Bioinformatics is a rapidly evolving field charged with cataloging, disseminating, and analyzing biological data. Bioinformatics started with genomics, but while genomics focuses more narrowly on the genes comprising a genome, bioinformatics now encompasses a much broader range of omics technologies. Overcoming barriers of scale and effort that plagued earlier sequencing methods, bioinformatics adopted an ambitious strategy involving high-throughput and highly automated assays. However, as the list of omics technologies continues to grow, the field of bioinformatics has changed in two fundamental ways. Despite enormous success in expanding our understanding of the biological world, the failure of bulk methods to account for biologically important variability among cells of the same or different type has led to a major shift toward single-cell and spatially resolved omics methods, which attempt to disentangle the conflicting signals contained in heterogeneous samples by examining individual cells or cell clusters. The second major shift has been the attempt to integrate two or more different classes of omics data in a single multimodal analysis to identify patterns that bridge biological layers. For example, unraveling the cause of disease may reveal a metabolite deficiency caused by the failure of an enzyme to be phosphorylated because a gene is not expressed due to aberrant methylation as a result of a rare germline variant. Conclusions: There is a fine line between superficial understanding and analysis paralysis, but like a detective novel, multi-omics increasingly provides the clues we need, if only we are able to see them.

Prediction of hepatocellular carcinoma (HCC) risk is an urgent unmet need in patients with nonalcoholic fatty liver disease (NAFLD). In cohorts of 409 patients with NAFLD from multiple global regions, we defined and validated hepatic transcriptome and serum secretome signatures predictive of long-term HCC risk in patients with NAFLD. A 133-gene signature, prognostic liver signature (PLS)–NAFLD, predicted incident HCC over up to 15 years of longitudinal observation. High-risk PLS-NAFLD was associated with IDO1 ⁺ dendritic cells and dysfunctional CD8 ⁺ T cells in fibrotic portal tracts along with impaired metabolic regulators. PLS-NAFLD was validated in independent cohorts of patients with NAFLD who were HCC naïve (HCC incidence rates at 15 years were 22.7 and 0% in high- and low-risk patients, respectively) or HCC experienced (de novo HCC recurrence rates at 5 years were 71.8 and 42.9% in high- and low-risk patients, respectively). PLS-NAFLD was bioinformatically translated into a four-protein secretome signature, PLSec-NAFLD, which was validated in an independent cohort of HCC-naïve patients with NAFLD and cirrhosis (HCC incidence rates at 15 years were 37.6 and 0% in high- and low-risk patients, respectively). Combination of PLSec-NAFLD with our previously defined etiology-agnostic PLSec-AFP yielded improved HCC risk stratification. PLS-NAFLD was modified by bariatric surgery, lipophilic statin, and IDO1 inhibitor, suggesting that the signature can be used for drug discovery and as a surrogate end point in HCC chemoprevention clinical trials. Collectively, PLS/PLSec-NAFLD may enable NAFLD-specific HCC risk prediction and facilitate clinical translation of NAFLD-directed HCC chemoprevention.

The tumor microenvironment can be classified into immunologically active "inflamed" tumors and inactive "non-inflamed" tumors based on the infiltration of cytotoxic immune cells. Previous studies on liver cancer have reported a superior prognosis for inflamed tumors compared to non-inflamed tumors. However, liver cancer is highly heterogeneous immunologically and genetically, and a finer classification of the liver cancer microenvironment may improve our understanding of its immunological diversity and response to immune therapy. We characterized the immune gene signatures of 234 primary liver cancers, mainly virus-related, from a Japanese population using RNA-Seq of tumors and matched non-tumorous hepatitis livers. We then compared them with the somatic alterations detected using the whole-genome sequencing. Liver cancers expressed lower levels of immune marker genes than non-tumorous hepatitis livers, indicating immunosuppression in the tumor microenvironment. Several immunosuppression mechanisms functioned actively and mutually exclusively, resulting in four immune subclasses of liver cancer: tumor-associated macrophage (TAM), CTNNB1, cytolytic activity (CYT), and regulatory T cell (Treg). The CYT and Treg subclasses represented inflamed tumors, while the TAM and CTNNB1 subclasses represented non-inflamed tumors. The TAM subclass, which comprised 31% of liver cancers, showed a poor survival, expressed elevated levels of extracellular matrix genes, and was associated with somatic mutations of chromatin regulator ARID2. The results of cell line experiments suggested a functional link between ARID2 and chemokine production by liver cancer cells. Primary liver cancer was classified into four subclasses based on mutually exclusive mechanisms for immunosuppression. This classification indicate the importance of immunosuppression mechanisms, such as TAM and Treg, as therapeutic targets for liver cancer. The Japan Agency for Medical Research and Development (AMED).

In adult syringomyelia associated with Chiari I malformation, the spinal deformity, the configuration of cerebellar tonsillar descent, the configuration of syrinx, and the clinical evaluation before and after surgery were investigated. To investigate the characteristics of the scoliosis in syringomyelia associated with Chiari I malformation. In previous studies, the clinical characteristics of pediatric scoliosis associated with syringomyelia have been reported. In this study, 42 patients with syringomyelia were treated. All the patients were 20 years of age or older. They were divided into three groups: Group 1 comprising those without scoliosis, Group 2 composed of those with scoliosis of 10° or more but less than 20°, and Group 3 consisting of those with scoliosis of 20° or more. Investigations conducted with the three groups included determining the curve patterns of scoliosis, the degree of thoracic kyphosis, the configuration of cerebellar tonsillar descent, the configuration of syrinx, the morbidity period, and the clinical evaluation before and after surgery. There were 12 patients in Group 1, 21 patients in Group 2, and 9 patients in Group 3. The concomitant rate of adult syringomyelia with scoliosis was 71.4%. As scoliosis advanced, the kyphotic angle also increased. The concordance in laterality between the cerebellar tonsil and curve convex was 70%. Findings showed that the more advanced the scoliosis was, the more aggravated the neurologic symptoms were, and the poorer the surgical outcomes tended to be. In adult syringomyelia with scoliosis, the morbidity period is long, the syrinx is long, the neurologic symptoms are aggravated, and the surgical outcomes tend to be poor.

Background: Lenvatinib, a multiple receptor tyrosine kinase inhibitor, might exert antitumor effects via tumor immune modulation. However, changes in the tumor immune microenvironment induced by lenvatinib are poorly understood. We investigated the effect of lenvatinib on immune features in clinical samples from patients with hepatocellular carcinoma. Methods: Fifty-one patients with advanced hepatocellular carcinoma who received lenvatinib monotherapy as first-line treatment were enrolled. We collected blood sample (n = 51) and tumor tissue (n, baseline/four weeks after treatment initiation/post-progression = 50/8/12). DNA, RNA, and proteins extracted from the tissues were subjected to multi-omics analysis, and patients were classified into two groups according to baseline immune status. Each group was investigated in terms of the dynamics of tumor signaling. We also longitudinally analyzed circulating immune proteins and chemokines in peripheral blood. Results: Here we show that lenvatinib has similar anti-tumor efficacy with objective response rate and progression-free survival in both Immune-Hot and Immune-Cold subtypes. Immune signatures associated with T-cell functions and interferon responses are enriched in the early phase of treatment, while signatures associated with immunoinhibitory cells are downregulated along with efficient vascular endothelial growth factor receptor and fibroblast growth factor receptor blockades. These findings are supported by imaging mass cytometry, T-cell receptor repertoire analysis and kinetics of circulating proteins. We also identify interleukin-8 and angiopoietin-2 as possible targets of intervention to overcome resistance to existing immunotherapies. Conclusions: Our findings show the ability of lenvatinib to modulate tumor immunity in clinical samples of hepatocellular carcinoma.