Discovering Novel Prognostic Biomarkers of Hepatocellular Carcinoma using eXplainable Artificial Intelligence.

Hepatocellular carcinoma (HCC) remains a global health challenge with high mortality rates, largely due to late diagnosis and suboptimal efficacy of current therapies. With the imperative need for more reliable, non-invasive diagnostic tools and novel therapeutic strategies, this study focuses on the discovery and application of novel genetic biomarkers for HCC using explainable artificial intelligence (XAI). Despite advances in HCC research, current biomarkers like Alpha-fetoprotein (AFP) exhibit limitations in sensitivity and specificity, necessitating a shift towards more precise and reliable markers. This paper presents an innovative XAI framework to identify and validate key genetic biomarkers for HCC prognosis. Our methodology involved analyzing clinical and gene expression data to identify potential biomarkers with prognostic significance. The study utilized robust AI models validated against extensive gene expression datasets, demonstrating not only the predictive accuracy but also the clinical relevance of the identified biomarkers through explainable metrics. The findings highlight the importance of biomarkers such as TOP3B, SSBP3, and COX7A2L, which were consistently influential across multiple models, suggesting their role in improving the predictive accuracy for HCC prognosis beyond AFP. Notably, the study also emphasizes the relevance of these biomarkers to the Hispanic population, aligning with the larger goal of demographic-specific research. The application of XAI in biomarker discovery represents a significant advancement in HCC research, offering a more nuanced understanding of the disease and laying the groundwork for improved diagnostic and therapeutic strategies.

Early-adulthood spike in protein translation drives aging via juvenile hormone/germline signaling.

Protein translation (PT) declines with age in invertebrates, rodents, and humans. It has been assumed that elevated PT at young ages is beneficial to health and PT ends up dropping as a passive byproduct of aging. In Drosophila, we show that a transient elevation in PT during early-adulthood exerts long-lasting negative impacts on aging trajectories and proteostasis in later-life. Blocking the early-life PT elevation robustly improves life-/health-span and prevents age-related protein aggregation, whereas transiently inducing an early-life PT surge in long-lived fly strains abolishes their longevity/proteostasis benefits. The early-life PT elevation triggers proteostatic dysfunction, silences stress responses, and drives age-related functional decline via juvenile hormone-lipid transfer protein axis and germline signaling. Our findings suggest that PT is adaptively suppressed after early-adulthood, alleviating later-life proteostatic burden, slowing down age-related functional decline, and improving lifespan. Our work provides a theoretical framework for understanding how lifetime PT dynamics shape future aging trajectories.

Deep Learning in Visual Tracking: A Review.

Deep learning (DL) has made breakthroughs in many computer vision tasks and also in visual tracking. From the beginning of the research on the automatic acquisition of high abstract feature representation, DL has gone deep into all aspects of tracking to date, to name a few, similarity metric, data association, and bounding box estimation. Also, pure DL-based trackers have obtained the state-of-the-art performance after the community's constant research. We believe that it is time to comprehensively review the development of DL research in visual tracking. In this article, we overview the critical improvements brought to the field by DL: deep feature representations, network architecture, and four crucial issues in visual tracking (spatiotemporal information integration, target-specific classification, target information update, and bounding box estimation). The scope of the survey of DL-based tracking covers two primary subtasks for the first time, single-object tracking and multiple-object tracking. Also, we analyze the performance of DL-based approaches and give meaningful conclusions. Finally, we provide several promising directions and tasks in visual tracking and relevant fields.

The Impact of Aging on the Lung Alveolar Environment, Predetermining Susceptibility to Respiratory Infections.

Respiratory infections are one of the top causes of death in the elderly population, displaying susceptibility factors with increasing age that are potentially amenable to interventions. We posit that with increasing age there are predictable tissue-specific changes that prevent the immune system from working effectively in the lung. This mini-review highlights recent evidence for altered local tissue environment factors as we age focusing on increased tissue oxidative stress with associated immune cell changes, likely driven by the byproducts of age-associated inflammatory disease. Potential intervention points are presented.

Characterizing the Electron Transport Chain: Structural Approach.

The mitochondrial respiratory chain which carries out the oxidative phosphorylation (OXPHOS) consists of five multi-subunit protein complexes. Emerging evidences suggest that the supercomplexes which further consist of multiple respiratory complexes play important role in regulating OXPHOS function. Dysfunction of the respiratory chain and its regulation has been implicated in various human diseases including neurodegenerative diseases and muscular disorders. Many mouse models have been established which exhibit mitochondrial defects in brain and muscles. Protocols presented here aim to help to analyze the structures of mitochondrial respiratory chain which include the preparation of the tissue samples, isolation of mitochondrial membrane proteins, and analysis of their respiratory complexes by Blue Native Polyacrylamide Gel Electrophoresis (BN-PAGE) in particular.

Characterizing the Electron Transport Chain: Functional Approach Using Extracellular Flux Analyzer on Mouse Tissue Samples.

The Seahorse Extracellular Flux Analyzer enables the high-throughput characterization of oxidative phosphorylation capacity based on the electron transport chain organization and regulation with relatively small amount of material. This development over the traditional polarographic Clark-type electrode approaches make it possible to analyze the respiratory features of mitochondria isolated from tissue samples of particular animal models. Here we provide a description of an optimized approach to carry out multi-well measurement of O2 consumption, with the Agilent Seahorse XFe96 analyzer on mouse brain and muscles to determine the tissue-specific oxidative phosphorylation properties. Protocols include the preparation of the tissue samples, isolation of mitochondria, and analysis of their function; in particular, the preparation and optimization of the reagents and samples.

Creating Cell Model 2.0 Using Patient Samples Carrying a Pathogenic Mitochondrial DNA Mutation: iPSC Approach for LHON.

Leber's Hereditary Optic Neuropathy is the most prevalent mitochondrial neurological disease caused by mutations in mitochondrial DNA encoded respiratory complex I subunits. Although the genetic origin for Leber's hereditary optic neuropathy was identified about 30 years ago, the underlying pathogenesis is still unclear primarily due to the lack of a relevant system or cell model. Current models are limited to lymphoblasts, fibroblasts, or cybrid cell lines. As the disease phenotype is limited to retinal ganglion cells, induced pluripotent stem cells will serve as an excellent model for studying this tissue-specific disease, elucidating its underlying molecular mechanisms, and identifying novel therapeutic targets. Here, we describe a detailed protocol for the generation of retinal ganglion cells, and also cardiomyocytes for proof of iPSC pluripotency.

Mitochondrial chaperones in human health and disease.

Molecular chaperones are a family of proteins that maintain cellular protein homeostasis through non-covalent peptide folding and quality control mechanisms. The chaperone proteins found within mitochondria play significant protective roles in mitochondrial biogenesis, quality control, and stress response mechanisms. Defective mitochondrial chaperones have been implicated in aging, neurodegeneration, and cancer. In this review, we focus on the two most prominent mitochondrial chaperones: mtHsp60 and mtHsp70. These proteins demonstrate different cellular localization patterns, interact with different targets, and have different functional activities. We discuss the structure and function of these prominent mitochondrial chaperone proteins and give an update on newly discovered regulatory mechanisms and disease implications.

Melatonin inhibits lung cancer development by reversing the Warburg effect via stimulating the SIRT3/PDH axis.

Recently, the morbidity and mortality from lung cancer have continued to increase. Mitochondrial dysfunction plays a key role in apoptosis, proliferation, and the bioenergetic reprogramming of cancer cells, especially for energy metabolism. Herein, we investigated the ability of melatonin (MLT) to influence lung cancer growth and explored the association between mitochondrial functions and the progression of lung tumors. The deacetylase, sirtuin 3 (Sirt3), is a pivotal player in maintenance of mitochondrial function, among participating in ATP production by regulating the acetylone and pyruvate dehydrogenase complex (PDH). We initially found that MLT inhibited lung cancer growth in the Lewis mouse model. Similarly, we observed that MLT inhibited the proliferation of lung cancer cells (A549, PC9, and LLC cells), and the underlying mechanism of MLT was related to reprogramming cancer cell metabolism, accompanied by a shift from cytosolic aerobic glycolysis to oxidative phosphorylation (OXPHOS). These changes were accompanied by higher ATP production, an elevated ATP production-coupled oxygen consumption rate (QCR), higher ROS levels, higher mito-ROS levels, and lower lactic acid secretion. Additionally, we observed that MLT improved mitochondrial membrane potential and the activities of complexes Ⅰ and Ⅳ in the electron transport chain. Importantly, we also found and verified that the foregoing changes resulted from activation of Sirt3 and PDH. As a result of these changes, MLT significantly enhanced mitochondrial energy metabolism to reverse the Warburg effect via increasing PDH activity with stimulation of Sirt3. Collectively, these findings suggest the potential use of melatonin as an anti-lung cancer therapy and provide a mechanistic basis for this proposal.

A novel sweetpotato RING-H2 type E3 ubiquitin ligase gene IbATL38 enhances salt tolerance in transgenic Arabidopsis.

Arabidopsis Toxicos en Levadura (ATL) proteins compose a subfamily of E3 ubiquitin ligases and play major roles in regulating plant growth, cold, drought, oxidative stresses response and pathogen defense in plants. However, the role in enhancing salt tolerance has not been reported to date. Here, we cloned a novel RING-H2 type E3 ubiquitin ligase gene, named IbATL38, from sweetpotato cultivar Lushu 3. This gene was highly expressed in the leaves of sweetpotato and strongly induced by NaCl and abscisic acid (ABA). This IbATL38 was localized to nucleus and plasm membrane and possessed E3 ubiquitin ligase activity. Overexpression of IbATL38 in Arabidopsis significantly enhanced salt tolerance, along with inducible expression of a series of stress-responsive genes and prominently decrease of H2O2 content. These results suggest that IbATL38 as a novel E3 ubiquitin ligase may play an important role in salt stress response.

Diagnostic value of circulating cell-free mtDNA in patients with suspected thyroid cancer: ND4/ND1 ratio as a new potential plasma marker.

Thyroid cancer is the most common endocrine malignancy, and its incidence continues to rise. For clinicians with cancer patients, choosing and interpreting diagnostic laboratory studies has become increasingly important. Previously, changes in plasma free mitochondrial DNA levels have been found in colorectal, breast, lung, and urinary cancers, and have demonstrated diagnostic value. In this study, we investigated whether the occurrence and development of thyroid cancer might be predicted using mtDNA copy number (ND1), mtDNA integrity (ND4/ND1) and levels of cell-free nDNA (GAPDH). We analyzed ND1, ND4, and GAPDH levels in plasma and blood cells from 75 patients with thyroid cancer, 40 patients with nodular goiter, and 107 normal controls using real-time PCR. Although both the thyroid nodule and thyroid cancer patients had significantly increased ND1 levels, the ND4/ND1 ratio in the thyroid cancer group was higher than the thyroid nodule group (P < 0.05), and significantly higher than the normal control group (P < 0.01). Plasma levels of nuclear DNA (GAPDH) in the thyroid cancer group were also higher compared to normal (P < 0.05). These results indicate that increased intactness of plasma free mtDNA is associated with increased levels of plasma cell-free nDNA, and that the ND4/ND1 ratio has the potential to be a new detection indicator in thyroid cancer. Furthermore, we classified thyroid cancer patients according to clinical data including age, tumor size, and metastasis. We found significantly higher levels of GAPDH in malignant tissues. Because ND4/ND1 correlated with plasma GAPDH in the plasma studies, this also suggests a potential relationship between ND4 intactness and thyroid tumor tissue size. Taken together, our findings suggest a tumor-specific process involving increased release of intact mtDNA, detectable in the plasma, which differentiates normal patients from patients with thyroid cancer.

BHRF1 Enhances EBV Mediated Nasopharyngeal Carcinoma Tumorigenesis through Modulating Mitophagy Associated with Mitochondrial Membrane Permeabilization Transition.

Epstein-Barr virus (EBV) is a major contributor to nasopharyngeal carcinoma (NPC) tumorigenesis. Mitochondria have been shown to be a target for tumor viral invasion, and to mediate viral tumorigenesis. In this study, we detected that mitochondrial morphological changes in tumor tissues of NPC patients infected with EBV were accompanied by an elevated expression of BHRF1, an EBV encoded protein homologue to Bcl-2. High expression of BHRF1 in human NPC cell lines enhanced tumorigenesis and metastasis features. With BHRF1 localized to mitochondria, its expression induced cyclophlin D dependent mitochondrial membrane permeabilization transition (MMPT). The MMPT further modulated mitochondrial function, increased ROS production and activated mitophagy, leading to enhanced tumorigenesis. Altogether, our results indicated that EBV-encoded BHRF1 plays an important role in NPC tumorigenesis through regulating cyclophlin D dependent MMPT.

Redox regulation by SOD2 modulates colorectal cancer tumorigenesis through AMPK-mediated energy metabolism.

Colorectal cancer (CRC) is a common malignancy. Many reports have implicated aberrant mitochondrial activity in the progression of CRC, with particular emphasis on the dysregulation of redox signaling and oxidative stress. In this study, we focused on manganese superoxide dismutase (MnSOD/SOD2), a key antioxidant enzyme, which maintains intracellular redox homeostasis. Current literature presents conflicting mechanisms for how SOD2 influences tumorigenesis and tumor progression. Here, we explored the role of SOD2 in CRC specifically. We found high levels of SOD2 expression in CRC tissues. We carried out a series of experiments to determine whether knockdown of SOD2 expression in CRC cell lines would reverse features of tumorigenesis. We found that reduced SOD2 expression decreased cell proliferation, migration, and invasion activity in CRC cells. Results from an additional series of experiments on mitochondrial function implicated a dual role for SOD2 in promoting CRC progression. First, proper level of SOD2 helped CRC cells maintain mitochondrial function by disposal of superoxide (O2.- ). Second, over-expression of SOD2 induced H2 O2 -mediated tumorigenesis by upregulating AMPK and glycolysis. Our results indicate that SOD2 may promote the occurrence and development of CRC by regulating the energy metabolism mediated by AMPK signaling pathways.

Emerging model systems and treatment approaches for Leber's hereditary optic neuropathy: Challenges and opportunities.

Leber's hereditary optic neuropathy (LHON) is a mitochondrial disease mainly affecting retinal ganglion cells (RGCs). The pathogenesis of LHON remains ill-characterized due to a historic lack of effective disease models. Promising models have recently begun to emerge; however, less effective models remain popular. Many such models represent LHON using non-neuronal cells or assume that mutant mtDNA alone is sufficient to model the disease. This is problematic because context-specific factors play a significant role in LHON pathogenesis, as the mtDNA mutation itself is necessary but not sufficient to cause LHON. Effective models of LHON should be capable of demonstrating processes that distinguish healthy carrier cells from diseased cells. In light of these considerations, we review the pathophysiology of LHON as it relates to old, new and future models. We further discuss treatments for LHON and unanswered questions that might be explored using these new model systems.

Thioredoxin overexpression in mitochondria showed minimum effects on aging and age-related diseases in male C57BL/6 mice.

Objective: In this study, the effects of overexpression of thioredoxin 2 (Trx2) on aging and age-related diseases were examined using Trx2 transgenic mice [Tg(TXN2]+/0]. Because our previous studies demonstrated that thioredoxin (Trx) overexpression in the cytosol (Trx1) did not extend maximum lifespan, this study was conducted to test if increased Trx2 expression in mitochondria shows beneficial effects on aging and age-related pathology. Methods: Trx2 transgenic mice were generated using a fragment of the human genome containing the TXN2 gene. Effects of Trx2 overexpression on survival, age-related pathology, oxidative stress, and redox-sensitive signaling pathways were examined in male Tg(TXN2)+/0 mice. Results: Trx2 levels were significantly higher (approximately 1.6- to 5-fold) in all of the tissues we examined in Tg(TXN2)+/0 mice compared to wild-type (WT) littermates, and the expression levels were maintained during aging (up to 22-24 months old). Trx2 overexpression did not alter the levels of Trx1, glutaredoxin, glutathione, or other major antioxidant enzymes. Overexpression of Trx2 was associated with reduced reactive oxygen species (ROS) production from mitochondria and lower isoprostane levels compared to WT mice. When we conducted the survival study, male Tg(TXN2)+/0 mice showed a slight extension (approximately 8-9%] of mean, median, and 10th percentile lifespans; however, the survival curve was not significantly different from WT mice. Cross-sectional pathological analysis (22-24 months old) showed that Tg(TXN2)+/0 mice had a slightly higher severity of lymphoma; however, tumor burden, disease burden, and severity of glomerulonephritis and inflammation were similar to WT mice. Trx2 overexpression was also associated with higher c-Jun and c-Fos levels; however, mTOR activity and levels of NFκB p65 and p50 were similar to WT littermates. Conclusions: Our findings suggest that the increased levels of Trx2 in mitochondria over the lifespan in Tg(TXN2)+/0 mice showed a slight life-extending effect, reduced ROS production from mitochondria and oxidative damage to lipids, but showed no significant effects on aging and age-related diseases.

Thioredoxin and aging: What have we learned from the survival studies?

Our laboratory has conducted the first systematic survival studies to examine the biological effects of the antioxidant protein thioredoxin (Trx) on aging and age-related pathology. Our studies with C57BL/6 mice overexpressing Trx1 [Tg(act-TRX1)+/0 and Tg(TXN)+/0) demonstrated a slight extension in early lifespan compared to wild-type (WT) mice; however, no significant effects were observed in the later part of life. Overexpression of Trx2 in male C57BL/6 mice [Tg(TXN2)+/0] demonstrated a slightly extended lifespan compared to WT mice. The pathology results from two lines of Trx1 transgenic mice showed a slightly higher incidence of age-related neoplastic diseases compared to WT mice, and a slight increase in the severity of lymphoma, a major neoplastic disease, was observed in Trx2 transgenic mice. Together these studies indicate that Trx overexpression in one compartment of the cell (cytosol or mitochondria alone) has marginal beneficial effects on lifespan. On the other hand, down-regulation of Trx in either the cytosol (Trx1KO) or mitochondria (Trx2KO) showed no significant changes in lifespan compared to WT mice, despite several changes in pathophysiology of these knockout mice. When we examined the synergetic effects of overexpressing Trx1 and Trx2, TXNTg x TXN2Tg mice showed a significantly shorter lifespan with accelerated cancer development compared to WT mice. These results suggest that synergetic effects of Trx overexpression in both the cytosol and mitochondria on aging are deleterious and the development of age-related cancer is accelerated. On the other hand, we have recently found that down-regulation of Trx in both the cytosol and mitochondria in Trx1KO x Trx2KO mice has beneficial effects on aging. The results generated from our lab along with our ongoing study using Trx1KO x Trx2KO mice could elucidate the key pathways (i.e., apoptosis and autophagy) that prevent accumulation of damaged cells and genomic instability leading to reduced cancer formation.

Interval and continuous exercise overcome memory deficits related to ß-Amyloid accumulation through modulating mitochondrial dynamics.

Exercise is a non-pharmacological strategy that may help to protect against cognitive decline and reduce the risk of Alzheimer's disease. However, the optimal exercise modes for cognitive benefits are controversial. Mitochondrial function has been related to both exercise and cognition. The present study aimed to investigate the effects of two exercise modes on cognitive function and mitochondrial dynamics in APP/PS1 transgenic mice. The results showed that 12-week high-intensity interval training (HIIT) and moderate-intensity continuous training (MICT) could improve exploratory behavior, spatial learning and memory ability of APP/PS1 transgenic mice. Both HIIT and MICT interventions significantly alleviated the hippocampal ß-Amyloid (Aß) burden and mitochondrial fragmentation and improved mitochondrial morphology in hippocampus. Furthermore, both HIIT and MICT interventions down-regulated dynamin-related protein 1 (DRP1) and fission 1 (FIS1), whereas mitofusin 1 (MFN1), mitofusin 2 (MFN2) and optic atrophy 1 (OPA1) were up-regulated. Hippocampal levels of total reactive oxygen species (ROS), malondialdehyde (MDA) and hydrogen peroxide (H2O2) were decreased, whereas activities of superoxide dismutase (SOD) and catalase (CAT) were elevated by HIIT and MICT. The study suggests that both HIIT and MICT alleviate cognitive decline and down-regulat Aß level in the hippocampus in APP/PS1 transgenic mice, which may be mediated by improvements in mitochondrial morphology and dynamics.

Oncocytic tumors are marked by enhanced mitochondrial content and mtDNA mutations of complex I in Chinese patients.

Oncocytic tumors are composed of oncocytes characterized by acidophilic granular and reticular cytoplasm. Such features have been attributed to the distinctive aggregation of abnormal mitochondria. Sporadic mitochondrial DNA (mtDNA) mutations, particularly those in complex I subunit genes, have been identified as one of the most noticeable alterations. We reviewed 11,051 cases of patients with thyroid tumors who visited the First Affiliated Hospital of Wenzhou Medical University from January 2011 to August 2017, and we were able to identify 123 cases as oncocytic tumors. We found that older people are at higher risk (P < 0.001) for oncocytic tumors. We confirmed an increased mitochondrial mass in representative samples. Furthermore, a comprehensive analysis of the mitochondrial genomes in patients with oncocytomas revealed 1) haplogroups D5 and A exhibit increased risk of oncocytomas; 2) 60% of mtDNA mutations are in genes encoding respiratory complex subunits while 8% occur in rRNA and 4% in tRNA regions; 3) among mutations in coding regions, 50% are in Complex I genes, including most of the disruptive mutations; 4) 64% of mtDNA mutations are heteroplasmic. Our studies imply a tumorigenesis mechanism for oncocytomas involving mitochondrial alterations mediated by genome instability and modified by mitochondrial haplogroups.