bluuebunny/crossref_metadata_2025_split huggingface dataset:
Association of phosphatidylinositol 3-kinase (PI3K) pathway activation with increased immune checkpoint expression in colorectal cancer (CRC) patients.
Authors: Nusrat Maliha , Roszik Jason , Katkhuda Riham , Menter David , Raghav Kanwal Pratap Singh , Morris Van Karlyle , Sharma Padmanee , Allison James Patrick , Blando Jorge M , Maru Dipen M. , Overman Michael J. , Kopetz Scott 
Published: January 2019

653 Background: PI3K pathway is a known modulator of anti-tumor immune response and is frequently activated in CRC through genetic alterations such as PTEN loss (PTENloss) and PIK3CA mutations (PIK3CAmut). This study aims to determine the impact of these alterations on immune cell infiltration, priming and activation in early stage CRC patients (pts). Methods: Immune infiltrates and checkpoints were evaluated using quantitative immunohistochemistry (IHC) on primary CRC (N = 59) for both center of tumor (CT) and invasive margin (IM). Pts were evaluated by presence or absence of either PTENloss or PIK3CAmut (collectively termed PI3K pathway alterations). Microsatellite unstable (MSI) and stable (MSS) tumors were analyzed separately. Clinicopathologic data was examined for potential associations with PI3K pathway alterations. Separately, mRNA data (Agilent) was obtained for immune related genes from an internal cohort with PTEN and PIK3CA annotation (N = 73). Results: 59 pts comprised IHC cohort (40 MSS, 19 MSI); 23 pts (39%) had PTENloss or PIK3CAmut. In Agilent cohort, 16 of 73 pts (22%) had PI3K pathway alterations. In MSS CRC, these alterations were more common in CMS1 (p = 0.03), on right side (p = 0.048) and with peritumoral lymphocytes (p = 0.031). MSS pts with PI3K pathway alterations had higher PD1 protein expression (p = 0.04), 2.1 and 2.3 times increased density of CD3+ (p = 0.01) and CD8+ (p = 0.04) cells respectively, and higher Granzyme B protein expression (p = 0.04) in the CT. These pts also had higher PDL1 gene expression (p = 0.046). MSS CRC pts with PIK3CAmut similarly had 2 times more PDL1 protein expression in epithelial cells of the IM (p = 0.01). Alternate checkpoints were also increased in pts with PI3K pathway alterations, including higher protein expression of LAG3 in CT (P = 0.046) and higher gene expression of CTLA4, TIM3, and TIGIT (P < 0.05 for all). Conclusions: PI3K pathway activated MSS CRC is associated with increased immune engagement, but also upregulation of key immune checkpoints in early stage tumors resulting in an ineffective immune response. Combination of PI3K pathway inhibition with immunotherapy merits investigation in this subset of pts.
Characterizing heterogeneity in KRAS mutant colorectal cancers (CRC) using cellular, mutation, and immune profiles.
Authors: Sadanandam Anguraj , Poudel Pawan , Fontana Elisa , Ragulan Chanthirika 
Published: January 2019

657 Background: Approximately 30%-50% of CRC patients have KRAS mutation, and they are associated with lack of treatment response to anti-EGFR therapy. KRAS mutant CRCs are heterogeneous that not all mutant tumors are dependent on its downstream signaling. At this era of the search for therapeutic targets related to mutant KRAS, it is essential to understand the underlying heterogeneity in KRAS mutant metastatic CRCs with a goal of identifying personalized therapeutic vulnerabilities. To understand KRAS mutation further, in this study we classified KRAS mutant CRCs based on individual cell types in the normal colon crypt and associated them with PIK3CA mutations and interferon-gamma responsive signature. Methods: Publicly available RNAseq gene expression data from KRAS mutant samples were used. Classification of CRC samples into CRCassigner subtypes, KRAS mutation dependents/independent groups, and interferon gamma-responsive status was performed using published signatures. Results: CRC samples (n>200) with KRAS mutant and wild-type statuses were classified into all the five CRCAssigner subtypes (goblet-like, enterocyte, transit-amplifying, stem-like and inflammatory) that represent individual cell types in the normal colon crypt. Interestingly, goblet-like subtype was found to be enriched for KRAS mutation. Among those KRAS mutant CRCs from all the subtypes (n=61), goblet-like samples showed significant enrichment (false discovery rate <0.05; hypergeometric test) for KRAS dependent signature, whereas stem-like subtype showed KRAS independent signature. KRAS independent stem-like CRCs showed increased PIK3CA mutation and expression of interferon-gamma responsive genes compared to dependent CRCs. Conclusions: Overall, KRAS mutant CRCs are heterogeneous with differentiated subtype highly dependent on the mutation and its signalling pathway, whereas less differentiated/stem-like subtype CRCs are independent of the mutation. Also, the enrichment of PIK3CA mutation and interferon-gamma responsive genes mainly in KRAS independent CRC subtype present a potential opportunity to target them using combination immunotherapeutics.
The prognostic role of CpG island methylator phenotype in metastatic colorectal cancer.
Authors: Chen Kuo-Hsing , Lin Liang-In , Tseng Li-Hui , Lin Yu-Lin , Liau Jau-Yu , Tsai Jia-Huei , Liang Jin-Tung , Lin Been-Ren , Cheng Ann-Lii , Yeh Kun-Huei 
Published: January 2019

667 Background: The prognostic role of CpG Island Methylator Phenotype (CIMP) in colorectal cancer (CRC) is still controversial, especially in metastatic CRC. Methods: We retrospectively analyzed the CpG island methylator phenotype (CIMP) in stage I to IV CRC specimens, which were diagnosed during 2005-2013. CIMP status was determined using a 5- gene MethyLight-based assay ( p16, MINT1, MINT2, MINT31, and MLH1). Tumors were designated as CIMP if 3 or more of 5 genes gave percent of methylated reference value ≧ 10. The clinicopatholoical characteristics, anti-cancer therapies, and the overall survival outcome were reviewed. Overall survival (OS) was compared between patients with CIMP CRC and those with non-CIMP CRC. Results: Among 450 patients with successfully determined CIMP status, 259 (57.56%) were male, 312 (70.31%) were stages I-III, 316 (70.69%) were left-sided CRC. In the survival analyses in stages I-IV patients, there was no significant difference in OS between those with or without CIMP (long rank test, p = 0.4526). Importantly, patients with metastatic CIMP CRC had poor OS than those with metastatic non-CIMP CRC (median survival, CIMP vs. non-CIMP: 1.36 vs. 3.11 years, log rank test, p = 0.0047). In a multivariate analysis, which adjusted prognostic variables such as: KRAS and BRAF mutations, microsatellite instability status, age, sex, grade, primary site, metastatic site number, chemotherapies and targeted therapies, CIMP remained an independent poor prognostic factor for OS (HR = 6.213, 95% confidence interval: 2.443 to 15.799, p = 0.0001) in metastatic CRC. In an exploratory analysis, there were more tumors with liver metastases at diagnosis in CIMP CRC than in non-CIMP CRC (94.4% vs. 71.3%, p = 0.0416). Conclusions: Our data demonstrated CIMP might independently predict poor survival in metastatic CRC in a large East Asian cohort.
Identification of biomarkers for TAS-102 efficacy in metastatic colorectal cancer patients based on preclinical analysis and clinical validation.
Authors: Suenaga Mitsukuni , Mashima Tetsuo , Kawata Naomi , Dan Shingo , Wakatsuki Takeru , Shinozaki Eiji , Ichimura Takashi , Ogura Mariko , Takahari Daisuke , Osumi Hiroki , Ota Yumiko , Chin Keisho , Seimiya Hiroyuki , Yamaguchi Kensei , Yamaguchi Toshiharu 
Published: January 2019

669 Background: Trifluridine (FTD) incorporation into DNA is the main anti-tumor mechanism of action of TAS-102. We performed preclinical analysis and translational validation study to identify the candidate cytokines for TAS-102 efficacy in metastatic colorectal cancer (mCRC) patients (pts). Methods: As a first preclinical process, we selected candidate cytokines according to our transcriptomic and cell biological analysis. We then validated predictive value of the cytokines in mCRC pts receiving TAS-102 (discovery) and regorafenib (control). Blood samples were obtained at baseline (BL), before second cycle (2nd) and progressive disease (PD), and cytokine levels were measured using ELISA. The change patterns were defined as ‘increased’ or ‘decreased’ from BL. Results: 93 pts were included in this study: 67 received TAS-102 and 26 received regorafenib. Preclinical cDNA microarray analysis with colon cancer cell lines demonstrated marked changes in the RNA expression of interleukin-8, VEGF-A and epiregulin (EREG) after FTD treatment. Particularly, in preclinical model, EREG secretion was highly measured after FTD treatment in FTD-sensitive cells, while not in FTD-resistant cells. In the discovery cohort, increased EREG levels at 2nd showed trend toward longer PFS and OS than decreased changes (2.6 vs 2.3 mos, P= 0.096; 10.8 vs 6.2 mos, P= 0.091). Meanwhile, decreased EREG levels at PD were marginally associated with longer PFS and significantly with longer OS than increased (4.0 vs 2.3 mos, P= 0.130; 9.8 vs. 6.2 mos, P= 0.016). Combined analysis of EREG changes showed that pts with either increased at 2nd or decreased at PD had significantly longer PFS and OS compared to those with both decreased at 2nd and increased at PD (3.0 vs 2.0 mos, HR: 0.47, 95%CI: 0.24-0.93, P= 0.031; 10.8 vs 5.3 mos, HR: 0.30, 95%CI: 0.14-0.61, P= 0.001). The findings were confirmed in the multivariate analysis for OS (HR: 0.311, 95%CI: 0.15-0.66, P= 0.002), and no significant differences were observed in the control cohort. Conclusions: Our preclinical data-based translational validation study suggests that serum EREG levels may predict clinical outcome in mCRC pts receiving TAS-102.
Genomic landscapes of brain metastasis patients of colorectal cancer to reveal clinical potential of individualized therapies.
Authors: Sun Jing , Wang Cheng , Gu Yayun , Yu Jian , Hu Zhibin , Gu Yanhong 
Published: January 2019

674 Background: Brain metastasis (BM) from colorectal cancer (CRC) is rare with 0.6-2.9% incidence rising in decades partly due to improved systemic treatment and prolonged survival. CRC patients had poor prognosis after BM because of lack of effective therapy. Commonly, only isolated BM of CRC patients are candidates for surgery and decisions for individualized therapies in patients with BM are often made according to primary-tumor biopsies, however, whether genomic features were similar in BMs and in primary CRC remained unknown. Thus, it is urgent to describe the molecular landscapes of BM genomics and to identify potentially clinically informative alterations. Methods: We conducted whole-exome sequencing on 15 “trios” of patient-matched brain metastases, primary CRC tumors, and adjacent-normal samples. Sequencing data processing and analysis were performed using pipeline of GATK best practice. Mutect2 algorithm were used to identify somatic substitutions in targeted exons. Clonal Evolution Suite was applied to evaluatecancer-cell fraction (CCF) for each mutation. Results: We identified 24,988 somatic mutations from CRC and their paired BM. In addition to the signature of age, we deciphered two mutational signatures, which was indicators of homologous recombination deficiency (HRD) and DNA mismatch repair deficiency (MMRD) respectively. The fraction of two signatures were significantly higher in BM than in primary CRC samples ( P< 0.001). Further analysis revealed BM-specific mutations (CCFBM= 1 and CCFPrimary< 0.5) in BRCA1 and BRCA2 and a significantly higher microsatellite instability status in BM patients ( P< 0.05). Additional BM-specific mutations were identified in genes from TARGET database for which somatic alterations have therapeutic or prognostic implications. We identified recurrent BM-specific mutations in voltage-gated sodium channel proteins ( SNC7A and SCN2A). Conclusions: It has been proved that patients with advanced HRD and MMRD are sensitive to PARP inhibitors and PD-1 blockade respectively. We provide new candidate targets for molecular therapies. Our findings provide new clinical potential for individualized therapies of BM patients of CRC.
Tumor sideness and mutational status: The potential effects on mCRC pts survival and treatment outcomes.
Authors: Sezer Emel , Eser Kadir , Onder Arif Hakan , Ozturk Banu 
Published: January 2019

682 Background: The treatment of mCRC has been changed with identification of different clinical behaviour of right and left sided tumors. Right-sided primary was associated with high mutational burden, worse prognosis and poor anti-EGFR response. We aimed to investigate the association between tumor site and survival, mutational status and treatment outcome of mCRC pts. Methods: The data of mCRC pts in two-cancer center in South Anatolia were retrospectively analyzed. The effects of tumor sidedness, treatment, braf on survival of mCRC pts were investigated using the log rank test. The Kaplan- Meier survival estimates were calculated. Results: A total of 210 (F/M=128/82) pts were included to study. Median age was 59.5 (range: 23-88) years. Right and left-sided tumour rates were 45 (21.7%) and 153 (72.9%), respectively. Kras, nras and braf mutation rates were 32.9, 5.5 and 6.7 %, respectively. Median follow-up was 27.5 (range: 1.3-274.3) months. In the right-sided tumors, kras (52.5 vs. 33.8 %, p=0.0034) and braf (33.3 vs. 11.1%, p=0.022) mutation rates were more than left-sided ones. Median PFS (15.1 vs. 14.2 months) and OS (27.5 vs. 23.9 months) were higher in the pts with left-sided tumors, the difference was not significant. First line bevacizumab was used in 76 (55%) in left, 15 (36%) in right, anti-EGFR was used in 27 (20%) in left, 11 (25%) in right-sided tumors. According to tumor side, there was no significant survival difference between treatment arms. In the pts with left-sided tumors, median OS was 39.3 months with anti-EGFR, 27.3 months with bevacizumab. Right-sided primary was associated with worse survival. Median OS was similar between braf wild and mutant tumours. Conclusions: Our mutation rates were similar with the literature. Braf mutations were more frequent in right-side tumors. Right-sided primary was associated with poor prognosis. However, the survival difference was not significant. Best survival rates were found with first-line anti-EGFR treatment in the pts with left-sided tumors, but only 20% pts used anti-EGFR at first line in this group. Due to low anti-EGFR usage at first line, survival rates were similar between treatment arms.
Platinum deposition in skin as a possible mechanism for peripheral sensory neuropathy (PSN) in patients (pts) with colorectal cancer (CRC) following oxaliplatin-based therapy.
Authors: Cao Yanshuo , Chang Qing , Zhang Wenjiang , Ornatsky Olga , Chen Eric Xueyu 
Published: January 2019

685 Background: Oxaliplatin plus fluorouracil (FOLFOX) is a standard treatment for CRC pts. One of the most common and dose-limiting side effects of oxaliplatin is PSN. The mechanism of this phenomenon is poorly understood. Previous studies suggested that higher serum platinum levels were related to more severe neuropathy in testicular cancer pts. Methods: CRC pts who completed adjuvant FOLFOX at least 6 months prior to enrollment are eligible. Baseline demographic and treatment information were collected. EORTC CIPN20 (with EORTC QLQ-C30) questionnaire was used for self-reported PSN symptom assessment. Peripheral blood samples were collected for total/free platinum concentrations using high-performance liquid chromatography with tandem mass spectrometry (HPLC/MS-MS). Skin biopsies were obtained from the lower leg of consented pts. Imaging mass cytometry (IMC) was used to visualize platinum deposition (195Pt) and intra-epidermal nerve fiber (IENF) (PGP9.5-154Sm) in formalin-fixed paraffin embedded (FFPE) skin biopsy samples stained with a metal-conjugated antibody cocktail. Results: Nine patients were enrolled. Median age was 51.8 yr (range: 34.5-69.4 yr); male/ female: 5/4; mean cumulative dose of oxaliplatin was 800.7 ± 188.2 mg/m2; median time from last dose of oxaliplatin to enrollment was 48 months (range: 7.2-65.6 months). The mean sensory score from CIPN20 was 15.4 ± 4.3 (range: 10-25). Platinum was undetectable in plasma samples collected from all 9 patients. In skin samples, IMC showed significant platinum depositions and IENF. Conclusions: Severity of PSN was not related to cumulative dose of oxaliplatin or interval from last dose of oxaliplatin. Although platinum was undetectable in plasma in these patients, platinum was readily detectable in skin biopsies up to 65.6 months post completion of FOLFOX. This is the first demonstration of platinum deposition in skin post oxaliplatin treatment and it provides a possible mechanism for oxaliplatin-induced PSN.
The prognostic impact of neutrophil to lymphocyte ratio in patients with recurrent or metastatic esophageal squamous cell carcinoma receiving immune checkpoint inhibitors.
Authors: Guo Jhe-Cyuan , Lin Chia-Chi , Huang Ta-Chen , Hsieh Min-Shu , Hsu Chih-Hung 
Published: January 2019

69 Background: The study explored the prognostic impacts of clinical parameters including neutrophil to lymphocyte ratio (NLR) in recurrent/metastatic esophageal squamous cell carcinoma (R/M ESCC) patients receiving anti-programmed cell death protein-1 (PD-1)/PD ligand 1 (PD-L1)-based therapy. Methods: Thirty-eight patients were enrolled. Tumor response evaluation was made according to Response Evaluation Criteria in Solid Tumours 1.1, and the clinical benefit response (CBR) was defined as complete response, partial response or stable disease at least 6 months. Clinical factors were analyzed for their impacts on patients' overall survival (OS) and progression-free survival (PFS). Formalin-fixed, paraffin-embedded tissues from 8 patients were analyzed by NanoString nCounter Human PanCancer Immune Profiling (NanoString Technologies, Seattle, WA, US). Results: Twenty-six recurrent and 12 de novo metastatic ESCC patients were enrolled. The response rate is 11.8%, and the CBR rate was 21.1%. The median PFS and OS are 2.7 and 5.5 months, respectively. The CBR group has lower blood white blood cells (WBC) ( P = 0.029), monocytes (p = 0.003), and NLR (p = 0.005). In univariate analysis, WBC, neutrophils, and NLR were statistically associated with PFS; performance status (PS), disease extent, albumin, WBC, neutrophils, and NLR were statistically associated with OS. In multivariate analysis, NLR (p = 0.007) was statistically associated with PFS; PS (p = 0.029) and NLR (p = 0.050) were statistically associated with OS. On examining the immune-related genes in ESCC tissues’ microenvironment, the ratios of mast cells, neutrophils, and macrophages relative to tumor-infiltrating lymphocytes (TILs) have significantly lower in the CBR group than in the non-CBR group. Conclusions: High NLR was associated with inferior prognosis in R/M ESCC patients receiving anti-PD-1/PD-L1-based therapy. The increased ratio of neutrophil to TILs in the ESCC tumor microenvironment of non-CBR patients may suggest a mechanistic role of neutrophils in affecting the efficacy of anti-PD-1/PD-L1 therapy. (Supported by the grant of MOST 105-2314-B-002 -186 -MY3)
Next-generation expression analysis (NanoString) to develop prognostic and predictive gene signatures for patients with locally advanced rectal cancer treated with neoadjuvant chemoradiotherapy.
Authors: Milano Annalisa , Borro Marina , Pilozzi Emanuela , Montori Andrea , Mazzotta Marco , Lorenzon Laura , Caivano Donatella , Chiloiro Giuditta , Botticelli Andrea , Mazzuca Federica , Osti Mattia Falchetto , Simmaco Maurizio , Ruco Luigi , Valentini Vincenzo , Marchetti Paolo 
Published: January 2019

700 Background: The standard of care for locally advanced rectal cancer (RC) is neoadjuvant chemoradiotherapy (CRT) with 5FU aimed to tumor downstaging prior to radical resection but there is a wide spectrum of responses to it, from none to complete. The aim of this project is to validate top candidate genes previously identified by microarray studies as prognostic and predictive classifiers of locally advanced RC, using the NanoString nCounter Platform. Methods: Two cohorts of RC patients were identified according to tumor regression grade (TRG) of AJCC Staging Manual (7th) system: 1) good prognosis: patients that after neoadjuvant CRT obtained TRG0 (complete response); 2) poor prognosis: patients with TRG1 (moderate response), patients with TRG2 (minimum response rate) and patients with TRG3 (poor response). Pre-treatment biopsies tissues from ten TRG0 patients (ID TRG0bio) and thirteen TRG1-3 patients (ID TRG1-3bio) were macro-dissected from FFPE sections, RNA isolated and used for expression profiling of a 305 genes custom code set consisting of 12 normalizer genes, 101 prognostic genes (markers of stemness, invasiveness, proliferation, drug-resistance), 192 predictive genes (involved in response to 5-FU, to radiation therapy and in the response to CRT). All samples were normalized using the geometric mean of the housekeeper genes. P-values were calculated by student’s t-test and was consider significance if was less than 0.05. Gene-specific RNA expression profiles were compared using Spearman's correlation. The heat map was generated using MeV 4.9.0. Results: When we compared TRG0bio to TRG1-3bio tissues, among the 305 genes assayed, changes in expression levels of 18 genes (SSB, GAPDH, TXNDC9, DUT, PKM, STAT1,SLC28A3, DAG1, TYMS, FERMT1, ARNT,SLC6A6, SMAD3, SCRN1, POU5F1, GNG4, PDRG1, ATP5E) were statistically significant. Conclusions: Results suggest that TRG0 RC is characterized by distinct molecular events compared TRG1-3 disease. Next steps will be: to amplify sample size, to understand signaling pathways of top differentially expressed genes and to validate prospectively our gene signature.