Primary liver cancer classification from routine tumour biopsy using weakly supervised deep learning

Deep Learning to Enhance Diagnosis and Management of Intrahepatic Cholangiocarcinoma

Intrahepatic cholangiocarcinoma (iCCA) is associated with a poor prognosis and necessitates a multimodal, multidisciplinary approach from diagnosis to treatment to achieve optimal outcomes. A noninvasive preoperative diagnosis using abdominal imaging techniques can represent a clinical challenge. Given the differential response of iCCA to localized and systemic therapies compared with hepatocellular carcinoma and secondary hepatic malignancies, an accurate diagnosis is crucial. Deep learning (DL) models for image analysis have emerged as a promising adjunct for the abdominal radiologist, potentially enhancing the accurate detection and diagnosis of iCCA. Over the last five years, several reports have proposed robust DL models, which demonstrate a diagnostic accuracy that is either comparable to or surpasses that of radiologists with varying levels of experience. Recent studies have expanded DL applications into other aspects of iCCA management, including histopathologic diagnosis, the prediction of histopathological features, the preoperative prediction of survival, and the pretreatment prediction of responses to systemic therapy. We herein critically evaluate the expanding body of research on DL applications in the diagnosis and management of iCCA, providing insights into the current progress and future research directions. We comprehensively synthesize the performance and limitations of DL models in iCCA research, identifying key challenges that serve as a translational reference for clinicians.

Automatic quality control of brain 3D FLAIR MRIs for a clinical data warehouse

Clinical data warehouses, which have arisen over the last decade, bring together the medical data of millions of patients and offer the potential to train and validate machine learning models in real-world scenarios. The quality of MRIs collected in clinical data warehouses differs significantly from that generally observed in research datasets, reflecting the variability inherent to clinical practice. Consequently, the use of clinical data requires the implementation of robust quality control tools. By using a substantial number of pre-existing manually labelled T1-weighted MR images (5,500) alongside a smaller set of newly labelled FLAIR images (926), we present a novel semi-supervised adversarial domain adaptation architecture designed to exploit shared representations between MRI sequences thanks to a shared feature extractor, while taking into account the specificities of the FLAIR thanks to a specific classification head for each sequence. This architecture thus consists of a common invariant feature extractor, a domain classifier and two classification heads specific to the source and target, all designed to effectively deal with potential class distribution shifts between the source and target data classes. The primary objectives of this paper were: (1) to identify images which are not proper 3D FLAIR brain MRIs; (2) to rate the overall image quality. For the first objective, our approach demonstrated excellent results, with a balanced accuracy of 89%, comparable to that of human raters. For the second objective, our approach achieved good performance, although lower than that of human raters. Nevertheless, the automatic approach accurately identified bad quality images (balanced accuracy >79%). In conclusion, our proposed approach overcomes the initial barrier of heterogeneous image quality in clinical data warehouses, thereby facilitating the development of new research using clinical routine 3D FLAIR brain images.

Multi-omics identification of a polyamine metabolism related signature for hepatocellular carcinoma and revealing tumor microenvironment characteristics

Background

Accumulating evidence indicates that elevated polyamine levels are closely linked to tumor initiation and progression. However, the precise role of polyamine metabolism in hepatocellular carcinoma (HCC) remains poorly understood.

Methods

We conducted differential expression analysis on bulk RNA sequencing data from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) to identify 65 polyamine metabolism-related genes. By employing unsupervised consensus clustering, AddModuleScore, single-sample gene set enrichment analysis (ssGSEA), and weighted gene co-expression network analysis (WGCNA), we identified polyamine metabolism-related genes at both the bulk RNA-seq and single-cell RNA-seq (scRNA-seq) levels. Utilizing 101 machine learning algorithms, we constructed a polyamine metabolism-related signature (PMRS) and validated its predictive power across training, testing, and external validation cohorts. Additionally, we developed a prognostic nomogram model by integrating PMRS with clinical variables. To explore immune treatment sensitivity, we assessed tumor mutation burden (TMB), tumor immune dysfunction and exclusion (TIDE) score, mutation frequency, and immune checkpoint genes expression. Immune cell infiltration was analyzed using the CIBERSORT algorithm. Finally, RT-qPCR experiments were conducted to validate the expression of key genes.

Results

Using 101 machine learning algorithms, we established a polyamine metabolism-related signature comprising 9 genes, which exhibited strong prognostic value for HCC patients. Further analysis revealed significant differences in clinical features, biological functions, mutation profiles, and immune cell infiltration between high-risk and low-risk groups. Notably, TIDE analysis and immune phenotype scoring (IPS) demonstrated distinct immune treatment sensitivities between the two risk groups. RT-qPCR validation confirmed that these 9 genes were highly expressed in normal cells but significantly downregulated in tumor cells.

Conclusions

Our study developed a polyamine metabolism-based prognostic risk signature for HCC, which may provide valuable insights for personalized treatment strategies in HCC patients.

Use of artificial intelligence for liver diseases: A survey from the EASL congress 2024

Artificial intelligence (AI) methods enable humans to analyse large amounts of data, which would otherwise not be feasibly quantifiable. This is especially true for unstructured visual and textual data, which can contain invaluable insights into disease. The hepatology research landscape is complex and has generated large amounts of data to be mined. Many open questions can potentially be addressed with existing data through AI methods. However, the field of AI is sometimes obscured by hype cycles and imprecise terminologies. This can conceal the fact that numerous hepatology research groups already use AI methods in their scientific studies. In this review article, we aim to assess the contemporaneous use of AI methods in hepatology in Europe. To achieve this, we systematically surveyed all scientific contributions presented at the EASL Congress 2024. Out of 1,857 accepted abstracts (1,712 posters and 145 oral presentations), 6 presentations (∼4%) and 69 posters (∼4%) utilised AI methods. Of these, 55 posters were included in this review, while the others were excluded due to missing posters or incomplete methodologies. Finally, we summarise current academic trends in the use of AI methods and outline future directions, providing guidance for scientific stakeholders in the field of hepatology.