Biology subjects

Fiorito, G.

Publications and source records attributed to Fiorito, G..

17 recordsLinked to original sources

bioRxiv2026

Recipient-driven metabolic and epigenetic remodeling of donor hematopoietic cells after transplantation in Fanconi Anemia.

Background Haematopoietic cell transplantation (HCT) restores donor-derived haematopoiesis in Fanconi anaemia (FA) but leaves recipient stromal and other non-haematopoietic cells genetically uncorrected. We investigated to what extent the persistent FA recipient environment influences the metabolic, redox, inflammatory and epigenetic phenotype of donor-derived haematopoietic cells after HCT. Methods Peripheral blood and, when available, bone marrow samples were analysed from healthy donors, patients with FA before and after HCT, and severe aplastic anaemia (SAA) patients after HCT as transplant controls. Mitochondrial function, cellular energy status, oxidative damage, antioxidant responses and circulating cytokines were assessed. Healthy donor mononuclear cells were exposed to conditioned media from FANCA-deficient mesenchymal stromal cells or FA fibroblasts, with FANCA-corrected fibroblasts as controls. DNA methylation profiling, acute inflammatory stimulation and pharmacological targeting of inflammatory pathways or mitochondrial oxidative stress were also performed. Results Despite stable full donor chimerism, FA recipients retained a pro-inflammatory and pro-oxidative circulating environment after HCT that was not observed in SAA transplant controls. Donor-derived mononuclear cells exposed to this environment acquired a distinct dysfunctional phenotype characterized by impaired mitochondrial oxidative phosphorylation and energy homeostasis, compensatory antioxidant and stress-response activation, and persistent lipid and protein oxidation. These alterations remained detectable after 96 h of ex vivo culture, suggesting relatively stable cellular remodelling, and were accompanied by a DNA methylation profile that, although globally shifted toward the donor state, retained an intermediate FA-associated episignature. Mechanistically, conditioned media from FANCA-deficient stromal cells and FA fibroblasts reproduced mitochondrial and oxidative abnormalities in healthy donor cells, whereas FANCA-corrected fibroblasts did not. Pharmacological targeting of inflammatory pathways or mitochondrial oxidative stress improved energy homeostasis and reduced oxidative damage, supporting a contributory role for chronic inflammation and oxidative stress in the microenvironment-driven phenotype acquired by donor-derived cells. Conclusions HCT corrects FA haematopoiesis without fully normalising the recipient environment. Persistent exposure to the FA milieu promotes metabolic, redox, signalling and epigenetic remodelling of donor-derived haematopoietic cells after transplantation. These findings identify the recipient environment as a determinant of post-HCT cell biology and highlight chronic inflammation and oxidative stress as mechanisms contributing to donor-cell remodelling in FA.

cell biology↗

bioRxiv2026

A configuration-resolved benchmark of differential abundance analysis methods for human gut 16S rRNA microbiome data

Tools for differential abundance testing of 16S rRNA data are conventionally treated as discrete methods, and benchmarks have accordingly sought to determine which tool performs best. However, each tool offers an array of configurations based on different normalisation, transformation, reference choice, and sensitivity filtering methods, and the specific impact of these configurations on performance has rarely been systematically investigated. We benchmarked five widely used tools (MaAsLin 2, MaAsLin 3, edgeR, ALDEx2, and ANCOM-BC2) across 18 configurations, using simulated communities and human gut profiles with implanted signals, at two taxonomic resolutions and across several design factors. Configuration accounted for as much performance variation as the choice of tool itself, with the ranking of two tools depending on which of their settings are compared. Individual parameters behaved as switches between opposite error regimes rather than as graded adjustments, and the settings carrying this weight are identifiable in advance. These behaviours were reproducible across data sources and resolutions. Our results define a configuration-aware framework for matching a tool and its settings to the cohort, study design, and feature resolution, establishing that a differential abundance result is interpretable only if the configuration used for the analysis is reported.

microbiology↗

bioRxiv2026

Conserved multiheme cytochrome machinery for extracellular electron transfer is widespread and transcriptionally active across deep peat profiles

Northern peatlands store approximately one-third of global soil organic carbon, yet the anaerobic respiratory pathways governing carbon turnover remain unclear. In ombrotrophic bogs, the scarcity of inorganic terminal electron acceptors (TEAs) and high CO2:CH4 ratios indicate that methanogenesis alone cannot account for the observed CO2 production. Peat particulate organic matter (POM) has been proposed as an alternative TEA, but whether resident microorganisms encode and express extracellular electron transfer (EET) machinery required to use such extracellular TEAs remains unknown. Using depth-resolved metagenomics and metatranscriptomics across peat profiles from four ombrotrophic Swedish bogs, we identified conserved EET machinery in dominant yet uncultured Acidobacteriota and Verrucomicrobiota, comprising multiheme cytochromes and outer-membrane porins arranged in syntenic gene clusters. This machinery was transcriptionally active up to several meters depth, alongside broader anaerobic respiratory pathways, while methane-cycling processes were more prominent in the upper layers. These results provide systematic genomic and transcriptomic evidence for EET capacity in peatland microorganisms, establishing a molecular foundation for EET-based respiration and its potential role in suppressing methane formation and emissions.

microbiology↗

bioRxiv2026

Identification and functional investigation of Octopus vulgaris TRPV channels as potential nociceptors in cephalopods

Nociception is an essential response for organisms to avoid potential harm and promote survival. Its molecular determinants are largely conserved across Eumetazoa. TRPV receptors are polymodal ion channels exhibiting selective peripheral expression and functional coupling that underpins nociception and pain modulation in complex organisms. However, the execution of protective behaviours triggered by TRPVs is also found in species with a simpler nervous organisation, thus encouraging their investigation in invertebrate model organisms to increase understanding of animal nociception. Cephalopods represent an interesting invertebrate phylum with respect to the evolution of the nervous system, whose complexity suggests it might support pain-like states that exist in vertebrates. This possibility is reflected by the inclusion of cephalopods in the UK and EU animal welfare legislations. Despite this, there is poor characterisation of cephalopod molecular nociceptors. For this reason, we used in silico analysis to identify two TRPV channels in Octopus vulgaris genome (Ovtrpv1 and Ovtrpv2). We validated the putative transcript sequences and highlighted prevalent expression in sensory tissues. We investigated the functional competence of these TRPVs by heterologously expressing Ovtrpv1 and Ovtrpv2 cDNA into Caenorhabditis elegans null mutants of the orthologous genes, ocr-2 and osm-9 respectively. Ovtrpvs successfully rescued the aversive response to chemical and mechanical noxious stimuli in the C. elegans mutants, suggesting these receptors are polymodal nociceptors. Additionally, complementary investigation using Xenopus laevis oocytes showed Ovtrpv1 and Ovtrpv2 form an active heteromeric channel gated by nicotinamide. This study highlights Ovtrpvs as an important route to better understand nociceptive detection in cephalopods.

neuroscience↗

bioRxiv2026

In silico identification and deorphanisation of an allatostatin C GPCR system in the cephalopod Octopus vulgaris reveals two receptors with distinct potency

Neuropeptide signalling is transversally important in all living animals as it constitutes the basis of cellular communication. The investigation of the functional roles of peptide signalling represents an important route to understanding evolution of specific physiological traits and behaviours in metazoans. Allatostatins and their cognate receptors are classically defined as invertebrate neuropeptide hormones. Among these, allatostatin C was firstly associated with insect development. However, accumulating evidence recognises the presence of allatostatin C as a conserved signalling molecule across all invertebrate lineages, with reported functions spanning from regulation of feeding and digestion to immune responses and modulation of core nociception. Here we combined in silico and experimental approaches to reveal the interacting molecular determinants of the allatostatin C signalling in the cephalopod Octopus vulgaris, a scientifically and culturally interesting invertebrate for its centralised nervous system, capable of top-down modulation of complex behaviours. This resolved a single prepropeptide encompassing allatostatin C peptide (OvAstC), whose conserved mature form (AVITACYFQAVSCY) was shown to differentially activate two identified cognate receptors (OvAstCR1 and OvAstCR2) when heterologously expressed in the recombinant system HEK293G5A. PCR analysis carried out in O. vulgaris tissues, showed a broad distribution of OvAstC and OvAstCRs. This wide expression across nervous, immune and digestive tissues is consistent with a pleiotropic role of this peptidergic system. Together, the opioid/somatostatin-related phylogenetic placement of OvAstCRs and the broad expression of OvAstC components in nervous and sensory tissues nominate this pathway as a candidate for neuromodulatory control of sensory processing, including nociception, with potential welfare relevance in cephalopods. Significance statementCephalopods represent an evolutionarily distinctive molluscan lineage that evolved a centralised nervous system capable of displaying advanced learning and behavioural complexity compared with other invertebrates. These features, speculated to allow elaboration of pain-like states, granted cephalopods inclusion as the only invertebrate taxon requiring protection under European legislations when used in research. Investigation of the neuropeptide signalling in cephalopods is currently understudied despite its crucial role in regulating broad physiological functions in organisms. This study identified for the first time a single allatostatin C peptide and two cognate receptors in Octopus vulgaris. Our characterisation of a putative endogenous allatostatin C system in octopus, the accumulating evidence of its central role in invertebrate antinociception and its evolutionary relationship with the vertebrate-exclusive analgesic opioid family, represent a critical starting point for a more in-depth analysis of the physiological role of allatostatin C in this subclass of molluscs, with important welfare implications.

evolutionary biology↗

bioRxiv2025

Identification of molecular nociceptors in Octopus vulgaris through functional characterisation in Caenorhabditis elegans

Nociception, a phenomenon crucial for animal survival, deploys evolutionarily conserved molecular mechanisms. Among invertebrate species, cephalopods are of particular interest as they possess a well-developed brain speculated to be able to encode pain-like states. This has led to their inclusion in the Directive 2010/63 EU for welfare protection. However, the molecular mechanisms of nociception in cephalopods are still poorly characterised and it is important to address this knowledge gap to better understand cephlapods capacity to express pain states. Here we describe a bioinformatic pipeline utilising conserved nociceptive genes, to identify the orthologous candidates in the Octopus vulgaris transcriptome. We identified 51 genes we predict to function in nociception. These add to the mechanosensory TRPN and the unique chemotactile receptors recently identified in octopus suckers, thus expanding the set of genes that merit further functional characterisation in cephalopods. We therefore selected 38 orthologues in Caenorhabditis elegans, a tractable experimental platform and tested loss of function mutant strains of distinct functional gene classes (e.g., osm-9, egl-3, frpr-3) in a low pH avoidance paradigm. This identified 18 nociceptive-related genes to be prioritised for further functional characterisation in O. vulgaris.

neuroscience↗

bioRxiv2025

Macroscale Connectivity in the Octopus brain

Comparative studies support the existence of functional analogies between given areas in the octopus and mammalian brains. Despite marked phylogenetic distance, the central nervous system of cephalopod mollusks is characterized by a complex network of anatomically interconnected and interacting neuronal populations. Previous studies provide a thorough description of the octopus neural network through neuronal tracing of axonal projections, offering a unique opportunity to systematically examine the brains network architecture. Here, we chart the topological organization of Octopus vulgaris neural network including information on the macroscale interregional pathways between 32 cortical and subcortical regions as provided by a high-quality historical dataset. We found more than 350 main neural connections (afferent, efferent) encompassing the three masses of octopus brain (supra-, sub-oesophageal masses, optic lobes). The octopus brain network possesses multiple nonrandom features promoting segregation and integration, including near-minimal path length, multiscale community structure, hubs, small-world features, and motif composition. Taken together, these attributes support an association between network architecture and function and are consistent with studies in a range of other species, suggesting the existence of a set of universal organizational principles across phylogeny. These findings expand our understanding of neuronal structures by highlighting brain regions that had previously received less attention.

neuroscience↗

bioRxiv2023

A chromosome-level reference genome for the common octopus, Octopus vulgaris (Cuvier, 1797)

Cephalopods are emerging animal models and include iconic species for studying the link between genomic innovations and physiological and behavioral complexities. Coleoid cephalopods possess the largest nervous system among invertebrates, both for cell counts and brain-to-body ratio. Octopus vulgaris has been at the center of a long-standing tradition of research into diverse aspects of cephalopod biology, including behavioral and neural plasticity, learning and memory recall, regeneration, and sophisticated cognition. However, no chromosome-scale genome assembly is available for O. vulgaris to aid in functional studies. To fill this gap, we sequenced and assembled a chromosome-scale genome of the common octopus, O. vulgaris. The final assembly spans 2.8 billion basepairs, 99.34% of which are in 30 chromosome-scale scaffolds. Hi-C heatmaps support a karyotype of 1n=30 chromosomes. Comparisons with other octopus species genomes show a conserved octopus karyotype, and a pattern of local genome rearrangements between species. This new chromosome-scale genome of O. vulgaris will further facilitate research in all aspects of cephalopod biology, including various forms of plasticity and the neural machinery underlying sophisticated cognition, as well as an understanding of cephalopod evolution.

genomics↗

bioRxiv2022

A Deep Survival EWAS approach estimating risk profile based on pre-diagnostic DNA methylation: an application to Breast Cancer time to diagnosis

Previous studies for cancer biomarker discovery based on pre-diagnostic blood DNA methylation profiles, either ignore the explicit modeling of the time to diagnosis (TTD) as in a survival analysis setting, or provide inconsistent results. This lack of consistency is likely due to the limitations of standard EWAS approaches, that model the effect of DNAm at CpG sites on TTD independently. In this work, we argue that a global approach to estimate CpG sites effect profile is needed, and we claim that such approach should capture the complex (potentially non-linear) relationships interplaying between sites. To prove our concept, we develop a new Deep Learning-based approach assessing the relevance of individual CpG Islands (i.e., assigning a weight to each site) in determining TTD while modeling their combined effect in a survival analysis scenario. The algorithm combines a tailored sampling procedure with DNAm sites agglomeration, deep non-linear survival modeling and SHapley Additive exPlanations (SHAP) values estimation to aid robustness of the derived effects profile. The proposed approach deal with the common complexities arising from epidemiological studies, such as small sample size, noise, and low signal-to-noise ratio of blood-derived DNAm. We apply our approach to a prospective case-control study on breast cancer nested in the EPIC Italy cohort and we perform weighted gene-set enrichment analyses to demonstrate the biological meaningfulness of the obtained results. We compared the results of Deep Survival EWAS with those of a traditional EWAS approach, demonstrating that our method performs better than the standard approach in identifying biologically relevant pathways. Author summaryBlood-derived DNAm profiles could be exploited as new biomarkers for cancer risk stratification and possibly, early detection. This is of particular interest since blood is a convenient tissue to assay for constitutional methylation and its collection is non-invasive. Exploiting pre-diagnostic blood DNAm data opens the further opportunity to investigate the association of DNAm at baseline on cancer risk, modeling the relationship between sites methylation and the Time to Diagnosis. Previous studies mostly provide inconsistent results likely due to the limitations of standard EWAS approaches, that model the effect of DNAm at CpG sites on TTD independently. In this work we argue that an approach to estimate single CpG sites effect while modeling their combined effect on the survival outcome is needed, and we claim that such approach should capture the complex (potentially non-linear) relationships interplaying between sites. We prove this concept by developing a novel approach to analyze a prospective case-control study on breast cancer nested in the EPIC Italy cohort. A weighted gene set enrichment analysis confirms that our approach outperforms standard EWAS in identifying biologically meaningful pathways.

genomics↗

bioRxiv2022

Cell type diversity in a developing octopus brain

Octopuses are mollusks that have evolved intricate neural systems comparable with vertebrates in terms of cell number, complexity and size. The cell types within the octopus brain that control their amazingly rich behavioral repertoire are still unknown. Here we profile cell diversity of the paralarval Octopus vulgaris brain to build a comprehensive cell type atlas that comprises mostly neural cells, as well as multiple glial subtypes, endothelial cells and fibroblasts. Moreover, we spatially map cell types within the octopus brain, including vertical and optic lobe cell types. Investigation of cell type conservation reveals a shared gene signature between glial cells of mice, fly and octopus. Genes related to learning and memory are enriched in vertical lobe cells, which show molecular similarities with Kenyon cells in Drosophila. Taken together, our data sheds light on cell type diversity and evolution of the complex octopus brain. Highlights & Key findingsO_LICharacterization of different cell types present in the early paralarval brain C_LIO_LICross-species comparisons reveal a conserved glial gene expression signature C_LIO_LIVertical lobe amacrine cells in octopus have molecular similarities to fly Kenyon cells C_LIO_LIHomeobox genes are defining transcription factors for cell type identity C_LIO_LIRecently expanded gene families may underlie cellular diversification C_LI

developmental biology↗

bioRxiv2021

Identification of LINE retrotransposons and long non-coding RNAs expressed in the octopus brain

BackgroundTransposable elements (TEs) widely contributed to the evolution of genomes allowing genomic innovations, generating germinal and somatic heterogeneity and giving birth to long non-coding RNAs (lncRNAs). These features have been associated to the evolution, functioning and complexity of the nervous system at such a level that somatic retrotransposition of long interspersed element (LINE) L1 has been proposed to be associated to human cognition. Among invertebrates, octopuses are fascinating animals whose nervous system reaches a high level of complexity achieving sophisticated cognitive abilities. The sequencing of the genome of the Octopus bimaculoides revealed a striking expansion of TEs which were proposed to have contributed to the evolution of its complex nervous system. We recently found a similar expansion also in the genome of Octopus vulgaris. However a specific search for the existence of full-length transpositionally competent TEs has not been performed in this genus. ResultsHere we report the identification of LINE elements competent for retrotransposition in Octopus vulgaris and Octopus bimaculoides and show evidence suggesting that they might be active driving germline polymorphisms among individuals and somatic polymorphisms in the brain. Transcription and translation measured for one of these elements resulted in specific signals in neurons belonging to areas associated with behavioral plasticity. We also report the transcription of thousands of lncRNAs and the pervasive inclusion of TE fragments in the transcriptomes of both Octopus species, further testifying the crucial activity of TEs in the evolution of the octopus genomes. ConclusionsThe neural transcriptome of the octopus shows the transcription of thousands of putative lncRNAs and of a full lenght LINE element belonging to the RTE class. We speculate that a convergent evolutionary process involving retrotransposons activity in the brain has been important for the evolution of sophisticated cognitive abilities in this genus.

genomics↗

bioRxiv2020

Association of 4 epigenetic clocks with measures of functional health, cognition, and all-cause mortality in The Irish Longitudinal Study on Ageing (TILDA)

The aging process is characterized by the presence of high interindividual variation between individuals of the same chronical age prompting a search for biomarkers that capture this heterogeneity. The present study examines the associations of four epigenetic clocks - Horvath, Hannum, PhenoAge, GrimAge - with a wide range of clinical phenotypes, and with all-cause mortality at up to 10-year follow-up in a sample of 490 participants in the Irish Longitudinal Study on Ageing. Results indicate that the GrimAge clock represents a step-improvement in the predictive utility of the epigenetic clocks for identifying age-related decline in an array of clinical phenotypes.

genomics↗

bioRxiv2020

Epigenome-wide association meta-analysis of DNA methylation with coffee and tea consumption

Coffee and tea are extensively consumed beverages worldwide. Observational studies have shown contradictory findings for the association between consumption of these beverages and different health outcomes. Epigenetics is suggested as a mechanism mediating the effects of dietary and lifestyle factors on disease onset. We conducted epigenome-wide association studies (EWAS) on coffee and tea consumptions in 15,789 participants of European and African-American ancestries from 15 cohorts. EWAS meta-analysis revealed 11 CpG sites significantly associated with coffee consumption (P-value <1.1x10-7), nine of them annotated to the genes AHRR, F2RL3, FLJ43663, HDAC4, GFI1 and PHGDH, and two CpGs suggestively associated with tea consumption (P-value<5.0x10-6). Among these, cg14476101 was significantly associated with expression of its annotated gene PHGDH and risk of fatty liver disease. Knockdown of PHGDH expression in liver cells showed a correlation with expression levels of lipid-associated genes, suggesting a role of PHGDH in hepatic-lipid metabolism. Collectively, this study indicates that coffee consumption is associated with differential DNA methylation levels at multiple CpGs, and that coffee-associated epigenetic variations may explain the mechanism of action of coffee consumption in conferring disease risk.

genomics↗

bioRxiv2020

Complex sex-specific age-related changes in DNA methylation including variability, epimutations and entropy

In humans, females live longer than males but experience a worse longevity, as genome-wide autosomal DNA methylation differences between males and females have been reported. So far, few studies have investigated if DNA methylation is differently affected by aging in males and females. We performed a meta-analysis of 4 large whole blood datasets, comparing 4 aspects of epigenetic age-dependent remodeling between the two sexes: differential methylation, variability, epimutations and entropy. We reported that a large fraction (43%) of sex-associated probes undergoes age-associated DNA methylation changes, and that a limited number of probes shows age-by-sex interaction. We experimentally validated 2 regions mapping in FIGN and PRR4 genes, and showed sex-specific deviations of their methylation patterns in models of decelerated (centenarians) and accelerated (Down syndrome) aging. While we did not find sex differences in the age-associated increase in epimutations and in entropy, we showed that the number of probes showing age-related increase in methylation variability is 15 times higher in males compared to females. Our results can offer new epigenetic tools to study the interaction between aging and sex and can pave the way to the identification of molecular triggers of sex differences in longevity and age-related diseases prevalence.

genomics↗

bioRxiv2019

From injury to full repair: nerve regeneration and functional recovery in the common octopus, Octopus vulgaris

Spontaneous nerve regeneration in cephalopod molluscs occurs in a relative short time after injury, achieving functional recovery of the lost capacities. In particular, transection of the pallial nerve in the common octopus (Octopus vulgaris) determines loss and subsequent restoring of two functions fundamental for survival, i.e. breathing and skin patterning, the latter involved in communication between animals and concealing. The phenomena occurring after lesion have been investigated in a series of previous studies, but a complete analysis of the changes occurring at the level of the axons and the effects on animals appearance during the whole regenerative process is still missing. Our goal is to determine the course of events following injury. Our goal is to determine the course of events following injury, from impairment to full recovery.\n\nWe observed nerve regeneration, end-target re-innervation and functional reconnections between central brain and periphery, using the contralateral nerve in the same animal as internal control. The final architecture of the regenerated nervous tissue does not mirror the original structure, however functionality returns to match the phenotype of an intact octopus, and with no visible impact on the behaviour of the animal. This provides exceptional value to these findings for future studies.\n\nSummary statementHere we report events occurring after interruption of the peripheral neural circuitry in Octopus vulgaris, from the dramatic loss of normal functioning to full recovery.

neuroscience↗

bioRxiv2018

Determinants of accelerated metabolomic and epigenetic ageing in a UK cohort

Markers of biological ageing have potential utility in primary care and public health. We developed an elastic net regression model of age based on untargeted metabolic profiling across multiple platforms, including nuclear magnetic resonance spectroscopy and liquid chromatography-mass spectrometry in urine and serum (almost 100,000 features assayed), within a large sample (N=2,239) from the UK occupational Airwave cohort. We investigated the determinants of accelerated ageing, including genetic, lifestyle and psychological risk factors for premature mortality. The metabolomic age model was well correlated with chronological age (r=0.85 in independent test set). Increased metabolomic age acceleration (mAA) was associated (p<0.0025) with overweight/obesity and depression and nominally associated (p<0.05) with high alcohol use and low income. DNA methylation age acceleration (N=1,102) was nominally associated (p<0.05) with high alcohol use, anxiety and post-traumatic stress disorder, but not correlated with mAA. Biological age acceleration may present an important mechanism linking psycho-social stress to age-related disease.

epidemiology↗

bioRxiv2017

An epigenome-wide association study of educational attainment (n = 10,767)

The epigenome has been shown to be influenced by biological factors, such as disease status, and environmental factors, such as smoking, alcohol consumption, and body mass index. Although there is a widespread perception that environmental influences on the epigenome are pervasive and profound, there has been little evidence to date in humans with respect to environmental factors that are biologically distal. Here, we provide evidence on the associations between epigenetic modifications--in our case, CpG methylation--and educational attainment (EA), a biologically distal environmental factor that is arguably among of the most important life-shaping experiences for individuals. Specifically, we report the results of an epigenome-wide association study meta-analysis of EA based on data from 27 cohort studies with a total of 10,767 individuals. While we find that 9 CpG probes are significantly associated with EA, only two remain associated when we restrict the sample to never-smokers. These two are known to be strongly associated with maternal smoking during pregnancy, and thus their association with EA could be due to correlation between EA and maternal smoking. Moreover, their effect sizes on EA are far smaller than the known associations between CpG probes and biologically proximal environmental factors. Two analyses that combine the effects of many probes--polygenic methylation score and epigenetic-clock analyses--both suggest small associations with EA. If our findings regarding EA can be generalized to other biologically distal environmental factors, then they cast doubt on the hypothesis that such factors have large effects on the epigenome.

genetics↗