bluuebunny/crossref_metadata_2025 huggingface dataset:
Identification of mutation biomarkers underpinning colon cancer sidedness and cetuximab sensitivity.
Authors: Yeatman Timothy Joseph , Yang Mingli , Schell Michael J. , Loboda Andrey , Nebozhyn Michael , Li Jiannong , Teer Jamie K. , Rocha Lima Caio Max S. , Pledger Jack
Published: January 2019

629

Background: Currently, extended RAS testing ( KRAS/ NRAS) in colorectal cancer (CRC) patients identifies only non-responders to EGFR inhibitor (EGFRi) therapies, and accurate prediction of drug-sensitive subpopulations remains problematic in patients, even with wild-type RAS. Moreover, the molecular basis for the laterality of anti-EGFR sensitivity is poorly understood. Methods: 468 CRCs were analyzed by global gene expression analysis, DNA sequencing (1321 cancer related genes) and MSI analysis. Tumors were stratified by a validated gene expression cetuximab sensitivity (CTX-S) score, and then correlated with identified high frequency mutations, resulting in a ranking of CTX-S score-associated mutated genes (see Table). Results: Ranking analysis revealed MSI-H status and KRAS mutation as the most negatively-correlated among all patients and MSS patients, respectively. Conversely, APC and TP53 were the most highly positively-correlated mutant genes in both all patient- and MSS-cases. Deeper analysis revealed that the combination of mutant APC + TP53 ( A + P) was more common in left vs. right CRCs (52% vs 21%), and even more pronounced in MSS vs MSI cases (47% vs 2%). CTX-S scores were highest in mutant A + P patients with WT RAS, but surprisingly, were nearly as high in mutant A + P patients with mutant RAS. CRC PDX models validated these results with a favorable CR/PR/SD vs PD association. Conclusions: Here we report the discovery of a cooperative role of APC and TP53 mutations in identifying EGFRi-sensitive CRC subpopulations. Our data suggest that addition of the routine sequencing of APC and TP53 to extended RAS testing may expand the EGFRi therapeutic opportunity (by up to 25%), regardless of RAS mutation status. [Table: see text]
ColotypeR: A tool to classify colon cancers by consensus molecular subtype and subtype-specific risk of recurrence.
Authors: Buechler Steven Allen , Badve Sunil S. , Gokmen-Polar Yesim , Herring Emily , Ludwig Katelyn , Hummon Amanda
Published: January 2019

632

Background: Colon cancer is highly heterogeneous in prognosis and response to treatment. The consensus molecular subtypes (CMS1-4, and mixed) partition colon cancers into distinct groups. CMS4 tumors, a mesenchymal subtype, have the worst prognosis and poor response to standard chemotherapies. There is a critical need for accurate molecular subtyping, and subtype-specific management. Methods: Affymetrix microarrays colon cancer datasets (N = 813; GSE39582, GSE14333) were partitioned into training (AT; N = 370) and validation sets (AV; N = 443) balanced for clinical traits. A novel multistate gene methodology was used to predict CMS, and prognosticate subtype-specific relapse-free survival (RFS) in the training set. Accuracy of CMS prediction and prognostic significance was validated in the AV and TCGA colon cancer (COAD; N = 458) sets. Results: In the training set, a 20-gene panel (ColotypeR-CMS) predicts CMS subtype. Mean accuracy for CMS1-4 prediction was 0.87 in AV and 0.81 in COAD. In AV, 5-year RFS is 0.52 (95%CI 0.43 – 0.63) in the predicted CMS4, and 0.70 (95%CI 0.65 – 0.77) in the non-CMS4 samples. The risk of relapse for non-CMS4 samples was refined by a genomic score (ColotypeR-Risk) computed using expression of 25 genes in the training set. ColotypeR-Risk was prognostic of RFS (p = 0.0004) among the AV non-CMS4 samples, and also prognostic (p = 0.0001) among the stage II non-CMS4 AV samples not treated with chemotherapy. The prognostic significance of ColotypeR-Risk among non-CMS4 samples is independent of tumor location (right or left) and CMS subtype (CMS1-3 or mixed). ColotypeR-Risk was also prognostic of RFS in non-CMS4 samples in COAD (p = 0.005). Conclusions: ColotypeR identifies the consensus molecular subtypes (CMS1, CMS2, CMS3, CMS4, or mixed), and assesses subtype-specific risk of recurrence of colon cancer. ColotypeR identifies prognostic risk and molecular features that could help guide the management of colon cancer patients.
Initial therapy with FOLFOXIRI plus bevacizumab (bev) for RAS mutant metastatic colorectal cancer (mCRC) and gene mutations in circulating tumor DNA (ctDNA) as a predictive marker for the efficacy: JACCRO CC-11.
Authors: Sunakawa Yu , Satake Hironaga , Usher Joshua L. , Jaimes Yolanda S , Miyamoto Yuji , Nakamura Masato , Nakayama Hiroshi , Sugano Nobuhiro , Takagane Akinori , Gotoh Masahiro , Watanabe Takanori , Ishigure Kiyoshi , Tanaka Chihiro , Takeuchi Masahiro , Fujii Masashi , DANENBERG KATHLEEN , Lenz Heinz-Josef , Sekikawa Takashi , Ichikawa Wataru
Published: January 2019

635

Background: We have reported that modified (m)-FOLFOXIRI plus bev was feasible and had a good objective response rate (ORR) for Japanese patients (pts) in a phase II trial of the JACCRO CC-11 (ESMO 2017 #543P). In addition, a pre-planned research was performed to investigate if the change of gene mutations in ctDNA during therapy can serve as a predictor for clinical outcomes in RAS mutant mCRC. Methods: The efficacy of m-FOLFOXIRI (irinotecan 150 mg/m², oxaliplatin 85 mg/m², levofolinate 200 mg/m², and fluorouracil 2400 mg/m² repeated biweekly) plus bev was evaluated prospectively in 62 pts (median age 63, 55% male, 92% PS0, and 27% right-sided tumors) with mCRC harboring RAS mutation (mt). The primary endpoint was ORR. Progression-free survival (PFS), overall survival, early tumor shrinkage (ETS), depth of response (DpR), and safety were secondary endpoints. Plasma samples for extraction of ctDNA were collected at 3 points (pre-, 8w, and progression) and analyzed for specific KRAS, NRAS, BRAF, and PIK3CA variants with real-time PCR assays. Results: Updated median follow-up time was 10.2 months. ORR and disease control rate were 75.8% and 96.8%, respectively. ETS was 73.8%, and median DpR was 49.6%. Median PFS was 11.5 months (95%CI 9.5-14.0). KRAS/ NRAS mt from pre-treatment plasma was confirmed in 79% of pts. In 41 pts with RAS mt at pre-treatment, mt status at 8 weeks predicted clinical outcomes (Table). Moreover, combined assessment of mt in ctDNA and ETS served as a refined predictor for efficacy. Pts with PIK3CA mt at pre-treatment had a poor outcome (ORR, 43%; median PFS, 8.8 months). Conclusions: FOLFOXIRI plus bev regimen is active for RAS mutant mCRC. RAS mt in ctDNA and ETS evaluation might potentially be a useful on-treatment biomarker in mCRC pts with RAS mt. Clinical trial information: UMIN000015152. [Table: see text]
Histopathologic response and growth patterns of colorectal cancer liver metastases (CRCLM) in patients treated with triplets plus bevacizumab (bev) or anti-EGFRs.
Authors: Marmorino Federica , Cremolini Chiara , Pietrantonio Filippo , Pellegrinelli Alessio , Zucchelli Gemma , Loupakis Fotios , Lonardi Sara , Aprile Giuseppe , Morano Federica , Prisciandaro Michele , Masi Gianluca , Mennitto Alessia , Bergamo Francesca , Cardellino Giovanni Gerardo , Fassan Matteo , Casagrande Mariaelena , Milione Massimo , Fontanini Gabriella , de Braud Filippo , Falcone Alfredo
Published: January 2019

636

Background: The histopathological response to pre-operative chemotherapy is associated with clinical outcome in patients (pts) undergoing secondary resection of CRCLM. Three different histopathological growth patterns (HGPs) of CRCLM have been described: desmoplastic (i.e. with a capsule of stroma separating tumor and normal cells), pushing (i.e. with limited infiltration of normal hepatic plates by tumor cells) and replacement (i.e. with abundant infiltration of normal hepatic plates by tumor cells and vessel cooption). Methods: Histopathological parameters of response were evaluated in specimens from 159 pts who underwent secondary resection of CRCLM, after receiving triplet (FOLFOXIRI or COI) plus bev (N = 103) or anti-EGFR (N = 56) in 5 first-line clinical studies (TRIBE, MOMA, MACBETH, COI-B and COI-E). The aims of this analysis were to evaluate the prognostic role of histopathologic response and to investigate the prognostic role of HGPs and their potential different sensitivity to targeted agents. Results: When compared with partial (TRG 3) and no (TRG 4-5) pathologic response (N = 118), major response (TRG 1-2, N = 41) was associated with longer RFS (mRFS: 28.0 versus 11.0 mos, HR = 0.57, 95%CI = 0.39–0.86; p = 0.007) and OS (mOS: unreached versus 42.1 mos, HR = 0.54, 95%CI = 0.31-0.93; p = 0.027). No association of baseline clinical characteristics and RAS and BRAF status with major response was found. Major response was more frequent among pts treated with bev than with anti-EGFRs (OR = 2.83, 95%CI = 1.20–6.65; p = 0.015) and was associated with deepness of response as a continuous variable (HR = 1.02, 95% CI = 1.00–1.04; p = 0.011). In the desmoplastic HGP (N = 28) a higher percentage of major response was reported (57% vs 17% in pushing and 22% in replacement HGP, p < 0.001) and a numerical advantage from anti-EGFR vs bev was evident in terms of both major response and RFS. Conversely, in the pushing HGP (N = 66) a significant benefit from bev vs anti-EGFR in major response and RFS was observed. No difference was described in the replacement HGP (N = 65). Conclusions: The assessment of HGPs may be useful to predict benefit from available targeted agents.
Association of RAS mutations with race in metastatic colorectal cancer: CALGB/SWOG 80405 (ALLIANCE).
Authors: Sehdev Amikar , Niedzwiecki Donna , Venook Alan P. , Lenz Heinz-Josef , Innocenti Federico , Mahoney Michelle R. , Shaw James Edward , Polite Blase N. , Hochster Howard S. , Atkins James Norman , Goldberg Richard , Mayer Robert J. , Schilsky Richard L. , Bertagnolli Monica M. , Blanke Charles David , O'Neil Bert H. ,   Cancer and Leukemia Group B (Alliance) and SWOG
Published: January 2019

638

Background: Colorectal cancer (CRC) is a heterogeneous disease with distinct molecular subtypes in part based on RAS mutational status. It is plausible that RAS mutations are differentially distributed between CC and AA and may contribute to poor outcomes in AAs with CRC. Methods: We did a retrospective analysis of CALGB/SWOG 80405 trial patients. We divided the entire cohort into 2 groups: a) Common RAS: mutation in KRAS exon 2, codon 12 or 13; b) Extended RAS: any NRAS mutations or mutation in KRAS except those listed above. We then analyzed these two subgroups for association between RAS mutations and race (3 categories: Caucasian, AA, Others) using chi-square test for univariate analyses and logistic regression for multivariate analysis. We also analyzed the effect of extended RAS testing on prognosis of metastatic CRC by estimating the overall survival (OS) using Kaplan-Meier method and 95% confidence interval (CI). Cox proportional-hazard model was used for multivariate analyses. Results: There were 1729 CRC patients in common RAS group of which 357 (20.6%) had mutations present. Extended RAS group had 621 patients of which 95 (15.5%) had mutations present. There was no significant difference in the rate of common RAS mutations between CC and AA (20.5% vs. 24%, p=0.22). However, extended RAS mutations were significantly more in AA as compared to CC (25% vs. 14%, p=0.02). Multivariate analysis adjusted for age, gender, prior adjuvant chemotherapy and pelvic radiation confirmed higher odds of extended RAS mutation in AA compared to CC (adjusted OR 1.12; 95% CI 1.01-1.23; p=0.02). The median OS in patients with an extended RAS mutation was shorter as compared to those without extended RAS mutation (25.3 vs. 31.9 months; HR 1.26; 95% CI 0.99-1.62; p=0.05). Multivariate analyses adjusted for age, gender, race, prior adjuvant chemotherapy and pelvic radiation showed a trend towards longer OS in patients without extended RAS mutation as compared those with extended RAS mutation (adjusted HR= 1.24, 95% CI, 0.97-0.1.58, p=0.08). Conclusions: Extended RAS mutations are significantly more common in AA as compared to CC. Additionally, presence of extended RAS mutation may confer a poor prognosis in CRC patients.
Clinical prognostic score of BRAF V600E mutated (BM) metastatic colorectal cancer (mCRC): Results from the “BRAF, BeCool” platform.
Authors: Intini Rossana , Loupakis Fotios , Cremolini Chiara , Sartore-Bianchi Andrea , Pietrantonio Filippo , Pella Nicoletta , Santini Daniele , Rimassa Lorenza , Formica Vincenzo , Calvetti Lorenzo , Salvatore Lisa , Antonuzzo Lorenzo , De Luca Emmanuele , Morano Federica , Tosi Federica , Moretto Roberto , Fassan Matteo , De Maglio Giovanna , Zagonel Vittorina , Di Maio Massimo
Published: January 2019

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Background: BM mCRCs account around 10% of mCRCs, with a dismal prognosis. Intra-group heterogeneity has been recently studied, however, an extensive prognostic clinical analysis has not been provided yet. Methods: BM mCRCs tested on primary tumor (T) or on metastases (mets) were collected from 13 Italian Oncology Units. A prognostic score was derived by an internal cross-validation procedure: the whole population was splitted in a training (67%) and in a testing (33%) sample; this process was repeated 10 times. Primary endpoint was OS. Multivariate analysis (MA) was performed on each training sample, and covariates with independent prognostic value were included in the scoring system, assigning rounded scores to the covariates. Results: A total of 395 BM mCRC patients were included. At MA, independent prognosticators for OS were ECOG PS (1 vs 0; 2-3 vs 0), Ca19.9 (high vs normal); LDH (≥300 vs low); neutrophil/lymphocyte ratio ( > 3 vs low); T grading (3-4 vs 1-2); liver mets (yes vs no); lung mets (yes vs no); lymphnode mets (yes vs no). Two different scoring systems were built: a «complete» score (0-18) with all significant covariates; a «simplified» score (0-11), selecting only significant clinico-pathological covariates, excluding laboratory values. With «complete» score, proportion of patients with low (0-4), intermediate (5-8) and high (9-18) score was 39%, 46% and 15%, respectively. Median OS was 27.6, 18.7 (HR interm. vs low 1.89, 95%CI 1.25 – 2.86, p = 0.003) and 6.6 months (HR high vs low 4.95, 95%CI 2.89 – 8.47, p < 0.0001), respectively. Similar results were observed adjusting for type of first-line treatment. Median PFS was 11.1, 8.6 (HR interm. vs low 1.36, 95%CI 0.94 – 1.97, p = 0.11) and 4.1 months (HR high vs low 3.50, 95%CI 1.98 – 6.20, p < 0.0001). Similar results were obtained with the «simplified» score. Conclusions: A simple and ready-to-use prognostic score for BM mCRC was developed. The robustness of the internal cross-validation justifies the effort of a validation study. Identification of specific prognostic factors in distinct molecular subgroups is crucial for adjusting exploratory translational analyses and future clinical trial design.
A pilot case control study: Could a gastric cancer risk screening tool help identify high risk patients for endoscopic screening in the United States?
Authors: In Haejin , Langdon-Embry Marisa , Gordon Lauren , Wylie-Rosett Judith , Schechter Clyde , Castle Philip , Kemeny Margaret , Rapkin Bruce D.
Published: January 2019

64

Background: Gastric cancer incidence varies greatly among US racial/ethnic groups. Few studies have examined ethnicity, birth country, immigration and cultural diet as gastric cancer risk factors in the US. These factors, in combination with known risk factors may narrow a target population for gastric cancer screening. Methods: Two racially diverse hospital systems were used to recruit gastric cancer cases using the cancer registry, and primary care (PC) controls from waiting rooms or phone. Community controls were recruited at community gatherings. Participants were eligible if 40-85 years old, not under endoscopic surveillance and without genetic syndromes. The survey items (n = 227) included conventional risk factors, plus items about ethnicity, birth country, acculturation, and ethnic diet. Results: Of 150 participants, 39 cases, 41 PC-controls, and 44 community controls were eligible for analysis. PC-controls generally completed phone interviews (72% vs 28%), while community controls generally completed paper surveys (92% vs 8%). Gastric cancer cases were more likely to be foreign born (85% vs. 49%, p = < 0.01), from a country with gastric cancer incidence > 5 per 100,000: (62% vs. 30%, p = < 0.01) and report daily consumption of cultural food at ages 15 to 18 (69% vs. 35%, p = < 0.01) compared to controls. Cases were also older, male, Hispanic, and had stronger family history of gastric cancer. Cases and controls had similar frequency of alcohol consumption, smoking, acculturation, and barbequed food consumption. In multivariate analysis, increased age (per year, aOR 1.4, 95%CI 1.07-1.21), daily consumption of cultural foods at ages 15 to 18 (aOR 19.58, 95%CI 1.54-248.99), having less than high school education (aOR 7.24, 95%CI 1.49-35.10), and being foreign born (aOR 11.81, 95%CI 1.69-82.64) were associated with case status. Conclusions: A risk assessment tool that addresses awareness of gastric cancer risk factors, ethnicity, cultural habits and immigration patterns has potential to identify high-risk persons from multicultural areas within the US, who might benefit from endoscopic screening for gastric cancer. (Support: UG1CA189823)
Serial monitoring of ctDNA to highlight mutation profiles in colorectal cancer.
Authors: Loree Jonathan M. , Strickler John H. , Pereira Allan Andresson Lima , Lam Michael , Raghav Kanwal Pratap Singh , Morris Van Karlyle , Menter David , Banks Kimberly , Nagy Rebecca J , Raymond Victoria , Overman Michael J. , Talasaz AmirAli , Lanman Richard B. , Kopetz Scott
Published: January 2019

641

Background: Circulating tumor DNA (ctDNA) represents an ideal platform to obtain the most current genomic profile of a patient’s tumor. We aimed to investigate how stable these profiles remain during serial ctDNA assays in metastatic colorectal cancer (mCRC). Methods: In 77 patients (pts) with mCRC and serial Guardant360 assays with a detectable mutation (mt), we compared mt stability by assessing whether variants were gained/lost between serial assays and changes in relative mutant allele frequency (rMAF). rMAF of a mt was defined as (mt allele frequency / mt present at the maximum allele frequency in that assay). rMAF results were normalized to detected ctDNA concentration changes between assays to ensure changes in rMAF were not due to changes in ctDNA concentration. MAPK pathway mutations were defined as RAS, BRAF, EGFR, KIT, or MET mutations. Results: Of 77 pts, 64 (83%) had 2 serial assays and 13 (16.9%) had 3 or 4 assays performed. Serial assays occurred an average of 138 days apart (+/- SD of 111 days). Only 13/77 (17%) pts had no change in the number of mts detected between assays. A new mt was detected in 42/77 (55%) pts, while 43/77 (56%) lost a previously detected mt. Of 52 mts detected in patients with > 2 assays, 16 (31%) were gained and subsequently lost. After controlling for ctDNA concentration, mts were equally likely to have an increasing (129/308 – 42%) or decreasing (150/308 – 49%) allele frequency. Potentially clinically relevant MAPK variants were gained/lost in 29% of patients; though MAPK mts developed in a large number of pts (16/77 – 21%), many pts also lost MAPK mts (9/77 – 12%), showing ongoing subclonal dynamics. Median time between assays did not differ between pts with gain/lost mts or stable mt profiles (P = 0.73), however mt rMAF shift of > 25% was more common if assays were > 90 days apart (OR 4.3, P < 0.0001). Conclusions: Serial ctDNA assays demonstrate ongoing mutational changes in mCRC, with emergence/disappearance of MAPK variants being more common than expansion of a pre-existing clone. Our results suggest repeated sampling may be important to optimize selection of targeted therapies at each regimen alteration.
Survival outcome in HER2-amplified metastatic colorectal cancer (mCRC).
Authors: Sawada Kentaro , Okamoto Wataru , Nakamura Yoshiaki , Yamanaka Takeharu , Yuki Satoshi , Yoshino Takayuki , Komatsu Yoshito , Sakamoto Naoya , Fujii Satoshi
Published: January 2019

642

Background: HER2 amplifications have been observed in approximately 3% of patients (pts) with metastatic colorectal cancer (mCRC). Early clinical trials with combined HER2-targeted therapies showed promising activities. However, it remains unclear whether HER2 amplification in mCRC is as prognostic as RAS or BRAF V600E mutant (mt). We aimed to evaluate survival outcome for mCRC pts with HER2 amplification compared to those with RAS or BRAF mt. Methods: mCRC pts who received a palliative resection of the primary tumor with metastatic diseases at presentation, or recurred after curative resection of the primary tumor between 2005 and 2015, were analyzed. HER2 immunohistochemistry (IHC) was performed using formalin-fixed and paraffin-embedded (FFPE) sections obtained from the primary tumor, and HER2 amplification was confirmed by fluorescence in situ hybridization (FISH) in case of IHC 2+ or 3+. Criteria for HER2 amplification were a HER2- to CEP17- signal ratio of 2.0 or higher. RAS / BRAF status was centrally assessed by a PCR-based method. The pts were classified into four subgroups based on RAS, BRAF and HER2 status: Group R , RAS mt; Group B, BRAF V600E mt; Group H, HER2 amplification with RAS / BRAF wild-type (wt); and Group W, RAS / BRAF wt. Results: Among 370 pts, 359 pts (97%) were successfully analyzed. A total of 15 pts (4%) had HER2 amplifications, out of which four pts had overlapped RAS mt (subclassified as Group R). RAS or BRAF mutations are mutually exclusive. The number in Group R, B, H and W was 204 (57%), 13 (4%), 11 (3%) and 131 (36%), respectively. There was no remarkable difference in baseline characteristics among groups. With a median follow-up time of 63 months (mos), the median overall survival of the 359 pts was 27 mos (95%CI 24 - 29 mos); Group R, 24 mos; Group B, 14 mos; Group H, 20 mos; and Group W, 39 mos. The HR of R vs. H is 0.83 (95%CI 0.41-1.70, p= 0.618), B vs. H is 1.16 (95%CI 0.47-2.84, p= 0.748), and W vs. H is 0.52 (95%CI 0.25-1.08, p= 0.080), respectively. Conclusions: This study suggests that the prognosis of mCRC pts with HER2 amplification tends to be worse as compared to those with RAS / BRAF wt, similar to those with RAS mt, and better than those with BRAF mt, although these comparisons were not statistical significant.
Polymorphism in cancer-associated fibroblasts (CAFs) related genes and clinical outcome in metastatic colorectal cancer (mCRC) patients (pts) enrolled in two independent randomized phase III trials: TRIBE and FIRE-3.
Authors: Puccini Alberto , Berger Martin D. , Tokunaga Ryuma , Naseem Madiha , BATTAGLIN FRANCESCA , Cao Shu , Millstein Joshua , Soni Shivani , McSkane Michelle , Zhang Wu , Loupakis Fotios , Stintzing Sebastian , Heinemann Volker , Falcone Alfredo , Lenz Heinz-Josef
Published: January 2019

645

Background: Tumor microenvironment plays a critical role for CRC development and progression. CAFs are the most dominant cellular components which orchestrate tumor cell proliferation, survival and invasion and have been shown to be associated with prognosis in pts with CRC. We aimed to evaluate whether single-nucleotide polymorphisms (SNPs) in CAFs related genes predict outcome in mCRC pts treated with first-line FOLFIRI/bevacizumab (bev) in TRIBE and FIRE-3 trials. Methods: The OncoArray, a custom array by Illumina including 530K SNP markers, was used to genotype genomic DNA from blood samples and served as our database, from which 15 functional SNPs within 9 genes (OPN, CD44, TCN, CD63, TIMP1, SLIT2, ROBO1, LOXL2, INHBA) related to CAF pathway were analyzed. Results: A total of 451 pts were included. Those treated with FOLFIRI/bev in TRIBE (N = 215, median PFS/OS: 9.7/26.3 months (mts)) and FIRE-3 (N = 107, median PFS/OS: 11.6/31.5 mts) served as discovery and validation cohorts respectively, while FIRE-3 FOLFIRI/cetuximab arm (N = 129, median PFS/OS: 12.8/49.8 mts) was used as the control. In overall pts in discovery set, OPN (osteopontin) rs11728697 any C variants showed longer PFS (median 10.8 vs 9.0 mts; HR = 0.68, 95%CI = 0.49-0.95; p = 0.025) and OS (median 30.6 vs 23.8 mts; HR = 0.69, 95%CI = 0.50-0.95; p = 0.025) than the homozygous wild type genotype (T/T) in multivariable analysis. These data were validated in the FIRE-3 cohort in OS both in univariate (median 49.3 vs 23.7 mts; HR = 0.40, 95%CI = 0.21-0.77; p < 0.001) and in multivariable analyses (HR = 0.31, 95%CI = 0.16-0.60; p < 0.001). However, the favorable impact on outcome was not shown among C allele carriers treated with FOLFIRI/cetuximab in the control arm. Conclusions: Our findings confirm that CAFs play a crucial role in mCRC and suggest that OPN polymorphisms could serve as predictive biomarkers for mCRC pts treated with first-line FOLFIRI/bev.
Genetic variants in methylation and demethylation pathways to predict clinical outcome in metastatic colorectal cancer (mCRC) patients (pts) treated with first-line FOLFIRI/Bev: Data from TRIBE and FIRE-3 trials.
Authors: Puccini Alberto , Loupakis Fotios , Stintzing Sebastian , Berger Martin D. , Tokunaga Ryuma , Naseem Madiha , BATTAGLIN FRANCESCA , Cao Shu , Millstein Joshua , Soni Shivani , McSkane Michelle , Zhang Wu , Heinemann Volker , Falcone Alfredo , Lenz Heinz-Josef
Published: January 2019

646

Background: DNA hypermethylation in CpG islands (CIMP) has been shown to promote CRC by silencing the expression of tumor suppressor genes. However, global DNA hypomethylation is now considered a common characteristic of CRC. A new family of genes (TET) has been shown to play a crucial role in actively demethylating the DNA. We explored whether genetic polymorphisms in the genes which promote DNA methylation and demethylation are associated with outcome in pts enrolled in TRIBE and FIRE-3 trials. Methods: Genomic DNA from blood samples was genotyped through the OncoArray, a custom array by Illumina including 530K SNP markers. 17 functional SNPs within 11 genes related to methylation (DNMT1/3A/3B, MDM2) and demethylation pathways (TET1/2/3, IDH1/2, MBD4, TDG) were analyzed. Results: A total of 451 pts were included. FOLFIRI/bevacizumab (bev) arms from TRIBE (N = 215, median PFS/OS: 9.7/26.3 months (mts)) and FIRE3 (N = 107, median PFS/OS: 11.6/31.5 mts) served as discovery and validation cohorts respectively. FIRE-3 FOLFIRI/cetuximab arm (N = 129, median OFS/OS: 12.8/49.8 mts) served as control. In the discovery cohort, overall pts carrying TET1 rs3814177 C/C variant showed lower response rate (RR) (42.1% vs 61.8%, p = 0.026) and shorter median PFS (9.5 vs 10.3 mts; HR = 1.54, 95%CI = 1.04-2.27; p = 0.024, univariate analysis) compare to those with any T allele. The effect was more significant among KRAS mutant pts in RR (21.4% vs 60.8%, p = 0.007) and median PFS (8.6 vs 9.5 mts) both in univariate (HR = 2.00, 95%CI = 1.07-3.73; p = 0.020) and multivariable analysis (HR = 2.01, 95%CI = 1.03-3.92 p = 0.041). These findings were validated in overall pts in FIRE-3 cohort in median OS both in univariate (23.7 vs 41.9 mts; HR = 2.08, 95%CI = 1.07-4.05; p = 0.023), and multivariable analysis (HR = 2.36, 95%CI = 1.15-4.81; p = 0.019). No significant association was observed in the control arm. Conclusions: Our results provide the first evidence that TET1 polymorphism may be used as a predictive biomarker in mCRC pts treated with FOLFIRI/bev. Therefore, TET enzymes could serve as promising new treatment targets for mCRC pts.
DNA damage repair (DDR) pathway defects in gastrointestinal (GI) malignancies.
Authors: Thota Ramya , Fulde Gail , Lewis Mark Andrew , Haslem Derrick S. , Nadauld Lincoln , Moulton Bryce , Romero Robin , Abraham Tyler , Christensen Bryce , Raghunath Sharanya , Barker Tyler
Published: January 2019

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Background: The clinical significance of the genomic alterations associated with DDR pathway in GI tumors (besides MMR defects) is largely unknown. These patients can potentially derive benefit from targeted therapy with poly ADP ribose polymerase (PARP) inhibitors, which have already shown promising activity in ovarian, breast and prostate cancers. In this study, we investigated the frequency and clinical significance of DDR repair defects (other than MMR defects) in GI tumors. Methods: We performed a retrospective analysis of all patients who had tumor next generation sequencing performed between January 2013 and August 2017 on GI cancers harboring DDR pathway defects. Data including demographics, clinical history, and treatment were extracted from patients' records. Results: Of 299 patients with GI tumors sequenced, 35 cases (12%) were noted to have DDR defects. The most commonly mutated genes – 6 (17%) BRCA2, 5 (14%) PALB2, 4 (11%) ATM, 3 (8.6%) BRCA1, 2 (5.7%) each of NBN, MUTYH, ERCC3, PARP1 amplification and 1 (2.8%) each of ERCC2, CDK12, and PARP2 amplification. Two patients had both ATM and BRCA2 mutations. Combination of ATM and MRE11, ATM and BRCA1, BRCA1 and ERCC6, BRCA2 and CDK12 were noted in 1 patient each. Of the 23 patients with available clinical data, the median age at diagnosis was 65 (range 30–85) years with male and female prevalence rates of 60.8% and 39.2%, respectively. Stage at diagnosis was I (n = 3), II (n = 3), III (n = 8), and IV (n = 9). The primary site of tumor was found in 8 (34.8%) colon, 4 (17.4%) liver, 4 (17.4%) pancreas, 2 (8.7%) esophagus, 2 (8.7%) anus, 2 (8.7%) appendix, 1 (4.3%) rectum. Seventeen patients received platinum‐based therapy, 7 were treated with PARP inhibitors and 5 patients received both platinum and PARP inhibitor. Median overall survival from diagnosis for patients with stage I/II was 65.3 months, stage III was 23.1 months, and stage IV was 22.4 months. The median survival of patients treated with olaparib was 24.5 months. Conclusions: DDR pathway defects in GI tumors are uncommon. However, they can potentially be targeted with PARP inhibitors with durable survival. Future clinical trials are warranted to explore the role to PARP inhibitors in these unique subset of patients.
Assessment and prognostic impact of a new classification using HER2 and HER3 status in resected gastric cancer in a european cohort.
Authors: Martinez Lago Nieves , Abdulkader Ihab , Santamaria Dora Insua , Nuñez Patricia Viaño , Carrera Juan Jose , Antunez Lopez Jose Ramón , Padin Iruegas Maria Elena , López López Rafael
Published: January 2019

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Background: HER2 status is a predictive biomarker to response to trastuzumab in metastatic gastric adenocarcinomas. However, relatively little is known about the role of HER2 and HER3 in the non-metastatic disease in European population. Methods: Immunohistochemical expression of HER2 was analyzed using DAKO-HercepTest™ and gene amplification using DAKO-DuoCISH kit; both was scored according to published reports. HER3 expressión was analyzed using HER3 clon DAK-H3-ICHER3 and scored as follows: 0 = no staining, 1+ = light staining, 2+ = moderate staining, and 3+ = strong staining. Slides with score 0 or 1+ were classified as low expression or negative and slides with score 2-3+, as high expression or positive. According HER2 and HER3 status patients were classified into six subtypes: HER2-HER3 negative, HER2 equivocal expression HER3 negative, HER2 positive – HER3 negative, HER2 negative – HER3 positive, HER2 equivocal expression – HER3 positive and HER2-HER3 positive. The relationship between this classification and the clinicopathological characteristics and survival was analyzed retrospectively. Results: We included 106 patients between January 2007 and June 2014. The HER2 positivity was 13.2% and HER3 high expression was identified in 27.4% of patients. HER2 status was significantly associated with HER3 status (p = 0.018). HER2 equivocal or positive subtypes were associated with intestinal subtype (0.020) and HER2 or HER3 positive subtypes were associated with low histological grade (0.050). Our classification have demonstrated prognostic impact (p = 0.032) with a specific mortality rate due to gastric cancer of 45-50% for patients with equivocal or positive HER2 subtypes with HER3 low expression, 30% for patients with HER3 high expression independently of HER2 status, and 18% for patients HER2-HER3 negative. Conclusions: Our classification, using HER2 and HER3 status, stratifies patients into 6 subtypes with differentiated clinical and pathological characteristics and prognostic impact.
Impact of adyuvant chemotherapy treatment according to tumor primary location in colorectal cancer: Experience at University Hospital Ramon y Cajal (HURyC) Madrid.
Authors: Barquín García Arantzazu Martínez , Martinez Saez Olga , Corral de la Fuente Elena , Serrano Domingo Juan José , Martín Huertas Roberto , Villamayor Delgado Maria , Saavedra Serrano Cristina , Rodríguez Garrote Mercedes , Pachón Olmos Vanesa , Reguera Puertas Pablo , LONGO FEDERICO , Guillen Carmen , Carrato Alfredo , Ferreiro REYES
Published: January 2019

655

Background: Adyuvant chemotherapy is a unified therapeutic principle in colon cancer (CC). However, many prognostic factors are arising to determine who really benefits from adyuvant chemotherapy in order to avoid overtreatment. Primary tumor location of CC is emerging as an important prognostic factor owing to distinct biological features. However, there is hardly any evidence showing the benefit of treatment according to primary tumor location. Methods: We retrospectively included patients with stage II and III CC that underwent surgical resection between 2009 and 2014 HURyC. We performed a multivariable Cox model analysis to estimate the benefit of chemotherapy according to tumor location in terms of DFS and OS. The model was further adjusted by including the following confounders: ECOG-PS, number of removed nodes ( < 12 or ≥ 12), use of adyuvant chemotherapy and age. A covariate was considered a confounder factor if the difference between the adjusted and unadjusted coefficient of chemotherapy varied > 10%. Stata 13.1 was used to analyze the data. Results: 564 patients were identified (267 left sided and 297 right sided). The median follow-up of the entire cohort was 49 months. Globally, chemotherapy did not improve DFS neither in right sided or left sided CC (HR: 0.81, p: 0.58; HR 1.31, p: 0.4, respectively). As for OS, it was improved when adding chemotherapy in both sides (right sided CC HR 0.51, p: 0.061 and left sided CC HR 0.42, p: 0.009). By stages, chemotherapy did not improve DFS or OS according to tumor localization in stage II. In right sided stage III, there was a trend to improve both DFS and OS (HR: 0.54, p: 0.14; HR: 0.39, p: 0.1, respectively). In left sided stage III, there was a trend to improve DFS (HR: 0.66, p: 0.36) and there was an improvement in OS (HR: 0.23, p < 0.001). Conclusions: The multivariable analysis showed benefit of chemotherapy in both right and left sided CC in terms of OS, exhibiting more benefit those patients with left sided CC.
Association of differential mucosal microbiome composition with clinicopathologic characteristics of rectal adenocarcinoma.
Authors: Lee Michael Sangmin , Carlson Cheryl Ann , Calvo Benjamin F. , O'Neil Bert H. , McCoy Nicole Amber , Keku Temitope O
Published: January 2019

656

Background: Alterations in gut microbial composition are associated with development and progression of colorectal cancer (CRC), and may contribute to interpatient biologic and clinical heterogeneity. While recent studies have emphasized primary CRC tumor site as explaining much of these differences, there is still marked heterogeneity in clinical outcomes among the more homogeneous subgroup of rectal cancers. As such, we hypothesized that differential mucosal microbial populations are associated with distinct clinicopathologic characteristics among patients with locally advanced rectal cancer. Methods: Patients with T3-4 or N+ rectal adenocarcinoma were prospectively identified and underwent endoscopic tumor biopsy before starting neoadjuvant chemoradiation. Tumor samples were fresh frozen, bacterial DNA was extracted, and the V1-V2 region of the 16S bacterial ribosomal RNA was sequenced (IonTorrent). Sequences were processed through QIIME and an average of 16,189 reads per sample was obtained after quality filtering. Multivariate analyses were conducted using PRIMER VII and SPSS v24 software. P-values were determined using Mann-Whitney tests, and Benjamini-Hochberg procedure for false discovery rate was used and only results with false discovery rate < 0.25 are presented. Results: Among the 37 patients, mean age at diagnosis was 54 (range 30-77) and pre-treatment clinical stage was II (30%) vs. III-IV (70%). Younger patients (age < 50) had samples underrepresented for Streptococcus (0.9% vs 7.1%, p = 0.016, FDR 0.224) genus. Higher clinical stage was associated with enrichment of Fusobacterium (16.2% vs 5.6%, p = 0.019) and Parvimonas (4.6% vs 1.4%, p = 0.033) genera. Conclusions: Differential composition of tumor mucosal microbiota is associated with key clinical features among rectal adenocarcinomas, including age of diagnosis and tumor stage. Further investigation to determine associations between gut dysbiosis and transcriptomic subtypes may shed light on etiology of interpatient heterogeneity of rectal cancers.
Correlation between tumor infiltrating immune cells and peripheral regulatory T cell determined by methylation analyses and its prognostic significance in gastric cancer.
Authors: Suh Koung Jin , Kim Jin Won , Kim Ji Eun , Koh Jiwon , Kim Ji-Won , Lee Hye Seung , Lee Keun-Wook
Published: January 2019

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Background: Peripheral regulatory T cells (pTregs) might involve in tumor immune microenvironment. We aim to evaluate the correlation between pTregs and tumor immune microenvironment. Methods: pTregs status was determined from assessment of the pTreg/total T cell ratio (ratio of Foxp3 Treg-specific demethylated region (TSDR) to CD3G/CD3D demethylation) through epigenetic pattern of bisulfite pyrosequencing in long-term stored peripheral blood of 442 gastric cancer patients who received curative surgery. Immunohistochemical staining of multiple immune-related markers including CD3, CD4, CD8, Foxp3, 1-selectin arginase, ADAM metallopeptidase domain 17, CD163 and CD45RO within tumor microenvironment were performed in resected gastric tumor specimen. Results: The median value of FoxP3-TSDR and CD3G/CD3D demethylation was 5.8% and 32.3%, respectively. When pTreg/total T cell ratio was divided into eight equal groups from the lowest to the highest value, the extreme pTreg/total T cell ratio of the upper eighth and the lower eighth was significantly associated with lower CD45RO expressed cell counts within tumor microenvironment. In terms of arginase and CD163, inverse results were observed. Patients with extreme pTreg/total T cell ratio had significantly shorter disease-free survival (DFS) and overall survival (OS) compared to the patients with non-extreme pTreg/total T cell ratio. Multivariate analysis which included age, stage, lymphatic invasion, vascular invasion, and perineural invasion as covariates demonstrated that the extreme pTreg/total T cell ratio was an independent predictor for shorter DFS (HR 1.740, 95% CI 1.128 – 2.682; p = 0.012) and OS (HR 1.900, 95% CI 1.175 – 3.070; p = 0.003). Conclusions: Our results suggest that the pTreg/total T cell ratio determined by epigenetic methylation analysis is correlated with specific immune cell infiltration within tumor microenvironment in resected gastric tumors, and gives prognostic information in gastric cancer patients. pTreg/total T cell ratio could be an easy-obtained potential biomarker for prognosis and future immunotherapeutic treatment strategies.
A precision medicine strategy to identify the FGFR pathway as a novel target in colorectal cancer liver metastasis.
Authors: Altunel Erdem , Somarelli Jason , Kim So Young , Glover Wayne , Rupprecht Gabrielle , Hsu Shiaowen David
Published: January 2019

660

Background: Colorectal cancer liver metastasis (CRCLM) continues to be a major health problem and despite extensive efforts to develop new drugs, median survival remains at a mere 30 months. The purpose of our study is 1. Develop a precision medicine strategy for patients with CRCLM and 2. Discover novel pathways and treatments to improve outcomes. Methods: In order to develop a precision medicine strategy, 6 matched patient derived xenografts (PDX) and cell lines were established from patients undergoing resection of their CRCLM. A high-throughput drug screen containing over 100 FDA approved drugs was first used in vitro on 3 cell lines to identify therapeutic targets. The top therapeutic targets were validated in vivo. RNA seq was then performed to identify potential predictive markers of response. Results: Our high-throughput drug screen performed on 3 early passage CRC cell lines (CRC057, CRC119 and CRC240) identified ponatinib, a multi TKI, as the only agent to inhibit all 3 cell lines. Subsequent growth inhibition analysis identified the fibroblast growth factor receptor (FGFR) as the main target of ponatinib. In vitro findings were confirmed in vivo in matched PDXs. Western blot analysis post treatment showed evidence of decreased phospho-FGFRs. Further analysis of the main downstream signaling pathways of FGFR (RAS/PI3K/AKT, RAS/MEK/ERK and STAT) demonstrated that the STAT pathway was effectively targeted in all 3 cell lines. In contrast, the ERK pathway was targeted in CRC240 and CRC057 while the p-AKT was targeted in CRC119. Finally, RNAseq revealed different isoforms and mutations in these samples. Conclusions: We have developed a precision medicine strategy for patients with CRCLM using matched cell lines and PDXs coupled with high throughput drug screens and genomic analysis to identify novel targets and specifically identified the FGFR/STAT axis as a therapeutic target. Furthermore, co-targeting FGFR and its downstream pathways may provide synergy and lead to combinatorial therapies that can improve patient outcomes. Finally, RNAseq data can be used to develop predictive markers of therapy.
Detection and description of ERBB2 amplification using circulating cell free tumor DNA (ctDNA) genomic analysis in metastatic colorectal cancer (mCRC).
Authors: Raghav Kanwal Pratap Singh , Loree Jonathan M. , Morris Jeffrey , Manuel Shanequa , Crosby Shadarra , Meric-Bernstam Funda , Menter David , Raymond Victoria , Lanman Richard B. , Talasaz AmirAli , Kopetz Scott
Published: January 2019

661

Background: ERBB2 amplification (HER2amp) is evolving as a distinct subset of mCRC with therapeutic implications. Although seen in 3-4% of mCRC in tumor tissue, little is known about occurrence of HER2amp in ctDNA. The purpose of this study was to assess the value of ctDNA in detection of HER2amp in blood and to delineate its landscape in mCRC. Methods: We performed a retrospective analysis of mCRC patients (pts) who underwent plasma-derived NGS of ctDNA in a CLIA-certified lab (Guardant Health, Inc.) using a high sensitivity assay that reports copy-number variations using pre-specified algorithms. Pts with no detectable alterations were excluded. The cohort was divided into 2 groups: HER2amp and ERBB2 non-amplified (HER2NA). Descriptive statistics and Fisher’s exact test were used. Results: Between 5/2014 and 5/2016, 1625 mCRC pts had a ctDNA NGS assay and of these 1387 met our inclusion criteria. Among these, HER2amp was seen in 69 pts (4.9%, 95%CI: 3.9 – 6.3). HER2amp were found to be enriched in RAS wild-type (WT) (6.4% v 2.9%, OR 2.3, P = 0.002) and RAS/BRAFV600E WT (6.9% v 2.7%; OR 2.7, P < 0.001). When co-existing with RAS mutations, HER2amps were seen more with sub-clonal ( < 50% relative mutation allele frequency) RAS mutations than clonal RAS mutations (6.6% v 2.1%, OR 3.1, P = 0.03). The most common co-occurring mutations were TP53 (77%), APC (59%), EGFR (25%), PIK3CA (25%) and KRAS (23%). HER2 (13% v 5%, OR 2.6, P = 0.017) and TP53 (77% v 62%, OR 2.1, P = 0.011) mutations co-occurred more frequently with HER2amp than with HER2NA cases. No significant association was seen with PIK3CA, EGFR and APC mutation status. Conclusions: In one of the largest series of CRC pts with ctDNA NGS, ERBB2 amplification were confirmed to be enriched in RAS/BRAF WT mCRC. In these pts, co-existing clonal RAS mutations are uncommon, but concurrent PIK3CA and ERBB2 mutations are present in a sizable minority of cases. These findings may have implications for anticipated innate/acquired resistance mechanisms to HER2-targeting therapies under evaluation for CRC.
Polymorphisms in beta-defensin pathways and clinical outcomes in metastatic colorectal cancer patients treated with FOLFIRI-bevacizumab in two randomized phase III trials.
Authors: Naseem Madiha , Berger Martin D , Puccini Alberto , Tokunaga Ryuma , BATTAGLIN FRANCESCA , Barzi Afsaneh , Soni Shivani , McSkane Michelle , Cao Shu , Millstein Joshua , Zhang Wu , Loupakis Fotios , Stintzing Sebastian , Heinemann Volker , Falcone Alfredo , Lenz Heinz-Josef
Published: January 2019

662

Background: Beta defensin 1 (DEFB1) and 2 (DEFB4A) are antimicrobial peptides secreted from colonic epithelial cells in response to inflammation. DEFB1 has been shown to serve as a tumor suppressor, whereas high concentrations of DEFB4A are linked with angiogenesis. This study examines the impact of single nucleotide polymorphisms (SNPs) in beta-defensin pathways in two independent phase III trials: FIRE-3 and TRIBE. Methods: The OncoArray database containing 530K SNP markers provided by Illumina was used to find associations between clinical outcomes and 10 functional SNPs from DEFB1, DEFB4A, PPARG, NFKB1, MUC2, and TLR4 genes. Patients treated with first-line FOLFIRI/bevacizumab (bev) in the randomized phase III FIRE-3 trial (n = 107) and TRIBE trial (n = 215) served as discovery and validation cohorts respectively. The FIRE-3 FOLFIRI and cetuximab (cet) arm served as a negative control (n = 129). Results: A total of 451 patients were included. The NFKB1 rs3821958 SNP showed significant association with OS and PFS in overall pts and those with left-sided CRC. Compared to pts carrying the mutant A allele, those with the wild-type G/G genotype had a shorter median OS (19 vs 40 mts) and PFS (9.2 vs 11.7 mts) in both univariate ((OS: HR = 2.32, 95%CI 1.21-4.42, p = 0.006) (PFS: HR = 1.93, 95%CI: 1.11-3.37, p = 0.014)) and multivariable analysis ((OS: HR = 2.90, 95%CI 1.47-5.70, p = 0.002) (PFS: HR = 2.08, 95%CI:1.18-3.67, p = 0.012)). This finding was validated in TRIBE, where carriers of G allele had shorter PFS in univariate analysis (HR = 1.44, p = 0.019). Opposite results were observed in pts receiving cet, where G/G carriers had improved OS in univariate analysis (HR = 0.46, p = 0.048). Pts with left-sided CRC who carried the wild-type allele had poorer OS and PFS in both trials. Conclusions: NFKB1 rs3821958 SNP is known to activate DEFB1 and is downstream of EGFR. Harboring a mutant allele in this SNP confers a mortality benefit in left-sided and overall pts treated with bev, and worsens OS in pts receiving cet. Hence, NFKB1 could serve as an important predictive biomarker. Future studies are warranted to further elucidate its role in colorectal cancer.