System-level metabolic modeling facilitates unveiling metabolic signature in exceptional longevity

Genome-scale models in human metabologenomics

Metabologenomics integrates metabolomics with other omics data types to comprehensively study the genetic and environmental factors that influence metabolism. These multi-omics data can be incorporated into genome-scale metabolic models (GEMs), which are highly curated knowledge bases that explicitly account for genes, transcripts, proteins and metabolites. By including all known biochemical reactions catalysed by enzymes and transporters encoded in the human genome, GEMs analyse and predict the behaviour of complex metabolic networks. Continued advancements to the scale and scope of GEMs - from cells and tissues to microbiomes and the whole body - have helped to design effective treatments and develop better diagnostic tools for metabolic diseases. Furthermore, increasing amounts of multi-omics data are incorporated into GEMs to better identify the underlying mechanisms, biomarkers and potential drug targets of metabolic diseases.

Specific differences and novel key regulatory genes of sex in influencing exceptional longevity phenotypes

BACKGROUND AND AIMS

Although the life expectancy of women systematically and robustly exceeds that of men, specific differences and molecular mechanisms of sex in influencing longevity phenotypes remain largely unknown. Therefore, we performed transcriptome sequencing of peripheral blood samples to explore regulatory mechanisms of healthy longevity by incorporating sex data.

METHODS

We selected 34 exceptional longevity (age: 98.26 ± 2.45 years) and 16 controls (age: 52.81 ± 9.78) without advanced outcomes from 1363 longevity and 692 controls recruited from Nanning of Guangxi for RNA sequencing 1. The transcriptome sequencing 1 data of 50 samples were compared by longevity and sex to screen differentially expressed genes (DEGs). Then, 121 aging samples (40-110 years old) without advanced outcomes from 355 longevity and 294 controls recruited from Dongxing of Guangxi were selected for RNA sequencing 2. The genes associated with aging from the transcriptome sequencing 2 of 121 aging samples were filtered out. Finally, the gender-related longevity candidate genes and their possible metabolic pathways were verified by cell model of aging and a real-time polymerase chain reaction (RT-PCR).

RESULTS

Metabolism differs between male and female and plays a key role in longevity. Moreover, the principal findings of this study revealed a novel key gene, UGT2B11, that plays an important role in regulating lipid metabolism through the peroxisome proliferator activated receptor gamma (PPARG) signalling pathway and ultimately improving lifespan, particularly in females.

CONCLUSION

The findings suggest specific differences in metabolism affecting exceptional longevity phenotypes between the sexes and offer novel therapeutic targets to extend lifespan by regulating lipid homeostasis.

SIRT6 activates PPARα to improve doxorubicin-induced myocardial cell aging and damage

The Sirtuins family, formally known as the Silent Information Regulator Factors, constitutes a highly conserved group of histone deacetylases. Recent studies have illuminated SIRT6's role in doxorubicin (DOX)-induced oxidative stress and apoptosis within myocardial cells. Nevertheless, the extent of SIRT6's impact on DOX-triggered myocardial cell aging and damage remains uncertain, with the associated mechanisms yet to be fully understood. In our research, we examined the influence of SIRT6 on DOX-induced cardiomyocyte senescence using β-galactosidase and γ-H2AX staining. Additionally, we gauged the mRNA expression of senescence-associated genes, namely p16, p21, and p53, through Real-time PCR. Employing ELISA assay kits, MDA, and total SOD activity assay kits, we measured inflammatory factors TNF-α, IL-6, and IL-1β, alongside oxidative stress-related indicators. The results unequivocally indicated that SIRT6 overexpression robustly inhibited DOX-induced cardiomyocyte senescence. Furthermore, we established that SIRT6 overexpression suppressed the inflammatory response and oxidative stress induced by DOX in cardiomyocytes. Conversely, silencing SIRT6 exacerbated DOX-induced cardiomyocyte injury. Our investigations further unveiled that SIRT6 upregulated the expression of genes CD36, CPT1, LCAD, MCAD associated with fatty acid oxidation through its interaction with PPARα, thereby exerting anti-aging effects. In vivo, the overexpression of SIRT6 was observed to restore DOX-induced declines in EF and FS to normal levels in mice. Echocardiography and HE staining revealed the restoration of cardiomyocyte alignment, affording protection against DOX-induced myocardial senescence and injury. The findings from this study suggest that SIRT6 holds significant promise as a therapeutic target for mitigating DOX-induced cardiomyopathy.

Longevity-Associated Transcription Factor ATF7 Promotes Healthspan by Suppressing Cellular Senescence and Systematic Inflammation

Aging is characterized by persistent low-grade systematic inflammation, which is largely responsible for the occurrence of various age-associated diseases. We and others have previously reported that long-lived people (such as centenarians) can delay the onset of or even escape certain major age-related diseases. Here, by screening blood transcriptome and inflammatory profiles, we found that long-lived individuals had a relatively lower inflammation level (IL6, TNFα), accompanied by up-regulation of activating transcription factor 7 (ATF7). Interestingly, ATF7 expression was gradually reduced during cellular senescence. Loss of ATF7 induced cellular senescence, while overexpression delayed senescence progress and senescence-associated secretory phenotype (SASP) secretion. We showed that the anti-senescence effects of ATF7 were achieved by inhibiting nuclear factor kappa B (NF-κB) signaling and increasing histone H3K9 dimethylation (H3K9me2). In Caenorhabditis elegans, ATF7 overexpression significantly suppressed aging biomarkers and extended lifespan. Our findings suggest that ATF7 is a longevity-promoting factor that lowers cellular senescence and inflammation in long-lived individuals.

Single-nucleus transcriptome inventory of giant panda reveals cellular basis for fitness optimization under low metabolism

BACKGROUND

Energy homeostasis is essential for the adaptation of animals to their environment and some wild animals keep low metabolism adaptive to their low-nutrient dietary supply. Giant panda is such a typical low-metabolic mammal exhibiting species specialization of extremely low daily energy expenditure. It has low levels of basal metabolic rate, thyroid hormone, and physical activities, whereas the cellular bases of its low metabolic adaptation remain rarely explored.

RESULTS

In this study, we generate a single-nucleus transcriptome atlas of 21 organs/tissues from a female giant panda. We focused on the central metabolic organ (liver) and dissected cellular metabolic status by cross-species comparison. Adaptive expression mode (i.e., AMPK related) was prominently displayed in the hepatocyte of giant panda. In the highest energy-consuming organ, the heart, we found a possibly optimized utilization of fatty acid. Detailed cell subtype annotation of endothelial cells showed the uterine-specific deficiency of blood vascular subclasses, indicating a potential adaptation for a low reproductive energy expenditure.

CONCLUSIONS

Our findings shed light on the possible cellular basis and transcriptomic regulatory clues for the low metabolism in giant pandas and helped to understand physiological adaptation response to nutrient stress.

Biomarkers of aging

Aging biomarkers are a combination of biological parameters to (i) assess age-related changes, (ii) track the physiological aging process, and (iii) predict the transition into a pathological status. Although a broad spectrum of aging biomarkers has been developed, their potential uses and limitations remain poorly characterized. An immediate goal of biomarkers is to help us answer the following three fundamental questions in aging research: How old are we? Why do we get old? And how can we age slower? This review aims to address this need. Here, we summarize our current knowledge of biomarkers developed for cellular, organ, and organismal levels of aging, comprising six pillars: physiological characteristics, medical imaging, histological features, cellular alterations, molecular changes, and secretory factors. To fulfill all these requisites, we propose that aging biomarkers should qualify for being specific, systemic, and clinically relevant.

Metabolic Modeling Identifies a Novel Molecular Type of Glioblastoma Associated with Good Prognosis

Glioblastoma (GBM) is one of the most aggressive forms of cancer. Although IDH1 mutation indicates a good prognosis and a potential target for treatment, most GBMs are IDH1 wild-type. Identifying additional molecular markers would help to generate personalized therapies and improve patient outcomes. Here, we used our recently developed metabolic modeling method (genome-wide precision metabolic modeling, GPMM) to investigate the metabolic profiles of GBM, aiming to identify additional novel molecular markers for this disease. We systematically analyzed the metabolic reaction profiles of 149 GBM samples lacking IDH1 mutation. Forty-eight reactions showing significant association with prognosis were identified. Further analysis indicated that the purine recycling, nucleotide interconversion, and folate metabolism pathways were the most robust modules related to prognosis. Considering the three pathways, we then identified the most significant GBM type for a better prognosis, namely N⁺P^-. This type presented high nucleotide interconversion (N⁺) and low purine recycling (P^-). N⁺P^--type exhibited a significantly better outcome (log-rank p = 4.7 × 10^-7) than that of N^-P⁺. GBM patients with the N⁺P^--type had a median survival time of 19.6 months and lived 65% longer than other GBM patients. Our results highlighted a novel molecular type of GBM, which showed relatively high frequency (26%) in GBM patients lacking the IDH1 mutation, and therefore exhibits potential in GBM prognostic assessment and personalized therapy.

Effect of Familial Longevity on Frailty and Sarcopenia: A Case-Control Study

Familial longevity confers advantages in terms of health, functionality, and longevity. We sought to assess potential differences in frailty and sarcopenia in older adults according to a parental history of extraordinary longevity. A total of 176 community-dwelling subjects aged 65-80 years were recruited in this observational case-control study, pair-matched 1:1 for gender, age, and place of birth and residence: 88 centenarians' offspring (case group) and 88 non-centenarians' offspring (control group). The main variables were frailty and sarcopenia based on Fried's phenotype and the European Working Group on Sarcopenia in Older People (EWGSOP) definitions, respectively. Sociodemographics, comorbidities, clinical and functional variables, the presence of geriatric syndromes, and laboratory parameters were also collected. Related sample tests were applied, and conditional logistic regression was performed. Cases had a higher percentage of robust patients (31.8% vs. 15.9%), lower percentages of frailty (9.1% vs. 21.6%) and pre-frailty (59.1% vs. 62.5%) (p = 0.001), and lower levels of IL-6 (p = 0.044) than controls. The robust adjusted OR for cases was 3.00 (95% CI = 1.06-8.47, p = 0.038). No significant differences in muscle mass were found. Familial longevity was also associated with less obesity, insomnia, pain, and polypharmacy and a higher education level and total and low-density lipoprotein cholesterol. The results suggest an inherited genetic component in the frailty phenotype, while the sarcopenia association with familial longevity remains challenging.

[Modern approaches to developing a system of valid methods for monitoring individual health and maintaining active longevity]

Life expectancy In Russia in 2023, according to preliminary data, exceeded 73 years, returning to the pre-pandemic level. The increase in life expectancy is associated both with an improvement in the quality of medical care In Russia and with a more responsible attitude towards the health of citizens, which is confirmed by an improvement in the quality of nutrition, a decrease in alcohol consumption and an increase in the number of people involved in sports. At the same time, there are many signs of aging, both cellular and molecular, some of the main ones are genome stability, telomere shortening, epigenetic alterations, impaired proteostasis and nutrient recognition, mitochondrial dysfunction, depletion of the stem cell pool and changes in intercellular interactions, extracellular matrix rigidity, as well as retrotransposon activation and chronic inflammation. For these reasons, in modern healthcare, the tasks of preventing premature aging and treating age-related diseases are becoming priorities.

MATERIAL AND METHODS

In total, at the first stage of work (in 2023), we examined 80 people, whose average age was 59.6±0.7 years. When analyzing and assessing data, the study adopted a division into age groups (WHO). The following indicators were studied: HbA1, fructosamine, HDL cholesterol, LDL cholesterol, insulin, homocysteine, C-peptide, TSH, free T4, prolactin, total testosterone, cortisol, arginine, asymmetric dimethylarginine, leptin, TNF-a, ferritin, interleukin 1 and 6, telomere length, creatinine, uric acid and urea.

RESULTS

As a result of the study, it was revealed that the aging process of the body affects many indicators, while the main markers that changed in men aged 18 to 44 years were total testosterone, leptin and telomere length; aged 44 to 60 years - HbA1, fructosamine, HDL cholesterol, homocysteine, C-peptide, total testosterone, leptin and telomere length; from 60 to 75 years - fructosamine, HDL cholesterol and telomere length and for 75-90 years - HbA1, HDL cholesterol, insulin, total testosterone, leptin and telomere length, interleukin 6 and uric acid. In women aged 18 to 44 years, only an increase in leptin was observed against the background of shortening telomere length; at the age of 44 to 60 years, the main markers that changed were total testosterone, leptin and telomere length; for the age group 60-75 years - indicators of HbA1, homocysteine, C-peptide, prolactin, total testosterone and leptin, interleukin 6 and uric acid, telomere length was shorter by only 2%; in the age group of 75-90 years, the main markers that changed were insulin, total testosterone, leptin, interleukin 6, while the indicators of uric acid, urea and telomere length differed from the reference values by 2-4%. Shortening of telomere length in all age groups, both men and women, indicates the presence of signs of premature aging. In an individual analysis, data were obtained on a more dramatic shortening of telomeres in 16 subjects in the presence of impaired glucose tolerance and insulin secretion, especially in comparison with healthy subjects, which was confirmed by the data of glycated hemoglobin (HbA1c), while, with shortening of telomere length, the HbA1 indicator was significantly higher (6.8±0.5) than in individuals with long telomeres and no chronic pathology (5.1±0.4).

CONCLUSION

A system of highly valid methods and panels of markers has been developed that indicate the presence of aging processes, taking into account gender and age characteristics, which can be used to identify premature aging processes, monitor individual health and maintain active longevity, as well as for the prevention of age-associated diseases.

Functional transcriptomic analysis of centenarians' offspring reveals a specific genetic footprint that may explain that they are less frail than age-matched non-centenarians' offspring

Centenarians exhibit extreme longevity and compression of morbidity and display a unique genetic signature. Centenarians' offspring seem to inherit centenarians' compression of morbidity, as measured by lower rates of age-related pathologies. We aimed to ascertain whether centenarians' offspring are less frail and whether they are endowed with a "centenarian genetic footprint" in a case-control study, matched 1:1 for gender, age ±5 years, and place of birth and residence. Cases must have a living parent aged 97 years or older, aged 65-80 years, community-dwelling, not suffering from a terminal illness, or less than 6 months of life expectancy. Controls had to meet the same criteria as cases except for the age of death of their parents (not older than 89 years). Centenarians were individuals 97 years or older. Frailty phenotype was determined by Fried's Criteria. We collected plasma and peripheral blood mononuclear cells from 63 centenarians, 88 centenarians' offspring, and 88 non-centenarians' offspring. miRNA expression and mRNA profiles were performed by the GeneChip miRNA 4.0 Array (Thermo Fisher Scientific) and GeneChip Clariom S Human Array (Thermo Fisher Scientific), respectively. We found a lower incidence of frailty among centenarians' offspring when compared to their contemporaries' non- centenarians' offspring (p <0.01). Both miRNA and mRNA expression patterns in centenarians' offspring were more like those of centenarians than those of non-centenarians' offspring (p <0.01). in conclusion, centenarians' offspring are less frail than age-matched non-centenarians' offspring, and this may be explained by their unique genetic endowment.

Specific Gain and Loss of Co-Expression Modules in Long-Lived Individuals Indicate a Role of circRNAs in Human Longevity

Deep RNA sequencing of 164 blood samples collected from long-lived families was performed to investigate the expression patterns of circular RNAs (circRNAs). Unlike that observed in previous studies, circRNA expression in long-lived elderly individuals (98.3 ± 3.4 year) did not exhibit an age-accumulating pattern. Based on weighted circRNA co-expression network analysis, we found that longevous elders specifically gained eight but lost seven conserved circRNA-circRNA co-expression modules (c-CCMs) compared with normal elder controls (spouses of offspring of long-lived individuals, age = 59.3 ± 5.8 year). Further analysis showed that these modules were associated with healthy aging-related pathways. These results together suggest an important role of circRNAs in regulating human lifespan extension.

Construction and contextualization approaches for protein-protein interaction networks

Protein-protein interaction network (PPIN) analysis is a widely used method to study the contextual role of proteins of interest, to predict novel disease genes, disease or functional modules, and to identify novel drug targets. PPIN-based analysis uses both generic and context-specific networks. Multiple contextualization methodologies have been described, such as shortest-path algorithms, neighborhood-based methods, and diffusion/propagation algorithms. This review discusses these methods, provides intuitive representations of PPIN contextualization, and also examines how the quality of such context-specific networks could be improved by considering additional sources of evidence. As a heuristic, we observe that tasks such as identifying disease genes, drug targets, and protein complexes should consider local neighborhoods, while uncovering disease mechanisms and discovering disease-pathways would gain from diffusion-based construction.