ATAC-clock: An aging clock based on chromatin accessibility

The establishment of aging clocks highlighted the strong link between changes in DNA methylation and aging. Yet, it is not known if other epigenetic features could be used to predict age accurately. Furthermore, previous studies have observed a lack of effect of age-related changes in DNA methylation on gene expression, putting the interpretability of DNA methylation-based aging clocks into question. In this study, we explore the use of chromatin accessibility to construct aging clocks. We collected blood from 159 human donors and generated chromatin accessibility, transcriptomic, and cell composition data. We investigated how chromatin accessibility changes during aging and constructed a novel aging clock with a median absolute error of 5.27 years. The changes in chromatin accessibility used by the clock were strongly related to transcriptomic alterations, aiding clock interpretation. We additionally show that our chromatin accessibility clock performs significantly better than a transcriptomic clock trained on matched samples. In conclusion, we demonstrate that the clock relies on cell-intrinsic chromatin accessibility alterations rather than changes in cell composition. Further, we present a new approach to construct epigenetic aging clocks based on chromatin accessibility, which bear a direct link to age-related transcriptional alterations, but which allow for more accurate age predictions than transcriptomic clocks.

Trigonelline is an NAD+ precursor that improves muscle function during ageing and is reduced in human sarcopenia

Mitochondrial dysfunction and low nicotinamide adenine dinucleotide (NAD+) levels are hallmarks of skeletal muscle ageing and sarcopenia1-3, but it is unclear whether these defects result from local changes or can be mediated by systemic or dietary cues. Here we report a functional link between circulating levels of the natural alkaloid trigonelline, which is structurally related to nicotinic acid4, NAD+ levels and muscle health in multiple species. In humans, serum trigonelline levels are reduced with sarcopenia and correlate positively with muscle strength and mitochondrial oxidative phosphorylation in skeletal muscle. Using naturally occurring and isotopically labelled trigonelline, we demonstrate that trigonelline incorporates into the NAD+ pool and increases NAD+ levels in Caenorhabditis elegans, mice and primary myotubes from healthy individuals and individuals with sarcopenia. Mechanistically, trigonelline does not activate GPR109A but is metabolized via the nicotinate phosphoribosyltransferase/Preiss-Handler pathway5,6 across models. In C. elegans, trigonelline improves mitochondrial respiration and biogenesis, reduces age-related muscle wasting and increases lifespan and mobility through an NAD+-dependent mechanism requiring sirtuin. Dietary trigonelline supplementation in male mice enhances muscle strength and prevents fatigue during ageing. Collectively, we identify nutritional supplementation of trigonelline as an NAD+-boosting strategy with therapeutic potential for age-associated muscle decline.

Initiation phase cellular reprogramming ameliorates DNA damage in the ERCC1 mouse model of premature aging

Unlike aged somatic cells, which exhibit a decline in molecular fidelity and eventually reach a state of replicative senescence, pluripotent stem cells can indefinitely replenish themselves while retaining full homeostatic capacity. The conferment of beneficial-pluripotency related traits via in vivo partial cellular reprogramming in vivo partial reprogramming significantly extends lifespan and restores aging phenotypes in mouse models. Although the phases of cellular reprogramming are well characterized, details of the rejuvenation processes are poorly defined. To understand whether cellular reprogramming can ameliorate DNA damage, we created a reprogrammable accelerated aging mouse model with an ERCC1 mutation. Importantly, using enhanced partial reprogramming by combining small molecules with the Yamanaka factors, we observed potent reversion of DNA damage, significant upregulation of multiple DNA damage repair processes, and restoration of the epigenetic clock. In addition, we present evidence that pharmacological inhibition of ALK5 and ALK2 receptors in the TGFb pathway are able to phenocopy some benefits including epigenetic clock restoration suggesting a role in the mechanism of rejuvenation by partial reprogramming.

Urbanization associates with restricted gut microbiome diversity and delayed maturation in infants

Alterations of the microbiome are linked to increasingly common diseases such as obesity, allergy, and inflammatory bowel disease. Post-industrial lifestyles are thought to contribute to the gut microbiome alterations that cause or aggravate these diseases. Comparing communities across the industrialization spectrum can reveal associations between gut microbiome alterations and lifestyle and health, and help pinpoint which specific aspect of the post-industrial lifestyle is linked to microbiome alterations. Here, we compare the gut microbiomes of 60 mother and infant pairs from rural and urban areas of Senegal over two time points. We find that urban mothers, who were more frequently overweight, had different gut microbiome compositions than rural mothers, showing an expansion of Lachnospiraceae and Enterobacter. Urban infants, on the other hand, showed a delayed gut microbiome maturation and a higher susceptibility to infectious diseases. Thus, we identify new microbiome features associated with industrialization, whose association with disease may be further investigated.

MAST: a hybrid Multi-Agent Spatio-Temporal model of tumor microenvironment informed using a data-driven approach

Motivation

Recently, several computational modeling approaches, such as agent-based models, have been applied to study the interaction dynamics between immune and tumor cells in human cancer. However, each tumor is characterized by a specific and unique tumor microenvironment, emphasizing the need for specialized and personalized studies of each cancer scenario.

Results

We present MAST, a hybrid Multi-Agent Spatio-Temporal model which can be informed using a data-driven approach to simulate unique tumor subtypes and tumor-immune dynamics starting from high-throughput sequencing data. It captures essential components of the tumor microenvironment by coupling a discrete agent-based model with a continuous partial differential equations-based model.The application to real data of human colorectal cancer tissue investigating the spatio-temporal evolution and emergent properties of four simulated human colorectal cancer subtypes, along with their agreement with current biological knowledge of tumors and clinical outcome endpoints in a patient cohort, endorse the validity of our approach.

Availability and implementation

MAST, implemented in Python language, is freely available with an open-source license through GitLab (https://gitlab.com/sysbiobig/mast), and a Docker image is provided to ease its deployment. The submitted software version and test data are available in Zenodo at https://dx.doi.org/10.5281/zenodo.7267745.

Supplementary information

Supplementary data are available at Bioinformatics Advances online.

A comparative in vitro study of the toxic potency of five inorganic lead compounds on a rat liver epithelial cell line (REL)

Relative insolubility of inorganic Pb compounds is one of the major problems in the evaluation of the toxicological profile of this metal. Different characteristics of Pb-containing solutions may, in fact, alter the biological properties of Pb compounds and influence their toxic potency. To investigate these aspects, we used selected experimental conditions to evaluate and compare the specific biological effects of five inorganic Pb compounds (soluble salts and oxide) on the viability and proliferation rate of a rat liver-derived cell line (REL cells). The study was performed according to classical toxicological criteria (dose- and time-response, reversibility/transience of the effect). Each Pb compound was accurately solubilised and the quantification of the real concentration of Pb(II) ions was performed either on the culture media used for each treatment, or on the extracts of exposed cells. Our study shows that four, out of the five Pb compounds we tested, induce the same dose- and time-related anti-proliferative effects on REL cells, being these effects also reversible, transient and directly related to the intracellular content of the metal. Since the intracellular concentration of the metal and, consequently, its biological effects on REL cells, directly depends on the bioavailability of the Pb(II) cation present in the treatment solutions, our results indicate that, in the experimental procedures aimed to assess the toxic potency of this metal, the solubility of each Pb compound should be carefully evaluated and taken into account.

[Inorganic lead stimulates endothelin secretion in the MDCK cell line]

BACKGROUND

Lead (Pb) is an environmental toxin whose acute intoxication causes haematological, gastrointestinal and neurological dysfunctions. Moreover it is well-established that prolonged exposure to low levels of inorganic Pb compounds is closely related to hypertension in experimental animals and occupationally exposed humans. Previous reports have suggested that endothelins (ETs), a family of peptides with potent vasoconstrictive properties, might be involved in the pathogenesis of lead-induced hypertension. In vivo studies demonstrated that rats chronically exposed to Pb low levels exhibited blood pressure elevation coupled with an increase of ET-3 concentration in plasma and urine in comparison with control animals.

OBJECTIVE

Since kidney is one of the target organs of lead injury, as well as the site of production/action of ETs, we investigated the effects of an inorganic Pb compound (Pb chloride) on the synthesis and secretion of these peptides, using, as in in vitro model, a renal-derived cell line (MDCK).

METHODS

The ETs assays in culture media of sub-confluent cell cultures exposed to different concentration of PbCl2 were performed by Enzyme linked Immunoassay (EIA), using two experimental procedures: a) cultures were exposed to 1100 and 200 microM PbCl2 for 30 min, next cells received Pb-free culture medium up to 24 h (pulse/chase experiment); b) cultures were fed continuously up to 24 h with treatment media containing the same PbCl2 concentrations (pulse experiment). Concomitantly, the Pb influence on cell viability was evaluated by different cytotoxicity assays (LDH release, DAPI staining and cell density assays). The mRNA expression of ET-1 was evaluated in pulse experiments by RT-PCR analysis before and after cell exposure to PbCl2. The Pb2+ cellular content of parallel MDCK cell cultures was assessed by AAS analysis.

RESULTS

In our experimental conditions, the administration of PbCl2 to sub-confluent MDCK cell cultures did not significantly affect cell viability. Either in pulse or in pulselchase experiments, the ETs content, evaluated in culture media of cells exposed to 100 microM PbCl2, significantly increased. On the contrary, cell treatment with 1 or 200 microM PbCl2 did not modify the ETs secretion. Because the amounts of ETs released in culture media were similar in both kinds of experiment, our results suggest that the metal induces the ETs secretion already after 30 min of cell exposure to the toxicant. Moreover, the ET-3 EIA specific assay did not reveal any immunoreactivity, excluding the involvement of this isoform in the Pb-induced secretion of ETs. Additionally, our results seem to exclude any Pb-induced up-regulation of ET-1 transcripts. The Pb2+ quantification in cell extracts demonstrated that the uptake of the metal is dose- and time-dependent and, in pulse experiments, it was maximum after six hours from the beginning of treatments, then the intracellular Pb2+ content decreased. This last phenomenon suggests the involvement of an ATP-dependent transporter in the mechanism of Pb cell excretion. Moreover, the ETs cell release in culture media of MDCK cells appears to depend on the intracellular content of Pb ions reached within 30 min of treatment.

CONCLUSION

Our results indicate that there is a range of PbCl2 doses (100 microM) at which MDCK cells enhance their ETs secretion. Lower doses (1 microM) of Pb salt seem to be ineffective to stimulate ETs release, while, doses equivalent to 200 microM seem to inhibit this phenomenon.

Antioxidant potential and gap junction-mediated intercellular communication as early biological markers of mercuric chloride toxicity in the MDCK cell line

In this study, the early nephrotoxic potential of mercuric chloride (HgCl(2)) has been evaluated in vitro, by exposing a renal-derived cell system, the tubular epithelial Madin-Darby canine kidney (MDCK) cell line, to the presence of increasing HgCl(2) concentrations (0.1-100 microM) for different periods of time (from 4 to 72 h). As possible biological markers of the tubular-specific toxicity of HgCl(2) in exposed-MDCK cultures we analysed: (i) critical biochemical parameters related to oxidative stress conditions and (ii) gap-junctional function (GJIC). HgCl(2) cytotoxicity was evaluated by cell-density assay. The biochemical analysis of the pro-oxidant properties of the mercuric ion (Hg(2+)) was performed by evaluating the effect of the metal salt on the antioxidant status of the MDCK cells. The cell glutathione (GSH) content and the activity of glutathione peroxidase (Gpx) and catalase (Cat), two enzymes engaged in the H(2)O(2) degradation, were quantified. HgCl(2) influence on MDCK GJIC was analysed by the microinjection/dye-transfer assay. HgCl(2)-induced morphological changes in MDCK cells were also taken into account. Our results, proving that subcytotoxic (0.1-10 microM) HgCl(2) concentrations affect either the antioxidant defences of MDCK cells or their GJIC, indicate these critical functions as suitable biological targets of early mercury-induced tubular cell injury.

[In vitro study of the nephrotoxic mechanism of mercuric chloride]

OBJECTIVES

Mercury (Hg), one of the most diffused and hazardous organ-specific environmental contaminants, exists in a wide variety of physical and chemical states, each of which with unique characteristics of target organ specificity. Exposure to Hg vapour and to organic mercurials specifically affects the CNS, while the kidney is the target organ for inorganic Hg compounds. Despite the increasing number of studies, the molecular bases of the nephrotoxic potential of Hg has not, up to now, been clarified, even if there is evidence suggesting that the ability of the metal to interact with proteins (thiol groups) or to generate oxygen radicals may play a major role. Within this context, the aim of the present study was to investigate, in vitro, the mechanism(s) of the early nephrotoxic potential of mercury chloride (HgCl2), one of the most diffused and biologically active mercury (Hg2+) compounds. For this purpose, two kidney-derived in vitro systems (the MDCK and the LLC-PK1 cell lines) were tested for their sensitivity to the salt, and MDCK was chosen as the most suitable in vitro model for our study. As possible biological markers of the organ-specific toxicity of the metal we analysed: i) critical biochemical parameters related to oxidative stress conditions (effect of Hg2+ on the anti-oxidant status of the cell), and ii) gap-junctional function (GJIC).

METHODS

Classical toxicity tests (MTT and NR) were used for assessing the sensitivity (IC50) of LLP-CK1 and MDCK cell lines to the mercuric salt. Complete solubilisation of the salt in the culture media was verified by inductively coupled plasma mass spectrometry (ICP-MS). The influence of the metal on cell growth rate and viability were evaluated by conventional proliferation assays. For the following mechanistic studies, cells were exposed for different time periods (4 to 72 hours) to non-cytotoxic (0.1-50 microM) HgCl2 concentrations. The biochemical analysis of the pro-oxidant properties of the mercuric compound was performed by the measurement of anti-oxidant cellular defences against H2O2 [catalase (Cat), glutathione peroxidase (Gpx), and total glutathione (GSH)]. The influence of the metal on the GJIC capacity of MDCK cells was assessed by the "microinjection/dye-coupling" assay.

RESULTS

Among the two kidney-derived in vitro systems, MDCK cell line was the most specifically sensitive to the toxic effect of HgCl2: it was, consequently, chosen as a "tubular cell model" for the following experimental steps. Tested for various time periods at increasing concentrations, the HgCl2 effect on MDCK cell proliferation and viability was found to be time- and dose-related. For concentrations < or = 50 microM, HgCl2 inhibits MDCK cell growth rate, being this effect significant (> 50% in respect to untreated controls) from the 24th from the beginning of the treatment, while, for concentrations > 50 microM, the metal causes cell death. Concerning the influence of HgCl2 on MDCK anti-oxidant defences, the most interesting results were obtained by analysing the influence of the mercury salt on the GSH cell content and Gpx activity. Both were, in fact, significantly affected by the presence of the mercury ion. HgCl2 also induced a rapid, dose- and time-related inhibitory effect on the GJIC capacity of the cells.

CONCLUSIONS

Even if further investigations are needed to better clarify the possible causal relationship between our findings, they indicate that: a) MDCK cells represent a suitable in vitro model for the study of Hg nephrotoxicity; b) GJIC function is, among those considered in our study, one of the most sensitive biological endpoints for investigating the mechanism(s) of Hg2+ specific toxicity.

Colimetric determination of amphetamine salts in dosage forms

A colorimetric method for the determination of primary amines has been applied to the assay of amphetamine salts in dosage forms. Aqueous solutions of amphetamine salts heated in acidic medium with 2,5-dimethoxytetrahydrofuran and subsequently reacted with p-(dimethylamino)benzaldehyde, give a red colour. This reaction is useful for photometric determinations at 557 nm. Secondary and tertiary amines do not interfere.