Deep Learning-based Pathway-Centric approach to characterize Recurrent Hepatocellular Carcinoma after Liver Transplantation
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE249913 | GEO | 2024/06/06
REPOSITORIES: GEO
Similar Datasets
Project description:Deep Learning-based Pathway-Centric approach to characterize Recurrent Hepatocellular Carcinoma after Liver Transplantation
| PRJNA1051125 | ENA
Project description:Many applications in speech, robotics, finance, and biology deal with sequential data, where ordering matters and recurrent structures are common. However, this structure cannot be easily captured by standard kernel functions. To model such structure, we propose expressive closed-form kernel functions for Gaussian processes. The resulting model, GP-LSTM, fully encapsulates the inductive biases of long short-term memory (LSTM) recurrent networks, while retaining the non-parametric probabilistic advantages of Gaussian processes. We learn the properties of the proposed kernels by optimizing the Gaussian process marginal likelihood using a new provably convergent semi-stochastic gradient procedure, and exploit the structure of these kernels for scalable training and prediction. This approach provides a practical representation for Bayesian LSTMs. We demonstrate state-of-the-art performance on several benchmarks, and thoroughly investigate a consequential autonomous driving application, where the predictive uncertainties provided by GP-LSTM are uniquely valuable.
| S-EPMC6334642 | biostudies-other
Project description:Engineered RNA elements are programmable tools capable of detecting small molecules, proteins, and nucleic acids. Predicting the behavior of these tools remains a challenge, a situation that could be addressed through enhanced pattern recognition from deep learning. Thus, we investigate Deep Neural Networks (DNN) to predict toehold switch function as a canonical riboswitch model in synthetic biology. To facilitate DNN training, we synthesized and characterized in vivo a dataset of 91,534 toehold switches spanning 23 viral genomes and 906 human transcription factors. DNNs trained on nucleotide sequences outperformed (R2=0.43-0.70) previous state-of-the-art thermodynamic and kinetic models (R2=0.04-0.15) and allowed for human-understandable attention-visualizations (VIS4Map) to identify success and failure modes. This deep learning approach constitutes a major step forward in engineering and understanding of RNA synthetic biology.
2020-08-12 | GSE149225 | GEO
Project description:BackgroundFlowering is one of the most important processes for flowering plants such as cotton, reflecting the transition from vegetative to reproductive growth and is of central importance to crop yield and adaptability. Conventionally, categorical scoring systems have been widely used to study flowering patterns, which are laborious and subjective to apply. The goal of this study was to develop a deep learning-based approach to characterize flowering patterns for cotton plants that flower progressively over several weeks, with flowers distributed across much of the plant.ResultsA ground mobile system (GPhenoVision) was modified with a multi-view color imaging module, to acquire images of a plant from four viewing angles at a time. A total of 116 plants from 23 genotypes were imaged during an approximately 2-month period with an average scanning interval of 2-3 days, yielding a dataset containing 8666 images. A subset (475) of the images were randomly selected and manually annotated to form datasets for training and selecting the best object detection model. With the best model, a deep learning-based approach (DeepFlower) was developed to detect and count individual emerging blooms for a plant on a given date. The DeepFlower was used to process all images to obtain bloom counts for individual plants over the flowering period, using the resulting counts to derive flowering curves (and thus flowering characteristics). Regression analyses showed that the DeepFlower method could accurately (R2?=?0.88 and RMSE?=?0.79) detect and count emerging blooms on cotton plants, and statistical analyses showed that imaging-derived flowering characteristics had similar effectiveness as manual assessment for identifying differences among genetic categories or genotypes.ConclusionsThe developed approach could thus be an effective and efficient tool to characterize flowering patterns for flowering plants (such as cotton) with complex canopy architecture.
| S-EPMC7720604 | biostudies-literature
Project description:ObjectivesTo utilize a deep learning model for automatic detection of abnormalities in chest CT images from COVID-19 patients and compare its quantitative determination performance with radiological residents.MethodsA deep learning algorithm consisted of lesion detection, segmentation, and location was trained and validated in 14,435 participants with chest CT images and definite pathogen diagnosis. The algorithm was tested in a non-overlapping dataset of 96 confirmed COVID-19 patients in three hospitals across China during the outbreak. Quantitative detection performance of the model was compared with three radiological residents with two experienced radiologists' reading reports as reference standard by assessing the accuracy, sensitivity, specificity, and F1 score.ResultsOf 96 patients, 88 had pneumonia lesions on CT images and 8 had no abnormities on CT images. For per-patient basis, the algorithm showed superior sensitivity of 1.00 (95% confidence interval (CI) 0.95, 1.00) and F1 score of 0.97 in detecting lesions from CT images of COVID-19 pneumonia patients. While for per-lung lobe basis, the algorithm achieved a sensitivity of 0.96 (95% CI 0.94, 0.98) and a slightly inferior F1 score of 0.86. The median volume of lesions calculated by algorithm was 40.10 cm3. An average running speed of 20.3 s ± 5.8 per case demonstrated the algorithm was much faster than the residents in assessing CT images (all p < 0.017). The deep learning algorithm can also assist radiologists make quicker diagnosis (all p < 0.0001) with superior diagnostic performance.ConclusionsThe algorithm showed excellent performance in detecting COVID-19 pneumonia on chest CT images compared with resident radiologists.Key points• The higher sensitivity of deep learning model in detecting COVID-19 pneumonia were found compared with radiological residents on a per-lobe and per-patient basis. • The deep learning model improves diagnosis efficiency by shortening processing time. • The deep learning model can automatically calculate the volume of the lesions and whole lung.
| S-EPMC7331494 | biostudies-literature
Project description:Determining transcriptional factor binding sites (TFBSs) is critical for understanding the molecular mechanisms regulating gene expression in different biological conditions. Biological assays designed to directly mapping TFBSs require large sample size and intensive resources. As an alternative, ATAC-seq assay is simple to conduct and provides genomic cleavage profiles that contain rich information for imputing TFBSs indirectly. Previous footprint-based tools are inheritably limited by the accuracy of their bias correction algorithms and the efficiency of their feature extraction models. Here we introduce TAMC (Transcriptional factor binding prediction from ATAC-seq profile at Motif-predicted binding sites using Convolutional neural networks), a deep-learning approach for predicting motif-centric TF binding activity from paired-end ATAC-seq data. TAMC does not require bias correction during signal processing. By leveraging a one-dimensional convolutional neural network (1D-CNN) model, TAMC make predictions based on both footprint and non-footprint features at binding sites for each TF and outperforms existing footprinting tools in TFBS prediction particularly for ATAC-seq data with limited sequencing depth.
| S-EPMC9499209 | biostudies-literature
Project description:Liver transplantation (LT) is an optimal treatment for a selected group of hepatocellular carcinoma (HCC) patients. However, about 10%-25% of LT cases develop post-transplant HCC recurrence, which drastically reduces the long-term survival of HCC patients. This study gives an analysis of the recurrent HCC after LT and the corresponding primary tumor. Results provide insight into the molecular mechanisms underlying post-LT HCC recurrence.
2021-08-27 | GSE102759 | GEO
Project description:Current selection criteria for liver transplant in patients with HCC (the Milan criteria) do not incorporate biologic metrics. MiRNA expression profiles correlate with HCC recurrence after transplant and can add significant value to the Milan criteria. MiRNA expression profiles were studied in HCC specimens from patients undergoing liver transplant and correlated with their tumor recurrence status and Milan criteria status.
2011-10-14 | E-GEOD-30297 | biostudies-arrayexpress
Project description:Background: Liver transplantation (LT) for Hepatocellular carcinoma (HCC) can be offered to patients beyond Milan criteria. However, there are currently no molecular markers that can be used on HCC explant histology to predict recurrence, which arises in up to 20% of LT recipients. The goal of our study was to identify proteins on HCC explant predictive of recurrence post-transplant, thereby guiding surveillance strategies and identifying patients beyond Milan criteria who would fare well following LT. Methods: LT recipients who had been transplanted at the University Health Network for HCC beyond Milan criteria in the context of Hepatitis B cirrhosis were identified. Snap-frozen samples from the dominant tumors of recurrent (N=7) and non-recurrent (N=4) patients were analyzed using LC-MS/MS on a Q-Exactive Plus mass spectrometer to delineate a distinctive proteomic signature. These tumors were also profiled by a Human Gene 2.0 ST microarray platform to identify a transcriptomic signature predictive of recurrence and analyzed with R packages. STRING database was used to characterize the implicated pathways. Kaplan-Meier estimator was used to generate a combined proteomic/transcriptomic signature predictive of HCC recurrence in patients with HCC beyond Milan criteria at time of LT. Significantly predictive proteins were verified and internally validated by immunoblotting or immunohistochemistry. Results: A total of 79 proteins and 636 genes were significantly differentially expressed in recurrent HCC, compared to non-recurrent (p<0.05). Among these, LGALS3, LGALS3BP, HAL, THBS1, and BLMH, were significantly increased in recurrent HCC at the protein and gene expression level. In turn, ALDH1A1 protein and gene expression were significantly decreased in recurrent HCC. Univariate survival analysis depicted ALDH1A1 (HR=0.084, 95%CI 0.01-0.68, p=0.02), LGALS3BP (HR=7.14, 95%CI 1.20-42.96, p=0.03), and LGALS3 (HR=2.89, 95%CI 1.01-8.3, p=0.049) as the key dysregulated proteins and genes in the patients with HCC recurrence versus those with non-recurrence by both proteomic and transcriptomic analysis. Decreased ALDH1A1 and significantly increased LGALS3 protein expression in recurrent HCC was verified by immunoblotting. Increased LGALS3BP protein expression in recurrent HCC was orthogonally verified and validated by immunohistochemistry in 30 independent HCC samples. Conclusion: Protein and gene expression of the cancer stem cell marker ALDH1A1 was protective against cancer recurrence in patients transplanted for HCC beyond Milan criteria. Conversely, increased expression of LGALS3 and LGALS3BP on explant was significantly predictive of post-transplant recurrence. These findings were internally validated, suggesting potential utility in identifying patients with HCC beyond Milan who would clearly benefit from transplant with limited recurrence risk and guiding post-transplant surveillance.
2022-02-22 | PXD022881 | Pride
Project description:Background and aims: Liver transplantation (LT) is the most radical treatment for hepatocellular carcinoma (HCC) with high rates of long-term survival, but tumor recurrence after LT is an unresolved problem. The aim of our study was to identify predictive markers for tumor recurrence after liver transplantation. Methods: In a retrospective single-center study, we included all patients with LT for HCC in our institution (01/2007-12/2012). Beside demographic data, we analyzed course, bridging therapies, Serum-AFP, time point of tumor recurrence, as well as the correlation of imaging and histopathology of our recipients. Additionally, we performed a microarray analysis to identify different miRNA profiles of patients with and without HCC recurrence after LT. Single assay stem-loop real-time PCR (Q-RT-PCR) was used for validation of the results. Results: During the study period, we performed 92 LT in patients with HCC (22 women, 70 men). Twenty-two (23.9%) patients developed a recurrent HCC after LT. Our subgroup with tumor recurrence after LT, presented with a mean disease-free survival of 10 months (3-55 months) and an overall survival of 25.5 months (4-77 months). Milan criteria, AFP levels and pathologic grading had an influence on the tumor recurrence. Performing miRNA analysis, we could identify significant upregulation of 8 miRNAs and downregulation of another 5 miRNAs in patients with tumor recurrence. Consecutively, array data were successfully validated using Q-RT-PCR. Multivariate Cox regression, ROC analysis and Kaplan-Meier showed that a score consisting of two miRNAs and Milan criteria are an independent predictor for tumor recurrence-free survival. Conclusions: Despite careful selection of patients, an early recurrence of HCC after LT cannot be avoided completely. Reliable prognostic markers related to tumor biology are still missing. Analysis and validation of specific miRNAs combined with radiological parameters might lead to a promising strategy for the prediction of tumor recurrence, but prospective studies have to follow. 8 macrodissected hepatocellular carcinoma (recurrent HCC) and 10 macrodissected hepatocellular carcinoma (non-recurrent HCC).
2016-03-01 | E-GEOD-64989 | biostudies-arrayexpress