used to identify associations between overall survival after diagnosis of PM (OS) with clinical, histopathologic and somatic mutation data. Results: Of 526 PM patients, 179 (34.2%) also had synchronous liver metastases, and these patients had worse OS compared to PM alone (HR 1.67, [1.26-2.22], p=0.0003). Lung metastases were identified in 57 (10.8%) and were not associated with worse OS (HR 1.34, [0.90-1.97], p=0.15). Poorly differentiated grade (HR 2.08, [1.42-3.04], p=0.0002), mucinous histology (HR 1.44, [1.07-1.94], p=0.016), male gender (HR 1.37, [1.05-1.78), p=0.019), and age (HR 1.02, [1.01-1.04], p=0.004) were independently associated with OS. Tumor sequencing data was available for 442 (87%) patients. TP53 was the most common mutation (61.5% of patients) and was associated with decreased OS (HR=1.51 [1.12-2.02], p=0.005). BRAF mutation (85% of which were V600E) was identified in 9.7% of patients and was also associated with decreased OS (HR=1.88 [1.23-2.86], p=0.003). In contrast, PTEN mutation (4.3%) was associated with improved OS (0.41 (0.17-0.99), p=0.049), while both KRAS (51.4%) and SMAD4 mutations (16%) were not (KRAS: HR 0.94, [0.72-1.24], p=0.68; SMAD4: HR 0.78, [0.53-1.16], p=0.21). Conclusions: Mutational data for PM patients has a distinct profile and unique associations with OS when compared to other sites of metastatic disease. TP53 and BRAF mutations were associated with worse survival, while PTEN mutation was associated with improved OS. KRAS mutation was more prevalent than expected in an unselected cohort, and not associated with OS. A better understanding of PM-specific associations with survival may influence treatment strategies for this difficult disease site.

Resistance Mechanisms to Anti-Epidermal Growth Factor Receptor Therapy in RAS/RAF Wild-Type Colorectal Cancer Vary by Regimen and Line of Therapy

PURPOSE

Acquired resistance to anti-epidermal growth factor receptor (EGFR) inhibitor (EGFRi) therapy in colorectal cancer (CRC) has previously been explained by the model of acquiring new mutations in KRAS/NRAS/EGFR, among other MAPK-pathway members. However, this was primarily on the basis of single-agent EGFRi trials and little is known about the resistance mechanisms of EGFRi combined with effective cytotoxic chemotherapy in previously untreated patients.

METHODS

We analyzed paired plasma samples from patients with RAS/BRAF/EGFR wild-type metastatic CRC enrolled in three large randomized trials evaluating EGFRi in the first line in combination with chemotherapy and as a single agent in third line. The mutational signature of the alterations acquired with therapy was evaluated. CRC cell lines with resistance to cetuximab, infusional fluorouracil, leucovorin, and oxaliplatin, and SN38 were developed, and transcriptional changes profiled.

RESULTS

Patients whose tumors were treated with and responded to EGFRi alone were more likely to develop acquired mutations (46%) compared with those treated in combination with cytotoxic chemotherapy (9%). Furthermore, contrary to the generally accepted hypothesis of the clonal evolution of acquired resistance, we demonstrate that baseline resistant subclonal mutations rarely expanded to become clonal at progression, and most remained subclonal or disappeared. Consistent with this clinical finding, preclinical models with acquired resistance to either cetuximab or chemotherapy were cross-resistant to the alternate agents, with transcriptomic profiles consistent with epithelial-to-mesenchymal transition. By contrast, commonly acquired resistance alterations in the MAPK pathway do not affect sensitivity to cytotoxic chemotherapy.

CONCLUSION

These findings support a model of resistance whereby transcriptomic mechanisms of resistance predominate in the presence of active cytotoxic chemotherapy combined with EGFRi, with a greater predominance of acquired MAPK mutations after single-agent EGFRi. The proposed model has implications for prospective studies evaluating EGFRi rechallenge strategies guided by acquired MAPK mutations, and highlights the need to address transcriptional mechanisms of resistance.

Abstract B028: Changes in exosomal RNA expression associate with treatment response to BRAF + EGFR + PD-1 blockade in MSS, BRAFV600E colorectal cancer: A liquid biopsy approach

Introduction: BRAF + EGFR inhibition induces decreased expression of mismatch repair (MMR) genes in preclinical models of microsatellite stable (MSS), BRAFV600E metastatic colorectal cancer (mCRC) but has not been reported in patients. We evaluated exosomal RNA (exoRNA) isolated from serial blood specimens collected from patients (pts) with MSS, BRAFV600E mCRC treated with encorafenib (E) + cetuximab (C) + nivolumab (N) as a novel blood-based approach to compare differences in gene expression according to treatment response. Methods: Pts with refractory MSS, BRAFV600E mCRC were treated with E (300 mg daily), C (500 mg/m2 q2 weeks), and N (480 mg q4 weeks) on an IRB-approved clinical trial at MD Anderson. Responses to treatment were assessed every 8 weeks (RECIST v1.1). ExoRNA isolated from pretreatment and on-treatment (week 8) blood samples were sequenced (SMART-seq) and deconvoluted (DeMix) in order to estimate cancer-specific gene expression. Previously validated MAPK and interferon (IFN)-γ gene expression signatures were used for measuring transcriptomic changes following treatment with E+C+N. Scores between responders and non-responders were compared by unpaired t-tests. For Gene Set Enrichment Analysis (GSEA), an adjusted false discovery rate (FDR) &lt; 0.25 was applied to find significantly enriched pathways between on-treatment and pretreatment samples separately for responders and non-responders. Results: 26 pts were treated with E+C+N, and 24 were evaluable for response. Overall response rate was 50% (95% confidence interval (CI), 29-71), and median progression-free survival was 7.4 months (95% CI, 6.0-NA). Four pts remained on study &gt; 12 months. Between responders vs non-responders (N=12 each), mean changes in MAPK signature score was decreased (-0.63 vs 0.15, respectively; p=.13). Both patients with response &gt; 18 months demonstrated dramatic increases in IFN-γ score following treatment with E+C+N (+13.1 and +14.6), a trend not observed in all other patients (range, -18.0 to 3.6). Among responders to E+C+N, GSEA analysis demonstrated dynamic pathway changes in normalized enrichment score (NES) for DNA repair (NES -2.3; p-adj=.008), IL6/JAK/STAT3 (NES -2.1, p-adj=.02), and IFN-α response (NES -2.0, p-adj=.03). For non-responders, relative increases in NES were observed for angiogenesis (NES 2.1, p-adj=.02) and IL-2/STAT5 (NES 2.0, p-adj= .02). Conclusions: Transcriptome analysis using exoRNA isolated from serial blood samples is feasible for assessing treatment response in pts with mCRC. Decreased MAPK score in exoRNA may be associated with treatment response to E+C+N in pts with MSS, BRAFV600E mCRC. Changes in immune NES scores following treatment may distinguish responders from non-responders to MAPK + PD-1 blockade and highlight targets for novel immune-mediated combinations for MSS, BRAFV600E mCRC.

Citation Format: Van Karlyle Morris, Kimal I. Rajapakshe, Vahid Bahrambeigi, Christine M. Parsehgian, Benny Johnson, Kanwal P. Raghav, Arvind Dasari, Ryan W. Huey, Michael J. Overman, Jason Willis, Michael S. Lee, Robert A. Wolff, Bryan K. Kee, Phat Le, Paola A. Guerrero, Scott Kopetz, Anirban Maitra. Changes in exosomal RNA expression associate with treatment response to BRAF + EGFR + PD-1 blockade in MSS, BRAFV600E colorectal cancer: A liquid biopsy approach [abstract]. In: Proceedings of the AACR Special Conference on Colorectal Cancer; 2022 Oct 1-4; Portland, OR. Philadelphia (PA): AACR; Cancer Res 2022;82(23 Suppl_1):Abstract nr B028.

Abstract PR005: Outcomes in colitis-associated metastatic colorectal cancer and intersection with early-onset and signet ring cell carcinoma

Patients with inflammatory bowel disease (IBD) have a higher risk of developing colorectal cancer (CRC) and mortality from colitis-associated CRC (CA-CRC) is currently rising. Clinical and molecular differences between CA-CRC and sporadic-CRC (S-CRC) have been previously identified, however there are conflicting reports on outcomes of CA-CRC, especially for those with metastatic CRC (mCRC). Due to the earlier onset of CA-CRC, undiagnosed IBD has been speculated to be a contributing factor to the rising prevalence of early-onset CRC (EOCRC), but confirmatory studies are lacking. In this retrospective study, three independent CRC patient datasets from MDACC were used – the mATTACC discover cohort (n=32 CA-mCRC; n=425 S-mCRC), a tumor registry (n=1696, excluding MSI-High samples), and a real-world evidence (RWE) validation dataset (n=269 CA-mCRC; n=29,596 S-mCRC). These cohorts were analyzed in order to explore characteristics of patients with CA-mCRC, evaluate the amount of EOCRC attributable to CA-mCRC, and compare outcomes of patient populations with CA-mCRC. Median age at diagnosis for patients with CA-mCRC (48yo) was significantly lower compared to S-mCRC (58yo; p&lt;0.001), and an association between CA-mCRC and EOCRC was confirmed (OR=4.04, p&lt;0.001). Prevalence of signet ring cell and mucinous (SRC/M) histology, a rare subtype of CRC, was analyzed within CA-mCRC and EOCRC cases in our cohorts. SRC/M histology was present in 28%-39% of CA-mCRC and 13%-15% of EOCRC cases, thus confirming the strong association of SRC/M histology with both CA-mCRC (OR=3.13, p&lt;0.001) and EOCRC (OR=1.35, p&lt;0.001). Therefore, by comparing the frequency of SRC/M in EOCRC and late-onset CRC, and correcting by the proportion of CA-mCRC cases with SRC/M histology, we estimate between 8.3% to 10.2% of EOCRC may be due to undiagnosed or subclinical IBD. Median overall survival (mOS) for patients with CA-mCRC (31m) was lower relative to S-mCRC (39m; HR=1.26, 95%CI: 1.06-1.48). In EOCRC, patients with CA-mCRC had worse outcomes (mOS=25m) compared to S-mCRC (40m; HR=1.61, 95%CI: 1.23-2.11). Prevalence of SRC/M histology stratified by CA-mCRC or EOCRC status revealed an increasing trend of SRC/M occurrence specifically within CA-mCRC (1995-2015). Additionally, for patients with CA-mCRC the mOS for those with SRC/M (21m) was lower than those with mucinous (51m) histology, highlighting the poor prognosis of SRC/M in this patient population (HR=1.89, 95%CI: 1.06-3.33). Patients with CA-mCRC have worse outcomes than S-mCRC, and those with early-onset or SRC/M have lower survival rates. Tumor biology consistent with CA-CRC, including SRC/M histology, may be present in 8.3%–10.2% of patients with EOCRC without a clinical diagnosis of IBD. Although other confounding biology may be underlying this association, recognition of undiagnosed IBD in mCRC patients is important as it may impact prognosis and treatment strategies for this high-risk patient population.

Citation Format: Oscar E. Villarreal, Fadl Zeineddine, Ray Chacko, Christine Parseghian, Benny Johnson, Jason Willis, Michael Lee, Van Karlyle Morris, Arvind Dasari, Kanwal Raghav, Michael Overman, Y. Nancy You, Yinghong Wang, Dipen Maru, John Paul Shen, Scott Kopetz. Outcomes in colitis-associated metastatic colorectal cancer and intersection with early-onset and signet ring cell carcinoma [abstract]. In: Proceedings of the AACR Special Conference on Colorectal Cancer; 2022 Oct 1-4; Portland, OR. Philadelphia (PA): AACR; Cancer Res 2022;82(23 Suppl_1):Abstract nr PR005.

Antibiotic Exposure Does Not Impact Immune Checkpoint Blockade Response in MSI-H/dMMR Metastatic Colorectal Cancer: A Single-Center Experience

BACKGROUND

Immune checkpoint blockade (ICB) has improved outcomes for patients with microsatellite instability high (MSI-H)/deficient mismatch repair (dMMR) tumors. However, not all MSI-H/dMMR patients will exhibit the same ICB efficacy. Previous studies suggest that concomitant antibiotic use while receiving ICB may result in poorer outcomes. We aimed to evaluate this association in patients with MSI-H/dMMR metastatic colorectal cancer (mCRC).

MATERIALS AND METHODS

A single-site, retrospective review of 57 patients with MSI-H/dMMR mCRC that received ICB was completed. Data collected included patient demographics, ICB information, and antibiotic use. Antibiotic exposure was considered from 90 days prior to ICB through 6 weeks after initiation. Primary endpoint was overall response rate (ORR).

RESULTS

The majority of patients received pembrolizumab (27 [47%]) or nivolumab (17 [30%]) monotherapy as their ICB agent. Of the 57 patients, 19 (33.3%) had antibiotic exposure from 90 days prior to ICB initiation through 6 weeks after initiation with most (13 [68%]) having antibiotic use in the 30 days preceding ICB initiation. Similar ORRs were seen in both groups (P-value > .99). No difference was observed in OS (P-value .29) or PFS (P-value .36) between groups.

CONCLUSION

Our data show no association of lower response rates or survival in those MSI-H/dMMR patients with mCRC who receive antibiotics around the initiation of ICB. This information needs to be confirmed in a larger prospective cohort.

Phase 2 study of anti-EGFR rechallenge therapy with panitumumab with or without trametinib in advanced colorectal cancer

3520

Background: In RAS/RAF WT colorectal cancer (CRC), rechallenge with anti-EGFR therapy (EGFRi) in patients (pts) with prior response leads to clinical benefit, with response rates up to 30% in prior trials. However, secondary MTs in the MAPK signaling pathway have been implicated in resistance to EGFRi. We designed a phase 2 trial to evaluate the efficacy of EGFRi rechallenge +/- a MEK inhibitor (trametinib) based on pre-treatment ctDNA MTs. Methods: This trial evaluated the efficacy and safety of EGFRi rechallenge +/- trametinib in pts with RAS/BRAF WT, MSS, treatment refractory mCRC who achieved clinical benefit with prior EGFRi based therapy for ≥16 weeks with subsequent progression. Pre study ctDNA was used to enroll in one of 3 arms: Arm A: Pts with an acquired EGFR ECD MT but absence of RAS/BRAF/MAP2K1 or with absence of any acquired resistance MT (Arm C) at time of study initiation received panitumumab 6 mg/kg IV Q2 wks. Arm B: Pts with an acquired RAS/BRAF/MAP2K1 MT received panitumumab 4.8 mg/kg plus trametinib 1.5 mg PO daily. Pts in Arms A and C were allowed to cross over on progression. The primary endpoint was ORR by RECIST v1.1. Results: 54 pts were enrolled, with 52 evaluable for efficacy. Median age is 59 yrs (range, 37-78), and 23 (46%) are female. Median number of prior therapies was 3. Three, 20, and 31 pts were enrolled in Arms A, B, C, respectively. Grade 3 TREAs occurred in 29 (54%) pts (all receiving the doublet regimen) and included acneiform rash in 17 (31%) and others occurring in < 5% of pts. There were no grade 4 TRAEs. In pts with no acquired MTs (Arm C), ORR was 20% (6/30) (95% CI, 0.07-0.37), DCR 67% (20/30) (95% CI, 0.45- 0.81), and median PFS and OS 4.1 mo and 11.2 mo, respectively. The median DOR was 5.5 mo. 22 patients crossed over to add trametinib at time of progression, without any responses. In contrast, in pts with acquired RAS/RAF/MAP2K1 MTs (Arm B), there were no responses, with DCR of 63% (12/19) (95% CI, 0.36-0.81), and median PFS and OS 2.1 mo and 5.9 mo, respectively. Only 3 pts were identified with EGFR ECD MTs (Arm A), and ORR is 0% (0/3) in this cohort, with DCR 67% (2/3) (95% CI, 0.09-0.99). Pts with PR had a longer median interval from prior EGFRi and longer time on prior EGFRi than those with SD+PD (5.5 vs 3.6 mo; p = 0.03, and 9.5 vs. 8.8 mo; p = 0.03, respectively). Conclusions: CtDNA guided rechallenge leads to responses in 20% of pts without acquired resistance MTs, with DCR of 67%. This exceeds current third line standard options. While panitumumab has the potential to block EGFR ECD mutations arising from cetuximab, these mutations in isolation were uncommon and there were no signals of efficacy. Although the acneiform rash induced by the combination of MEK and EGFR inhibition was manageable with close dermatologic management, the combination failed to improve outcomes for pts with acquired resistance. Alternative approaches to downstream MAPK blockade should be explored to improve outcomes. Clinical trial information: NCT03087071.

RAS co-mutation and early onset disease represent an aggressive phenotype of atypical (non-V600) BRAF mutant metastatic colorectal cancer

3592

Background: While BRAFV600E accounts for the majority of BRAF mutations in mCRC, non-V600 BRAF variants (a BRAF) have emerged in recent years as a distinct molecular subtype. There are no consensus recommendations regarding management. This study provides a comprehensive profile of a BRAF, their clonalities and co-mutations in mCRC using a large genomic database as well as a prospective treatment cohort of patients with a BRAF and mCRC managed at a single center. Methods: A systematic analysis was performed of patients with mCRC who underwent ctDNA testing (Guardant360 platform, Guardant Health) from September 2014 to May 2021. A variant was defined as clonal if the mutant allele frequency (MAF) was greater than 50% of the highest somatic MAF in the sample; otherwise it was defined as subclonal. Co-mutation analysis was conducted with BRAF, KRAS, NRAS, NF1, ERBB2, PIK3CA and SMAD4. Treatment history and overall survival (OS) for patients with a BRAF mCRC from MD Anderson Cancer Center were included. Results: 1,733 out of 14,742 mCRC patients had at least one BRAF variant, including 6.5% of patients with BRAFV600E variants and 6.2% with a BRAF variants (1.1% with class II, 1.9% with class III, and 3.2% with unclassified variants). 431 unique BRAF variants were identified in a total of 1,905 BRAF variants. BRAF class II and III variants showed a higher rate of co-occurring KRAS mutations (25.6% and 21.5%) and co-occurring NRAS mutations (5.8% and 2.7%) compared with BRAFV600E variants (2.4% for KRAS and 0.1% for NRAS); however, co-occurring KRAS G12C was only noted in one patient. In our MDACC cohort, 38 patients were included in the analysis. The median age was 55, 81% were Caucasian, and 74 % had left sided primary tumors (45% rectal, 24% sigmoid) with 37% being exposed to at least 2 lines of therapy. The most common mutations in clinical practice were class III, D594G (39%), followed by class II G469A (10%), & class III G466E (7%). The median follow-up time was 23.8 months (mo). While there were no survival differences between a BRAF classes II and III, there was a significant difference in OS in patients with RAS co-mutation (28.3 mo vs not reached [NR], p = 0.05) or liver involvement (28.8 mo vs NR, p = 0.02). Patients < 50 years of age had extremely poor survival with OS of 16.3 mo (vs. NR) and HR 7.51 (95% CI 1.82-31.0, p = 0.005). Treatment with anti-EGFR or use of metastasectomy was not associated with improved survival. Conclusions: a BRAF mutations have historically been considered a favorable prognostic marker in mCRC. Co-mutation with RAS is frequent for both classes and portends poor survival in our real-world cohort. Furthermore, early onset a BRAF mCRC is associated with more aggressive disease. These factors highlight the need for dedicated clinical trials for this unique subset of mCRC and may represent an opportunity to improve management in early onset colorectal cancer.

Phase I/II trial of encorafenib, cetuximab, and nivolumab in patients with microsatellite stable (MSS), BRAFV600E metastatic colorectal cancer

3598

Background: Treatment with encorafenib (E) and cetuximab (C) offers response and survival benefit for patients (pts) with MSS, BRAFV600E metastatic colorectal cancer (CRC). BRAF + EGFR inhibition induced a transient MSI-H phenotype in preclinical models of MSS, BRAFV600E CRC and may prime these tumors for response to immunotherapy with anti-PD-1 antibodies like nivolumab (N). Methods: In this single-arm, single-institution, phase I/II clinical trial, pts with treatment-refractory MSS, BRAFV600E metastatic CRC were eligible. No prior BRAF, MEK, or ERK inhibitors, anti-EGFR antibody, or immunotherapy was permitted. Pts received E (300 mg PO daily), C (500 mg/m2 IV q14 days), and N (480 mg IV q28 days). The primary endpoints were best overall response (RECIST 1.1) and safety/tolerability (CTCAE v5). A Simon two-stage design (H0: p≤.22; Ha: p≥.45, where p = percentage of pts with radiographic response) was employed using a one-sided α =.05 and β =.20. Median progression-free survival (PFS) and overall survival (OS) were estimated via Kaplan-Meier. To measure ex vivo treatment responses with an E-slice assay (EMPIRI), 300 µm fresh tissue slices from core biopsies were generated and cultured in serum-free media with E, C, and N. Longitudinal changes in viability were measured at days 4, 8, and 12 and compared to baseline viability in each tissue. Ex vivo “response” was defined if < 1X baseline tumor cell viability. Results: With a data cutoff of 2/8/2022, all pts are enrolled: 26 evaluable for toxicity and 23 for response. Median age is 60 years (range, 32-85), and 16 (62%) are female. Grade 3-4 treatment-related adverse events (AE) have occurred in 5/26 (19%) patients: colitis, maculopapular rash, leukocytosis, and myositis/myocarditis (all N = 1); asymptomatic elevated amylase/lipase (N = 2). Overall response rate is 48% (95% CI, 27-69), and disease control rate is 96% (95% CI, 78-100). Median PFS is 7.4 months (95% CI, 5.6-NA). For the 11 pts with responses, median duration of response is 7.7 months (95% CI, 4.5-NA). Median OS is 15.1 months (95% CI, 7.7-NA). E-slices showed concordance between pts with radiographic responses and reduction in cell viability, and between non-responders and increase in cell viability. Final results will be presented. Conclusions: E + C + N appears to be effective and well-tolerated for pts with MSS, BRAFV600E metastatic CRC. Ex vivo analysis of pretreatment tissue predicted eventual clinical response in matched patients. A follow-up randomized phase II trial (SWOG 2107) to evaluate encorafenib/cetuximab with or without nivolumab in pts with MSS, BRAFV600E metastatic CRC will activate in 2022. Clinical trial information: NCT04017650.

Prognostic role of systemic inflammatory markers in patients with metastatic MSI-h/dMMR colorectal cancer receiving immunotherapy

3524

Background: Markers of systemic inflammation including neutrophil-to-lymphocyte ratio (NLR), platelet-to-lymphocyte ratio (PLR), and monocyte-to-lymphocyte ratio (LMR) are prognostic in patients with metastatic colorectal cancer receiving systemic chemotherapy. The presence of liver metastases has also been hypothesized to modulate response to immunotherapy. In this study, we assess the prognostic role of these markers in patients with microsatellite high (MSI-H)/deficient mismatch repair (dMMR) tumors receiving immunotherapy for metastatic or unresectable colorectal cancer (CRC). Methods: This was a single-institution retrospective analysis of patients with dMMR/MSI-H CRC who received anti-PD-(L)1 and/or anti-CTLA-4 therapy for metastatic or unresectable disease at between 2015 and 2021 (n = 59). NLR, PLR, and LMR were calculated based on the complete blood count obtained within 1 week prior to treatment. Patient and tumor characteristics were obtained from the clinical record. Patient characteristics were compared using Fisher’s exact test and Mann-Whitney U where appropriate. Progression free survival (PFS) and overall survival (OS) were the primary endpoints and log-rank test was used for comparison of survival distribution among groups. Results: 59 patients with metastatic dMMR/MSI-H CRC were identified. Median age was 60, 53% (n = 31) had right-sided tumors, 35% (n = 35) of patients with testing available had RAS-mutated tumors, and 37% (n = 22) received prior chemotherapy. Most common sites of metastatic disease were peritoneum (n = 23, 39%) and liver (n = 17, 29%). Patients were divided into NLR-High (NLR ≥ 3, n = 20) and NLR-Low (NLR < 3, n = 39), and both groups had similar baseline characteristics. The rate of progressive disease as best response was not different in NLR-Low versus NLR-High (15% vs 30%, p = 0.3). At a median follow-up of 32 months, neither median PFS nor median OS were reached. 74% (n = 29) remained progression free at 1 year in the NLR-Low group versus 60% (n = 12) in NLR-High group which was not statistically significant (p = 0.37); 90% (n = 35) remained alive at 2 years in the NLR-low versus 80% (n = 16) in the NLR-High group (p = 0.4). Similarly, using a cut-off of 150 and 3 for PLR and LMR respectively, there was no significant difference between PFS at 1 year in the PLR-Low (n = 32) vs PLR-High (n = 27) (66% vs 74%, p = 0.58) and LMR-Low (n = 35) vs LMR-High (n = 24) (60% vs 83%, p = 0.084) groups. The presence of liver metastasis or the presence of a RAS mutation did not influence PFS at 1 year (p = 0.35 and p = 1.00, respectively). Conclusions: Markers of systemic inflammation may have a limited prognostic role for patients with dMMR/MSI-H CRC receiving immunotherapy.

Clinical outcomes following termination of immunotherapy due to long-term benefit in MSI-H colorectal cancer

3585

Background: Immune checkpoint blockade therapy improves survival in patients (pts) with microsatellite instability-high (MSI-H) advanced colorectal cancer (CRC). Oncologists often discontinue immunotherapy after 2 years of disease control based on prior trial data. Recurrence outcomes following discontinuation of immunotherapy and clinicopathologic features associated with recurrence remain underreported given the recent advent of these agents for pts with MSI-H advanced CRC. Methods: Records from pts with MSI-H CRC from MD Anderson Cancer Center who received immunotherapy between 2015-2022 and stopped after clinical benefit were reviewed. Median survival was estimated according to the Kaplan-Meier method. Associations between the event of recurrence and coexisting mutations ( KRAS, NRAS, BRAFV600E, PIK3CA, APC, TP53, POLE/POLD), metastatic site (lung, liver, lymph nodes, or peritoneum), primary tumor sidedness (right vs. left colon), and prior immunotherapy (anti-PD-(L)1 alone or with anti-CTLA-4 antibodies) were measured by Fisher’s exact tests. Results: Thirty-six pts with MSI-H CRC without progression on immunotherapy were reviewed. Of these 29 and 7 received anti-PDL1 antibody alone or in combination with anti-CTLA-4 antibody, respectively. Median exposure to prior immunotherapy was 24 months (range, 5-43). After a median follow-up of 19 months (95% CI, 14-26) after stopping immunotherapy, 30 of 36 pts (83%) remained without disease progression. For the 6 patients with progression after stopping, median time to relapse was 13 months (range, 5-31). Median disease-free survival (DFS) was not reached. The estimated 1-year, 2-year, and 3-year DFS probabilities were 90% (95% CI, 79-100), 79.1% (95% CI, 64-98), and 68% (95% CI, 47-98), respectively. Median overall survival from the time that immunotherapy was stopped was 54 months (95% CI, 47-NA). Only 1 pt died due to unrelated illness. There were no observed associations between disease recurrence and co-existing mutations, metastatic organ involvement, primary tumor sidedness, or immunotherapy used. Conclusions: Most pts with MSI-H advanced CRC who achieve initial clinical benefit and do not progress on immunotherapy do not recur after treatment is stopped. Our data suggest that favorable outcomes do occur following cessation of immunotherapy in this setting even with concomitant prognostically unfavorable clinical features (RAS, BRAFV600E mutations; liver, peritoneal metastases).

Resistance mechanisms to anti-EGFR therapy in RAS/RAF wildtype colorectal cancer varies by regimen and line of therapy

3554

Background: The conventional theory for the development of treatment resistance to anti-EGFR for metastatic colorectal cancer (mCRC) is the selective growth advantage of pre-existing therapy-resistant subclones with genomic mechanisms such as RAS mutations, leading to treatment resistance and disease progression. However, the impact of cytotoxic chemotherapy in combination with anti-EGFR on the mechanisms of resistance has not been assessed. Methods: We analyzed paired plasma samples from RAS/BRAF/EGFR wild-type mCRC patients enrolled in three large randomized phase 3 trials of anti-EGFR rechallenge in whom paired baseline and time of progression plasma samples had been collected for sequencing of ctDNA on a platform optimized for very low allele frequencies. 569 patients had paired baseline and progression ctDNA samples analyzed, including 147 in the first line study of FOLFOX +/- panitumumab, 91 patients in third line with panitumumab vs best supportive care, and 331 patients in the third line study of cetuximab vs. panitumumab. The mutational signature of the alterations acquired with therapy was evaluated. We also established colon cancer cell lines with resistance to cetuximab, FOLFOX, and SN38, and profiled transcriptional changes. Results: Using serial plasma samples, we demonstrate that patients whose tumors were treated with and responded to anti-EGFR alone were approximately 5-times more likely to develop acquired mutations at progression compared to those treated with an EGFR inhibitor in combination with cytotoxic chemotherapy (46% vs. 9%, respectively; p < 0.001). Consistent with this clinical finding, cell lines with non-genomic acquired resistance to cetuximab were cross-resistant to cytotoxic chemotherapy and vice-versa, with transcriptomic profiles consistent with epithelial to mesenchymal transition. In contrast, common acquired genomic alterations in the MAPK pathway that drive resistance to EGFR monoclonal antibodies do not impact sensitivity to cytotoxic chemotherapy. Further, contrary to the generally accepted hypothesis of clonal expansion of acquired resistance, in our work we demonstrate that baseline resistant subclonal mutations rarely expanded to become clonal at the time of progression (8%), and most remained subclonal (44%) or disappeared (49%). Conclusions: Collectively, this work outlines a model of resistance where non-genomic mechanisms of resistance common to both EGFR inhibitors and cytotoxic chemotherapy predominate in patients treated with EGFR and chemotherapy combinations. With EGFR inhibitor monotherapy, genomic acquired resistance mechanisms predominate, although only rarely through expansion of pre-existing subclones. These findings have important implications for strategies of EGFR-inhibitor rechallenge studies.

Phase I study of hydroxychloroquine plus binimetinib in patients with metastatic pancreatic cancer (the HOPE trial)

TPS634

Background: Pancreatic ductal adenocarcinoma (PDAC) is a devastating malignancy with a dearth of effective therapeutic options. Over 90% of PDAC harbor activating mutations in the KRAS oncoprotein, which in turn leads to activation of downstream effector proteins in the the RAF-MEK-ERK mitogen-activated protein kinase (MAPK) signaling cascade serving to promote tumor cell survival, growth and metastasis. Unfortunately, single agent treatment with MAPK-inhibitors have had limited therapeutic efficacy in patients with PDAC owing to development of various tumor-cell intrinsic resistance mechanisms, including upregulation of autophagy. Hydroxychloroquine is an antimalarial drug that functions to inhibit autophagy by inhibiting acidification of lysosomes. Previously published preclinical data suggest combination therapy with binimetinib, a MEK 1/2 inhibitor, and hydroxychloroquine leads to enhanced killing of PDAC cells in vitro and in vivo. Methods: This is a single arm, single center phase I trial of binimetinib plus hydroxychloroquine in patients with metastatic pancreatic cancer harboring a KRAS mutation. All patients will receive binimetinib at a fixed dose of 45mg PO twice daily (14-day cycles) while hydroxychloroquine will be dosed at 400mg PO twice daily (14-day cycles) and dose escalated using a Bayesian optimal interval design with a target toxicity rate of 0.3. Key eligibility criteria include histologically confirmed metastatic pancreatic adenocarcinoma, prior treatment with at least one line of systemic therapy and a documented KRAS mutation. An estimated 24 patients will be enrolled in the first phase of this study and up to 15 patients in the dose expansion cohort. The primary endpoint of this study is to determine the maximum tolerated dose (MTD) of hydroxychloroquine when combined with a fixed dose of binimetinib. Key secondary endpoints include safety and toxicity profile, response rate, progression free survival (PFS) and overall survival (OS). This study is ongoing and has enrolled 10 patients at the time of submission. Clinical trial information: NCT04132505.

Outcomes of IBD-associated colorectal cancer and implications in early-onset colorectal cancer

22

Background: Inflammatory bowel disease (IBD) increases the risk of developing colorectal cancer (CRC), and colitis-associated CRC (CA-CRC) mortality is on the rise. It has been postulated that CA-CRC may be contributing to the increasing prevalence of early-onset CRC (EOCRC) but supportive studies are currently lacking. Molecular and clinical differences between CA-CRC and sporadic-CRC (S-CRC) have been reported, however outcomes for CA-CRC remains unclear. Signet ring cell carcinoma (SRC) is a rare subtype of CRC which is seen at higher frequencies, along with mucinous histology, in both CA-CRC and EOCRC. In this study, we validate the association of SRC and mucinous (SRC/M) histology with CA-CRC and EOCRC, and utilize it to estimate the amount of EOCRC attributable to undiagnosed or subclinical IBD. Methods: A retrospective study was conducted using three independent mCRC patient datasets from MDACC. The mATTACC discovery cohort consisted of 32 IBD- and 425 S-mCRC patients enrolled in a prospective biomarker trial. Validation of tumor histology was completed with a tumor registry (n=1696), excluding the MSI-High samples, and a real-world evidence (RWE) cohort from MDACC containing 269 CA-mCRC and 29,596 S-mCRC patients, was used as our validation cohort. Results: In the mATTACC cohort SRC/M histology was found in 37.5% of CA-mCRC and 11.7% of S-mCRC, showing a strong association between SRC/M and CA-mCRC (OR = 4.54, 95% CI: 2.19-9.43). The RWE cohort confirmed the correlation of SRC/M with CA-mCRC (28.6%) relative to S-mCRC (11.4%) patients (OR = 3.13, 95%CI: 2.39-4.09). An association was found between SRC/M and EOCRC (OR = 1.35; 95% CI: 1.24-1.47). By comparing the prevalence of SRC/M in EOCRC and late-onset CRC and correcting by the proportion of CA-CRC cases with SRC/M histology, we estimate that between 8.28% to 10.15% of EOCRC may attributable to undiagnosed/subclinical IBD. Using the RWE cohort, median overall survival was determined to be lower for CA-mCRC (31m) relative to S-mCRC (39m; p=0.007), yielding a HR of 1.26 (95% CI: 1.06-1.48). CA-mCRC patients with EOCRC (25m) were also found to have significantly worse outcomes than S-mCRC patients (40m) with EOCRC (p=0.0005; HR = 1.61, 95%CI: 1.23-2.11). Within CA-mCRC, patients with SRC or SRC/M histology (21m) had decreased OS compared to mucinous histology (51m), indicating the poor prognosis of SRC in CA-mCRC (p=0.028; HR=0.53, 95% CI: 0.3-0.94). Conclusions: Tumor biology consistent with CA-CRC, including SRC/M histology, may be present in 8.3% – 10.2% of patients with EOCRC without a clinical diagnosis of IBD, and harbors worse outcomes. Although other confounding biology may be underlying this association, recognition of undiagnosed IBD in CRC patients, especially those with metastatic disease, is important as it may impact prognosis and treatment strategies for this high-risk patient population.

Phase I/II trial of encorafenib, cetuximab, and nivolumab in patients with microsatellite stable, BRAFV600E metastatic colorectal cancer

12

Background: Encorafenib (E) and cetuximab (C) offers short-lived response and survival benefit for patients (pts) with MSS, BRAFV600E metastatic colorectal cancer (CRC). BRAF + EGFR inhibition induced a transient MSI-H phenotype in preclinical models of MSS, BRAFV600E CRC and may prime these tumors for response to immunotherapy with anti-PD-1 antibodies like nivolumab (N). Methods: In this single-arm, single-institution, phase I/II clinical trial, pts with treatment-refractory MSS, BRAFV600E metastatic CRC were eligible. No prior BRAF inhibitors, anti-EGFR antibody, or immunotherapy was permitted. Pts received E (300 mg PO daily), C (500 mg/m2 IV q14 days), and N (480 mg IV q28 days). The primary endpoints were best overall response (RECIST 1.1) and safety/tolerability (CTCAE v5). A Simon two-stage design (H0: p≤.22; Ha: p≥.45, where p= percentage of pts with radiographic response) was employed using a one-sided α=.05 and β=.20. In the first stage, ≥ 4/15 responses were needed in order for the trial to enroll 11 additional pts. Median progression-free survival (PFS) and overall survival (OS) were estimated via Kaplan-Meier. Results: All 26 pts have been enrolled - 23 patients treated, and 21 evaluable for response so far. Median age is 59 years (range, 32-85), and 14 (54%) are female. No dose-limiting toxicities occurred. Grade 3-4 treatment-related adverse events (AE) occurred in 4/22 (18%) patients. Grade 3 AEs included colitis, maculopapular rash, leukocytosis, and elevated amylase/lipase (all N=1). Grade 4 AEs in a single patient were myositis/myocarditis. Overall response rate is 45% (95% CI, 23-68), and disease control rate is 95% (95% CI, 75-100). Median PFS is 7.3 months (95% CI, 5.5-NA). Median OS is 11.4 months (95% CI, 7.6-NA). For the 9 pts thus far with responses, median duration of response is 8.1 months (95% CI, 7.3-NA). Updated results will be presented. Conclusions: E + C + N is effective and well-tolerated for pts with MSS, BRAFV600E metastatic CRC. The E+C+N regimen met its predefined efficacy endpoint and suggests a role for immunotherapy as a novel combination approach for this specific subpopulation of MSS metastatic CRC. A follow-up randomized phase II trial (SWOG 2107) to evaluate encorafenib/cetuximab with or without nivolumab in pts with MSS, BRAFV600E metastatic CRC will activate in early 2022. Clinical trial information: NCT04017650.

First Direct Detection Constraints on Planck-Scale Mass Dark Matter with Multiple-Scatter Signatures Using the DEAP-3600 Detector

Dark matter with Planck-scale mass (≃10^{19}  GeV/c^{2}) arises in well-motivated theories and could be produced by several cosmological mechanisms. A search for multiscatter signals from supermassive dark matter was performed with a blind analysis of data collected over a 813 d live time with DEAP-3600, a 3.3 t single-phase liquid argon-based detector at SNOLAB. No candidate signals were observed, leading to the first direct detection constraints on Planck-scale mass dark matter. Leading limits constrain dark matter masses between 8.3×10^{6} and 1.2×10^{19}  GeV/c^{2}, and ^{40}Ar-scattering cross sections between 1.0×10^{-23} and 2.4×10^{-18}  cm^{2}. These results are interpreted as constraints on composite dark matter models with two different nucleon-to-nuclear cross section scalings.

Sensei: how many samples to tell a change in cell type abundance?

Cellular heterogeneity underlies cancer evolution and metastasis. Advances in single-cell technologies such as single-cell RNA sequencing and mass cytometry have enabled interrogation of cell type-specific expression profiles and abundance across heterogeneous cancer samples obtained from clinical trials and preclinical studies. However, challenges remain in determining sample sizes needed for ascertaining changes in cell type abundances in a controlled study. To address this statistical challenge, we have developed a new approach, named Sensei, to determine the number of samples and the number of cells that are required to ascertain such changes between two groups of samples in single-cell studies. Sensei expands the t-test and models the cell abundances using a beta-binomial distribution. We evaluate the mathematical accuracy of Sensei and provide practical guidelines on over 20 cell types in over 30 cancer types based on knowledge acquired from the cancer cell atlas (TCGA) and prior single-cell studies. We provide a web application to enable user-friendly study design via https://kchen-lab.github.io/sensei/table_beta.html .

Right ventricular assessment of the adolescent footballers heart: impact of ethnicity

Introduction

Athletic training often results in electrical and structural changes that may mimic phenotypical features of pathological cardiomyopathies. These physiological changes are influenced by age, ethnicity and sporting discipline. The presence of such changes that overlap with diseases implicated in exercise related sudden cardiac death may require comprehensive assessment to confirm or refute the presence of disease. One such potential physiological overlap with pathological change in athletes can occur in arrhythmogenic right ventricular dysplasia (ARVD), with features including chamber dilatation and T-wave inversion (TWI). An erroneous interpretation may have profound consequences ranging from false reassurance in a vulnerable athlete to unfair disqualification in a healthy individual. Therefore, it is important for the clinician to distinguish physiology from pathology.

Purpose

Studies detailing the physiological adaptation to exercise on the right ventricle (RV) of adolescent athletes are fewer compared to the left ventricle, with even fewer reports describing the impact of ethnicity on the RV. We set out to describe the normal dimensions of the RV of academy football players.

Results

ECG and echocardiographic data of 3000 academy male footballers were analysed, aged between 13 and 18 years old (mean age 16.4±0.5 years), who underwent mandatory cardiac screening. Ethnicity was categorised as white (n=1000), black (African/Caribbean; n=1000) and mixed-race (one parent white and one parent black; n=1000). ARVD major criteria for TWI was seen in 6.3% of the cohort. This was more prevalent in black footballers (3.7%) when compared to mixed race footballers (2%) or white footballers (0.6%), p&lt;0.05. In up to 67% of the overall cohort, RV values exceeded those for normal adult reference ranges. There were no differences in RV dimensions between ethnicities (Tables 1 & 2). If ARVD criteria was applied, 13.2% would fulfil major ARVD criteria for right ventricular outflow tract. This was also demonstrated for RVOT dimensions (6.1% - 23.6%; Figure 1). Overall, 0.2% of the cohort would fulfil diagnosis for “definite” ARVD and 2.2% would fulfil diagnosis for “borderline” ARVD. This was seen more frequently in black footballers (9.9%) than mixed race footballers (3.9%) or white footballer (0.6%), P=0.0005. Among athletes meeting definite or borderline ARVD criteria, no cardiomyopathy was identified after comprehensive clinical assessment.

Conclusion

This is the largest study to our knowledge that reports RV dimension data among adolescent footballers of different ethnicities. Right heart sizes in excess of standard adult ranges occurred in as many as one in 22 athletes. It is not unusual to observe values that would overlap with criteria for ARVD. As with LV parameters, variations in terms of ethnicity should be accounted for when considering RV dimensions and ECG changes when performing routine cardiac assessments of adolescent athletes.

Funding Acknowledgement

Type of funding sources: Other. Main funding source(s): National Institute for Health Research

Pulse-shape discrimination against low-energy Ar-39 beta decays in liquid argon with 4.5 tonne-years of DEAP-3600 data

The DEAP-3600 detector searches for the scintillation signal from dark matter particles scattering on a 3.3 tonne liquid argon target. The largest background comes from 39 Ar beta decays and is suppressed using pulse-shape discrimination (PSD). We use two types of PSD estimator: the prompt-fraction, which considers the fraction of the scintillation signal in a narrow and a wide time window around the event peak, and the log-likelihood-ratio, which compares the observed photon arrival times to a signal and a background model. We furthermore use two algorithms to determine the number of photons detected at a given time: (1) simply dividing the charge of each PMT pulse by the mean single-photoelectron charge, and (2) a likelihood analysis that considers the probability to detect a certain number of photons at a given time, based on a model for the scintillation pulse shape and for afterpulsing in the light detectors. The prompt-fraction performs approximately as well as the log-likelihood-ratio PSD algorithm if the photon detection times are not biased by detector effects. We explain this result using a model for the information carried by scintillation photons as a function of the time when they are detected.

A novel clinical tool to estimate risk of false negative KRAS mutation in circulating tumor DNA testing

3594

Background: Recently, in metastatic colorectal cancer (mCRC), the detection of RAS mutations by circulating tumor (ct) DNA has recently emerged as a valid and non-invasive alternative approach, overall showing a high concordance with the standard tissue genotyping, giving information on response to EGFRi treatment and resistant mechanisms. However, RAS mutations may be missed due to low levels of any ctDNA in the blood (false-negative), and it has been difficult to distinguish this from patients without a RAS mutation in the tumor (true-negative). We propose a methodology that can be applied to multi-gene ctDNA testing panels to accurately distinguish true- and false-negative tests. Methods: 357 subjects with tissue and multi-panel ctDNA testing from MD Anderson (MDACC) were used as a training dataset and 295 subjects from Massachusetts General Hospital (MGH) dataset as the testing dataset. CtDNA panels contained between 65 and 70 genes, allowing evaluation of tumor ctDNA shedding from variant allele fraction (VAF) levels in the plasma from other genes (such as APC and TP53). Based on the relationship between KRAS and the VAFs of other gene, we established a Bayesian model providing a posterior probability of false negative in the ctDNA test, using thresholds of < 5% (low), 5-15% (medium), and > 15% (high). This model was validated on the MGH database. Results: Across both cohorts, 431 patients were ctDNA wild type for KRAS. Of those, 29 had tissue documenting a KRAS mutation for a false negative rate of 8%. The model provides the posterior probability that a KRAS mutation is indeed present in the tissue given the observed values of allele frequencies for other mutated genes in the plasma. In the validation cohort, a predicted low false negative had no false negatives (0/62, 95% CI 0%-5.8%), while a predicted medium false negative rate was associated with 3% false negative (1/32, 95% CI 0%-16%). In contrast, a high predicted false negative rate was associated with 5% false negative (5/100, 95% CI 1.6%-11%). The results demonstrate the ability of our tool to discriminate between subjects with true negative and false negatives, as a higher proportion of false negatives are observed at higher posterior probabilities. Conclusions: In conclusion, our approach provides increased confidence in KRAS ctDNA mutation testing in clinical practice, thereby facilitating the identification patients who will benefit from EGFR inhibition while reducing the risk of false negative tests. Extension of this methodology to NRAS and BRAF is possible, with clinical application enabled by a freely available online tool.

Rarity of acquired mutations (MTs) after first-line therapy with anti-EGFR therapy (EGFRi)

3514

Background: Colorectal cancers (CRC) lacking RAS MTs treated with EGFRi are thought to evolve by a repetitive process of genetic diversification and clonal evolution. Acquired MTs in KRAS, NRAS, BRAF, MAP2K1, and EGFR are known mechanisms of acquired resistance in the EGFRi refractory population. However, the prevalence of MTs in the first line (1L) setting is not well established as most experience with EGFRi has been beyond the 1L setting. Methods: We analyzed paired plasma samples from RAS/BRAF/EGFRWT mCRC patients (pts) enrolled in 3 large randomized phase 3 trials who had been treated with EGFRi and in whom paired baseline (BL) and time of progression (PRO) plasma samples had been collected for sequencing of ctDNA on a platform optimized for very low allele frequencies (Plasma Select-R™ and Resolution Bio™). Prevalence of MTs at BL and PRO from a 1L study (‘203; FOLFOX ± panitumumab) were compared with 2 studies in the third line setting (3L; ‘007; panitumumab + best supportive care [BSC] vs BSC; and 3L; ‘763; panitumumab vs. cetuximab), to assess the frequency of acquired resistance mutations via ctDNA analysis. Results: For pts with available paired plasma samples (n = 112 for ‘203; n = 89 for ‘007; n = 274 for ‘763), acquisition of at least one KRAS, NRAS, BRAF, MAP2K1, or EGFR MT was significantly less common in post-progression samples in the EGFR containing arms of the 1L ‘203 study compared to the 3L ‘763 and ‘007 studies (6.8% vs 50.4% vs 39.6%, respectively; p < 0.001). In the non EGFR containing arms of the ‘203 and ‘007 study, the rate of acquired MTs was 7.5% and 0%, respectively (p = 1). While this difference in the rate of acquired MTs between the EGFR and non EGFR containing arms was statistically significant for the 3L study (p < 0.001) it was not significant for the 1L study. Further, pts on both 3L studies treated with EGFRi who experienced CR, PR or SD acquired more MTs than those who had PD as best response (53.6% vs 33.3%, respectively; p < 0.001). This relationship was not significant in the 1L setting (7.7% vs 0%; p = 1). Subclonal MTs (rMAF < 25%) in KRAS, NRAS, EGFR, BRAF and MAP2K1 were present at BL in 129 pts (27%). Based on the hypothesis that EGFRi is selecting for rare existing mutated cells in the tumor, we would expect expansion of any preexisting subclones in the BL samples. However, in contrast to expectations, these subclones rarely expanded to become clonal at the time of progression (12.4%). Conclusions: In contrast to expectations, acquired KRAS, NRAS, BRAF, EGFR, or MAP2K1 MTs rarely develop after 1L therapy. While selective pressure appears to increase the frequency of acquired MTs in the 3L setting, preexisting subclonal MTs do not appear to be the dominant source of acquired MTs at progression, implying that there may also be a transient mutational process driving resistance rather than expansion of preexisting clones. These findings have significant implications for ongoing and planned EGFRi rechallenge studies.

ARID1A Mutation May Define an Immunologically Active Subgroup in Patients with Microsatellite Stable Colorectal Cancer

PURPOSE

AT-rich interactive domain 1A (ARID1A) is commonly mutated in colorectal cancer, frequently resulting in truncation and loss of protein expression. ARID1A recruits MSH2 for mismatch repair during DNA replication. ARID1A deficiency promotes hypermutability and immune activation in preclinical models, but its role in patients with colorectal cancer is being explored.

EXPERIMENTAL DESIGN

The DNA sequencing and gene expression profiling of patients with colorectal cancer were extracted from The Cancer Genome Atlas and MD Anderson Cancer Center databases, with validation utilizing external databases, and correlation between ARID1A and immunologic features. IHC for T-cell markers was performed on a separate cohort of patients.

RESULTS

Twenty-eight of 417 patients with microsatellite stable (MSS) colorectal cancer (6.7%) had ARID1A mutation. Among 58 genes most commonly mutated in colorectal cancer, ARID1A mutation had the highest increase with frameshift mutation rates in MSS cases (8-fold, P < 0.001). In MSS, ARID1A mutation was enriched in immune subtype (CMS1) and had a strong correlation with IFNγ expression (Δz score +1.91, P < 0.001). Compared with ARID1A wild-type, statistically significant higher expression for key checkpoint genes (e.g., PD-L1, CTLA4, and PDCD1) and gene sets (e.g., antigen presentation, cytotoxic T-cell function, and immune checkpoints) was observed in mutant cases. This was validated by unsupervised differential expression of genes related to immune response and further confirmed by higher infiltration of T cells in IHC of tumors with ARID1A mutation (P = 0.01).

CONCLUSIONS

The immunogenicity of ARID1A-mutant cases is likely due to an increased level of neoantigens resulting from increased tumor mutational burden and frameshift mutations. Tumors with ARID1A mutation may be more susceptible to immune therapy-based treatment strategies and should be recognized as a unique molecular subgroup in future immune therapy trials.

COMT Genotype and Efficacy of Propranolol for TMD Pain: A Randomized Trial

Propranolol is a nonselective β-adrenergic receptor antagonist that is efficacious in reducing facial pain. There is evidence that its analgesic efficacy might be modified by variants of the catechol-O-methyltransferase (COMT) gene. We tested the hypothesis in a subset of 143 non-Hispanic Whites from a randomized controlled trial of patients with painful temporomandibular disorder (TMD). Patients were genotyped for rs4680, a single nucleotide polymorphism of COMT, and randomly allocated to either propranolol 60 mg twice daily or placebo. During the 9-wk follow-up period, patients recorded daily ratings of facial pain intensity and duration; the product was computed as an index of facial pain. Postbaseline change in the index at week 9 (the primary endpoint) was analyzed as a continuous variable and dichotomized at thresholds of ≥30% and ≥50% reduction. Mixed models for repeated measures tested for the genotype × treatment group interaction and estimated means, odds ratios (ORs), and 95% confidence limits (95% CLs) of efficacy within COMT genotypes assuming an additive genetic model. In secondary analysis, the cumulative response curves were plotted for dichotomized reductions ranging from ≥20% to ≥70%, and genotype differences in area under the curve percentages (%AUC) were calculated to signify efficacy. Mean index reduction did not differ significantly (P = 0.277) according to genotype, whereas the dichotomized ≥30% reduction revealed greater efficacy among G:G homozygotes (OR = 10.9, 95%CL = 2.4, 50.7) than among A:A homozygotes (OR = 0.8, 95%CL = 0.2, 3.2) with statistically significant interaction (P = 0.035). Cumulative response curves confirmed greater (P = 0.003) efficacy for G:G homozygotes (%AUC difference = 43.7, 95%CL = 15.4, 72.1) than for A:A homozygotes (%AUC difference = 6.5, 95%CL = -30.2, 43.2). The observed antagonistic effect of the A allele on propranolol’s efficacy was opposite the synergistic effect hypothesized a priori. This unexpected result highlights the need for better knowledge of COMT’s role in pain pathogenesis if the gene is to be used for precision-medicine treatment of TMD (ClinicalTrials.gov NCT02437383).

ARID1A mutation to define an immunologically active subgroup in patients with microsatellite-stable colorectal cancer

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Background: AT-rich interactive domain 1A (ARID1A) is a chromatin regulator mutated in human cancers, frequently resulting in truncation and loss of expression of this protein. ARID1A recruits MSH2 during DNA replication to perform mismatch-repair. ARID1A deficiency has been shown to increase mutational load and immune activation in preclinical models (Shen J, Nat Med 2018) but its role in colorectal cancer (CRC) patients (pts) is being explored. Methods: The DNA sequencing and gene expression profiling of microsatellite-stable (MSS) CRC pts were extracted from TCGA and MD Anderson Cancer Center databases. The expression levels were normalized according to the mean values of each dataset. The mutational burden and expression signatures for IFN-γ and various immune markers were compared according to the ARID1A mutational status. Results: Among 417 pts with MSS CRC, 28 pts (6.7%) had a non-silent mutation in ARID1A. Out of the 58 genes most commonly mutated in CRC, non-silent mutation in ARID1A had the strongest association with the frame-shift mutation rate in MSS cases (8-fold increase, p< .001). ARID1A mutation had also a strong correlation with the IFN-γ expression signature in MSS CRC (Δz score +1.91, p< .001) . Compared with ARID1A wild-type pts, higher expression signatures for cytotoxic T cell function, NK cells, and immune checkpoints were observed in MSS ARID1A mutated cases. ARID1A mutant cases showed higher expressions of various immune checkpoint genes (CD274, CTLA4, HAVCR2, IDO1, LAG3, PDCD1, and PDCD1LG2) compared to wild-type cases (all p < .05). All findings were observed independently in both datasets. Conclusions: In MSS CRC, ARID1A mutation is associated with a high expression of IFN-γ pathway and immune signatures (such as cytotoxic T cell function and immune checkpoint markers). The immunogenicity of ARID1A mutant cases is likely due to the increased level of neoantigens resulting from the increased rate of frame-shift mutations. Tumors with ARID1A mutation may be more susceptible to immune therapy-based treatment strategies and should likely be recognized as a unique molecular subgroup in future immune therapy trials.

NeoRAS: Incidence of RAS reversion from RAS mutated to RAS wild type

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Background: RAS mutations are found in ~50% of patients (pts) with metastatic colorectal cancer (mCRC) and associated with resistance to anti-EGFR. Circulating tumor DNA (ctDNA) enables detection of resistant RASMUT arising from RASWT. Recently there has been interest in defining the converse: RASMUT tumors that revert to RASWT, with early results suggesting rates of ~7%. Clinical trials in this population are in development, though the incidence has not been validated with robust methodologies. Methods: 1) We identified 74 mCRC pts with baseline RASMUT and longitudinal ctDNA or tissue data enrolled in ATTACC (NCT01196130), a prospective genomic matching protocol utilizing paired tissue/ctDNA samples at baseline. We evaluated serial samples for RAS loss. 2) Using an external cohort of pts with mCRC and serial ctDNA with a targeted NGS assay sequencing all KRAS/ NRAS exons (Guardant360, Guardant Health), we screened pts for baseline RASMUT with no evidence of prior anti-EGFR exposure and evaluated for RAS loss. Results: 74 pts met criteria of RASMUT CRC with serial samples in ATTACC. Of these, 51 retained RASMUT. 22 pts had very low or absent levels of other clonal alterations such as APC or TP53 and are therefore unable to reliably detect RAS loss. One patient had true RAS loss with NRAS G13R, APC and TP53 mutations at baseline and persistent high-level APC and TP53 mutations without a detectable NRAS mutation, for an overall rate of RAS loss of 2% (1/52). In the second cohort we identified 162 pts, 34 of which had insufficient ctDNA to assess RAS loss on the serial sample as defined by loss of clonal alterations like APC and TP53. Of the remaining 128 patients, 11 had RAS loss (8.5%, with 1 NRAS, 10 KRAS). We next compared the relative mutant allele frequency (rMAF) between RAS retainers and RAS loss. The median baseline rMAF for pts who lost RAS was 0.74, compared to 0.86 in pts retaining RAS (p = 0.045). Conclusions: RAS reversion in mCRC from RASMUT to RASWT is uncommon and occurs at a rate between 2-8% in our two cohorts. RAS reversion is associated with a lower rMAF at baseline, suggesting subclonality. Liquid biopsies must be interpreted carefully, such that a determination of RAS mutation status is most informative in the presence of truncal APC and/or TP53 mutations.

Validation of Microsatellite Instability Detection Using a Comprehensive Plasma-Based Genotyping Panel

PURPOSE

To analytically and clinically validate microsatellite instability (MSI) detection using cell-free DNA (cfDNA) sequencing.

EXPERIMENTAL DESIGN

Pan-cancer MSI detection using Guardant360 was analytically validated according to established guidelines and clinically validated using 1,145 cfDNA samples for which tissue MSI status based on standard-of-care tissue testing was available. The landscape of cfDNA-based MSI across solid tumor types was investigated in a cohort of 28,459 clinical plasma samples. Clinical outcomes for 16 patients with cfDNA MSI-H gastric cancer treated with immunotherapy were evaluated.

RESULTS

cfDNA MSI evaluation was shown to have high specificity, precision, and sensitivity, with a limit of detection of 0.1% tumor content. In evaluable patients, cfDNA testing accurately detected 87% (71/82) of tissue MSI-H and 99.5% of tissue microsatellite stable (863/867) for an overall accuracy of 98.4% (934/949) and a positive predictive value of 95% (71/75). Concordance of cfDNA MSI with tissue PCR and next-generation sequencing was significantly higher than IHC. Prevalence of cfDNA MSI for major cancer types was consistent with those reported for tissue. Finally, robust clinical activity of immunotherapy treatment was seen in patients with advanced gastric cancer positive for MSI by cfDNA, with 63% (10/16) of patients achieving complete or partial remission with sustained clinical benefit.

CONCLUSIONS

cfDNA-based MSI detection using Guardant360 is highly concordant with tissue-based testing, enabling highly accurate detection of MSI status concurrent with comprehensive genomic profiling and expanding access to immunotherapy for patients with advanced cancer for whom current testing practices are inadequate.See related commentary by Wang and Ajani, p. 6887.

Identification of Actionable Fusions as an Anti-EGFR Resistance Mechanism Using a Circulating Tumor DNA Assay

PURPOSE

Gene fusions are established oncogenic drivers and emerging therapeutic targets in advanced colorectal cancer. This study aimed to detail the frequencies and clinicopathological features of gene fusions in colorectal cancer using a circulating tumor DNA assay.

METHODS

Circulating tumor DNA samples in patients with advanced colorectal cancer were analyzed at 4,581 unique time points using a validated plasma-based multigene assay that includes assessment of fusions in FGFR2, FGFR3, RET, ALK, NTRK1, and ROS1. Associations between fusions and clinicopathological features were measured using Fisher's exact test. Relative frequencies of genomic alterations were compared between fusion-present and fusion-absent cases using an unpaired t test.

RESULTS

Forty-four unique fusions were identified in 40 (1.1%) of the 3,808 patients with circulating tumor DNA detected: RET (n = 6; 36% of all fusions detected), FGFR3 (n = 2; 27%), ALK (n = 10, 23%), NTRK1 (n = 3; 7%), ROS1 (n = 2; 5%), and FGFR2 (n = 1; 2%). Relative to nonfusion variants detected, fusions were more likely to be subclonal (odds ratio, 8.2; 95% CI, 2.94 to 23.00; P < .001). Mutations associated with a previously reported anti-epidermal growth factor receptor (anti-EGFR) therapy resistance signature (subclonal RAS and EGFR mutations) were found with fusions in FGFR3 (10 of 12 patients), RET (nine of 16 patients), and ALK (seven of 10 patients). For the 27 patients with available clinical histories, 21 (78%) had EGFR monoclonal antibody treatment before fusion detection.

CONCLUSION

Diverse and potentially actionable fusions can be detected using a circulating tumor DNA assay in patients with advanced colorectal cancer. Distribution of coexisting subclonal mutations in EGFR, KRAS, and NRAS in a subset of the patients with fusion-present colorectal cancer suggests that these fusions may arise as a novel mechanism of resistance to anti-EGFR therapies in patients with metastatic colorectal cancer.

A rare presentation of carcinosarcoma of the bone in a young female; response with gemcitabine and docetaxel

Background

Sarcomatoid carcinoma, or carcinosarcoma, is a neoplasm that contains both sarcomatous and carcinomatous elements. It is an extremely rare cancer most often arising from visceral organs. Here we report the seventh documented de novo case of carcinosarcoma of the bone, in a young female who showed initial clinical improvement with gemcitabine and docetaxel.

Case presentation

A 36-year-old Caucasian female presented with diffuse musculoskeletal pain that had progressed from her shoulder to her back, arm, and knee over 6 months. Imaging revealed diffuse sclerotic lesions of bilateral humeral heads, iliac and ischial bones, and thoracic and lumbar spine. Histopathologic examination of biopsies from the T9 vertebra and left femur showed mainly sarcomatous spindle cells with focal osteoid production. Immunostaining showed the cells to be OSCAR cytokeratin, patchy positive for pankeratin, and negative for CK7, GATA3, S100, SOX10, CD99, EMA, AE1/AE3, and HMW keratin indicative of an epithelial origin. After thorough clinical correlation, sarcomatoid carcinoma of a visceral organ was excluded and the diagnosis of primary sarcomatoid carcinoma of the bone was ultimately favored. She received chemotherapy with gemcitabine and docetaxel, and showed improvement at 6 months but ultimately passed 1 year post diagnosis.

Conclusions

Primary carcinosarcoma of the bone is an extremely rare malignancy. Early diagnosis is crucial as localized disease may be curable with resection. As shown in this case, combination chemotherapy with gemcitabine and docetaxel is a potential option in patients with unresectable or metastatic disease.

Identifying anti-EGFR (EGFRi) response subgroups using evidence of ctDNA selective pressure

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Background: Metastatic colorectal cancers (mCRC) that respond to EGFRi display a robust circulating tumor DNA (ctDNA) signature that reflects selective pressure and clonal evolution. Conversely, non-responding tumors do not exhibit this signature. On this basis, we developed a novel method that defines EGFRi sensitivity with improved biological confidence with fewer patients (pts), and does not rely on clinical trial outcomes where responses may be confounded by concurrent chemotherapy. We used this method to further elucidate the association of several features that have been previously reported to be associated with EGFRi resistance, namely tumor sidedness, BRAF, PIK3CA, or ERBB2 ( HER2) MTs, and the absence of APC/ TP53MT. Methods: We analyzed 112 pts with baseline tissue based RASWT mCRC who had progressed following EGFRi, and with plasma samples available for ctDNA sequencing using a blood based NGS assay. Using our previously validated EGFRi exposure signature, we identified pts with evidence of selective pressure. Results: Post EGFRi ctDNA found 37% and 33% of pts with left sided and transverse tumors displayed evidence of selective pressure, respectively. 0 pts with right sided tumors displayed evidence of selective pressure; p= 0.01. Similarly, BRAFV600EMT displayed no evidence of selective pressure vs 30% of WT pts; in contrast, selective pressure was evident in pts with PIK3CAMT, ERBB2MT and pts with absence of APC/TP53MT (42% vs 28%, 67% vs 28%, 24% vs 43%, respectively for MT vs WT, p= NS for all). BRAF, PIK3CA, ERBB2, and APC/TP53 MT were present in 4/117, 12/108, 3/118 and 30/91 pts, respectively. ctDNA shedding was similar for all subgroups, as was time from previous EGFRi, indicating that these factors were not confounders. Conclusions: Consistent with prior large randomized studies, no pts with right sided tumors or BRAFMT had evidence of biologic benefit as assessed by presence of selective pressure. In contrast a number of pts with transverse tumors, ERBB2MT, PIK3CAMT or absence of APC/TP53MT had evidence of EGFR selective pressure, confirming that these are not absolute predictors of EGFR resistance and suggesting a subset of these pts were deriving benefit from EGFR inhibition. This biology based approach has the potential to more efficiently evaluate biomarkers of targeted therapy in the future without reliance on large randomized datasets.

Exploring the genetic basis of Lynch-like syndrome through paired germline and tumor exome sequencing

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Background: Lynch-like syndrome (LLS) is characterized by a diagnosis of mismatch repair deficient (dMMR) malignancy where somatic bi-allelic mutations in canonical MMR pathway genes ( MLH1, MSH2, MSH6, PMS2) have been identified as the main cause. Yet, a substantial proportion of cases remain unexplained by MMR somatic bi-allelic events or germline mutations. We hypothesize that LLS cases with young-onset cancers carry cryptic germline alterations in other pathways. To explore this contribution, we performed analyses of the germline and tumor mutation landscapes in LLS patients diagnosed with dMMR cancers. Methods: 18 probands with young-onset (age <50 years) dMMR colorectal or uterine cancers were selected from a familial cancer registry. The absence of deleterious germline MMR mutation and/or somatic MLH1inactivation was confirmed by standard clinical testing. We performed whole-exome sequencing (Illumina HiSeq) of germline (peripheral blood) DNA. Variant calls, quality-control, allele-frequency filtering (<1% in reference cohorts), and in silicoannotation were performed using the GATK and polyphen/SIFT tools. Pathway analysis was performed using the DAVID suite. For 16 of 18 patients, targeted exon sequencing of 408 cancer-related genes was performed on paired tumor/normal tissue samples (Ion Torrent AmpliSeq) and analyzed with VarScan 2. Results: 237,055 rare germline variants were detected in our cohort. We enriched a subset of 758 variants with putative frameshift (45.1%), stop gain or loss (25%), or splice site alteration (29.9%). Pathway analysis of genes altered by this subset revealed excess events in DNA damage repair (e.g. ERCC5, POLM, POLN, EXO5) and mRNA splicing (e.g. SCAF1, SRSF4) pathways. Preliminary analysis of somatic mutations profiles shows frequent alteration of known drivers including APC(64%) and NOTCH1(36%). Conclusions: Our exploratory analysis provides novel evidence that LLS patients may harbor an excess of deleterious germline mutations in DNA damage repair- and mRNA splicing-related genes. Future studies will identify genes which are targeted by both germline and somatic mutation with the goal of nominating putative causal genes. Defining additional mechanisms of dMMR in LLS cancers may help to refine prevention strategies for (un)affected individuals.

A Type 1 Diabetes Genetic Risk Score Predicts Progression of Islet Autoimmunity and Development of Type 1 Diabetes in Individuals at Risk

OBJECTIVE

We tested the ability of a type 1 diabetes (T1D) genetic risk score (GRS) to predict progression of islet autoimmunity and T1D in at-risk individuals.

RESEARCH DESIGN AND METHODS

We studied the 1,244 TrialNet Pathway to Prevention study participants (T1D patients' relatives without diabetes and with one or more positive autoantibodies) who were genotyped with Illumina ImmunoChip (median [range] age at initial autoantibody determination 11.1 years [1.2-51.8], 48% male, 80.5% non-Hispanic white, median follow-up 5.4 years). Of 291 participants with a single positive autoantibody at screening, 157 converted to multiple autoantibody positivity and 55 developed diabetes. Of 953 participants with multiple positive autoantibodies at screening, 419 developed diabetes. We calculated the T1D GRS from 30 T1D-associated single nucleotide polymorphisms. We used multivariable Cox regression models, time-dependent receiver operating characteristic curves, and area under the curve (AUC) measures to evaluate prognostic utility of T1D GRS, age, sex, Diabetes Prevention Trial-Type 1 (DPT-1) Risk Score, positive autoantibody number or type, HLA DR3/DR4-DQ8 status, and race/ethnicity. We used recursive partitioning analyses to identify cut points in continuous variables.

RESULTS

Higher T1D GRS significantly increased the rate of progression to T1D adjusting for DPT-1 Risk Score, age, number of positive autoantibodies, sex, and ethnicity (hazard ratio [HR] 1.29 for a 0.05 increase, 95% CI 1.06-1.6; P = 0.011). Progression to T1D was best predicted by a combined model with GRS, number of positive autoantibodies, DPT-1 Risk Score, and age (7-year time-integrated AUC = 0.79, 5-year AUC = 0.73). Higher GRS was significantly associated with increased progression rate from single to multiple positive autoantibodies after adjusting for age, autoantibody type, ethnicity, and sex (HR 2.27 for GRS >0.295, 95% CI 1.47-3.51; P = 0.0002).

CONCLUSIONS

The T1D GRS independently predicts progression to T1D and improves prediction along T1D stages in autoantibody-positive relatives.

Impact of microsatellite instability (MSI) on tumor clonal evolution in metastatic colorectal cancer (mCRC)

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Background: For mCRC, the contribution of clinical and pathologic factors to concordance between formalin-fixed, paraffin-embedded (FFPE) tissue-based and ctDNA-based mutation profiling remains unclear. MSI is hypothesized to confer a higher rate of somatic alteration resulting in clonal evolution over time compared to microsatellite stable (MSS) patients, but this has not been previously confirmed. Methods: All mCRC patients were consented for a prospective genomic matching protocol (Assessment of Targeted Therapies Against Colorectal Cancer [ATTACC]) using CLIA-certified platforms. Archived tumor DNA from primary or metastatic tissue was sequenced on a 46- or 50-gene panel (Ion Torrent). Paired ctDNA samples were isolated from blood and sequenced with an ultra high-sensitivity assay (Guardant360). Mutation data were normalized by excluding genomic regions not covered on both platforms and were filtered to remove germline or synonymous variants. Results: An initial cohort of 139 patients was included in our analyses, with a median of two lines of intervening chemotherapy between FFPE and plasma DNA collection; 6 (4.3%) of the patients had MSI (MSI-H) mCRC. We detected 472 total mutations in either tissue or ctDNA, with a global concordance rate of 34.5%. Global concordance was not associated with tissue source, nor treatment with specific standard cytotoxic and/or biologic agents. Mutations detected in MSI-H CRC showed significantly greater discordance compared to MSS CRC (OR = 2.5, p = 0.025). This finding was validated using an independent cohort of 17 MSI-H mCRC patients (OR = 2.78, p = 0.00015). Among recurrently altered genes, we found that MSI-H cases were significantly more likely to have gained new TP53 mutations (OR = 8.17, p = 0.001) and to have lost PIK3CA mutations (OR = 8.04, p = 0.036) in ctDNA compared to MSS cases. Conclusions: MSI correlates with discordance between tissue DNA and ctDNA-based mutation profiling, which suggests that MSI-H CRC undergoes distinct patterns of clonal evolution including acquisition of new TP53 mutations. This may have implications for targeted and immunologic therapies in this unique population, and suggests a utility for repeated molecular testing.