bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcriptomic profiles to differentiate colon and rectal adenocarcinomas.
Authors: Hogan John , Dejulius Kathryn , Li Xiaoxia , Coffey John Calvin , Kalady Matthew 
Published: February 2017

468 Background: Dissimilarity exists between colon and rectal cancer at a genetic, clinical, and molecular level. This is likely to reflect variation at a transcriptomic level. Transcriptional studies of colorectal cancer have previously combined colonic and rectal adenocarcinoma in a single group. Consequently few studies accurately describe the transcriptional profile of colon and/or rectal cancer. This study aims to develop classifiers based on transcriptomic differences between colon and rectal cancer and utilize these classifiers to predict tumor origin (colon vs. rectum). Methods: Comparisons were made between cDNA microarrays derived from colon (87) and rectal (125) adenocarcinomas. Gene expression data was filtered according to standard deviation to retain only highly dysregulated genes. Genes differentially expressed between colon and rectal adenocarcinoma were identified on two groups t test (p<0.05, Bonferroni p value adjustment) and further analysed. Genes were rank ordered in terms of descending fold change. Comparisons included a) colon adenocarcinoma vs. rectal adenocarcinoma (stages I - III), b) stage II colon adenocarcinoma vs. stage II rectal adenocarcinoma and c) stage III colon adenocarcinoma vs. stage III rectal adenocarcinoma. For each comparison, those five genes with the greatest positive fold change were grouped in a classifier. Five separate tests were applied to evaluate the discriminatory capacity of each classifier and summary receiver operating characteristic curves generated for each classifier. Results: Genetic classifiers dervied from a comparison of stage II colon and stage II rectal adenocarcinoma were the most accurate in distinguishing tumor type (mean sensitivity 82.5%, mean specificity 81.7%). Classifiers derived from a pooled analysis comparing colon and rectal cancers (stages I - III) (mean sensitivity 79.8%, mean specificity 71.1%) and those derived from a comparison of stage III colon and stage III rectal cancers (mean sensitivity 57.1%, mean specificity 98.6%) were also accurate in determining tumor type (colon vs. rectum). Conclusions: Colon and rectal adenocarcinoma differs at a transcriptomic level. These findings provide insight into underlying biologic differences.
Molecular epidemiology of RAS/RAF-mutant colorectal cancer metastases.
Authors: Atreya Chloe Evelyn , Watters James , Rowley Steve , Lee Joon Sang , Iartchouk Oleg , Light Madelyn , Warren Robert S. , Venook Alan Paul 
Published: February 2017

470 Background: A comprehensive molecular characterization of primary colorectal cancers (CRC) was recently reported. Less is known about mutation patterns in CRC metastases and association with survival. Our sequencing analysis focused on CRC liver metastases with RAS/RAF mutations, representing a patient population with limited therapeutic options. Methods: DNA was extracted from formalin-fixed paraffin-embedded CRC liver metastases. Fifty tumors found by Sequenom MassARRAY to harbor KRAS, NRAS or BRAF mutations underwent next generation sequencing on the Ion AmpliSeq Comprehensive Cancer Panel of 409 genes. Co-investigators were blinded to Sequenom mutations identified at UCSF. Variants called by Strelka and VarScan were extensively filtered to control the False Positive Rate and find mutations occurring with > 5-10% variant allele frequency compared to normals. The dataset was evaluated for significant co-mutations, biclustering, and population probabilities of mutations. Results: Following sequencing, 37,744 variants were called in 409 genes with a median coverage depth of 1053x. After filtering to minimize false positives, 2335 variants in 315 genes remained. ARID1A and PIK3R1 were the most significantly associated co-mutation pair, P < 3.5e-5. Biclustering showed no stratification of patients; genes stratified only by mutation frequency. Further filtering yielded 1,186 variants present at < 1% allele frequency within 1,000 Genomes, of which 131 variants in 24 genes are referenced in the Catalog of Somatic Mutations in Cancer. In addition to anticipated mutations in mismatch repair genes and the RTK/RAS/PI3K, Wnt, TP53, and TGF beta pathways, infrequent mutations were found in Akt1, mTOR, MET and PPP2R1a. After APC, TP53 was the most commonly mutated gene, in 44% of the tumors (95% cl: 31.1% - 57.8%). Survival was similar with mutation of RAS/RAF plus either TP53 or PIK3CA. Conclusions: Next generation sequencing was used to characterize co-variants in RAS/RAF mutated CRC liver metastases. The complexity of our results is consistent with the clinical observation that targeting RAS/RAF mutated metastatic CRC is a formidable challenge. These analyses may nonetheless inform the design of future clinical trials.
Cancer stem cells profile and clinical outcome in stage III colon cancer patients receiving adjuvant oxaliplatin-based chemotherapy.
Authors: Giampieri Riccardo , Scartozzi Mario , Loretelli Cristian , Del Prete Michela , Faloppi Luca , Bianconi Maristella , Bittoni Alessandro , Mandolesi Alessandra , Bearzi Italo , Cascinu Stefano 
Published: February 2017

474 Background: Although an oxaliplatin-based adjuvant treatment is a widely accepted option for radically resected stage III colorectal cancer patients, it is not uncommon to observe an heterogeneous clinical outcome independently from stage. Cancer stem cells (CSC) profile has been suggested to regulate key steps leading to progression, relapse and metastasis and therefore may be responsible for this otherwise unpredictable heterogeneity. ALCAM, CD133, CD24, LRG5, SOX2, ALDH1A1 have been reported as potential markers for CSC, particularly in digestive system cancer. Aim of our study was to assess the role of these markers in determining clinical outcome for stage III colon cancer patients receiving adjuvant chemotherapy. Methods: Patients undergoing radical surgical resection for stage III colon cancer and receiving adjuvant oxaliplatin in combination with either 5FU or capecitabine were eligible for our analysis. CSC profile (ALCAM, CD133, CD24, LGR5, SOX2, ALDH1A1) was analysed by RT-PCR in primary tumour samples. The multivariate analysis also included adjustments for other variables such as T and N stage, sex, age and tumour location. Results: Seventy-eight patients were eligible for analysis. Only high ALCAM expression was associated with clinical outcome. In particular in colon tumours overexpressing ALCAM we observed a significant interaction for a higher risk of relapse (p = 0.04) and a reduced time to relapse (not reached vs. 33.24 months, HR:0.46, 95%CI:0.23-0.89, p = 0.02). There were no significant differences according to main stratification factors between the high ALCAM group vs. low ALCAM group. In our series N stage (N1 vs. N2-3) resulted also relevant for clinical outcome. Conclusions: Our analysis supports the hypothesis that ALCAM expression may represent a crucial marker for a better risk stratification in stage III colon cancer patients receiving adjuvant chemotherapy. According to our data we also suggest that other potential markers of CSC are probably ineffective for patients stratification. Patients expressing high ALCAM levels may be optimal candidates for therapy intensification and possibly different treatment options.
Correlation of peripheral blood lymphocyte counts with outcome and histopathologic features of lymphocytic inflammation in patients with stage II colorectal carcinoma.
Authors: Li-Chang Hector Hugo , Assarzadegan Naziheh , Messenger David , Grin Andrea , Howlett Christopher , Kirsch Richard 
Published: February 2017

475 Background: The prognostic importance of the local antitumor immune response in colorectal carcinoma (CRC) is well established. Recent studies suggest that systemic antitumor immunity may also impact on survival. This study aimed to determine the relationship between peripheral blood lymphocyte counts (PBLCs), reactive features in regional lymph nodes, local tumoral/peri-tumoral lymphocytic inflammation and survival in stage II CRC. Methods: Resection specimens from 185 patients with stage II CRC were assessed for peri-tumoral lymphocytic inflammation, tumor-infiltrating lymphocytes, lymph node yield, lymph node size, and reactive changes in individual lymph nodes. Reactive changes were scored semi-quantitatively and given a reactivity [R] score of 1-4 based on the presence and size of germinal centers. Pre-operative PBLCs and neutrophil counts were recorded. Results: Lower peripheral lymphocyte counts were associated with advanced age (p = 0.016), T4 disease (p = 0.006), venous invasion (p = 0.006), lymph node yields <12 (p = 0.024), smaller mean nodal diameters (p = 0.021), absence of tumor-infiltrating lymphocytes (p = 0.002) and fewer highly-reactive lymph nodes (R score 4) per case (p = 0.032). Cox regression analysis revealed that advanced age (Hazard Ratio, 1.03 per year [95% confidence interval, 1.01-1.05]; p = 0.015) and higher peripheral lymphocyte counts (HR, 0.52 per 1x109cells/L [95% CI, 0.31-0.86]; p = 0.011) were independently predictive of disease-free survival. Neutrophil counts were not associated with outcome. A higher neutrophil to lymphocyte ratio was associated with worse survival on univariate, but not multivariable analysis. Conclusions: The PBLC is an independent predictor of survival in stage II CRC, and is significantly associated with the immune status of regional lymph nodes and the local lymphocytic immune response.
Potential regulators of HER2 activity in HER2-overexpressing gastric and gastroesophageal tumors: Analysis of HER3 and heregulin expression.
Authors: Kudla Arthur J. , Paragas Violette , Geretti Elena , Onsum Matthew D. , McDonagh Charlotte Fenton 
Published: February 2017

48 Background: HER2 is overexpressed in gastric and gastroesophageal junction (GEJ) tumors. Though treatment of these tumors with the HER2-targeted agent trastuzumab offers clinical benefit, patients ultimately progress. Signaling by HER2/HER3 heterodimers following activation by HER3’s ligand heregulin has been shown to be a resistance mechanism to trastuzumab. The objective of this study was to quantitate HER2, HER3 and heregulin in gastric and GEJ tumor samples to determine whether these tumors express components for signaling through this complex and thus have potential for developing trastuzumab resistance. Methods: A novel immunofluorescent assay was used to quantitate HER2 and cytokeratin in 236 gastric and GEJ tumors. Using image analysis, each cell within a section was classified as tumor or non-tumor based on cytokeratin level. HER2 fluorescence was also quantitated in each cell and converted to number of HER2 receptors per cell using a standard curve from an array of cell lines with defined HER2. The assay’s single cell output enables an assessment of HER2 heterogeneity in any tissue. In those tumors overexpressing HER2, HER3 and heregulin were quantitated using immunofluorescence as for HER2 and by RT-PCR. Results: In concordance with published data, HER2 was overexpressed in ~10% of gastric and ~20% of GEJ tumors. HER2-overexpressing tumors could be divided into two groups with levels of HER2 consistent with IHC scores of 2+ and 3+ as assessed by clinical assays. All HER2-overexpressing samples also expressed HER3 and heregulin. Heregulin expression was detected in both tumor cells and/or in adjacent stroma. Conclusions: HER3 and heregulin are present in HER2-overexpressing gastric and GEJ tumors. To evaluate the importance of HER3 and heregulin in these patients, a randomized open label second line Phase 2 trial has been initiated with MM-111, a HER2/HER3 bispecific antibody that inhibits HER3 activity in HER2-overexpressing cells by blocking heregulin binding. HER2, HER3 and heregulin expression will be retrospectively analyzed in tumor samples from patients in this trial, providing further insight into the role of this complex in gastric and GEJ cancer.
SDF-1 and VEGF-C as potential circulating angiogenic biomarkers for bevacizumab in patients with metastatic colorectal cancer.
Authors: Suenaga Mitsukuni , Matsusaka Satoshi , Shinozaki Eiji , Ogura Mariko , Ozaka Masato , Nakayama Izuma , Wakatsuki Takeru , Chin Keisho , Mizunuma Nobuyuki , Yamaguchi Toshiharu 
Published: February 2017

480 Background: Bevacizumab (BV) plus chemotherapy (chemo) has been shown to improve survival for metastatic colorectal cancer (mCRC). Stromal cell-derived factor-1 (SDF-1) is known as a ligand for CXCR-4. We previously reported that proportion of CXCR4-positive circulating endothelial cells at baseline was correlated with the prognosis of BV plus chemo (Matsusaka, et al. Cancer. 2011). The aim of this study was to investigate changes during treatment in serum candidate cytokines including SDF-1 as potential markers of treatment response to BV. Methods: Patients receiving first-line BV plus chemo with mCRC were enrolled in this prospective study. Serum samples were analyzed before initiation of treatment and during treatment (on days 14 and 56) and at the time of progressive disease. Correlation between tumor response and changes in serum levels of the cytokines (such as VEGF, SDF-1, Ang-1 and -2, etc.) were investigated. Differences in the means of continuous measurements were tested by the Student’s t test. A two-way repeated-measures analysis of variance was used to evaluate differences between sequential continuous variables. Results: 24 were enrolled at the first interim analysis. 14 patients were assessable; some who got conversion surgery or discontinued treatment due to toxicity in early were excluded. Tumor response was achieved in 57% of the patients. SDF-1 levels at baseline (p=0.045) and on days 14 (p=0.049) were significantly lower in tumor responder, while a trend toward higher on days 56 compared to non-responder. The results of a two-way repeated-measures analysis of variance to evaluate differences between sequential continuous variables showed significant differences in VEGF-C (p=0.043) and SDF-1 (p=0.02), influenced by tumor response. Serum levels of SDF-1 trended toward increase on days 14 and decrease on days 56, whilst VEGF-C trended toward decrease on days 14 and 56. Conclusions: Changes Serum levels of SDF-1 and VEGF-C showed correlation with tumor response to BV plus chemo, suggesting that these surrogate markers may represent anti-angiogenic condition for BV treatment. This study is currently ongoing, and further analysis will be performed in more population.
The role of the organic anion transporting polypeptide OATP4A1 in immunactivation in colorectal cancer and inflammatory colon disease.
Authors: Ausch Christoph Alexander , Zotter Simone , Scheikh Maidah , Bauer Heike , Mollik Marina , Bajna Erika , Sebesta Christian , Reiner Angelika , Thalhammer Theresia , Buxhofer-Ausch Veronika 
Published: February 2017

481 Background: OATP-transporter proteins, such as OATP4A1, present influence cancer progression by providing compounds (hormones, prostaglandins, cyclic nucleotides, second messenger proteins, drugs) which either inhibit or stimulate tumor cells growth. Therefore, OATP expression in cancer cells and in the stroma, i.e., the microenvironment surrounding the epithelial cells can become a critical parameter. Methods: OATP4A1 was investigated in paraffin-embedded specimens from 148 patients with colorectal cancer and 20 with diverticulitis by immunohistochemistry (IHC) on an automatic quantitative microscopic image analysis system (TissuesFaxs). With the Histoquest program, the immunoreactive score (IRS), was calculated from the degree of the staining intensity and the number of OATP4A1-positive cells. To identify OATP4A1+-cells, double-immunofluorescence staining (IF) was done with antibodies against appropriate cellular markers. Results: OATP4A1 was located in the membrane and cytosol of colon cancer cells and immune cells, while membranous OATP4A1staining was seen in normal mucosa. OATP4A1 levels were higher in cancer cells in patients without tumor recurrence for up to 5 years (NR) than in patients with an early relapse (R) having IRS of 4391±231 and 3026±373 (Mean±SEM), respectively. Highest OATP4A1 levels were observed in immune cells in the tumors of Rs (IRS, 5712 ±254, while in NRs they were lower (IRS: 3549±358; p=0.05). In both groups, OATP4A1 levels in stroma cells were low (288±54 vs. 611±82). OATP4A1 expressing immune cell subtypes in cancer and diverticulitis sections were identified as CD45+ leukocytes, CD3+ T- and CD20+ B-cells, CD68+ macrophages, CD34+precursor cells. OATP4A1 was not detectable in Conclusions: High levels of OATP4A1 in immune cells in malignant and non-malignant colon disease suggest a role of the transporter in the activation of the immune system in malignant and non-malignant colon disease. Whether OATP4A1 might be a therapeutical target has to be established.
A novel and robust technique for determining lymph node status in colorectal cancer.
Authors: Hogan John , O Callaghan Michael , Judge Conor , O Connor Cormac , Aziz A , Burke John , Dunne Cormac , Kalady Matthew , Walsh Stewart , Coffey Calven 
Published: February 2017

483 Background: Currently, techniques that determine lymph node positivity (prior to resection) have poor sensitivity and specificity. The ability to determine lymph node status, based on preoperative biopsies, would greatly assist in planning treatment in colorectal cancer. This is particularly relevant in polyp-detected cancers. This study aims to harness the potential of public gene expression repositories, to develop gene expression profiles that could accurately determine nodal status in colorectal cancer. Methods: Public gene expression repositories were screened for experiments comparing metastatic and non-metastatic colorectal cancer. A customized graphic user interface was developed to extract genes dysregulated across the majority of identified studies (i.e., consensus profiles or “CP”). The utility of CP was tested by determining if classifiers could be derived that determined nodal positivity or negativity. CP-derived classifiers were tested on separate Affymetrix and Illumina–based experiments and collated outputs compiled in summary-receiver operator curve characteristic format. The association between classification and oncologic outcome was determined using an additional, independent data set. Results: Four consensus profiles were generated from which classifiers were derived that accurately determined node positive and negative status (pooled AUC were 0.79 ± 0.04 and 0.8 ± 0.03 for nodal positivity and negativity respectively). Overall AUC ranged from 0.73 to 0.86 demonstrating high accuracy across consensus profile type, classification technique and array platform used. As CP enabled classification of nodal status, survival outcomes could be compared for those predicted node negative or positive. Patterns of disease-free and overall survival were identical to those observed for standard histopathologic nodal status. Genes contained within consensus profiles were strongly linked to the metastatic process and included FYN, WNT5A, COL8A1 and BMP. Conclusions: Microarray expression data available in public gene expression repositories can be harnessed to generate consensus profiles. The latter are a source of classifiers that have prognostic and predictive properties.
Association between KRAS mutation and lung metastasis in advanced colorectal cancer.
Authors: Pereira Allan Andresson Lima , Rego Juliana Florinda De Mendonga , Morris Van Karlyle , Overman Michael J. , Eng Cathy , Garrett Chris R. , Ferrarotto Renata , Lee Michael Sangmin , Jiang Zhiqin , Hoff Paulo Marcelo , Vauthey Jean-Nicolas , Vilar Sanchez Eduardo , Maru Dipen M. , Kopetz Scott 
Published: February 2017

494 Background: The role of KRAS status in the time-dependent pattern of metastasis in colorectal cancer (CRC) patients has been reported but not validated in independent series of unresectable metastatic CRC. We aimed to determine its potential value as a predictive factor for development of lung metastasis. Methods: We retrospectively evaluated data from MD Anderson Cancer Center from 494 patients diagnosed with metastatic CRC with KRAS mutation testing (codons 12, 13, 61) by Sanger sequencing or mass spectroscopy genotyping in 2008 through 2010. Medical records and image reports were assessed to determine date of lung metastasis diagnosis, pattern of lung involvement and presence of thoracic lymph nodal metastasis. Time-to-lung metastasis (TTLM), lung-metastasis-free survival (LMFS) and overall survival (OS) were calculated from the time of diagnosis of first metastasis in any site according to the Kaplan-Meier method and were compared by log-rank test. Results: We included 494 patients (41% female) with a median age of 55 years. 292 tumors were KRAS wild type (WT, 59%) and 202 (41%) were KRAS mutants. OS was not different between the groups (45.5 months for KRAS mutants vs. 50.6 months for KRAS wild type; p=0.6). At the time of diagnosis of metastatic disease, 36% of patient had lung metastases, with 1.6-fold higher odds of lung metastases with a KRAS mutation (p=0.013, 95% CI 1.1 – 2.4). Compared to KRAS WT, KRAS mutations were associated with a shorter TTLM (15.2 vs. 22.4 months; p=0.002) and LMFS (12.9 vs. 16.7 months; p= 0.019). There was no difference in thoracic lymph node involvement (p= 0.18), number of lung metastasis (p=0.71), lung lobes involved (p=0.19) or disease in bilateral lung (p=0.27) according to KRAS status. There were no differences in lung metastasis frequency or pattern between codons 12, 13, and 61 mutations. Conclusions: In this retrospective analysis, lung metastases were more common at diagnosis of mCRC in KRAS mutant patients and more likely to develop during the disease course. This data suggests a potential role for KRAS mutations in determining a metastatic tropism of CRC to the lung and can be used to risk stratify patients.
Changes in circulating lymphocyte counts and tumor-infiltrating lymphocyte subpopulations among patients receiving endorectal brachytherapy for rectal adenocarcinoma.
Authors: Ellsworth Susannah G. , Sopha Sabrina C. , Drake Charles G. , Campian Jian Li , Gearhart Susan , Azad Nilofer Saba , Hacker-Prietz Amy , Grossman Stuart A. , Herman Joseph M. 
Published: February 2017

500 Background: Radiation-induced lymphopenia (RIL) is common in patients with rectal cancer and is associated with worse outcomes in rectal cancer and other solid tumors. We investigated whether endorectal brachytherapy (EB) is associated with milder RIL than external radiation treatment (XRT) in patients with rectal cancer and whether EB is associated with altered tumor-infiltrating lymphocyte (TIL) subpopulations. Methods: Records from 11 patients enrolled in a prospective study of EB for T2-3, N0-1 rectal cancer were reviewed; total lymphocyte counts (TLC) at baseline and 2 months after treatment were recorded. EB was given to tumor alone (6.5Gy x 4). XRT was given to the whole pelvis (median dose 50.4Gy). All patients underwent proctectomy after EB/XRT. TLCs from EB patients were compared to 62 rectal cancer patients receiving pelvic XRT + capecitabine. Proctectomy specimens were immunostained for TIL (CD3, CD4, CD8, FoxP3, and CD25) subtypes. Results: Median baseline TLC in EB patients was 1930 vs 1570 cells/uL in XRT patients (p>0.05). Two months after treatment, median TLC was 1550 in EB patients vs 520 in XRT patients (p<0.01). EB patients had higher absolute numbers of CD3, CD4, CD8, and FoxP3+ TILs (Table). Conclusions: EB spares circulating lymphocytes and is associated with increased TIL expression after therapy. Further investigation is needed to determine if there is a causal association between these phenomena and if the increased TIL expression in EB patients is associated with better outcomes in these patients. [Table: see text]