Features and Algorithms for Embedded Protein Sequence Classification with Class Imbalance

13301甲第5587号博士（学術）金沢大学博士論文本文Full 以下に掲載：Frontiers in Genetics 13(1) pp.Article No.885929-11p. 2022. Frontiers. 共著者：Fatma Indriani, Kunti Robiatul Mahmudah, Bedy Purnama, Kenji Sato

The expanding constellation of histone post-translational modifications in the epigenetic landscape

The emergence of a nucleosome-based chromatin structure accompanied the evolutionary transition from prokaryotes to eukaryotes. In this scenario, histones became the heart of the complex and precisely timed coordination between chromatin architecture and functions during adaptive responses to environmental influence by means of epigenetic mechanisms. Notably, such an epigenetic machinery involves an overwhelming number of post-translational modifications at multiple residues of core and linker histones. This review aims to comprehensively describe old and recent evidence in this exciting field of research. In particular, histone post-translational modification establishing/removal mechanisms, their genomic locations and implication in nucleosome dynamics and chromatin-based processes, as well as their harmonious combination and interdependence will be discussed

Molecular regulation of nutrient sensing and immunometabolism by calorie restriction

“‘You'll live longer and you'll be healthier too,’ he answered. ‘Because as we were saying today, there's nothing in the world like eating moderately to live a long life.’ ‘If that's the way things are,’ I thought to myself, ‘I never will die.’ Because I've always been forced to keep that rule, and with my luck I'll probably keep it all my life.”—Anonymous, The Life of Lazarillo de Tormes and of His Fortunes and Adversities 1554. Adaptive mechanisms in response to calorie restriction are evolutionarily conserved and necessary to promote longevity and increase health span. Caloric restriction (CR) without malnutrition, constitutes an effective strategy for weight reduction and ameliorates the chronic inflammatory burden of many chronic metabolic diseases. CR is known to impact nutrient sensing and immuno-metabolic processes in immune cells, but not much is known about skeletal muscle, the largest tissue in the body. We first delve into the literature that describes the interaction of CR and epigenetic mechanisms: DNA methylation, histone modifications, and microRNAs. We explore the impact of CR on nutrient sensing and immuno-metabolic processes and provide a comprehensive view of the adaptive and epigenetic machinery coordinated by CR. In our first study, we aimed to uncover the long-term effect of CR following early-life high fat-diet exposure. We analyzed physiological, biochemical, and transcriptional changes in muscle following chronic CR. Our results indicate that CR activates nutrient sensing pathways, promotes protein recycling, and stimulates myogenesis, possibly due to inhibition of cachexia-inducing inflammatory pathways. Then, our second experiment was designed to titrate the effects of CR by using a novel approach with clinical translatability. We used alternate-day CR (ADCR) in 1-3 days a week and 25-75 % energy restriction to delineate the physiological, biochemical, and transcriptional changes in muscle following chronic ADCR. Effective strategies with high translatable potential, such as 50% CR more than 2 days a week or 75% CR more than 1 day a week, produced similar effects to the gold standard of 25% chronic CR. Finally, on our third experiment we dissected the series of adaptive, epigenetic mechanisms employed by CR to decrease muscle inflammation. Chronic CR activates a series of inhibitors of inflammatory factor NF-kB, while increasing promoter DNA methylation and decreasing transcription factor binding of cytokine Tnf, as well as fine-tuning miRNA expression to prevent inflammation. Here we describe that CR orchestrates a series of adaptive nutrient sensing and anti-inflammatory checkpoints to inhibit inflammation and promote skeletal muscle maintenance

Lipid elongation and its role in prostate cancer

Prostate cancer is the most commonly diagnosed cancer in Australian men, and advanced stage disease is currently incurable. Prostate cancer development and progression is driven by androgens, male hormones such as testosterone, that control a suite of cellular processes via androgen receptor (AR) signalling. An important target of AR signalling in prostate cancer cells is lipid metabolism, as it is commonly dysregulated in cancer. Fatty acids are the building blocks of complex lipids within the cell (the lipidome), and fatty acid synthesis is one aspect of lipid metabolism controlled by AR signalling in prostate cancer. Recently, lipidomic analysis of prostate cancer cells stimulated by androgens demonstrated an increased abundance of long-chain phospholipid species compared to untreated control cells. This effect was found to be mediated by the elongation of very long chain fatty acid 5 (ELOVL5) enzyme. Knockdown of ELOVL5 reduced prostate cancer cell viability, suggesting that ELOVL5-mediated fatty acid elongation was important for prostate cancer cell homeostasis, however, the mechanisms to explain the effects of ELOVL5 were undefined. Therefore, this thesis aimed to determine the contribution of ELOVL5 and the production of long-chain fatty acids to prostate cancer cell phenotypes (Chapters 3 and 4), and analyse the accumulation of metabolic precursors and associated metabolic dysfunction following ELOVL5 targeting (Chapter 5). In Chapter 3, ELOVL5 protein levels were found to be positively correlated with mitochondrial respiration and inversely correlated with the levels of reactive oxygen species (ROS). Interestingly, only the monounsaturated fatty acid (MUFA) product of ELOVL5, cis-vaccenic acid (cVA) could rescue the effects of ELOVL5 knockdown on prostate cancer cell viability. Further investigation of cVA, in Chapter 4, demonstrated that cVA supplementation could increase prostate cancer cell viability and consistently rescue the effects of inhibition of the canonical MUFA-producing enzyme stearoyl-CoA desaturase 1 (SCD1), required for cVA production. Mechanistically, cVA was found to be incorporated into cardiolipins, a mitochondrial specific phospholipid, where it regulated mitochondrial-specific ROS production. Taken together, these findings from Chapters 3 and 4 identified the MUFA product of ELOVL5, cVA, as a novel oncogenic factor in prostate cancer. Finally, Chapter 5 considered the effects of targeting fatty acid elongation on malonyl-CoA accumulation. Malonyl-CoA is required for fatty acid elongation, and can reduce mitochondrial fatty acid oxidation (β-oxidation) through inhibition of carnitine palmitoyltransferase 1 (CPT1). Accordingly, ELOVL5 knockdown caused an accumulation of malonyl-CoA in prostate cancer cell lines, and reduced mitochondrial β-oxidation, identifying a previously unappreciated role for fatty acid elongation in the regulation of malonyl-CoA levels. Overall, this thesis demonstrates that ELOVL5 is a critical oncogenic factor in prostate cancer that promotes cell growth and proliferation through the production of the MUFA, cVA, and regulation of key substrate malonyl-CoA, that influence mitochondrial homeostasis and β-oxidation, respectively. These findings provide novel insight into the role of fatty acid elongation in prostate cancer, and highlight a potential therapeutic vulnerability of these cells that warrants further investigation.Thesis (Ph.D.) -- University of Adelaide, Adelaide Medical School, 202

Characterization and identification of lysine glutarylation based on intrinsic interdependence between positions in the substrate sites

Abstract Background Glutarylation, the addition of a glutaryl group (five carbons) to a lysine residue of a protein molecule, is an important post-translational modification and plays a regulatory role in a variety of physiological and biological processes. As the number of experimentally identified glutarylated peptides increases, it becomes imperative to investigate substrate motifs to enhance the study of protein glutarylation. We carried out a bioinformatics investigation of glutarylation sites based on amino acid composition using a public database containing information on 430 non-homologous glutarylation sites. Results The TwoSampleLogo analysis indicates that positively charged and polar amino acids surrounding glutarylated sites may be associated with the specificity in substrate site of protein glutarylation. Additionally, the chi-squared test was utilized to explore the intrinsic interdependence between two positions around glutarylation sites. Further, maximal dependence decomposition (MDD), which consists of partitioning a large-scale dataset into subgroups with statistically significant amino acid conservation, was used to capture motif signatures of glutarylation sites. We considered single features, such as amino acid composition (AAC), amino acid pair composition (AAPC), and composition of k-spaced amino acid pairs (CKSAAP), as well as the effectiveness of incorporating MDD-identified substrate motifs into an integrated prediction model. Evaluation by five-fold cross-validation showed that AAC was most effective in discriminating between glutarylation and non-glutarylation sites, according to support vector machine (SVM). Conclusions The SVM model integrating MDD-identified substrate motifs performed well, with a sensitivity of 0.677, a specificity of 0.619, an accuracy of 0.638, and a Matthews Correlation Coefficient (MCC) value of 0.28. Using an independent testing dataset (46 glutarylated and 92 non-glutarylated sites) obtained from the literature, we demonstrated that the integrated SVM model could improve the predictive performance effectively, yielding a balanced sensitivity and specificity of 0.652 and 0.739, respectively. This integrated SVM model has been implemented as a web-based system (MDDGlutar), which is now freely available at http://csb.cse.yzu.edu.tw/MDDGlutar/