Biology subjects

Longo, M.

Publications and source records attributed to Longo, M..

8 recordsLinked to original sources

bioRxiv2024

Artificial intelligence as a ploy to delve into the intricate relationship between genetics and mitochondria in MASLD patients

Background and AimsMitochondrial (mt-) dysfunction is a hallmark of progressive MASLD. MtDNA copy number (mtDNA-CN) and cell-free circulating mtDNA (ccf-mtDNA), which reflect mt-mass and mt-dysfunction, respectively, are gaining attention as non-invasive disease biomarkers. We previously demonstrated that PNPLA3/MBOAT7/TM6SF2 deficiency in HepG2 cells increased mt-mass, mtDNA-CN and ccf-mtDNA. This study furtherly explored mt-biogenesis, function and mt-biomarkers in biopsied MASLD patients from a Discovery (n=28) and a Validation (n=824) cohort, stratified by the number of risk variants (NRV=3). We took advantage of artificial intelligence (AI) to develop new risk scores, predicting MASLD evolution by integrating anthropometric and genetic data (Age, BMI, NRV) with mt-biomarkers. MethodsHepatic mt-morphology and dynamics were assessed by TEM, IHC and gene expression. mtDNA-CN and ccf-mtDNA were measured in PBMCs and serum samples. GPT-4 was employed as AI tool to support the construction of novel risk scores for MASLD progressive forms (MASH, fibrosis and HCC). ResultsIn the Discovery cohort, NRV=3 patients showed the highest mt-mass and significant mt-morphological changes (i.e. membranes rupture). An elevated PGC-1, OPA1, DRP1 and PINK1, markers of mt-biogenesis, fusion and fission were found in these patients, supporting an enhanced mt-dynamics. However, PRKN protein levels were reduced, suggesting a premature block of mitophagy. In the Validation cohort, PGC-1 mRNA levels and mtDNA-CN were significantly higher in NRV=3 compared to patients with 1,2 or no variants. Circulating mtDNA-CN and ccf-mtDNA were augmented in NRV=3 patients and correlated with genetics and MASLD severity at multivariate analysis, supporting that both may independently modulate mt-dynamics and activity. By exploiting rsGPT-4 we then optimized the combination of non-invasive variables to get prediction models named Mitochondrial, Anthropometric, and Genetic Integration with Computational intelligence ("MAGIC-") for assessing MASH, fibrosis, and HCC, respectively. The MAGIC-MASH and MAGIC-Fib models showed AUCs of 73% and 76% in detecting MASH and fibrosis >1. Of note, MAGIC-HCC achieved an AUC of 86% (95% CI: 0.823-0.885), with 78.6% sensitivity and 81.5% specificity thus resulting the best score for the desired outcome. ConclusionsmtDNA-CN and ccf-mtDNA may have pathological and prognostic significance in MASLD patients, especially in those genetically-predisposed.

genetics↗

bioRxiv2024

Serum mitochondrial bioenergetics as fingerprint of the hepatic one: how to monitor genetic MASLD

Background & AimsMetabolic Dysfunction-Associated Steatotic Liver Disease (MASLD) pathogenesis is shaped by genetics and mitochondrial dysfunction. Recently, we demonstrated that the co-presence of patatin- like phospholipase domain-containing 3 (PNPLA3), transmembrane 6 superfamily member 2 (TM6SF2) and membrane bound o-acyltransferase domain-containing 7 (MBOAT7) polymorphisms predisposes to disease progression in MASLD patients and that their deletion contributes to mitochondrial (mt) maladaptation in an in- vitro model. In this work we deepened the impact of genes silencing on mitochondrial dynamism. Then we restored TM6SF2 and/or MBOAT7 wild-type (WT) proteins in the in-vitro model to evaluate the rescue of organelles morphology/function. Finally, we compared hepatic and peripheral mt-bioenrgetics in MASLD patients carrying PNPLA3, MBOAT7 and/or TM6SF2 loss-of-function variations. MethodsWT proteins were overexpressed through lentiviral transfection, mt-respiration was assessed by Seahorse. ResultsThe restore of MBOAT7 and/or TM6SF2 wild-type proteins resulted in the assembly of spaghetti- shaped mitochondria with improved OXPHOS capacity. Mitochondrial activity was assessed in liver biopsies and peripheral blood mononuclear cells of biopsy-proven (n=44;Discovery cohort) and noninvasively assessed (n=45;Fibroscan-MASLD cohort) MASLD patients stratified according to the presence of the 3 at-risk variants alongside in unrelated liver disease patients (n=45;Unrelated liver disease cohort). In the Discovery cohort, the hepatic bioenergetic profile fully reflecting the circulating one, was impaired in carriers of the risk variants, more so when in combination. We confirmed the lowered serum respirometry in the Fibroscan-MASLD cohort. Finally, the circulating respiration did not change in unrelated liver disease patients, thus demonstrating that it was specifically impaired in MASLD. ConclusionsThese results boosted the relevance of mitochondrial circulating respirometry to outline genetically-based MASLD.

genetics↗

bioRxiv2023

Cholesterol-associated Locus EHBP1 Protects against NASH Fibrosis

SUMMARYHepatic free cholesterol contributes to fibrosis in nonalcoholic steatohepatitis (NASH), but how hepatic cholesterol metabolism becomes dysregulated in NASH is not completely understood. We show here that human fibrotic NASH livers have decreased EHBP1, a novel GWAS locus associated with LDL-cholesterol, and that the EHBP1 rs10496099 T>C variant in NASH patients is associated with decreased hepatic EHBP1 expression and augmented NASH fibrosis. Congruent with the human data, EHBP1 loss- and gain-of-function increases and decreases NASH fibrosis in mice, respectively. Mechanistic studies reveal that EHBP1 promotes sortilin (SORT1)-mediated PCSK9 secretion, leading to LDLR degradation, decreased LDL uptake, and reduced TAZ, a fibrogenic effector. Moreover, we show that the TNF/PPAR pathway suppresses EHBP1 in NASH. These data not only provide new mechanistic insight into the role of EHBP1 in cholesterol metabolism and NASH fibrosis by uncovering the interaction between EHBP1 and other cholesterol-related loci, including SORT1, PCSK9, and LDLR, but also elucidate a novel interplay between inflammation and EHBP1-mediated cholesterol metabolism. HighlightsHepatic EHBP1 is reduced in human and mouse fibrotic NASH EHBP1 rs10496099 T>C is associated with decreased hepatic EHBP1 and augmented NASH EHBP1 reduces LDLR, cholesterol uptake, and TAZ in hepatocytes EHBP1 promotes sortilin-mediated PCSK9 secretion in hepatocytes TNF suppresses EHBP1 expression in hepatocytes

pathology↗

bioRxiv2022

Remote sensing-based forest modeling reveals positive effects of functional diversity on productivity at local spatial scale

O_LIForest biodiversity is critical for many ecosystem functions and services at plot scale, but it is uncertain how biodiversity influences ecosystem functioning across environmental gradients and contiguous larger areas. We used remote sensing and process-based terrestrial biosphere modeling to explore functional diversity-productivity relationships at multiple scales for a heterogeneous forest site in Switzerland. C_LIO_LIWe ran the biosphere model with empirical data about forest structure and composition derived from ground-based surveys, airborne laser scanning and imaging spectroscopy for the years 2006-2015 at 10x10-m spatial resolution. We then related the model outputs forest productivity to functional diversity under observed and experimental model conditions. C_LIO_LIFunctional diversity increased productivity significantly (p < 0.001) across all simulations at 20x20-m to 30x30-m scale, but at 100x100-m scale positive relationships disappeared under homogeneous soil conditions. C_LIO_LIWhereas local functional diversity was an important driver of productivity, environmental context (especially soil depth, texture and water availability) underpinned the variation of productivity (and functional diversity) at larger spatial scales. Integration of remotely-sensed information on canopy composition and structure into terrestrial biosphere models helps fill the knowledge gap about how plant biodiversity affects carbon cycling and biosphere feedbacks onto climate over large contiguous areas. C_LI

ecology↗

bioRxiv2021

Liana optical traits increase tropical forest albedo and reduce ecosystem productivity

Lianas are a key growth form in tropical forests. Their lack of self-supporting tissues and their vertical position on top of the canopy make them strong competitors of resources. A few pioneer studies have shown that liana optical traits differ on average from those of colocated tree. Those trait discrepancies were hypothesized to be responsible for the competitive advantage of lianas over trees. Yet, in the absence of reliable modelling tools, it is impossible to unravel their impact on the forest energy balance, light competition and on the liana success in Neotropical forests. To bridge this gap, we performed a meta-analysis of the literature to gather all published liana leaf optical spectra, as well as all canopy spectra measured over different levels of liana infestation. We then used a Bayesian data assimilation framework applied to two radiative transfer models (RTMs) covering the leaf and canopy scales to derive tropical tree and liana trait distributions, which finally informed a full dynamic vegetation model. According to the RTMs inversion, lianas grew thinner, more horizontal leaves with lower pigment concentrations. Those traits made the lianas particularly efficient at light interception and completely modified the forest energy balance and its carbon cycle. While forest albedo increased by 14% in the shortwave, light availability was dramatically reduced in the understory (-30% of the PAR radiation) and soil temperature decreased by 0.5{degrees}C. Those liana-specific traits were also responsible for a significant reduction of tree (-19%) and ecosystem (-7%) gross primary productivity (GPP) while lianas benefited from them (their GPP increased by +27%). This study provides a novel mechanistic explanation to the increase in liana abundance, new evidence of the impact of structural parasitism on forest functioning, and paves the way for the evaluation of the large-scale impacts of woody vines on forest biogeochemical cycles.

plant biology↗

bioRxiv2020

TM6SF2/PNPLA3/MBOAT7 loss-of-function genetic variants impact on NAFLD development and progression both in patients and in in vitro models

Background and aimsThe I148M PNPLA3, the rs641738 in MBOAT7/TMC4 locus and the E167K TM6SF2 polymorphisms represent the main predisposing factors to non-alcoholic fatty liver disease (NAFLD) development and progression. We previously generated a full knockout of MBOAT7 in HepG2 cells (MBOAT7-/-), homozygous for the I148M PNPLA3. Therefore, we aimed to:1) investigate the synergic impact of the 3 at-risk variants on liver injury and hepatocellular carcinoma (HCC) in a large cohort of NAFLD patients;2) create in vitro models of genetic NAFLD by silencing TM6SF2 in both HepG2 and MBOAT7-/- cells. MethodsNAFLD patients (n=1380) of whom 121 had HCC were stratified with a semi-quantitative score ranging from 0 to 3 according to the number of PNPLA3, TM6SF2 and MBOAT7 at-risk variants. TM6SF2 was silenced in HepG2 (TM6SF2-/-) and MBOAT7-/- (MBOAT7-/-TM6SF2-/-) through CRISPR/Cas9. ResultsIn NAFLD patients, the additive weight of these mutations was associated with liver disease severity and increased risk to develop HCC. In HepG2 cells, TM6SF2 silencing altered lipid composition and induced the accumulation of micro-vesicular LDs, whereas the MBOAT7-/-TM6SF2-/- cells showed a mixed micro/macro pattern of LDs. TM6SF2 deletion strongly affected endoplasmic reticulum (ER) and mitochondria ultrastructures thus increasing ER/oxidative stress. Mitochondrial number raised in both TM6SF2-/- and MBOAT7-/-TM6SF2-/- models, suggesting an unbalancing in mitochondrial dynamics and the silencing of both MBOAT7 and TM6SF2 impaired mitochondrial activity with a shift towards anaerobic glycolysis. MBOAT7-/-TM6SF2-/- cells also showed the highest proliferation rate. ConclusionsThe co-presence of the 3 at-risk variants impacts on NAFLD course, in both patients and experimental models affecting LDs accumulation, mitochondrial functionality and metabolic reprogramming towards HCC.

genetics↗

bioRxiv2019

Reconstructing neural representations of tactile space

Psychophysical experiments have demonstrated large and highly systematic perceptual distortions of tactile space. We investigated the neural basis of tactile space by analyzing activity patterns induced by tactile stimulation of nine points on a 3 x 3 square grid on the hand dorsum using functional magnetic resonance (fMRI). We used a searchlight approach within pre-defined regions of interests (ROIs) to compute the pairwise Euclidean distances between the activity patterns elicited by tactile stimulation. Then, we used multidimensional scaling (MDS) to reconstruct tactile space at the neural level and compare it with skin space at the perceptual level. Our reconstructions of the shape of skin space in contralateral primary somatosensory (SI) and motor (M1) cortices reveal that it is distorted in a way that matches the perceptual shape of skin space. This suggests that early sensorimotor areas are critical to processing tactile space perception.\n\nSignificant StatementHere, we show that the primary somatosensory (SI) and motor (M1) cortices, rather than higher-level brain areas, are critical to estimating distances between tactile stimuli on the hand dorsum. By combining functional magnetic resonance (fMRI), Procrustes alignment, and multidimensional scaling, we reconstructed the shape of skin space in the brain. Strikingly, the shape of the skin that we reconstructed from neural data matches the distortions we found at the behavioral level, providing strong evidence that early sensorimotor areas are critical for the construction of tactile space. Our work therefore supports the view that tactile distance perception is computed at lower level in the somatosensory system than is usually supposed.

neuroscience↗

bioRxiv2018

Dysregulation of circular RNAs in myotonic dystrophy type 1

Circular RNAs (circRNAs) constitute a recently re-discovered class of non-coding RNAs functioning as sponge for miRNAs and proteins, affecting RNA splicing and regulating transcription. CircRNAs are generated by \"back-splicing\", linking covalently 3- and 5-ends of exons. Thus, circRNA levels might be deregulated in conditions associated to altered RNA-splicing. Indeed, increasing evidence indicates their role in human diseases. Specifically, myotonic dystrophy type 1 (DM1) is a multisystemic disorder caused by expanded CTG-repeats in the DMPK gene, resulting in abnormal mRNA-splicing. In this investigation, circRNAs expressed in DM1 skeletal muscles were identified by analyzing RNA-sequencing data-sets followed by qPCR validation. In muscle biopsies, out of 9 tested, 4 transcripts showed an increased circular fraction: CDYL, HIPK3, RTN4_03 and ZNF609. The circular fraction values correlated positively with skeletal muscle strength and Receiver-Operating-Characteristics curves showed that these four circRNAs allow to distinguish DM1 patients from controls. The identified circRNAs were also detectable in peripheral-blood-mononuclear-cells (PBMCs) and plasma of DM1 patients, but they were not regulated significantly, indicating a tissue-selectivity of the identified modulations. Finally, increased circular fractions of RTN4_03 and ZNF609 were also observed in differentiated myogenic cell lines derived from DM1 patients.\n\nIn conclusion, this proof-of-principle study identified circRNA dysregulation in DM1 patients.

molecular biology↗