bluuebunny/crossref_metadata_2025_split huggingface dataset:
Clinicopathological characteristics of patients with gastrointestinal stromal tumor according to progranulin expression.
Authors: Koo Dong-Hoe , Do In-Gu , Oh Sukjoong , Lee Yun-Gyoo , Kim Kyungeun , Sohn Jin Hee , Park Jung Ho , Sohn Chong Il , Son Byung Ho , Serrero Ginette , Yoo Chang Hak 
Published: January 2019

57 Background: As an autocrine growth factor, progranulin (PGRN) has been known to stimulate tumorigenesis and proliferation of several types of cancer cells. However, little is known about the clinicopathological features of patients with gastrointestinal stromal tumor (GIST) according to the PGRN expression. Methods: A retrospective analysis was performed for patients with GIST who underwent curative surgical resection between March 2007 and March 2018. PGRN expression in tumor cells was evaluated by immunohistochemical (IHC) analysis and semi-quantitatively categorized (no expression, 0; weak, 1+; moderate, 2+; strong, 3+). High expression was considered for tumors graded 2+ or 3+ staining intensity. Results: A total of 54 patients were analyzed, and 31 patients (57%) were male. Median age at surgery was 60 years (range, 33-79), and the most common primary site was stomach (36 patients, 67%). Spindle histology was observed in 35 patients (65%). Median tumor size was 8 cm (range, 2-47), and low mitotic count (≤ 5/50 HPF) was observed in 18 patients (33%). According to the modified NIH classification, 42 patients (78%) were grouped into high risk. With IHC evaluation, KIT and CD34 expression were observed in 51 patients (94%) and 40 patients (80%), respectively, and 27 patients (50%) had high PGRN-expressing tumors. Among the 34 patients whose tumors were genotyped, 25 patients (74%) had an exon 11 mutation, and D842V was observed in 3 patients (9%). According to the PGRN expression, high PGRN-expressing tumors had more epithelioid/mixed histology (68% vs. 32%; p = 0.046), and KIT exon 11 mutation (76% vs. 24%; p = 0.037). Regarding other clinicopathological characters, such as sex, age at surgery, primary site, size, mitotic count, risk classification, and KIT/CD34 expression, there was no significant difference between high PGRN-expressing tumors and low PGRN-expressing tumors. Conclusions: High PGRN-expressing GISTs had more epithelioid/mixed histology and more KIT exon 11 mutation in GIST patients who underwent curative surgical resection.
Chemoradiation-induced alteration of programmed death-ligand 1 and CD8+ tumor-infiltrating lymphocytes in rectal cancer.
Authors: Baretti Marina , Fu Wei , Wang Hao , Anders Robert A , Azad Nilofer Saba , Zhu Qingfeng 
Published: January 2019

570 Background: DNA damage and subsequent neoantigen formation has been hypothesized as a mechanismfor radiotherapy and PD-1/PD-L1 pathway inhibition to synergize in an antitumor immune response. We investigated neoadjuvant chemoradiotherapy (nCRT)-induced changes in CD8+ tumor infiltrating lymphocyte, PD-L1 and mucin expression in rectal cancer patients as compared to patients who did not receive nCRT. Methods: Tumor samples were collected from rectal adenocarcinoma patients who had undergone resection between 2008-2014 with (n = 62) or without (n = 17) nCRT treatment. Tissue sections were stained with CD8 and PD-L1 antibodies for immunohistochemistry. Whole slides images were acquired at 20x magnification. The prevalence of positive CD8 stained cells was recorded in tumor, interface tumor side, interface background rectal side. Image analysis (HALO Indica Labs) was used to determine the density (# of cells/surface area analyzed) of CD8 expressing lymphocytes. The percentage of PD-L1 membranous expression was manually counted in tumor cells (TC), tumor stroma (TS) and invasive front (IF). Mucin expression was determined as the percentage of the mucin area in the whole tumor mass area. Results: PD-L1 expression on TCs was identified in 7.7 % (6/78) of specimens. All 6 cases had received nCRT (p = 0.33). 80% and 75.5% of the nCRT cases showed PD-L1 expression on TS and IF respectively, versus 20% (p = 0.55) and 24.5% (p = 0.56) in non-nCRT cases. The median densities of CD8+ infiltrating T lymphocytes in tumor, interface tumor side, interface background rectal side did not differ significantly between the two groups (p = 0.79, p = 0.47, p = 0.22). No nCRT-changes in mucin expression observed in the 28 evaluable cases (p = 0.25). Conclusions: nCRT exposure was associated with a non-significant difference in PD-L1 expression on TS and IF cells in patients with rectal adenocarcinoma as compared to non-nCRT case, possibly due to sample size limitations. Further mechanistic investigations and comprehensive analysis of other immune checkpoints are needed to understand nCRT-induced immunologic shift in rectal cancer and to expand the potential applicability of checkpoint inhibitors in this setting.
The relationship between tumor budding, tumor microenvironment, and survival in patients with primary operable colorectal cancer.
Authors: Van Wyk Hester Catharina , Roseweir Antonia K. , Anderson Ditte , Sutton Elizabeth , Horgan Paul G. , McMillan Donald C , Edwards Joanne 
Published: January 2019

581 Background: Tumour budding is an independent prognostic factor in colorectal cancer and has recently been defined by the International Consensus Conference on Tumour Budding. The aim was to use the ITBCC budding evaluation method to examine relationships between tumour budding, tumour factors, tumour microenvironment, gene expression profiles and survival in patients with primary operable CRC. Methods: Hematoxylin and Eosin (H&E) stained slides of 953 CRC patients, diagnosed between 1997 and 2007 were evaluated for tumour budding according to the ITBCC-criteria. The tumour microenvironment was evaluated using tumour stroma percentage (TSP) and Klintrup–Makinen (KM) grade to assess the tumour inflammatory cell infiltrate. Differential gene expression was assessed using TempO-Seq gene expression profiling (BioSpyder Technologies Inc., CA, USA) using the Surrogate+Tox targeted panel (2,733 genes selected for biological diversity, maximal information content, and widespread pathway coverage). Results: High budding (n = 269/ 28%) was significantly associated with TNM stage (P < 0.001), venous invasion (P < 0.001), weak KM grade (P < 0.001), high TSP (P < 0.001) and reduced cancer specific survival (CSS) (HR = 5.04; 95% confidence interval [CI], 3.50-9.51; P < 0.001) and was independent of venous invasion, KM grade, and Ki67 proliferation index. RNA expression analysis was employed using TempO-Seq to determine differential gene expression between tumours with (n = 8) and without budding (n = 18). Three genes were identified as significantly differentially expressed: S100A2 (S100 calcium binding protein A2) was upregulated by 2.9 fold (padj < 0.00001); REG1A (regenerating family member 1 alpha) was downregulated by 4.7 fold (padj < 0.01) and LCN2 (lipocalin 2) was downregulated by 2.2 fold (padj < 0.01). Conclusions: Tumour budding stratifies patients’ survival in primary operable colorectal cancer and associates with differing gene expression profiles and factors of the tumour. Therefore, the ITBCC budding evaluation method should be used to assess tumour budding as supplement the TNM staging system and can help to further subdivide colorectal cancer into new prognostic groups.
Blood-based biomarkers in metastatic colorectal cancer patients treated with FOLFIRI plus regorafenib or placebo: Results from LCCC1029.
Authors: Liu Yingmiao , Burdett Kirsten , Starr Mark D. , Brady J. Chris , Hatch Ace Joseph , Ivanova Anastasia , Moore Dominic T. , Hammond Kelli , Lee Michael Sangmin , O'Neil Bert , Innocenti Federico , Owzar Kouros , Sanoff Hanna Kelly , Nixon Andrew B. 
Published: January 2019

587 Background: The LCCC1029 trial demonstrated that addition of the multitargeted kinase inhibitor regorafenib (Rego) to FOLFIRI in metastatic colorectal cancer (mCRC) patients (pts) modestly prolonged progression-free survival (PFS). In this preplanned analysis, circulating angiogenic and inflammatory proteins were explored as potential prognostic and predictive biomarkers of Rego benefit. Methods: Plasma samples from 149 mCRC pts (107 in Rego + FOLFIRI and 42 in placebo + FOLFIRI) were evaluated for 20 markers at baseline (n = 149) and cycle 1 day 21 (C1D21, n = 81). Predictive and prognostic values of each marker at baseline were analyzed for both PFS and overall survival (OS) using Cox proportional hazard models. On-treatment changes were quantified as fold change [log2(C1D21/baseline)] and differences between arms were evaluated using the Mann-Whitney test. Results: The primary objective of this study was to determine whether any marker was predictive of benefit with Rego for PFS. Although no treatment by marker interactions were significant after adjusting for multiple testing, the top three markers of interest were OPN (unadjusted p-values of 0.02), VCAM-1 (0.02), and PDGF-AA (0.04). VCAM-1 was also predictive for OS benefit in pts treated with Rego (unadjusted p = 0.01). Baseline levels of multiple markers (including HGF, IL-6, PlGF, VEGF-R1, OPN) were prognostic for both PFS and OS. Higher levels of these markers were associated with worse survival. Biomarker changes in response to treatment were explored and compared between arms. Fold change of three markers (PlGF, VEGF-A, VCAM-1) were significantly different between arms (p < 0.0001), all being markedly up-regulated in the Rego arm compared to the placebo after treatment. Conclusions: In this hypothesis generating report, VCAM-1, OPN, and PDGF-AA were the top biomarkers when analyzing the potential predictive association with PFS, where a lower hazard was observed for pts receiving Rego. Candidate prognostic markers were identified, including PlGF and VEGF-R1, key factors in VEGF biology. Biomarker changes observed here may offer insights into potential combinatorial strategies with Rego for future studies.
On-treatment changes of plasma protein biomarkers in CALGB/SWOG 80405 (Alliance).
Authors: Hatch Ace Joseph , Ou Fang-Shu , Zemla Tyler , Starr Mark D. , Brady John C. , Liu Yingmiao , Innocenti Federico , Meyerhardt Jeffrey A. , O'Reilly Eileen Mary , Lenz Heinz-Josef , Hurwitz Herbert , Venook Alan P. , Nixon Andrew B. 
Published: January 2019

588 Background: CALGB/SWOG 80405 found no difference in overall survival (OS) or progression-free survival (PFS) in 1137 patients with KRAS wild-type metastatic colorectal cancer (mCRC) treated with either the anti-VEGF agent bevacizumab (Bev) or the anti-EGFR agent cetuximab (Cet) in combination with chemotherapy (FOLFOX or FOLFIRI) as first-line therapy. Additional molecular biomarkers are required for the optimization of treatment choices for patients with mCRC. Methods: Levels of 24 proteins were assayed in EDTA-plasma samples using multiplex ELISA techniques. Plasma samples were collected at baseline and cycle 2 day 1 (C2D1). Analyses of baseline markers have been presented previously. Changes from baseline to C2D1 were expressed as an L-ratio (LR, log2 of C2D1 divided by baseline measure). LRs dichotomized at 0 were analyzed for potential prognostic and predictive effects on OS and PFS using Cox models while adjusting for confounders (post-hoc optimized cutpoints were used for PLGF, TIMP1, VCAM1, and VEGFR3 due to skew in the distributions of these markers). P-values are not corrected for multiple testing. Results: Baseline and matched C2D1 samples from 446 patients (212 Bev/234 Cet) were available for analysis. Thirteen markers were differentially modulated between arms (p < 0.05). Early increases in CD73 (p = 0.001), ICAM1 (p = 0.022), TIMP1 (p = 0.001), TSP2 (p = 0.024), and VEGFR3 (p = 0.006) were prognostic for shorter OS. Increases in ICAM1 (p = 0.008), TIMP1 (p = 0.042), and TGFB1 (p = 0.039) were prognostic for shorter PFS. Changes in VEGFR3 (pint = 0.097) and TGFBR3 (pint = 0.052) were predictive for OS and PFS, respectively. No other markers were predictive for OS or PFS (p < 0.1). Conclusions: Changes in circulating plasma protein biomarkers observed in patients enrolled in CALGB/SWOG 80405 were both prognostic and predictive for OS and PFS and warrant further study. Such changes could provide valuable information and help guide treatment decisions. Support: U10CA180821, U10CA180882, U10CA180888, U10CA180830; ClinicalTrials.gov: NCT00265850. [Table: see text]
Prognostic significance of circulating tumor cells in patients with gastric cancer: Epithelial mesenchymal transition and perioperative kinetics.
Authors: Ishiguro Yui 
Published: January 2019

59 Background: Circulating tumor cells (CTCs) have been shown to be heterogeneous. This study aimed to identify the prognostic significance of CTCs in patients with gastric cancer, focusing on epithelial mesenchymal transition and perioperative kinetics. Methods: Peripheral blood (7.5 ml) was taken from patients (n = 54) before curative resection, and at 7 days, 1 and 6 months postoperatively. CTCs were enriched using density gradient centrifugation and magnetic-activated cell sorting (negative selection). Cell suspensions were characterized by multi-immunofluorescence staining against cytokeratin (CK) and N-cadherin, and by DAPI staining. CTCs were defined as nucleated cells expressing CK or N-cadherin. Threshold analysis identified 1 CTC/7.5 ml as an optimal cut-off value. The median observation period was 735 days. Results: CTCs were detected in seven patients (24%) with early cancer and 14 patients (56%) with advanced cancer (p < 0.05). Cells were identified as either N-cadherin+/CK−/CD45− or N-cadherin+/CK+/CD45−, but no N-cadherin−/CK+/CD45− cells were observed. The median follow-up period was 24.5 months. After 2 years, postoperative recurrence was detected in nine patients, all of whom had advanced gastric cancer and N-cadherin+/CK−/CD45− CTCs preoperatively. In terms of perioperative kinetics (just before, 7 days and 1 month after surgery), we divided patients with advanced cancer into three risk groups: A, preoperative CTCs ≥1 and increased postoperatively; B, preoperative CTCs ≥1 and decreased postoperatively; C; no preoperative CTCs. The recurrence rates in the above groups were 80% (4/5), 44% (4/9), and 0% (0/11), respectively. Conclusions: Numerous CTCs expressed N-cadherin but not CK. Perioperative measurement of CTCs may be a useful surrogate marker for recurrence risk.
Association of DNA damage response and repair genes (DDR) mutations and microsatellite instability (MSI), PD-L1 expression, tumor mutational burden (TMB) in gastroesophageal cancers.
Authors: Cerniglia Michael , Xiu Joanne , Grothey Axel , Pishvaian Michael J. , Hwang Jimmy J. , Marshall John , Vanderwalde Ari M. , Shields Anthony Frank , Lenz Heinz-Josef , Salem Mohamed E. , Philip Philip Agop , Goldberg Richard M. , Korn W. Michael , Kim Sunnie S. 
Published: January 2019

60 Background: DDR mutations are associated with higher neoantigen load and tumor infiltrating lymphocytes, and are a potential biomarker for immunotherapy. We investigated the association of DDR mutations in gastric (GC), esophageal (EC), and gastroesophageal junction (GEJ) cancers with MSI, PD-L1, and TMB, known predictors for immune checkpoint inhibitors. Methods: 20 DDR mutations were tested by Next-Generation Sequencing (NGS) with a 592-gene panel on a total of 1935 (709 EC; 831 GC; 355 GEJ) cancers. TMB was assessed by NGS, MSI by NGS or fragment analysis, and PD-L1 by IHC (22c3 for CPS or SP142). Results: GC had the highest DDR mutation rate compared to EC and GEJ (27% vs. 20%, p = 0.0005 and 17%, p = 0.0002, respectively). MSI-High (MSI-H) was significantly more common in the DDR mutated cohort (DDR-M) compared to non-mutated cancers (18% vs. 1%; p < 0.0001). TMB-High (≥ 10 mutations/megabase [mt/MB]) was higher in DDR-M (35% vs. 21%; p < 0.0001); in DDR-M cohort, GC had the highest TMB compared to DDR-M EC and GEJ (mean: 13.8 vs. 9.4 vs. 10 mt/MB, respectively; p < 0.0001). DDR mutations were more frequent in the PD-L1 combined positive score (CPS) ≥ 50 group than CPS 0 (42.9% vs. 24%; p = 0.037) and CPS 1-9 (42.9% vs. 20.6%; p = 0.005). ARID1A, ATRX, BRCA2, and PTEN were the most prevalent DDR mutations in MSI-H (87%, 31%, 25%, 24%, respectively); ARID1A, ATRX, BRCA2, and PTEN in TMB-High (47%, 7.7%, 6.7%, 6.8%) and ARID1A, BRCA2, RAD50, and WRN in PD-L1 high (CPS ≥ 10) (48.5% vs. 5.2% vs. 2.5% vs. 3.4%). Conclusions: MSI-H, TMB-high and high PD-L1 expression were significantly more prevalent in the DDR-M cohort compared to non-DDR-mutated cancers, most pronounced in GC. Alterations in ARID1A, ATRX, BRCA2, and PTEN were correlated with MSI-H and TMB-high while ARID1A, BRCA2, RAD50, and WRN were correlated with increased PD-L1 expression. Our findings may help identify patients for tailored immunotherapy approaches in future clinical trials.
Comprehensive -omic analysis of 152 CRC patients allows greater subclassification than CMS or sidedness alone.
Authors: Szeto Christopher , Kazmierczak Kevin , Chambers Andrew , Kim Yeoun Jin , Nguyen Andrew , Tan Iain B. , Benz Stephen Charles , Vaske Charles Joseph 
Published: January 2019

601 Background: Despite relatively high TMB in CRC, immune checkpoint inhibition (ICI) response is lower than in similarly mutated tissues such as melanoma (ORR 10-20% vs. 20-50%). MSI-status can be used to pre-select likely-responders, however MSI is rare. There is a need to guide ICI candidacy in CRC. Four transcriptomic-based CRC consensus molecular subtypes (CMS) have been described with ad hocclinical associations. We sought to confirm these subtypes in proteomic assays and their clinical associations. Methods: 152 CRC tumors from the National Cancer Centre Singapore were available for analysis. Tumor/normal-paired DNAseq (WGS or WES) and deep RNAseq was performed. Mass-spec based global proteomics was successfully performed on 143/152 samples. Consensus between RNAseq and global proteomics was confirmed by correlation significance analysis. MSI-status was determined by both PCR and WGS/WES profiles. CMS types, checkpoint expression, and immune-infiltration deconvolution were calculated upon RNAseq data. A CMS-like clustering of proteomic data was identified by analyzing homogeneity of candidate clusterings with CMS types. Significant enrichment for MSI, immune status, CMS types, and clinical covariates was analyzed. Results: DNAseq-based MSI and PCR-based MSI were statistically equivalent (adj. p < 1.4E-14). 3075/5135 genes were significantly correlated between RNAseq and global proteomic assays. The most correlated genes within COSMIC cancer-related genes were enriched for MHC binding processes. Clustering of immune-expression deconvolution bifurcated into hot and cold tumors. Significant association was found between CMS1, MSI, transverse sides, and being immune hot. Conversely, CMS2 was found to be significantly MSS, left-sided, and immune cold. A semi-supervised clustering of global proteomic data significantly recapitulated some CMS subtypes, but grouped CMS1 (MSI enriched) and CMS3 (Ras mt enriched) subtypes. Genes driving this association were significantly enriched for ECM organization. Conclusions: CMS1 tumors are the best candidates for ICI therapy. CMS3 co-clusters with CMS1 in ECM genes within proteomic data, warranting further research of CMS3 ICI outcomes.
Characteristics of colorectal cancer (CRC) patients with BRCA1 and BRCA2 mutations.
Authors: Naseem Madiha , Xiu Joanne , Salem Mohamed E. , Goldberg Richard M. , Vanderwalde Ari M. , Grothey Axel , Philip Philip Agop , Seeber Andreas , Puccini Alberto , Tokunaga Ryuma , Battaglin Francesca , Berger Martin D. , Barzi Afsaneh , Hanna Diana L. , Zhang Wu , Hwang Jimmy J. , Shields Anthony Frank , Marshall John , Korn Wolfgang Michael , Lenz Heinz-Josef 
Published: January 2019

606 Background: Between 3-5% of CRC patients have BRCA1/2 pathogenic mutations. This study aims to identify associations between BRCA1 and BRCA2 mutations and clinical characteristics in CRC. Methods: A total of 6396 CRC tumor samples were tested with Next-Generation Sequencing (NGS) on a 592-gene panel, pathogenic or presumed pathogenic variants were counted as mutations (mt). Microsatellite instability (MSI) and tumor mutational burden (TMB) were tested by NGS. Statistical correlations were investigated using ANOVA, Chi-square and t-test. Results: Among tumors sampled, 53% derived from male patients and median age was 60 years. BRCA1 mt were detected in 1.1% (n = 72) of tumors, while BRCA2 in 2.8% (n = 179). BRCA1 mt were more frequent in women (W;65%) than men (M;35%) (p = 0.0019) while no relationship with sex was seen for BRCA2 mt (42% F vs. 58% M). No significant associations with age were noticed. Majority of pathogenic mt in BRCA1 (52%; n = 34) and BRCA2 (62%; n = 103) occurred in MSI-High (MSI-H) cases. MSI-H pts had more frameshift mt in both BRCA1/2 than MSS pts. MSS cases had lower rates of BRCA1 and 2 pathogenic mt (44% and 37%, respectively). Right-sided tumors were significantly associated with BRCA1 (p = 0.0056) and BRCA2 (p < 0.0001) mt in MSI-H cases only. BRCA1/2 mt were associated with higher TMB in all CRCs, including MSI-H and MSS cases (p < 0.001). POLE mt (n = 31) were associated with higher BRCA1/2 mt rates (9.6%, 55% respectively). Among MSS cases with POLE wild-type status, BRCA1 (p = 0.0269) and BRCA2 (p = 0.0151) mt were associated with high TMB and combining both BRCA1/2 mutations led to an even higher TMB (3.6%; p = 0.001). Conclusions: This is the first study to show that BRCA1/2 mutations are more frequent in MSI-H, and independently associated with higher TMB, pathogenic POLE mutations, and right-sided tumors in MSI-H CRCs. Given their relationship with TMB, the presence of BRCA1/2 mutations may be potential predictive biomarkers for checkpoint or PARP inhibitors in CRC, a finding that should be prospectively evaluated.
A systematic review and network meta-analysis of regorafenib and TAS-102 in refractory metastatic colorectal cancer.
Authors: Sonbol Mohamad Bassam , Benkhadra Raed , Wang Zhen , Firwana Belal , Mody Kabir , Kasi Pashtoon Murtaza , Hubbard Joleen Marie , Murad M. Hassan , Ahn Daniel H. , Bekaii-Saab Tanios S. 
Published: January 2019

619 Background: Regorafenib (at a starting dose of 160 mg/day, rego 160), regorafenib (with a weekly dose escalation, rego 80+) and TAS-102, are suggested treatment options for refractory metastatic colorectal cancer (mCRC). We aimed to evaluate the comparative effectiveness evidence supporting these 3 strategies. Methods: We searched PubMed, Embase, and Cochrane CENTRAL, for randomized controlled trials evaluating TAS 102 or regorafenib in refractory mCRC patients who progressed on/intolerant of previous oxaliplatin, irinotecan, and fluoropyrimidine. Outcomes of interest included OS and PFS. The overall effect was pooled using the DerSimonian random effects model. We conducted network meta-analysis based on White’s multivariate meta-regression to pool evidence from direct and indirect comparisons. Results: Six trials (3 of regorafenib and 3 of TAS-102) at low risk of bias (2,445 patients) were included. Direct comparisons showed that Rego 160 and TAS-102 as monotherapy were superior to BSC in terms of PFS (Rego 160: HR = 0.4, CI 0.26 to 0.63; TAS-102: HR = 0.46, CI 0.40 to 0.52) and OS (Rego 160: HR = 0.67, CI 0.48 to 0.93; TAS-102: HR = 0.67, CI 0.57 to 0.80). Network analysis showed that there was no difference in PFS or OS between Rego 160 and TAS-102. Rego 80+ was superior to BSC in terms of OS (HR = 0.44, CI 0.23 to 0.84) and PFS (HR = 0.37, CI 0.21 to 0.66). There was a numerical advantage for Rego 80+ compared to TAS-102 and Rego 160 (see table). Conclusions: Regorafenib 160 and TAS-102 appear to have similar efficacy. Rego 80+ is shown to be superior to BSC. A trend for improved OS was observed with Rego 80+ versus Rego 160 or TAS 102. [Table: see text]