Homology modeling of Homo sapiens lipoic acid synthase: Substrate docking and insights on its binding mode

Lnc-CNNM3-DT as a protective factor in cervical cancer: regulation of LIAS expression and intracellular copper levels

Background

Cervical cancer (CC) is the fourth leading cause of cancer-related death in women globally.While early screening has reduced mortality, tumor metastasis remains a significant concern, particularly in developing countries. Recent studies have identified cuproptosis, a copper-dependent cell death mechanism, as a potential factor in tumor progression. Long non-coding RNAs (lncRNAs) are key regulators of tumor progression. This study investigates the role of cuproptosis-related lncRNA (CRL) CNNM3-DT in CC, focusing on its impact on LIAS expression, intracellular copper levels, and tumor progression.

Methods

We analyzed the expression of lnc-CNNM3-DT and LIAS in clinical samples and CC cell lines using Real-time Polymerase Chain Reaction (RT-qPCR), Western blot, and immunohistochemistry (IHC). Functional assays, including CCK-8, wound healing, transwell invasion, and flow cytometry, were used to evaluate the effects of lnc-CNNM3-DT overexpression on cell proliferation, migration, invasion, and apoptosis. Intracellular copper ion levels were measured, and correlations between lnc-CNNM3-DT, LIAS, and clinicopathological features were analyzed.

Results

Lnc-CNNM3-DT expression was significantly higher in paracancerous tissues and normal cervical epithelial cells compared to tumor tissues and CC cell lines. Overexpression of lnc-CNNM3-DT suppressed proliferation, migration, and invasion of HeLa and SiHa cells while enhancing apoptosis. Additionally, lnc-CNNM3-DT overexpression downregulated LIAS expression and decreased intracellular copper ion levels. Correlation analysis indicated that lnc-CNNM3-DT expression was negatively associated with tumor diameter and depth of invasion, while LIAS expression showed no significant correlation with clinicopathological features.

Conclusion

Our findings suggest that lnc-CNNM3-DT functions as a protective factor in CC by inhibiting tumor progression through downregulation of LIAS expression and reduction of intracellular copper levels. These results highlight lnc-CNNM3-DT as a potential biomarker and therapeutic target in CC.

Potential relationship between cuproptosis and sepsis-acquired weakness: an intermediate role for mitochondria

Sepsis is defined as a life-threatening organ dysfunction caused by a dysregulated host response to infection. Skeletal muscle atrophy due to critical illness is a common phenomenon in the intensive care unit (ICU) and is referred to as ICU-acquired weakness (ICU-AW). The occurrence of ICU-AW in patients with sepsis is known as sepsis-acquired weakness (SAW). Furthermore, it is well known that maintaining normal muscle function closely relates to mitochondrial homeostasis. Once mitochondrial function is impaired, both muscle quality and function are affected. Copper plays a key role in mitochondrial homeostasis as a transition metal that regulates the function and stability of various enzymes. Copper is also involved in oxidation-reduction reactions, and intracellular copper overload causes oxidative stress and induces cell death. Previous studies have shown that excess intracellular copper induces cell death by targeting lipid-acylated proteins that regulate the mitochondrial tricarboxylic acid (TCA) cycle, which differs from the known canonical mechanisms of regulated cell death. Furthermore, inhibitors of cell death, such as apoptosis, necroptosis, pyroptosis and ferroptosis, are not effective in preventing copper-induced cell death. This new form of cell death has been termed "Cuproptosis"; however, the mechanism by which copper-induced cell death is involved in SAW remains unclear. In this paper, we review the possible relationship between cuproptosis and SAW. Cuproptosis may be involved in regulating the pathological mechanisms of SAW through mitochondria-related signaling pathways, mitochondria-related ferroptosis mechanisms, and mitochondria-related genes, and to provide new ideas for further investigations into the mechanism of SAW.

Characterization of tumor prognosis and sensitive chemotherapy drugs based on cuproptosis-related gene signature in ovarian cancer

BACKGROUND

Cuproptosis is a novel form of cell death, acting on the tricarboxylic acid cycle in mitochondrial respiration and mediated by protein lipoylation. Other cancer cell death processes, such as necroptosis, pyroptosis, and ferroptosis, have been shown to play crucial roles in the therapy and prognosis of ovarian cancer. However, the role of cuproptosis in ovarian cancer remains unclear.

METHODS

The expression profiles of 10 cuproptosis-related genes were extracted from GSE140082. Kaplan-Meier survival and Cox proportional hazards regression were used to identify prognostic genes for constructing risk models. Following this, Least Absolute Shrinkage and Selection Operator regression was employed to construct a risk score model. Next, a nomogram was constructed to predict overall survival in ovarian cancer. Ultimately, our analysis compared the two groups across various dimensions, including clinical characteristics, tumor progression, metabolism-related pathways, immune landscape, and drug sensitivity.

RESULTS

MTF1 and LIAS were identified as protective factors in ovarian cancer, with patients in the higher risk group being significantly associated with poorer survival. Furthermore, integrating the risk score with clinical characteristics in the nomogram demonstrated high specificity and sensitivity in predicting survival. A higher propotion of M2 macrophages, follicular helper T cells, and resting mast cells was observed in the high-risk group. Additionally, the IC50 values of Dasatinib, Bortezomib, Parthenolide, and Imatinib were significantly lower in the high-risk group.

CONCLUSIONS

The study highlights the prognostic significance of cuproptosis-related genes and provides new insights into developing pharmacological therapeutic strategies targeting cuproptosis for the prevention and treatment of ovarian cancer.

Predicting the Structural Impact of Human Alternative Splicing

Protein structure prediction with neural networks is a powerful new method for linking protein sequence, structure, and function, but structures have generally been predicted for only a single isoform of each gene, neglecting splice variants. To investigate the structural implications of alternative splicing, we used AlphaFold2 to predict the structures of more than 11,000 human isoforms. We employed multiple metrics to identify splicing-induced structural alterations, including template matching score, secondary structure composition, surface charge distribution, radius of gyration, accessibility of post-translational modification sites, and structure-based function prediction. We identified examples of how alternative splicing induced clear changes in each of these properties. Structural similarity between isoforms largely correlated with degree of sequence identity, but we identified a subset of isoforms with low structural similarity despite high sequence similarity. Exon skipping and alternative last exons tended to increase the surface charge and radius of gyration. Splicing also buried or exposed numerous post-translational modification sites, most notably among the isoforms of BAX. Functional prediction nominated numerous functional differences among isoforms of the same gene, with loss of function compared to the reference predominating. Finally, we used single-cell RNA-seq data from the Tabula Sapiens to determine the cell types in which each structure is expressed. Our work represents an important resource for studying the structure and function of splice isoforms across the cell types of the human body.

The implications and prospect of cuproptosis-related genes and copper transporters in cancer progression

Currently, cancer has become one of the major public health problems worldwide. Apoptosis is an important anti-cancer defense mechanism, which is used in the development of targeted drugs. Because cancer cells have endogenous resistance to apoptosis,the clinical efficacy of related drugs is not ideal. Therefore, non-apoptotic regulatory cell death may bring new therapeutic strategies for cancer treatment. Cuproptosis is a novel form of regulatory cell death which is copper-dependent, regulated and distinct from other known cell death regulatory mechanisms. FDX1,LIAS,and DLAT named cuproptosis-related genes play an essential role in regulating cuproptosis. Meanwhile, abnormal accumulation of copper can be observed in various malignant tumors. The correlation has been established between elevated copper levels in serum and tissues and the progression of several cancers. Copper transporters, CTR1 and Copper-transporting ATPases(ATP7A and ATP7B), are mainly involved in regulating the dynamic balance of copper concentration to maintain copper homeostasis. Thus,cuproptosis-related genes and copper transporters will be the focus of cancer research in future. This review elaborated the basic functions of cuproptosis-related genes and copper transporters by retrievalling PubMed. And then we analyzed their potential relationship with cancer aiming to provide theoretical support and reference in cancer progression, diagnosis and treatment for future study.

Cuproptosis and cuproptosis-related genes in rheumatoid arthritis: Implication, prospects, and perspectives

Rheumatoid arthritis (RA) is an autoimmune disease that severely affects patients' physical and mental health, leading to chronic synovitis and destruction of bone joints. Although various available clinical treatment options exist, patients respond with varying efficacies due to multiple factors, and there is an urgent need to discover new treatment options to improve clinical outcomes. Cuproptosis is a newly characterized form of cell death. Copper causes cuproptosis by binding to lipid-acylated components of the tricarboxylic acid cycle, leading to protein aggregation, loss of iron-sulfur cluster proteins, and eventually proteotoxic stress. Targeting copper cytotoxicity and cuproptosis are considered potential options for treating oncological diseases. The synovial hypoxic environment and the presence of excessive glycolysis in multiple cells appear to act as inhibitors of cuproptosis, which can lead to excessive survival and proliferation of multiple immune cells, such as fibroblast-like synoviocytes, effector T cells, and macrophages, further mediating inflammation and bone destruction in RA. Therefore, in this study, we attempted to elaborate and summarize the linkage of cuproptosis and key genes regulating cuproptosis to the pathological mechanisms of RA and their effects on a variety of immune cells. This study aimed to provide a theoretical basis and support for translating preclinical and experimental results of RA to clinical protocols.

Lipoic acid rejuvenates aged intestinal stem cells by preventing age-associated endosome reduction

The age‐associated decline of adult stem cell function is closely related to the decline in tissue function and age‐related diseases. However, the underlying mechanisms that ultimately lead to the observed functional decline of stem cells still remain largely unexplored. This study investigated Drosophila midguts and found a continuous downregulation of lipoic acid synthase, which encodes the key enzyme for the endogenous synthesis of alpha‐lipoic acid (ALA), upon aging. Importantly, orally administration of ALA significantly reversed the age‐associated hyperproliferation of intestinal stem cells (ISCs) and the observed decline of intestinal function, thus extending the lifespan of Drosophila. This study reports that ALA reverses age‐associated ISC dysfunction by promoting the activation of the endocytosis–autophagy network, which decreases in aged ISCs. Moreover, this study suggests that ALA may be used as a safe and effective anti‐aging compound for the treatment of ISC‐dysfunction‐related diseases and for the promotion of healthy aging in humans.

Identification and characterization of a sterically robust phenylalanine ammonia-lyase among 481 natural isoforms through association of in silico and in vitro studies

The enzyme phenylalanine ammonia lyase (PAL) is of special importance for the treatment of phenylketonuria patients. The aim of this study was to find a stable recombinant PAL with suitable kinetic properties among all natural PAL producing species using in silico and experimental approaches. To find such a stable PAL among 481 natural isoforms, 48,000 of 3-D models were predicted using the Modeller 9.10 program and evaluated by Ramachandran plot. Correlation analysis between Ramachandran plot and the energy of different thermodynamic components indicated that this plot could be an appropriate tool to predict protein stability. Hence, PAL6 from Lotus japonicus (LjPAL6) was selected as a stable isoform. Molecular dynamic (MD) simulation for 50 ns and docking has been conducted for LjPAL6-phenylalanine complex. The best PAL-phenylalanine frame was selected by re-docking with l-phenylalanine (L-Phe) and root-mean-square deviation (RMSD) value. MD simulation showed that the complex has a good stability, depicted by the low RMSD value, binding free energy and hydrogen bindings. Docking results showed that LjPAL6 has a high affinity toward l-Phe according to the low level of binding free energy. By overexpressing Ljpal6 in E. coli BL21, a total of 33.5 mg/l of protein was obtained, which has been increased to 83.7 mg/l via the optimization of LjPAL6 production using response surface methodology. The optimal pH and temperature were 8.5 and 50 °C, respectively. LjPAL6 showed a specific activity of 42 nkat/mg protein, with K_m, K_cat and K_cat/K_m values of 0.483 mM, 7 S^-1 and 14.5 S^-1 mM^-1 for l-phe, respectively. In conclusion, finding models with the most reasonable stereo-chemical quality and lowest numbers of steric clashes would result in easier folding. Hence, in silico analyses of bulk data from natural origin will lead one to find an optimal model for in vitro studies and drug design.