bluuebunny/crossref_metadata_2025_split huggingface dataset:
Gene expression subtype and p53 mutational status are correlated among neoadjuvantly treated breast cancers in UNC LCCC9819 and I-SPY1 (CALGB 150007/ACRIN 6657)
Authors: Carey L. A. , Oh D. , Sawyer L. , Edmiston S. , Tolbert D. , Moore D. , Buxton M. , Esserman L. , Perou C. , Conway K. 
Published: March 2020

10048 Background: LCCC9819 and I-SPY1 are designed to examine multiple potential predictive markers and assays simultaneously in biopsies from neoadjuvantly treated patients. Both p53 mutation status and molecular ‘intrinsic‘ subtype have been associated with chemosensitivity. In this preliminary analysis, we present the p53 mutation spectra by molecular subtype from patients enrolled in the combined LCCC 9819 and I-SPY1 datasets. Methods: Patients received neoadjuvant anthracycline-based chemotherapy with pre-therapy biopsies. p53 mutation analysis was performed by p53 GeneChip assay for point mutations/1 bp deletions followed by SSCP if GeneChip-negative. Abnormal GeneChip or SSCP were confirmed by sequencing. DNA microarrays used Agilent human microarrays and a common reference strategy approach. Results: 51 patients were treated on LCCC9819 and have available molecular analyses; 87 from I-SPY1. 111 patients have completed p53 mutation analysis, revealing a high proportion (42%) with abnormal p53. Of these, several were in known hotspots, including R175H (4 mutations), R248L (1), R273H (3), and R273C (2). Most were missense mutations (81%), however, there were 8 (17%) null and 1 (2%) silent mutations. Most (91%) mutations were in the DNA binding domain. Molecular subtypes are known on 111 tumors: 22% Luminal A, 22% Luminal B, 3% Normal-like, 23% HER2+/ER−, 27% Basal-like, and 3% unclassified. Among those with both assays complete, we found that p53 mutations differed by subtype (Table). Conclusions: P53 mutations are common in these independent neoadjuvant datasets, and differ in frequency between molecular subtypes, which may have implications for predictive factor identification. Future analyses will include aCGH, cell cycle protein analysis, proteomics, and clinical data including response to chemotherapy. (supported by UNC Breast SPORE-CA58223, NIH M01RR00046, DAMD 17–02–1-0521). [Table: see text] No significant financial relationships to disclose.
Identification of cancer of unknown primary with gene expression profiling
Authors: Li H. , Qu K. , Tokoro K. , Ren Y. , Liu J. Y. , Sferruzza A. , Bender R. 
Published: March 2020

10052 Background: Patients with metastatic cancer of unknown primary (CUP) generally have a poor prognosis, with a median survival of 2–10 months. Conventional diagnostic approaches for identifying the primary tumor site are successful in only 20%-30% of cases; however, such identification provides prognostic information and helps with selection of tumor-specific therapy, leading to improved survival. Recent studies indicate that gene expression-based classification of CUP is highly successful in predicting the site of origin. We report herein development and validation of a method that determines the site of tumor origin by comparing the gene expression profiles of CUP cases to those in a database created from known tumor types. Methods: RNA extracted from frozen and formalin-fixed, paraffin-embedded (FFPE) tissue wasis purified and amplified using the Paradise Reagent System System (Arcturus, Mountain View, CA). Following reverse-transcription, cDNA products wereare used in a semi-quantitative real-time PCR to detect 87 tumor-associated genes and 5 reference genes in an ABI PRISM 7900HT Detection System (Applied Biosystems, Foster City, CA). Gene expression data wereare then compared to those in a database, composed of gene expression profiles of 571 samples from 39 different tumor types, using k-nearest neighbor analysis to predict the most likely site of tumor origin. Intra- and interassay reproducibility was determined. Frozen and FFPE tissues (n=57) from a well-characterized, independent sample set were also tested in a blinded manner to further validate the method. Results: Based on the real-time PCR cycle threshold, the intra- and interassay reproducibility ranged from 0.1%-4.3% and 0.5%-8.2%, respectively. The primary tumor type was identified in 77% of cases. The assay determined the correct tumor type in 88% (44/50) of the samples. Seven samples were not reported: 3 failed to amplify adequately and 4 had an unacceptably low confidence level. Conclusions: We have shown that gene expression profiling can determine the most likely site of tumor origin. Our data suggest that this new method is able tomay identify the primary site of tumor origin in 77% of CUP cases. No significant financial relationships to disclose.
Chemokine receptor 5 (CCR5) Δ32 base pair somatic gene deletions from PBM predict survival of patients with advanced stage (IV) melanoma
Authors: Essner R. , Lee J. H. , Itakura H. , Huynh Y. , Scheri R. , Morton D. 
Published: March 2020

10056 Background: Chemokines are a family of secreted chemotactic cytokines that function in leukocyte trafficking and activation. Chemokine receptor 5 (CCR5) is involved in CD4+ T-cell mediated immunity and dendritic cell (DC) activation. A 32 base pair (bp) deletion mutation on chromosome 3p21 result in a non-functional CCR5 with defective immunity. We hypothesized that CCR5Δ32 bp mutations would result in a diminished immune response to melanoma and maybe predictive of outcome of patients with advanced-stage disease. Methods: We identified 160 AJCC stage IV melanoma patients from our database whom had been made NED (no evidence of disease) by surgical resection. 105 (66%) had received active specific immunotherapy in phase I/II trials. Genomic DNA was extracted from peripheral blood mononuclear cells (PBM) and screened by PCR for the presence of CCR5Δ32 bp deletions. PCR products were sequenced to verify the result. Statistical analysis was performed by using Log-rank, Chi-square & Student’s t-test. Results: Of 160 patients, 100 (63%) were men. Ages ranged from 19–82 (median 47 yrs.). 46 (29%) patients had M1a, 48 (30%) Mlb and 66 (41%) Mlc stage of metastases prior to surgical resection. Median follow-up was 47.5 mos. 135 (84%) patients had wild-type (Wt)CCR5 gene; 21 (13%) had heterozygous (HtM) and 4(3%) had homozygous mutations (HoM). 5-yr survival was significantly higher for patients with CCR5 Wt than those with HtM or HoM deletions (55.6%±6.1% vs. 21.4%±10.8%, p=0.031). None of the 21 patients with HtM survived 10yrs. Multivariate analyses demonstrated only CCR5 gene status (Wt vs. HtM/HoM) as predictive of survival (p=0.007). Age (p=0.23), gender (p=0.38), and M stage (M1a vs. M1b/c) (p=0.31) were not important in the statistical model. When immunotherapy responses (+ vs. -) were included in the model both responses and CCR5 mutation status were significant (p=0.0021, p=0.0063 respectively). Conclusions: Our results suggest CCR5Δ32bp somatic mutations from PBM are present in advanced-stage melanoma patients and are highly predictive of survival. Functional CCR5 may be used as a selection factor for surgery but more importantly essential for either active immunotherapy or the natural immune response to be effective for these patients. No significant financial relationships to disclose.
The adenocarcinoma-specific stage shift: Closely-repeated low-dose helical CT screening in a high-risk cohort for 10 years
Authors: Seki N. , Eguchi K. , Kaneko M. , Ohmatsu H. , Kakinuma R. , Matsui E. , Kusumoto M. , Tsuchida T. , Nishiyama H. , Moriyama N. 
Published: March 2020

1006 Background: Trials of CT screening for lung cancer have not yet proven the presence of a stage shift, to say nothing of a mortality benefit. On the basis of an update from Anti-Lung Cancer Association project, we investigated whether the stage shift did occur during the long-term closely-repeated low-dose helical CT screening in a high-risk cohort. Methods: A total of2,120 participants (mean age 63 yrs, 87% male, and 83% smoker) underwent low-dose helical CT screening semiannually from 1993 to 2004 (median, 3.5 years). Results: Nineteen prevalence and 57 incidence lung cancers were detected. In comparison between baseline and repeated screening, the detection rate was 0.90% vs. 0.32% (P < 0.001) and the tumor size was 24mm vs. 17mm (P = 0.018). Adenocarcinoma (74% and 63%) and stage IA (58% and 79%) were observed most commonly in both screen-groups, respectively, but their proportions showed no significant difference between groups, respectively. Regarding the survival of lung cancer patients, screening type was not a significant prognostic factor. In repeated screening,the detection rate oflung cancer except bronchioloalveolar carcinoma increased significantly depending on CT repeating times (r = 0.50, P = 0.020). Moreover, the proportion of stage II-IV and the tumor size decreased significantly only in invasive adenocarcinoma (r = -0.77, P = 0.007 and r = -0.60, P = 0.029, respectively). Conclusions: The adenocarcinoma-specific stage shift did occur in a high-risk cohort. Considering larger proportion of adenocarcinoma in this population, smokers might benefit from the long-term closely-repeated low-dose helical CT screening. No significant financial relationships to disclose.
Detection of mutations in the EGFR tyrosine kinase domain by DNA sequencing
Authors: Da Silva M. , Flynn K. E. , Choppa P. , Zhou Z. , Bell D. W. , Iafrate A. J. , Paler R. J. , Allitto B. A. , Rohlfs E. M. 
Published: March 2020

10060 Background: The presence of sequence alterations in the tyrosine kinase domain of the epidermal growth factor receptor gene (EGFR) have been documented as gefitinib/erlotinib sensitizing mutations and serve as indicators for targeted (Iressa/Tarceva) therapy in patients with non-small-cell lung carcinoma (NSCLC). We report results obtained from the development and validation of a sequencing-based assay for the detection of these somatic mutations. Methods: Specimens tested included4 DNA samples with known EGFR mutations and 59 formalin-fixed primary or metastatic lung carcinomas, 22 which had known EGFR genotypes and 37 which were untested. Forty-one were adenocarcinomas. The most tumor-rich area of the section was micro-dissected to minimize amplification of non-tumor cells. DNA was extracted following treatment to deparaffinize and dehydrate the tissue section. A quantitative EGFR PCR was used to determine if the quantity of isolated DNA was sufficient for sequence analysis. A first-round multiplex amplification was followed by four semi-nested PCR amplifications targeting EGFR exons 18–21 and the flanking splice sites. These products were then subjected to sequencing reactions and evaluated for alterations as compared to the wild type sequence. Results: All of the specimens met the minimum quantity of 750pg of EGFR DNA required for the analysis. Thirty-one of the 37 anonymous specimens showed no sequence alterations in exons 18–21. Four of the five specimens with sequence alterations had known sensitizing mutations; three were L858R and one was 2235–2249del15. One specimen had a novel W817X mutation in exon 20. One specimen failed analysis for three of the exons. The percent tumor in the area selected for analysis varied from 5–30% in the specimens with sequence alterations. Twenty-five of the 26 samples with known genotypes were correctly identified by this method. In one sample a reported mutation was not detected, possibly due to selection of a different tumor nodule for testing. Resequencing of the sample by an outside lab confirmed the negative result. Conclusions: We have developed a highly sensitive and accurate sequencing-based assay capable of detecting somatic mutations in EGFR exons 18–21 which is important in the treatment and management of patients with NSCLC. [Table: see text]
Therapeutic efficacy of an oncolytic adenovirus monitored by in vivo imaging of an ovarian cancer model
Authors: Tsuruta Y. , Pereboeva L. , Rein D. T. , Breidenbach M. , Curiel D. T. 
Published: March 2020

10061 Background: Although a number of advances in ovarian cancer treatment have occurred in the last decade, most patients will experience a recurrence after standard therapies. Recently, virotherapy has been proposed as a new therapeutic approach for ovarian cancer. Conditionally replicative adenovirus (CRAd) contains tumor-specific promoters that restrict virus replication to cancer cells and has shown particular promise as oncolytic viral agents. However, the lack of a tumor-volume monitoring system hinders the evaluation of CRAd impact on cancer treatment. Therefore, methods for analyzing CRAd efficacy and tumor response are required. Mesothelin, a cell surface glycoprotein, is overexpressed in ovarian cancer but not in normal ovarian tissues. The purpose of this study was to explore the therapeutic utility of a mesothelin promoter-based CRAd in a murine model of ovarian cancer, using a non-invasive biological imaging system. Methods: We constructed a mesothelin promoter based CRAd which also contains a modified fiber (Ad5/3 fiber) previously shown to improve infectivity of many ovarian cancer cells (Ad5/3MSLN). Viral replication and oncolysis were assessed in a panel of ovarian cancer cell lines. To test the oncolytic efficacy of Ad5/3MSLN in murine model, firefly luciferase-expressing SK-OV-3-luc cells were injected intraperitoneally (i.p.), followed by an i.p. injection of viruses. Then, bioluminescence imaging of tumor luciferase activity was carried out. Results: Ad5/3MSLN achieved up to 10,000-fold higher cell killing effect and up to 120-fold higher levels of viral replication in all ovarian cancer cell lines tested, compared to wild type Ad5. In vivo tumor imaging confirmed that Ad5/3MSLN significantly inhibited tumor growth, while the untreated mice had rapid tumor growth (p<0.05). Survival with Ad5/3MSLN was significantly enhanced when compared with no virus, or wild type Ad5-treated group (p<0.05). Conclusions: The robust replication, oncolysis, and in vivo therapeutic efficacy of Ad5/3MSLN demonstrated that this CRAd is a promising candidate for treating ovarian cancer. Importantly, we have established an in vivo non-invasive imaging system, which has allowed repeated and longitudinal measurements of tumor growth after CRAd treatment. No significant financial relationships to disclose.
Nuclear localization of NF-kappaB p65 in primary prostate tumors is predictive of pelvic lymph node metastases
Authors: Lessard L. , Bellon-Gagnon P. , Alam-Fahmy M. , Karakiewicz P. , Mes-Masson A. , Saad F. 
Published: March 2020

10077 Background: Pelvic lymph node metastases are associated with a greater risk of prostate cancer recurrence and peripheral metastasis. Unfortunately, markers predictive of lymph node metastasis and/or recurrence after radical prostatectomy are limited and new molecular markers are needed to identify patients at higher risk of progression. NF-kB (p65) is a candidate molecular marker already associated with poor clinical outcomes such as biochemical recurrence and bone metastasis. We have also reported elevated nuclear p65 expression in prostate cancer lymph node metastasis. Pertinent to this issue, we tested whether the nuclear localization of p65 in radical prostatectomy specimens could predict the presence of lymph node metastases. Methods: Following informed consent, 51 patients who underwent radical prostatectomy were included in the study: 20 patients had lymph node metastasis at surgery and 31 patients had no evidence of lymph node metastasis and were used as the control group. All cases in the control group had no biochemical relapse 5 years following radical prostatectomy. NF-kB expression in prostate tumor sections was assessed by immunohistochemistry using a monoclonal NF-kB p65 antibody. The relation between nuclear p65 expression in primary tumors and lymph node metastasis was tested in univariate and multivariate Cox regression models. Results: Primary tumors of metastatic patients had an average of 21.25% of tumor cells with nuclear p65 expression as opposed to 9.42% of tumor cells of control patients (p=0.001). Univariate Cox regression demonstrated a 7.5% increased risk of having lymph node metastases for each percent increase in p65 nuclear staining (p=0.003). In the multivariate model, after controlling for pre-operative PSA (p=0.175), Gleason patterns (p=0.382), pathological stage (p=0.436), extracapsular extension (p=0.243) and seminal vesicle invasion (p=0.016), nuclear p65 was associated with an 8.8% increased risk for lymph node metastases (p=0.024). Conclusion: In univariate and multivariate analyses, p65 nuclear expression was strongly predictive of lymph node invasion. We propose that nuclear NF-kB (p65) may serve as a useful independent molecular marker for stratifying patients at risk for lymph node metastases. No significant financial relationships to disclose.
Developing a predictive model for disease status in breast cancer patients using Th1 and Th2 serum cytokine profiles
Authors: Khoo S. , Kao T. , Dehqanzada Z. A. , Storrer C. E. , Harris K. A. , Jama Y. H. , Shriver C. D. , Ponniah S. , Peoples G. E. 
Published: March 2020

10078 Background: Using the Luminex multiplex assay, we have reported significant correlations between serum levels of MCP-1, eotaxin, and IL-6 and disease characteristics in breast cancer (BCa) patients. We now examine the potential of utilizing a general cytokine profile to develop a statistical model to predict certain disease states in these patients. Methods: Sera from 36 BCa patients (24 node-negative, 12 node-positive, 12 normals) were analyzed using the Luminex assay for levels of 21 cytokines (IL-1α, 1b, 2, 4, 5, 6, 8, 10, 12, 13, 15, 17, IFN-γ, G-CSF, GM-CSF, TNF-α, IP-10, MIP-1α, RANTES, MCP-1, eotaxin). Logistic regression models were used to assess if a binary outcome variable (Y) can be predicted by using serum cytokine levels (X). The area under a receiver operating characteristic (ROC) curve (c) was used to assess the potential utility of a biomarker. The larger the value of c, the better the biomarker. Results: MCP-1 was found to be a possible predictor of the presence of BCa while other potential biomarkers were IL-13, MIP-1α and eotaxin. The higher the MCP-1 level, the greater the likelihood that the patient would have BCa. Similar relationships applied to the other potential biomarkers. Among BCa patients, GM-CSF seemed to be a good predictor of nodal status with lower levels of GM-CSF predicting positive nodes. Other potential biomarkers with a similar expression pattern for nodal status were MCP-1, IL-6 and IL-5. Due to small sample sizes, we were unable to examine a potential “panel” of cytokines to develop a prognostic algorithm based on serum analysis. Conclusions: MCP-1, which was previously shown to be elevated in BCa, may also have some predictive value linking the presence of disease and disease severity as measured by nodal status. Other prominent cytokines from earlier studies (MIP-1α, eotaxin, IL-6) also displayed some possible predictive value. Our results warrant studying a larger population in order to establish a unified prognostic formula for BCa based on serum cytokine levels. [Table: see text] No significant financial relationships to disclose.
Oxygen saturation measured in vivo in bronchial tumors during bronchoscopy in patients with lung cancer using differential path length spectroscopy (DPS) correlates with survival, stage of the disease, and expression of HIF1a
Authors: Aerts J. G. , Bard M. P. , Amelink A. , Sterenborg D. , Bom F. , Van Meerbeeck J. , Hoogsteden H. , Lambrecht B. 
Published: March 2020

10084 Background: Tumor hypoxia is known to correlate with poor prognosis in solid cancers. In bronchial tumors direct determination of oxygen saturation is not possible and therefore indirect measures like hypoxia related proteins as HIF1a have been studied. We studied the prognostic significance on patient survival and tumor stage of microvascular oxygen saturation (StO2) measured in vivo in bronchial tumors using optical spectroscopy and compared this to HIF1a expression in bronchial biopsies. Methods: DPS is a non-invasive real-time measurement of hypoxia related parameters such as microvascular blood oxygenation (StO2) which can be used during bronchoscopy (Bard Am J Respir Crit Care Med 2005). Endobronchial tumors (12 squamous cell carcinomas, 5 adenocarcinomas, 15 large cell undifferentiated and 6 small cell carcinomas), were measured in 38 patients. In a subgroup of patients HIF1a expression was related to StO2 using linear regression analysis. Results: StO2 of bronchial tumors was predictive for patient survival. Patients with an endobronchial tumor and a saturation lower than the median value of 52% had a significant shorter overall survival than patients with a better saturated tumor. The StO2 was also related to the stage of the disease. StO2 was significantly lower in case of advanced lung tumors (stage III & IV, StO2= 44.7 ± 24.7%) in comparison with localized lung tumors (stage I&II, StO2 = 73.3 ± 12.4) (p<0.05). StO2 correlated to HIF1a expression levels (r = −0.65). Conclusions: StO2 using DPS correlates with HIF1a expression, is related to tumor stage and is a prognositc factor. This opens a new field for study of therapeutic agents in lung cancer and may also be important in the staging of lung cancer. No significant financial relationships to disclose.
A multi-gene algorithm as predictor of response to chemo-radiotherapy in head and neck cancer
Authors: Gasco M. , Syed N. , Smith P. , Numico G. , Colantonio I. , Garrone O. , Granetto C. , Di Costanzo G. , Merlano M. , Crook T. 
Published: March 2020

10086 Background: Chemo-radiotherapy results in clinical cure for stage III/IV head and neck cancer in approximately 40% of cases, with significant treatment-associated morbidity and mortality. Molecular genetic factors predictive of treatment outcome would clearly be of value in selection of patients with highest probability of response. We have analysed the structure and epigenetic regulation of specific genes as possible predictors of outcome to chemo-radiotherapy. The genes analyzed were: p53 (single nucleotide polymorphism (SNP) and mutation), MDM2 (SNP), Chfr (methylation), CRABP1 (methylation). Methods: 84 patients with locally advanced head and neck cancer receiving cisplatin-based chemo-radiotherapy were studied. SNP genotypes were determined by direct sequencing of DNA from normal tissue. Acquired mutations in p53 and aberrant methylation in the CpG islands of specific genes were analyzed by direct sequencing and methylation-specific PCR. Results: There were 6 treatment-related deaths in 84 patients, all occurring in cases with germ-line haplotype p53 72 Arg/Arg, MDM2 309T/T. At the time of analysis, 39/84 (46%) patients had progressed or died, with median time to progression or death = 17.3 months. Complete response was more common in patients whose genetic/epigenetic profile was p53 72 Arg/Arg wild type, MDM2 309 G/G, Chfr methylated, CRABP1 methylated, compared to the profile p53 72 Arg/Arg mutant, MDM2 309 T/T, Chfr unmethylated, CRABP1 unmethylated (91% vs 46%, log rank p = 0.002). Progression-free survival was significantly longer for patients with the profile p53 72 Arg/Arg wild type, MDM2 309 G/G, Chfr methylated, CRABP1 methylated, compared to those with p53 72 Arg/Arg mutant, MDM2 309 T/T, Chfr unmethylated, CRABP1 unmethylated (% surviving progression-free at 2 years = 74% vs 36%, p = 0.001). Overall survival was significantly longer in patients with the profile p53 72 Arg/Arg wild type, MDM2 309 G/G, Chfr methylated, CRABP1 methylated compared to those with p53 72 Arg/Arg mutant, MDM2 309 T/T, Chfr unmethylated, CRABP1 unmethylated (% surviving at 2 years = 88% vs 40%, p = 0.0004). Conclusions: Genetic and epigenetic parameters influence the toxicity and clinical outcome of chemo-radiotherapy in head and neck cancer. No significant financial relationships to disclose.