Pre-treatment plasma proteomic markers associated with survival in oesophageal cancer.
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ABSTRACT:
SUBMITTER: Kelly P
PROVIDER: S-EPMC3305965 | biostudies-other | 2012 Feb
REPOSITORIES: biostudies-other
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Project description:BackgroundCancer-associated fibroblasts (CAFs) form the major stromal component of the tumour microenvironment (TME). The present study aimed to examine the proteomic profiles of CAFs vs. normal fibroblasts (NOFs) from patients with oesophageal adenocarcinoma to gain insight into their pro-oncogenic phenotype.MethodsCAFs/NOFs from four patients were sub-cultured and analysed using quantitative proteomics. Differentially expressed proteins (DEPs) were subjected to bioinformatics and compared with published proteomics and transcriptomics datasets.ResultsPrincipal component analysis of all profiled proteins showed that CAFs had high heterogeneity and clustered separately from NOFs. Bioinformatics interrogation of the DEPs demonstrated inhibition of adhesion of epithelial cells, adhesion of connective tissue cells and cell death of fibroblast cell lines in CAFs vs. NOFs (p < 0.0001). KEGG pathway analysis showed a significant enrichment of the insulin-signalling pathway (p = 0.03). Gene ontology terms related with myofibroblast phenotype, metabolism, cell adhesion/migration, hypoxia/oxidative stress, angiogenesis, immune/inflammatory response were enriched in CAFs vs. NOFs. Nestin, a stem-cell marker up-regulated in CAFs vs. NOFs, was confirmed to be expressed in the TME with immunohistochemistry.ConclusionsThe identified pathways and participating proteins may provide novel insight on the tumour-promoting properties of CAFs and unravel novel adjuvant therapeutic targets in the TME.
| S-EPMC5943522 | biostudies-literature
Project description:Oesophageal adenocarcinoma (OAC) is an aggressive cancer with a five-year survival of <15%, and the incidence is predicted to double within the next 20 years. Current neo-adjuvant chemotherapy treatment strategies only benefit a minority (20-30%) of patients and there are currently no methods available to differentiate between responders and non-responders. Here we performed quantitative proteomics using Sequential Window Acquisition of all THeoretical fragment-ion spectra-Mass Spectrometry (SWATH-MS) on albumin/IgG-depleted and non-depleted plasma samples from 23 patients with locally advanced OAC or oesophageal gastric junction cancers prior to treatment. Individuals were grouped based on tumour regression (TRG) score (TRG1-3 vs TRG4 and 5) after chemotherapy and differentially abundant proteins were compared using univariate and multivariate analyses. Protein depletion led to the identification of around twice as many proteins in the samples compared to non-depletion. SWATH-MS revealed significant quantitative differences in the abundance of several proteins (p<0.05) between the two groups. These included all three c1q subunit proteins, C1QA, C1QB and C1QC, which were of higher abundance in the low TRG group (higher degree of regression in response to treatment). Of those that were found to be of higher abundance in the high TRG group, GSTP1 was found to exhibit the lowest p-value (univariate analysis) and highest accuracy and Cohen’s kappa value (multivariate analysis). The concentrations of c1q complex and GSTP1 were further examined and validated using ELISA-based assays. This study provides quantitative information relating to differences in the plasma proteome that underpin response to chemotherapeutic treatment in oesophageal cancers.
2022-08-22 | PXD032137 | Pride
Project description:BackgroundAs oesophageal cancer has short survival, it is likely pre-diagnosis health behaviours will have carry-over effects on post-diagnosis survival times. Cancer registry data sets do not usually contain pre-diagnosis health behaviours and so need to be augmented with data from external health surveys. A new algorithm is introduced and tested to augment cancer registries with external data when one-to-one data linkage is not available.MethodsThe algorithm is to use external health survey data to impute pre-diagnosis health behaviour for cancer patients, estimate misclassification errors in these imputed values and then fit misclassification corrected Cox regression to quantify the association between pre-diagnosis health behaviour and post-diagnosis survival. Data from US cancer registries and a US national health survey are used in testing the algorithm.ResultsIt is demonstrated that the algorithm works effectively on simulated smoking data when there is no age confounding. But age confounding does exist (risk of death increases with age and most health behaviours change with age) and interferes with the performance of the algorithm. The estimate of the hazard ratio (HR) of pre-diagnosis smoking was HR = 1.32 (95% CI 0.82,2.68) with HR = 1.93 (95% CI 1.08,7.07) in the squamous cell sub-group and pre-diagnosis physical activity was protective of survival with HR = 0.25 (95% CI 0.03, 0.81). But the method failed for less common behaviours (such as heavy drinking).ConclusionsFurther improvements in the I2C2 algorithm will permit enrichment of cancer registry data through imputation of new variables with negligible risk to patient confidentiality, opening new research opportunities in cancer epidemiology.
| S-EPMC8670692 | biostudies-literature
Project description:The current inability of clinical psychiatry to objectively select the most appropriate treatment is a major factor contributing to the severity and clinical burden of major depressive disorder (MDD). Here, we have attempted to identify plasma protein signatures in 39 MDD patients to predict response over a 6-week treatment period with antidepressants. LC-MS/MS analysis showed that differences in the levels of 29 proteins at baseline were found in the group with a favorable treatment outcome. Most of these proteins were components of metabolism or immune response pathways as well as multiple components of the coagulation cascade. After 6 weeks of treatment, 43 proteins were altered in responders of which 2 (alpha-actinin and nardilysin) had been identified at baseline. In addition, 46 proteins were altered in non-responders and 9 of these (alpha-actinin, alpha-2-macroglobulin, apolipoprotein B-100, attractin, C-reactive protein, fibrinogen alpha chain, fibrinogen beta chain, nardilysin and serine/threonine-protein kinase Chk1) had been identified at baseline. However, it should be stressed that the small sample size precludes generalization of the main results. Further studies to validate these as potential biomarkers of antidepressant treatment response are warranted considering the potential importance to the field of psychiatric disorders. This study provides the groundwork for development of novel objective clinical tests that can help psychiatrists in the clinical management of MDD through improved prediction and monitoring of patient responses to antidepressant treatments.
| S-EPMC5583163 | biostudies-literature
Project description:Background Less than 20 % of patients with resectable oesophageal adenocarcinoma obtain a pathological response following neoadjuvant chemotherapy. Studies using oesophageal cancer cell lines have shown that drug sensitive tumour cells undergo apoptosis in response to drug treatment, whereas resistant cells induce autophagy and can recover following withdrawal of drug. In this study, we evaluated markers of apoptosis (active/cleaved caspase-3) and autophagy (LC3B) to establish whether these markers are useful prognostic indicators following neoadjuvant therapy. Methods Oesophageal adenocarcinoma tumour tissue from the Northern Ireland Biobank at Queens University Belfast was examined retrospectively. Tumours from 144 patients treated with platinum-based neoadjuvant chemotherapy followed by surgical resection were assembled into tissue microarrays prior to immunohistochemical analysis. Kaplan-Meier survival curves and log-rank tests were used to assess the impact of cleaved caspase-3 and LC3B expression on survival. Cox regression was used to examine association with clinical risk factors. Results High levels of cleaved caspase-3 were found in 14.6 % of patients and this correlated with a significantly better overall survival (p = 0.03). 38.9 % of patients had high cytoplasmic LC3B expression, which correlated with poor overall survival (p = 0.041). In addition, a distinct globular pattern of LC3B expression was identified in 40.3 % of patients and was also predictive of overall survival (p < 0.001). LC3B globular structures are also associated with tumour recurrence (p = 0.014). When these markers were assessed in combination, it was found that patients who showed low/negative cleaved caspase-3 staining and high/positive staining for both patterns of LC3B had the worst overall survival (p < 0.001). Multi-variate analysis also indicated that this marker combination was an independent predictor of poor prognosis (p = 0.008; HR = 0.046, 95% CI = (0.005-0.443). Conclusions The expression of cleaved caspase-3 and specific LC3B staining patterns are associated with overall survival following neoadjuvant treatment. The combination of these markers is an independent indicator of outcome in neoadjuvant chemotherapy treated oesophageal adenocarcinoma. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-022-09981-8.
| S-EPMC9392302 | biostudies-literature
Project description:BackgroundSelf-expandable metal stents (SEMSs) are the main palliative modality used in inoperable oesophageal cancer. Other palliative modalities, including argon plasma coagulation (APC), have also been used.ObjectiveThe purpose of this study was to assess the relative efficacy of SEMS and APC regarding the survival of patients with inoperable oesophageal cancer, not receiving chemo/radiotherapy.MethodsSingle centre, retrospective analysis of all patients (n = 228) with inoperable oesophageal cancer between January 2000 and July 2014, not receiving chemo-radiotherapy, treated with SEMS (n = 160) or APC (n = 68) as primary palliation modalities. Cox regression analysis was performed to identify individual factors affecting survival and Kaplan-Meier curves were created for patients treated with APC and SEMS for stage III and IV disease. Survival intervals were compared by the log-rank test.ResultsType of treatment was the only statistically significant factor affecting survival, after disease stage stratification (hazard ratio (HR): 1.36, 95% confidence interval (CI): 1.13-1.65 of SEMS over APC, p: 0.002). Median survival for patients treated with APC and SEMS was 257 (interquartile range (IQR): 414, 124) and 151 (IQR: 241, 61) days respectively in stage III disease. It was 135 (IQR: 238, 43) and 70 (IQR: 148, 32) days respectively in stage IV disease. Both differences were statistically significant (p = 0.02 and 0.05 respectively).ConclusionsAPC is a promising palliation modality in inoperable oesophageal cancer, when patients are not candidates for chemo-radiotherapy. A randomized controlled trial will be needed to confirm those results.
| S-EPMC5384556 | biostudies-literature
Project description:PurposeTo prospectively evaluate the feasibility of solid gold marker placement in oesophageal cancer patients and to quantify inter-fractional and intra-fractional (baseline shift) marker motion during radiation treatment. Radiotherapy target margins and matching strategies were investigated.Materials/methodsThirty-four markers were implanted by echo-endoscopy in 10 patients. Patients received a planning 4D CT, daily pre-treatment cone-beam CT (CBCT) and a post-treatment CBCT for at least five fractions. For fractions with both pre- and post-treatment CBCT, marker displacement between planning CT and pre-treatment CBCT (inter-fractional) and between pre-treatment and post-treatment CBCT (intra-fractional; only for fractions without rotational treatment couch correction) were calculated in left-right (LR), cranio-caudal (CC) and anterior-posterior (AP) direction after bony-anatomy and soft-tissue matching. Systematic/random setup errors were estimated; treatment margins were calculated.ResultsNo serious adverse events occurred. Twenty-three (67.6%) markers were visible during radiotherapy (n = 3 middle oesophagus, n = 16 distal oesophagus, n = 4 proximal stomach). Margins for inter-fractional displacement after bony-anatomy match depended on the localisation of the primary tumour and were 11.2 mm (LR), 16.4 mm (CC) and 8.2 mm (AP) for distal markers. Soft-tissue matching reduced the CC margin for these markers (16.4 mm to 10.5 mm). The mean intra-fractional shift of 12 distal markers was 0.4 mm (LR), 2.3 mm (CC) and 0.7 mm (AP). Inclusion of this shift resulted in treatment margins for distal markers of 12.8 mm (LR), 17.3 mm (CC) and 10.4 mm (AP) after bony-anatomy matching and 12.4 mm (LR), 11.4 mm (CC) and 9.7 mm (AP) after soft-tissue matching.ConclusionThis study demonstrated that the implantation of gold markers was safe, albeit less stable compared to other marker types. Inter-fractional motion was largest cranio-caudally for markers in the distal oesophagus, which was reduced after soft-tissue compared to bony-anatomy matching. The impact of intra-fractional baseline shifts on margin calculation was rather small.
| S-EPMC7677672 | biostudies-literature
Project description:We evaluated and correlated gene expression profiles of pre-treatment endoscopic biopsies in a pre-defined patient population of resectable oesophageal adenocarcinoma who had received neoadjuvant platinum and fluoropyrimidine based chemotherapy with clinical outcome, the primary end-point being overall survival. At the time of pre-treatment staging EUS, tumour biopsies were collected (approximately 1.5 mm3). and immediately snap frozen and stored in liquid nitrogen. Total RNA was extracted from the biopsies and amplified using a T7 bacteriophage RNA polymerase based linear amplification protocol, then expression profiling was carried out. The expression levels of 47 genes selected by biological function, fold change and degree of significance were further validated using quantitative reverse transcription-PCR Keywords: Tumour vs normal comparison
2008-08-15 | GSE11595 | GEO
Project description:We aimed to identify novel markers for aggressive prostate cancer in a STAT3-low proteomics-derived dataset of mitochondrial proteins by immunohistochemical analysis and correlation with transcriptomic data and biochemical recurrence in a STAT3 independent PCa cohort. Formalin-fixed paraffin-embedded tissue (FFPE) sample selection for proteomic analysis and tissue-microarray (TMA) generation was conducted from a cohort of PCa patients. Retrospective data analysis was performed with the same cohort. 153 proteins differentially expressed between STAT3-low and STAT3-high samples were identified. Out of these, 46 proteins were associated with mitochondrial processes including oxidative phosphorylation (OXPHOS), and 45 proteins were upregulated, including NDUFS1/ATP5O. In a STAT3 independent PCa cohort, high expression of NDUFS1/ATP5O was confirmed by immunocytochemistry (IHC) and was significantly associated with earlier biochemical recurrence (BCR). mRNA expression levels for these two genes were significantly higher in intra-epithelial neoplasia and in PCa compared to benign prostate glands. NDUFS1/ATP5O levels are increased both at the mRNA and protein level in aggressive PCa. Our results provide evidence that NDUFS1/ATP5O could be used to identify high-risk PCa patients.
| S-EPMC8656993 | biostudies-literature
Project description:BackgroundConditional survival accounts for the time already survived after surgery and may be of additional informative value. The aim was to assess conditional survival in patients with oesophageal cancer and to create a nomogram predicting the conditional probability of survival after oesophagectomy.MethodsThis retrospective study included consecutive patients with oesophageal cancer who received neoadjuvant chemoradiation followed by oesophagectomy between January 2004 and 2019. Conditional survival was defined as the probability of surviving y years after already surviving for x years. The formula used for conditional survival (CS) was: CS(x|y) = S(x + y) /S(x) , where S(x) represents overall survival at x years. Cox proportional hazards models were used to evaluate predictors of overall survival. A nomogram was constructed to predict 5-year survival directly after surgery and given survival for 1, 2, 3 and 4 years after surgery.ResultsSome 660 patients were included. Median overall survival was 44·4 (95 per cent c.i. 37·0 to 51·8) months. The probability of achieving 5-year overall survival after resection increased from 45 per cent directly after surgery to 54, 65, 79 and 88 per cent given 1, 2, 3 and 4 years already survived respectively. Cardiac co-morbidity, cN category, ypT category, ypN category, chyle leakage and pulmonary complications were independent predictors of survival. The nomogram predicted 5-year survival using these predictors and number of years already survived.ConclusionThe probability of achieving 5-year overall survival after oesophagectomy for cancer increases with each additional year survived. The proposed nomogram predicts survival in patients after oesophagectomy, taking the years already survived into account.
| S-EPMC7317937 | biostudies-literature