Identification of novel molecular subgroups in esophageal adenocarcinoma to predict response to neo-adjuvant therapies
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE207526 | GEO | 2023/01/08
REPOSITORIES: GEO
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Project description:Oesophageal adenocarcinoma exome sequence data from samples before and after neo-adjuvant chemotherapy
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Project description:Treatment of locally advanced rectal cancer involves chemoradiation, followed by total mesorectum excision. Complete response after chemoradiation is an accurate surrogate for long-term local control. Predicting complete response from pre-treatment features could represent a major step towards conservative treatment. Patients with a T2-4 N0-1 rectal adenocarcinoma treated between June 2010 and October 2016 with neo-adjuvant chemoradiation from three academic institutions were included. All clinical and treatment data was integrated in our clinical data warehouse, from which we extracted the features. Radiomics features were extracted from the tumor volume from the treatment planning CT Scan. A Deep Neural Network (DNN) was created to predict complete response, as a methodological proof-of-principle. The results were compared to a baseline Linear Regression model using only the TNM stage as a predictor and a second model created with Support Vector Machine on the same features used in the DNN. Ninety-five patients were included in the final analysis. There were 49 males (52%) and 46 females (48%). Median tumour size was 48?mm (15-130). Twenty-two patients (23%) had pathologic complete response after chemoradiation. One thousand six hundred eighty-three radiomics features were extracted. The DNN predicted complete response with an 80% accuracy, which was better than the Linear Regression model (69.5%) and the SVM model (71.58%). Our model correctly predicted complete response after neo-adjuvant rectal chemoradiotherapy in 80% of the patients of this multicenter cohort. Our results may help to identify patients who would benefit from a conservative treatment, rather than a radical resection.
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Project description:Following exposure to chemoradiation, EAC cells increase their mitochondrial content and associated metabolic processes, which drives treatment resistance. Inhibition of this response using clinically applicable inhibitors of ESRRA in combination with (chemo)radiation shows promising anti-tumor activities and could be further developed for clinical use.
2022-10-17 | GSE184654 | GEO
Project description:BACKGROUND:Although radical surgery remains the cornerstone of cure in resectable gastric cancer, survival remains poor. Current evidence-based (neo)adjuvant strategies have shown to improve outcome, including perioperative chemotherapy, postoperative chemoradiotherapy and postoperative chemotherapy. However, these regimens suffer from poor patient compliance, particularly in the postoperative phase of treatment. The CRITICS-II trial aims to optimize preoperative treatment by comparing three treatment regimens: (1) chemotherapy, (2) chemotherapy followed by chemoradiotherapy and (3) chemoradiotherapy. METHODS:In this multicentre phase II non-comparative study, patients with clinical stage IB-IIIC (TNM 8th edition) resectable gastric adenocarcinoma are randomised between: (1) 4 cycles of docetaxel+oxaliplatin+capecitabine (DOC), (2) 2 cycles of DOC followed by chemoradiotherapy (45Gy in combination with weekly paclitaxel and carboplatin) or (3) chemoradiotherapy. Primary endpoint is event-free survival, 1 year after randomisation (events are local and/or regional recurrence or progression, distant recurrence, or death from any cause). Secondary endpoints include: toxicity, surgical outcomes, percentage radical (R0) resections, pathological tumour response, disease recurrence, overall survival, and health related quality of life. Exploratory endpoints include translational studies on predictive and prognostic biomarkers. DISCUSSION:The aim of this study is to select the most promising among three preoperative treatment arms in patients with resectable gastric adenocarcinoma. This treatment regimen will subsequently be compared with the standard therapy in a phase III trial. TRIAL REGISTRATION:clinicaltrials.gov NCT02931890 ; registered 13 October 2016. Date of first enrolment: 21 December 2017.
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Project description:Radiotherapy and adjuvant cisplatin (DDP) chemotherapy are standard administrations applied in the treatment of NPC. However, molecular change and functions of DDP chemo-resistance in nasopharyngeal carcinoma are still poorly understood.
2019-08-01 | GSE135083 | GEO
Project description:The development of human epidermal growth factor 2 (HER2)-directed therapy has resulted in significant improvement in outcomes for patients with early-stage HER2-overexpressing (HER2+) breast cancer. In recent years, newer HER2-directed agents and novel treatment strategies have been developed with ongoing improvements in overall outcomes. However, with the addition of newer agents, there is an increasing need to risk stratify patients to maximize efficacy and minimize toxicity of treatment. De-escalation of therapy with the potential to shorten the duration of adjuvant therapy and minimize chemotherapy administration in patients with favorable disease can be considered. On the other hand, escalation of therapy with the addition of novel HER2-directed agents and extended duration of therapy in patients at high risk of relapse can help improve long-term cure rates. Herein, we discuss recent developments in neoadjuvant and adjuvant strategies for the treatment of potentially curable HER2+ breast cancer.
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Project description:Background:We performed whole-exome sequencing of pretreatment biopsies and examined whether genome-wide metrics of overall mutational load, clonal heterogeneity or alterations at variant, gene, and pathway levels are associated with treatment response and survival. Patients and Methods:Two hundred and three biopsies from the NeoALTTO trial were analyzed. Mutations were called with MuTect, and Strelka, using pooled normal DNA. Associations between DNA alterations and outcome were evaluated by logistic and Cox-proportional hazards regression. Results:There were no recurrent single gene mutations significantly associated with pathologic complete response (pCR), except PIK3CA [odds ratio (OR)?=?0.42, P?=?0.0185]. Mutations in 33 of 714 pathways were significantly associated with response, but different genes were affected in different individuals. PIK3CA was present in 23 of these pathways defining a ‘trastuzumab resistance-network’ of 459 genes. Cases with mutations in this network had low pCR rates to trastuzumab (2/50, 4%) compared with cases with no mutations (9/16, 56%), OR?=?0.035; P?<?0.001. Mutations in the ‘Regulation of RhoA activity’ pathway were associated with higher pCR rate to lapatinib (OR?=?14.8, adjusted P?=?0.001), lapatinib?+?trastuzumab (OR?=?3.0, adjusted P?=?0.09), and all arms combined (OR?=?3.77, adjusted P?=?0.02). Patients (n?=?124) with mutations in the trastuzumab resistance network but intact RhoA pathway had 2% (1/41) pCR rate with trastuzumab alone (OR?=?0.026, P = 0.001) but adding lapatinib increased pCR rate to 45% (17/38, OR?=?1.68, P?=?0.3). Patients (n?=?46) who had no mutations in either gene set had 6% pCR rate (1/15) with lapatinib, but had the highest pCR rate, 52% (8/15) with trastuzumab alone. Conclusions:Mutations in the RhoA pathway are associated with pCR to lapatinib and mutations in a PIK3CA-related network are associated with resistance to trastuzumab. The combined mutation status of these two pathways could define patients with very low response rate to trastuzumab alone that can be augmented by adding lapatinib or substituting trastuzumab with lapatinib.
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Project description:Esophageal adenocarcinoma (EAC) is a highly aggressive malignancy that frequently develops from Barrettâs esophagus (BE), a premalignant pathological change occurring in the lower end of esophagus. To identify BE patients at high risk of malignant transformation is essential to the prevention of EAC. Although microRNA (miRNA) expression signatures have been associated with the etiology and prognosis of several types of cancers, their roles in the development of EAC have not been extensively evaluated. We analyzed the expression patterns of 470 human miRNAs using Agilent miRNA microarray in 32 disease/normal-paired tissues from 16 patients diagnosed with BE of either low or high grade dysplasia, or EAC
2010-05-16 | E-GEOD-16456 | biostudies-arrayexpress
Project description:The objective of this study is to assess gene expression changes and identify gene sets associated with chemo-radiotherapy (CRT) in colorectal cancer (CRC) patients. We performed RNA-seq based transcriptome profiling using primary tumor samples obtained from 22 CRC patients. By a number of statistical tests, a total of 575 genes were statistically significant, indicating a gene set profoundly responded to chemo-radiotherapy in CRC. To select the genes showing strong gene expression intensities and critically validate the differences between treatment-responded and non-responded patients, we applied more rigorous cut-off for gene selection, revealing a total of 8 final gene candidates. These genes were applied to the downstream experimental assays.
2020-12-25 | GSE80606 | GEO
Project description:Osteosarcoma (OS) is a primary bone sarcoma, manifesting as osteogenesis by malignant cells. Nowadays, patients' quality of life has been improved, however continuing high rates of limb amputation, pulmonary metastasis and drug toxicity, remain unresolved issues. Thus, effective osteosarcoma therapies are still required. Recently, the potentialities of biophysical treatments in osteosarcoma have been evaluated and seem to offer a promising future, thanks in this field as they are less invasive. Several approaches have been investigated such as hyperthermia (HT), high intensity focused ultrasound (HIFU), low intensity pulsed ultrasound (LIPUS) and sono- and photodynamic therapies (SDT, PDT). This review aims to summarize in vitro and in vivo studies and clinical trials employing biophysical stimuli in osteosarcoma treatment. The findings underscore how the technological development of biophysical therapies might represent an adjuvant role and, in some cases, alternative role to the surgery, radio and chemotherapy treatment of OS. Among them, the most promising are HIFU and HT, which are already employed in OS patient treatment, while LIPUS/SDT and PDT seem to be particularly interesting for their low toxicity.
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