The relationship between expression of aging-related genes in normal tissues and cancer patient survival has not been assessed. We developed a genome-wide transcriptomic analysis approach for normal tissues adjacent to the tumor to identify aging-related transcripts associated with survival outcome, and applied it to 12 cancer types. As a result, five aging-related genes (DUSP22, MAPK14, MAPKAPK3, STAT1, and VCP) in normal tissues were found to be significantly associated with a worse survival outcome in patients with renal cell carcinoma (RCC). This computational approach was investigated using nontumorigenic immune cells purified from young and aged mice. Aged immune cells showed upregulated expression of all five aging-related genes and promoted RCC invasion compared to young immune cells. Further studies revealed DUSP22 as a regulator and druggable target of metastasis. DUSP22 gene knockdown reduced RCC invasion and the small molecule inhibitor BML-260 prevented RCC dissemination in a tumor/immune cell xenograft model. Overall, these results demonstrate that deciphering the relationship between aging-related gene expression in normal tissues and cancer patient survival can provide new prognostic markers, regulators of tumorigenesis and novel targets for drug development.
High dimensional multi-omics data integration can enhance our understanding of the complex biological interactions in human diseases. However, most studies involving unsupervised integration of multi-omics data focus on linear integration methods. In this study, we propose a joint deep semi-non-negative matrix factorization (JDSNMF) model, which uses a hierarchical non-linear feature extraction approach that can capture shared latent features from the complex multi-omics data. The extracted latent features obtained from JDSNMF enabled a variety of downstream tasks, including prediction of disease and module analysis. The proposed model is applicable not only to sample-matched multiple data (e.g., multi-omics data from one cohort) but also to feature-matched multiple data (e.g., omics data from multiple cohorts), and therefore it can be flexibly applied to various cases. We demonstrate the capabilities of JDSNMF using sample-matched simulated data and feature-matched multi-omics data from Alzheimer’s disease cohorts, evaluating the feature extraction performance in the context of classification. In a test application, we identify AD- and age-related modules from the latent matrices using an explainable artificial intelligence and regression model. These results show that the JDSNMF model is effective in identifying latent features having a complex interplay of potential biological signatures.
MicroRNAs (miRNAs) are key molecules that regulate biological processes such as cell proliferation, differentiation, and apoptosis in cancer. Somatic copy number alterations (SCNAs) are common genetic mutations that play essential roles in cancer development. Here, we investigated the association between miRNAs and SCNAs in cancer. We collected 2538 tumor samples for seven cancer types from The Cancer Genome Atlas. We found that 32−84% of miRNAs are in SCNA regions, with the rate depending on the cancer type. In these regions, we identified 80 SCNA-miRNAs whose expression was mainly associated with SCNAs in at least one cancer type and showed that these SCNA-miRNAs are related to cancer by survival analysis and literature searching. We also identified 58 SCNA-miRNAs common in the seven cancer types (CC-SCNA-miRNAs) and showed that these CC-SCNA-miRNAs are more likely to be related with protein and gene expression than other miRNAs. Furthermore, we experimentally validated the oncogenic role of miR-589. In conclusion, our results suggest that SCNA-miRNAs significantly alter biological processes related to cancer development, confirming the importance of SCNAs in non-coding regions in cancer.
Background and purpose: Alzheimer disease (AD) is the most common type of dementia. Amyloidβ (Aβ) positivity is the main diagnostic marker for AD. Aβ positron emission tomography and cerebrospinal fluid are widely used in the clinical diagnosis of AD.However, these methods only assess the concentrations of Aβ, and the accessibility of these methods is thus relatively limited compared with structural magnetic resonance imaging (sMRI). Methods: We investigated whether regions of interest (ROIs) in sMRIs can be used to predict Aβ positivity for samples with normal cognition (NC), mild cognitive impairment (MCI), and dementia. We obtained 846 Aβ negative (Aβ−) and 865 Aβ positive (Aβ+) samples from the Alzheimer's Disease Neuroimaging Initiative database. To predict which samples are Aβ+, we built five machine learning models using ROIs and apolipoprotein E (APOE) genotypes as features. To test the performance of the machine learning models, we constructed a new cohort containing 97 Aβ− and 81 Aβ+ samples. Results:The best performing machine learning model combining ROIs and APOE had an accuracy of 0.798, indicating that it can help predict Aβ+. Furthermore, we searched ROIs that could aid our prediction and discovered that an average left entorhinal cortical region (L-ERC) thickness is an important feature. We also noted significant differences in L-ERC thickness between the Aβ− and Aβ+ samples even in the same diagnosis of NC, MCI, and dementia. Conclusions:Our findings indicate that ROIs from sMRIs along with APOE can be used as an initial screening tool in the early diagnosis of AD.
Cancer prognosis is one of the most important feats of cancer researchers, as a more precise prediction can promote proper clinical treatment for patients. However, cancer prognosis is challenging, as the heterogeneity and environment of different cancer types significantly affect their prognoses. 1 With the development of sequencing
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