Artificial Intelligence as Accelerator for Genomic Medicine and Planetary Health

Decoding Systems Biology of Inflammation Signatures in Cancer Pathogenesis: Pan-Cancer Insights from 12 Common Cancers

Chronic inflammation is an important contributor to tumorigenesis in many tissues. However, the underlying mechanisms of inflammatory signaling in the tumor microenvironment are not yet fully understood in various cancers. Therefore, this study aimed to uncover the gene expression signatures of inflammation-associated proteins that lead to tumorigenesis, and with an eye to discovery of potential system biomarkers and novel drug candidates in oncology. Gene expression profiles associated with 12 common cancers (e.g., breast invasive carcinoma, colon adenocarcinoma, liver hepatocellular carcinoma, and prostate adenocarcinoma) from The Cancer Genome Atlas were retrieved and mapped to inflammation-related gene sets. Subsequently, the inflammation-associated differentially expressed genes (i-DEGs) were determined. The i-DEGs common in all cancers were proposed as tumor inflammation signatures (TIS) after pan-cancer analysis. A TIS, consisting of 45 proteins, was evaluated as a potential system biomarker based on its prognostic forecasting and secretion profiles in multiple tissues. In addition, i-DEGs for each cancer type were used as queries for drug repurposing. Narciclasine, parthenolide, and homoharringtonine were identified as potential candidates for drug repurposing. Biomarker candidates in relation to inflammation were identified such as KNG1, SPP1, and MIF. Collectively, these findings inform precision diagnostics development to distinguish individual cancer types, and can also pave the way for novel prognostic decision tools and repurposed drugs across multiple cancers. These new findings and hypotheses warrant further research toward precision/personalized medicine in oncology. Pan-cancer analysis of inflammatory mediators can open up new avenues for innovation in cancer diagnostics and therapeutics.

Precision Oncology: An Ensembled Machine Learning Approach to Identify a Candidate mRNA Panel for Stratification of Patients with Breast Cancer

The rise of machine learning (ML) has recently buttressed the efforts for big data-driven precision oncology. This study used ensemble ML for precision oncology in breast cancer, which is one of the most common malignancies worldwide with marked heterogeneity of the underlying molecular mechanisms. We analyzed clinical and RNA-seq data from The Cancer Genome Atlas (TCGA) (844 patients with breast cancer and 113 healthy individuals) and the Molecular Taxonomy of Breast Cancer International Consortium (METABRIC) (1784 patients with breast cancer and 202 healthy individuals). We evaluated six algorithms in the context of ensemble modeling and identified a candidate mRNA diagnostic panel that can differentiate patients from healthy controls, and stratify breast cancer into molecular subtypes. The ensemble model included 50 mRNAs and displayed 82.55% accuracy, 79.22% specificity, and 84.55% sensitivity in stratifying patients into molecular subtypes in TCGA cohort. Its performance was markedly higher, however, in distinguishing the basal, LumB, and Her2+ breast cancer subtypes from healthy individuals. In overall survival analysis, the mRNA panel showed a hazard ratio of 2.25 (p = 5 × 10^-7) for breast cancer and was significantly associated with molecular pathways related to carcinogenesis. In conclusion, an ensemble ML approach, including 50 mRNAs, was able to stratify patients with different breast cancer subtypes and differentiate them from healthy individuals. Future prospective studies in large samples with deep phenotyping can help advance the ensemble ML approaches in breast cancer. Advanced ML methods such as ensemble learning are timely additions to the precision oncology research toolbox.

Multi-Omics and Artificial Intelligence-Guided Data Integration in Chronic Liver Disease: Prospects and Challenges for Precision Medicine

Chronic liver disease (CLD) is a significant planetary health burden. CLD includes a broad range of liver pathologies from different causes, for example, hepatitis B virus infection, fatty liver disease, hepatocellular carcinoma, and nonalcoholic fatty liver disease or the metabolic associated fatty liver disease. Biomarker and diagnostic discovery, and new molecular targets for precision treatments are timely and sorely needed in CLD. In this context, multi-omics data integration is increasingly being facilitated by artificial intelligence (AI) and attendant digital transformation of systems science. While the digital transformation of multi-omics integrative analyses is still in its infancy, there are noteworthy prospects, hope, and challenges for diagnostic and therapeutic innovation in CLD. This expert review aims at the emerging knowledge frontiers as well as gaps in multi-omics data integration at bulk tissue levels, and those including single cell-level data, gut microbiome data, and finally, those incorporating tissue-specific information. We refer to AI and related digital transformation of the CLD research and development field whenever possible. This review of the emerging frontiers at the intersection of systems science and digital transformation informs future roadmaps to bridge digital technology discovery and clinical omics applications to benefit planetary health and patients with CLD.

A Real-Time Effectiveness Evaluation Method for Remote Sensing Satellite Clusters on Moving Targets

Recently, remote sensing satellites have become increasingly important in the Earth observation field as their temporal, spatial, and spectral resolutions have improved. Subsequently, the quantitative evaluation of remote sensing satellites has received considerable attention. The quantitative evaluation method is conventionally based on simulation, but it has a speed-accuracy trade-off. In this paper, a real-time evaluation model architecture for remote sensing satellite clusters is proposed. Firstly, a multi-physical field coupling simulation model of the satellite cluster to observe moving targets is established. Aside from considering the repercussions of on-board resource constraints, it also considers the consequences of the imaging’s uncertainty effects on observation results. Secondly, a moving target observation indicator system is developed, which reflects the satellite cluster’s actual effectiveness in orbit. Meanwhile, an indicator screening method using correlation analysis is proposed to improve the independence of the indicator system. Thirdly, a neural network is designed and trained for stakeholders to realize a rapid evaluation. Different network structures and parameters are comprehensively studied to determine the optimized neural network model. Finally, based on the experiments carried out, the proposed neural network evaluation model can generate real-time, high-quality evaluation results. Hence, the validity of our proposed approach is substantiated.