bluuebunny/crossref_metadata_2025_split huggingface dataset:
Type II RAF inhibition predicts superior ERK suppression compared to type I RAF inhibition in different BRAF mutant types recurrently found in lung cancer.
Authors: Giron Philippe , Noeparast Amir , De Brakeleer Sylvia , De Ridder Ulrike , Teugels Erik , De Greve Jacques 
Published: September 2018

e23154 Background: Somatic driver BRAF mutations account for 6-8% of lung cancers. As opposed to melanoma in which V600E mutant BRAF predominates, the majority of lung cancer-derived BRAF mutations are non-V600. Yet, the efficacy of RAF-inhibitors and the possible resistance mechanisms in non-V600 BRAF mutant cells remain to be uncovered. Recently, we have shown that non-V600 BRAF mutations recurrently found in lung cancer predict sensitivity to the combination of type I RAF inhibitor Dabrafenib and a MEK inhibitor Trametinib. As a single agent, Dabrafenib shows only weak suppression of mutant BRAF-induced ERK signaling; moreover it can induce ERK paradoxical activation in CRAF overexpressing cells. Methods: Several recombinant BRAF expression vectors were generated by performing site-directed mutagenesis. We compared the effects of Dabrafenib and a type II RAF inhibitor (AZD-628) at clinically relevant dose as single agents or in combination with MEK inhibitor Trametinib on ERK activity in HEK293T cells expressing several tumor-derived BRAF mutants and a non-V600 BRAF mutant lung cancer cell line (H1666). Viability and caspase3/7 activation assays were performed using the H1666 cell line model. Results: In contrast to Dabrafenib, AZD-628 does not induce paradoxical ERK activation in CRAF expressing cells. Increased CRAF expression desensitizes BRAF-mutant expressing cells to Dabrafenib but not to AZD-628. Notably, AZD-628 has superior ERK-inhibitory effect in HEK293T cells co-expressing several different BRAF-mutants with CRAF and in H1666 cells. Combination of Trametinib and AZD-628 has superior MEK-inhibitory and pro-apoptotic effect in H1666 cells compared to combined Trametinib/Dabrafenib. Moreover, upon down titration of the RAF inhibitors with a steady dose of Trametinib, AZD-628 resulted in overall stronger effect on viability compared to Dabrafenib. Conclusions: In our in vitro model, we obtained strong indications that at conventional doses, type II RAF-inhibitor AZD628 is superior to type I RAF-inhibitor Dabrafenib in combination with MEK inhibitor Trametinib for the treatment of non-V600 BRAF mutant lung cancer.
Application of bioinformatics approach to identify indications for PFKFB3-mediated glycolysis inhibition as potential anticancer treatment.
Authors: Khodova Kristina , Pyatnitskiy Mikhail , Eremeeva Tatiana , Fedichev Peter 
Published: September 2018

e23158 Background: Glycolysis is one of the mechanisms which enables cancer cells to adapt to intermittent oxygen deprivation and obtain the best available metabolic strategy in the lack of resources. Therefore, inhibition of 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase-3 (PFKFB3) enzyme, one of the glycolysis pathway regulators, may result in decreased tumor metabolism, as well as suppressed cell growth. Additionally it has been shown that PFKFB3 is involved in angiogenesis regulation, which contributes to tumor growth, and in immune cells activation, which mediates anti-tumor immune response. Methods: We performed the analysis of available data on the role of PFKFB3 gene expression in various cancer types, i.e. patients’ stratification to identify tumors in which PFKFB3 inhibition improved survival. We exploited TCGA expression data and applied cluster analysis and Cox-regression analysis. The objective was to detect the relation between the increased level of PFKFB3 gene expression and patients’ survival. We also compared the clusters we identified with TCGA metadata to define whether any of them fall down into well-established tumor subtypes. Results: As a result we selected four clusters among solid tumor types, in which increased expression of the target was related to significant decrease in overall survival rate. These include breast cancer, renal cell carcinoma, cervical carcinoma, and leiomyosarcoma. We managed to cross-validate the obtained results on independent datasets. The results show potential indications for PFKFB3 inhibitors. Using our proprietary molecular modelling tool, we designed a series of novel small molecule PFKFB3 inhibitors to target the fructose binding pocket rather than occupying the ATP-pocket which leads to the highly selective inhibition and strong reduction of potential off-target binding. We proved target coverage by performing in vitro biochemical assays. Conclusions: Our current data provide strong rationale for further preclinical and clinical development of PFKFB3 inhibitors as novel anticancer treatment with the potential to overcome resistance to chemo- or radiotherapy.
The role of procollagen alpha 1 type 1 (Col1A1) on invasion and cellular signaling in glioma cells.
Authors: Savaraj Niramol , Chen Shumei , Wu Chunjing , Li Ying-Ying , Wangpaichitr Medhi , Benveniste Ronald , Feun Lynn G. 
Published: September 2018

e23165 Background: We have previously shown that Procollagen alpha 1 type 1 (Col1A1) is found more in low and intermediate grade glioma and less often in glioblastoma(GBM) (Cancer Invest. 23:577, 2005). We now investigate their role in cellular function. Methods: 4 glioma cell lines: Glioma 1 and U118 express high amount of Col1A1 ( Col1A1+) ; A172 and SW1783 express insignificant amount of Col1A1 ( Col1A1 - ) as the model . All four cell lines express SPARC. Scratch, transwell, and metrigel assay were used to study migration and invasion. Cell cycles were analyzed by flowcytometry. Results: U118 has the highest amount of SPARC followed by A172, SW1783 and Glioma 1. Thus it does not appear to have any relationship between these two proteins which are known as binding partner. Glioma 1 showed the least invasion and migration followed by U118, SW1783 and A172. Thus, Col1A1 expression appear to correlate with invasiveness. To further confirm this, we have silence Col1A1 in Glioma 1 and U118 using both siRNA and shRNA. All clones exhibit more migration and invasion. However, it does not affect both intracellular and extracellular levels of SPARC. Silencing Col1A1 results in increasing G2M arrest; 11% in U118 and 6% in Glioma 1. However it does not affect cellular proliferation. To further verify this, we have overexpressed Col1A1 in A172 and SW1783 using plasmid containing Col1A1 and DDK tag. These Col1A1 (+) A172 and SW1783 transfectants exhibit less migration and invasion. However, there is no effect on SPARC levels. These Col1A1 positive cells exhibit 12% increase in Go/G1 arrest and decrease in proliferation. A limited protein array also showed that silencing Col1A1 increase in STAT3, 5 and 6 and AKT levels. Interestingly, a difference in sensitivity to STAT3/5 inhibitors also noted in parental and their Col1A1 knock down transfectants. Conclusions: our results support the role of Col1A1 in glioma cell invasiveness, and hence confirm our previous data which showed that Col1A1 is found more in low grade and intermediate grade glioma. Thus, Col1A1 could be an additional useful marker to assess the aggressiveness of GBM beside histopathological grading. Col1A1 may also play a role in cellular signaling pathway.
Concordance of PD-L1 expression detection in non-small cell lung cancer (NSCLC) tissue biopsies between OncoTect iO single cell PD-L1 quantification assay and immunohistochemistry (IHC).
Authors: Chargin Amanda , Morgan Rian Janine , Patterson Bruce Kendrick 
Published: September 2018

e23172 Background: PD-1/PD-L1 therapy has been shown to be effective in patients with NSCLC, specifically those with 50% PD-L1 expression or greater by IHC. Response rates for those with lower PD-L1 expression do not consistently correlate with PD-L1 amount. The OncoTect iO Lung PD-L1 Assay was designed to provide non-subjective quantification of PD-L1 expression on tumor cells and immune cells from a multitude of tumor types. The objective of this study was to compare OncoTect iO and the current method of PD-L1 testing by immunohistochemistry (IHC) in NSCLC biopsies. Methods: Eleven NSCLC tissues were obtained from two IRB approved sites. Fresh tissues were processed into single cell suspensions using the IVD IncellPREP Kit (IncellDx, Inc). Normal lung tissue adjacent to tumor sites was obtained for 9 of the samples. Cell suspensions were tested with the OncoTect iO Lung Assay which contains antibodies directed against PD-L1 (28-8), CD45, CD3, and CD8. Suspensions are fixed and permeabilized, labeled with the antibodies, and then stained with DAPI to identify intact, single cells, and to analyze cell cycle including aneuploidy.Matched FFPE sections were taken from the tissue biopsies and were tested at BioReference Laboratories with the Dako PD-L1 IHC 28-8 PharmDx Kit. Results: A cut-off of 4% was used for the OncoTect iO Assay and a positive result for the Dako assay is ≥ 5% of the tumor cells (equivalent to 5 cells out of 100). PD-L1 expression ranged from 0% to 75% in the tumor samples which is consistent with reported ranges. Seven samples were positive by OncoTect iO Lung and 6 were positive by IHC. Twelve samples were negative by OncoTect iO Lung and 13 were negative by IHC demonstrating a concordance of 95%. Of note, one tumor that was negative by OncoTect iO and IHC demonstrated 5% of aneuploidy tumor cells that were positive and most likely very rare to be detected in the assays. Conclusions: In this study, the concordance between Oncotect iO and IHC was 95%, however, the Oncotect iO Single Cell PD-L1 Quantification Assay was fast ( < 3 hours), non-subjective, and provided addition expression information for aneuploid tumor cells.
A combination of anti-PD-L1 mAb plus Lm-LLO-E6 vaccine to suppress tumor growth and metastasis in HPV-infected cancers.
Authors: Lin Po Lin , Yen Yun , Lee Huei 
Published: September 2018

e23175 Background: PD-1/PD-L1 immunotherapy is viewed as having clinical benefits in advanced cancers but is effective in only a few patients, suggesting that an efficient combination approach is needed to improve efficacy for certain non-small cell lung cancer (NSCLC) patients. Methods: PD-L1 and E6 oncoprotein expressions in lung tumors from 122 NSCLC patients were examined by immunohistochemistry and their prognostic value was evaluated by Kaplain-Meier and Cox regression analysis. HPV16-postive and negative TL-1 and TL-4 lung cancer and SiHa and C33A cervical cancer cells were used to test whether PD-L1 expression could be regulated by E6, not by E7 oncoprotein. Immune deficiency nude mice were used to test the possibility that combining anti-PD-L1 mAb with Lm-LLO-E6 vaccine could have a higher antitumor activity compared with anti-PD-L1 mAb or Lm-LLO-E6 vaccine alone. Results: Immunohistochemistry analysis indicated that PD-L1 expression was correlated with the E6 expression in tumors from 122 lung cancer patients. The poorest survival occurred in PD-L1-positive/E6-positive tumor. PD-L1 expression was increased by the expression of E6, but not the E7, oncoprotein in lung and cervical cancer cells. PD-L1 expression was responsible for E6-mediated colony formation and soft agar growth. Therefore, PD-L1 secreted from tumor cells may directly promote tumor progression, particularly in E6-positive tumors. A greater antitumor activity was obtained with anti-PD-L1 mAb+Lm-LLO-E6 vaccine than with anti-PD-L1 mAb or Lm-LLO-E6 alone in subcutaneous and metastatic tumors induced by TL-1 and SiHa cells. The longest survival time for nude mice was observed in the anti-PD-L1 mAb+Lm-LLO-E6 vaccine group. Conclusions: An anti-PD-L1 mAb+Lm-LLO-E6 vaccine may be an efficient treatment for suppression of tumor growth and metastasis induced by HPV-infected cells.
Conversion of nontumorigenic dormant MOLT3 by lactate into a glycolytic cancer via epigenetic changes and lymphangiognesis.
Authors: Haaga John , Coller Hilary , Kao Hung-Ying , Lee Richard T. 
Published: September 2018

e23176 Background: Lactate considered a "waste product" lactate is a multifunctional modulator. Processes modulated by lactate are: 1. initiation of the transformation of the microenvironment 2.production of hyaluronan which interacts with RHAMM to cause cell motility, stabilize mitotic spindle, and supports stem cells. With these many processes, we hypothesized that lactate might interrupt the dormant state of the MOLT3 dormant cell line. Previous authors Indraccola et al, PNAS, 2006 reported that the dormant MOLT3 cell line implanted in SCID mice could be interrupted to become tumorigenic by co-implantation with VEGF,FGF, or irradiated (dead) Kaposi Sarcoma. We used this model to determine if lactate could stimulate tumorigenesis in a similar manner. Methods: In multiple cohorts of SCID mice, lactate was coimplanted with MOLT3 cells. In approximately 40 days, tumors grew rapidly in an exponential manner. Arterial perfusion was measured by contrast enhanced dual energy CT and MRI perfusion. Immunohistochemistry was performed for vascular stains CD21,VEGFR3, Notch 1, Ephrin B, VEGFA,VEGFD, Macrophages, VEGFD. Rna sequencing was performed on six samples, 3 Molt3 cell plugs, 3 MOLT3/lactate tumors (sequencing done at UCLA, data processed at Broad Street Institute MIT). Results: The data confirmed lactates's modulator role. Perfusion studies showed no arterial flow. The IHC showed many cancer cell with many mitotic figures and apoptosis.IHC confirmed presence of numerous macrophages, increased VEGFD, lymphatics and no arteries. Indraccola's reported their tumors showed no mitotic figures. 1114 genes were up/down regulated. In general rna showed: 1.mitochondrial dysfunction 2.Down regulated tumor suppressors 3) Up regulated oncogenes 4)Increased Stem cell markers 5) increased NFK-b and other pathways. Conclusions: Lactate induced an avascular "cancer" with features similar to natural pancreatic ductal and triple negative breast cancer. Results question the universality of the angiogenic switch. We hypothesize Lactate from marophages may be the cause of inflammation induced cancer.
The prognostic significance of infiltrating immune cells subtypes in invasive ductal carcinoma of the breast.
Authors: Zheng Qiuhong 
Published: September 2018

e23177 Background: To explore the correlation between tumour infiltrating immune cell subsets and breast cancer prognosis. Methods: Specimens of 102 patients with invasive breast ductal carcinoma were analyzed for immune -related markers (CD8, CD20, FoxP3 and CD68). The number of positive cells in 3 most highly-stained intratumoural stroma areas of the primary tumour was counted. The mean number of each marker was calculated and used to divide patients into two groups respectively (CD8high/CD8low group, CD20high/CD20low group, FOXP3high/ FOXP3 low group and CD68high/CD68 low group). Results: Kaplan–Meier survival analysis showed : (A) For all patients, high tumour-infiltrating CD8+ and CD20+ B lymphocytes , low tumour-infiltrating FoxP3+ Treg and CD68+ macrophages all increased the OS and DFS (P < 0.05); (B) For both the 35 ER negative and the 45 lymphonode negative patients, high CD8+ CTLs increased the OS and DFS(P < 0.05). Multivariate analysis of OS and DFS showed for all patients, high CD8+ CTLs and low FoxP3+ Treg were related to good OS and DFS(P < 0.05). Conclusions: high number of tumour-infiltrating CD8 and low FoxP3 T lymphocytes both could function as potential independent prognostic markers for invasive ductal breast carcinoma .
Molecular classification of cancers with an uncertain diagnosis as candidates for immunotherapy.
Authors: Barzi Afsaneh , Soifer Harris S , Israel Mason , Schnabel Catherine A. 
Published: September 2018

e23183 Background: FDA approvals of immunotherapy checkpoint inhibitors (CPIs) are based on organ site and thus cancers of unknown primary or with uncertain tumor type diagnoses have limited access to these revolutionary treatments. The 92-gene assay (CancerTYPE ID) is a validated gene expression classifier of 50 tumor type/subtypes for metastatic patients, six of which (lung adenocarcinoma, lung squamous cell, head & neck squamous cell, urinary bladder, kidney, and melanoma) have FDA-approved indications for CPIs. Study objectives were to analyze the distribution of the 6 tumor types with available CPIs in a large dataset of clinical cases and report patient and disease characteristics for this subset. Methods: A de-identified database was created under an IRB approved protocol that contains pathology and molecular information from consecutive cases submitted for clinical testing with the 92-gene assay. The distribution of molecular diagnoses was analyzed based on biopsy site, age, and gender. Chi-squared tests were used to compare between subgroups. Results: A total of 24,484 patients were available for analysis. Median age was 66y and 46% were male. The assay rendered a molecular diagnosis with an approved CPI in 27% (N = 6536) of cases. The most common biopsy sites were lymph node (23%), lung (15%) and liver (12%). Lung adenocarcinoma (31%) was the most common molecular diagnoses, followed by urinary bladder (20%), and head & neck squamous (16%). The proportion of melanoma molecular diagnoses decreased with age (11% in < 40y vs 4-6% across other age groups, p < 0.001), whereas the proportion of urinary bladder molecular diagnoses increased from 15% in < 40y to 23% in patients > 65y (p < 0.001). Women had a higher proportion of lung adenocarcinoma molecular diagnoses (36% vs 28% in men; p < 0.001), while kidney molecular diagnoses were more common in men (14% vs 8% in women; p < 0.001). Conclusions: These findings highlight the utility of molecular classification to identify metastatic cancers with unknown or uncertain tumor type diagnoses that are eligible for CPI. In addition, there was a significant difference in the distribution of 92-gene molecular diagnoses by age and gender among cancers susceptible to CPI.
Elucidation of the molecular and clinical impact of microsatellite instability in Brazilian colorectal cancer patients at Barretos Cancer Hospital.
Authors: Berardinelli Gustavo Noriz , Duraes Ronilson Oliveira , de Oliveira Marco Antonio , Scapulatempo Cristovam , Peixoto-Guimarães Denise , Pereira Rui , Reis Rui Manuel 
Published: September 2018

e23185 Background: Colorectal cancer (CRC) has a high incidence and mortality in the world and in Brazil. The microsatellite instability (MSI) pathway is associated with a distinct mutational profile, which affects MSI target genes contributing to a different clinical impact. Reports have suggested that CRC aspects may be influenced by patients’ ancestry. This study aims to elucidate the molecular and clinical impact of MSI, and to determine Brazilian patients’ genetic ancestry. Methods: We enrolled 1013 patients. MSI was evaluated by molecular analysis, and MSI-H cases were further analyzed for alterations in 24 MSI-target genes, BRAF V600E, and MLH1 methylation. Genetic ancestry was evaluated by an AIMs panel. Results: MSI-H was observed in 10.5% of the cases. MSI-H cases were significantly associated with: right colon localization, staging II, absence of metastasis, mucinous histological type, III/undifferentiated histological grade, presence of synchronic tumor, no disease recurrence, and complete cure response. The most altered MSI target genes was HSP110, followed by ATM and EGFR. The frequency of BRAF V600E mutation was 26.4% and of MLH1 methylation was 72.3% in MSI-H cases. No significant overall survival (OS) differences were observed among the MSI statuses, neither when stratified by 5-FU treatments, nor by HSP110 mutational status. The average ancestry proportion was 74% of European, 12% of African, 7% of Native Americans, and 7% of East Asian. We observed that African ancestry is associated with increased chance of being MSI-H, and that in MSI-H cases, the lower the Asian ancestral component the greater the probability of patient survival. Conclusions: The MSI frequency of 10% identified in Brazilian CRC is in agreement with literature. MSI-H status was found correlated with clinic-pathological features associated with less aggressive tumors, although we did not find significant differences in patient’s OS. The European ancestral component was the most representative one, confirming population genetic studies. In conclusion, this study constituted the deepest and most extensive analyses of the MSI impact in the CRC Brazilian patients.
Profiling analysis reveals potential prognostic biomarkers for esophageal cancer patients treated with radiotherapy.
Authors: Fan Yu , Li Tao , Wang Qifeng , Lv Jiahua , Li Qi , Wang Yi , Wang Junchao 
Published: September 2018

e23190 Background: Survival time among esophageal cancer patients undergoing radiotherapy varies considerably. Treatment failure resulting from local recurrence and metastasis reflects varying biological features such as radiosensitivity, invasion, and metastasis. This study aims to explore the genetic characterizations that are associated with prognosis of esophageal cancer patients who have undergone radiotherapy. Methods: We retrospectively reviewed specimens of 21 patients who were treated with radiotherapy. Based on the progression-free-survival (PFS), these patients were divided in to two groups: short PFS group with an average PFS of 6.9 months and long PFS group with an average PFS of 31.9 months. We extracted DNA from paraffin specimens for next generation sequencing. Mutation burden (the sum of mutation frequencies of targeted genes) and copy number aberrance were analyzed by targeted sequencing that covers 1086 genes. Results: We excluded six samples in the mutation burden analysis because of the shortage of coverage of the targeted genes. The mutation burden of 15 genes panel, which included ARID1A, BCL2, BRAF, CDH1, ERBB2, FAT1, LRP1B, MET, MTOR, NOTCH1,NOTCH2, PDGFRA, PTCH1, RB1, STK11, showed a statistically significant difference between the long PFS group and the short PFS group (p value = 0.001408). We then used copy number variation (CNV) kit to detect genes copy number variation between these two groups. The CNV of 9 genes panel, which include ASH1L, CD55, CDK4, CREBBP, FGFR1, MYC, TP53 , TYMS, XRCC3, showed a statistically significant difference between the long PFS group and the short PFS group (p value = 0.03147). Conclusions: Our results suggested that the gene mutation burden and CNV detected by targeted sequencing have a relationship with the prognosis of esophageal cancer patients who had undergone radiotherapy. In this exploratory study, we involved patients with extreme PFS ( < 1 year and > 2 years), which can be expanded in the future. To construct a predictive genetic model of prognosis in esophageal cancer patients, one may also consider analyzing circulating tumor DNA (ctDNA) in serum.