| 1. |
- Fallerini, Chiara, et al.
(author)
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Common, low-frequency, rare, and ultra-rare coding variants contribute to COVID-19 severity
- 2022
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In: Human Genetics. - : Springer Nature. - 0340-6717 .- 1432-1203. ; 141:1, s. 147-173
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Journal article (peer-reviewed)abstract
- The combined impact of common and rare exonic variants in COVID-19 host genetics is currently insufficiently understood. Here, common and rare variants from whole-exome sequencing data of about 4000 SARS-CoV-2-positive individuals were used to define an interpretable machine-learning model for predicting COVID-19 severity. First, variants were converted into separate sets of Boolean features, depending on the absence or the presence of variants in each gene. An ensemble of LASSO logistic regression models was used to identify the most informative Boolean features with respect to the genetic bases of severity. The Boolean features selected by these logistic models were combined into an Integrated PolyGenic Score that offers a synthetic and interpretable index for describing the contribution of host genetics in COVID-19 severity, as demonstrated through testing in several independent cohorts. Selected features belong to ultra-rare, rare, low-frequency, and common variants, including those in linkage disequilibrium with known GWAS loci. Noteworthily, around one quarter of the selected genes are sex-specific. Pathway analysis of the selected genes associated with COVID-19 severity reflected the multi-organ nature of the disease. The proposed model might provide useful information for developing diagnostics and therapeutics, while also being able to guide bedside disease management.
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| 2. |
- Gabbi, Chiara
(author)
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Studies on the oxysterol receptor LXRβ : linking cholesterol metabolism to water transport and cell proliferation
- 2011
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Doctoral thesis (other academic/artistic)abstract
- Liver X Receptor β (LXRβ) is a nuclear receptor, belonging to the superfamily of ligand-activated transcription factors. With its α isoform (LXRα), LXRβ shares more than 78% homology in its amino acid sequence, a common profile of oxysterol ligands and the heterodimerization partner, Retinoid X Receptor. LXRs have a crucial role in lipid metabolism, in particular in preventing cholesterol accumulation, in glucose homeostasis and in macrophage inflammatory response. The first evidence that, in spite of all the common properties, LXRα and LXRβ have distinct functions, came in 2001 with the creation of knock-out mice for each LXR isoform. LXRα-/- mice fed with 2% cholesterol diet show a severe cholesterol accumulation in the liver due to an inability to increase bile acid synthesis in response to high cholesterol intake. Surprisingly, LXRβ-/- mice had the same compensatory capacity of WT mice to avoid hepatic cholesterol accumulation suggesting that LXRβ may have a completely distinct role from LXRα. Indeed in 2005, it was shown that specifically in LXRβ-/- male mice cholesterol accumulates in big motor neurons of the spinal cord leading to their death and inducing a significant motor function impairment like amyotrophic lateral sclerosis (ALS). Starting from this neurological phenotype of LXRβ-/- mice and comparing the characteristics of knock-out mice for each LXR isoform, this thesis aims to define new and specific functions of the oxysterol receptor LXRβ. Paper I of this thesis aims to investigate the neurological phenotype of LXRβ-/- mice focusing in particular on the role of β-sitosterol in the pathogenesis ALS-Parkinson-Dementia complex. Administration of β-sitosterol to LXRβ-/- mice creates a severe motor-impairment and loss of dopaminergic neurons in the substantia nigra, activates microglia and decreases brain cholesterol indicating that LXRβ may have a protective role against the toxic action of β- sitosterol on the central nervous system. Paper II investigates the resistance to gain weight, characteristic of LXRβ-/- mice and demonstrates that they are affected by a severe pancreatic insufficiency with low serum levels of amylase, lipase, low fecal protease and abundant inflammatory infiltrates all around medium size pancreatic ducts. The water channel aquaporin-1 (AQP-1), responsible of transporting water into the pancreatic ductal lumen was markedly decreased in LXRβ-/- mice leading to the presence of plugs inside the ducts and in turn to a pancreatic insufficiency. In the digestive system AQP-1 is strongly expressed in the cholangiocytes of the gallbladder being, together with AQP-8, the mediator of the absorbing-secretory functions of this organ. Paper III shows that the male gallbladder cholangiocytes of LXRβ-/- mice express very low mRNA and protein levels of both AQP-1 and AQP-8 and morphologically they appear shrunk with loss of cell polarization. Treatment of WT mice with LXR-agonist increases the expression of the two water channels in the gallbladder together with the cholesterol transporters ATP Binding Cassette G5/G8 and it is associated with cholesterol crystals in the bile. The morphology of female LXRβ-/- gallbladders was studied in paper IV: at the age of 12 months a wide range of preneoplastic lesions are detectable, from dysplasia to metaplasia and adenomas, degenerating into carcinoma in situ, when the mice become 19 months old. The pathogenesis involves a complex interplay between LXRβ, Transforming Growth Factor β (TGFβ) and estrogens. Indeed, ovariectomy of LXRβ-/- mice prevents the development of preneoplastic lesions and normalizes the TGFβ signaling that is upregulated in LXRβ-/ mice. In conclusion, this thesis describes new emerging and specific roles for LXRβ in controlling not only cholesterol homeostasis in the central nervous system but also water channels in pancreas and gallbladder as well neoplastic transformation of cholangiocytes.
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| 3. |
- Gabbi, Chiara
(author)
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Studies on the phenotype of LXRβ-/- mice : from malabsorption to amyotrophic lateral sclerosis
- 2008
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Licentiate thesis (other academic/artistic)abstract
- Liver X Receptors, LXRalpha and LXRbeta (NR1H2) are nuclear receptors belonging to the superfamily of ligand-activated transcription factors with a key role in the control of lipid and glucose metabolism. Studies of the phenotype of LXRalpha-/-mice and LXRbeta-/-mice have shown that these nuclear receptors have specific and distinct roles, although they share very high sequence homology (78%). In particular, unlike LXRalpha-/-mice, LXRbeta-/-mice are resistant to obesity when fed with a high fat diet and have a decreased gonadal fat pad during standard diet feeding. In addition, they develop a motor neuron disease that resembles amyotrophic lateral sclerosis by the age of 7 months. The studies in this thesis are aimed at investigating the mechanisms through which loss of LXRbeta leads to disease. The first study investigated the pathogenesis of motor neuron disease in LXRbeta-/- mice. It has been shown that in the spinal cord of patients with amyotrophic lateral sclerosis, there is an accumulation of sphingomyelin, ceramides and cholesterol esters: phytosterols are known ligands of LXRs and are secreted into the intestinal lumen by ABCG transporters. These transporters are LXR-regulated genes. In the first study we treated LXRbeta-/- mice with beta-sitosterol, a known motoneuron toxin thought to be involved in ALS. After 3 weeks of treatment, in LXRbeta-/- mice but not in wild type littermates, there was a reduction in the number of motor neurons in the lumbar region of the spinal cord and in the surviving motor neurons there were aggregates of ubiquitin and TDP-43. In addition, in the substantia nigra there was a loss of tyrosine hydroxylasepositive dopaminergic neurons and an increase in the number of activated microglia. Brain cholesterol concentrations were higher in LXRbeta-/- than in their wild type counterparts, and treatment with beta-sitosterol reduced brain cholesterol in both WT and LXRbeta-/- mice. Levels of the intestinal transporters, ABCG5/8 and Niemann-Pick C1 Like 1, were not affected by the loss of LXRbeta and/or treatment with beta-sitosterol. In conclusion, these data indicate that multiple mechanisms are involved in the sensitivity of LXRbeta-/- mice to beta-sitosterol: activation of microglia, accumulation of protein aggregates in the cytoplasm of large motor neurons, and depletion of brain cholesterol. The second paper examined the resistance to gain weight of LXRbeta-/- mice. We demonstrated that these mice at 11 months of age on a standard diet, exhibit a pancreatic exocrine insufficiency that could explain their resistance to gain weight. Moreover, we showed a marked reduction in the expression of the water channel aquaporin-1 in pancreatic ducts of LXRbeta-/-mice. This reduction is likely responsible for the thick and dense secretion visualized in electron microscopy and for the pancreatic insufficiency. With a specific antibody we demonstrated the presence of LXRbeta in the nuclei of epithelial cells in pancreatic ducts and by treatment of wild type mice with an LXR agonist we could demonstrate an increase in the level of mRNA of aquaporin-1. These findings suggest that LXRbeta plays an important role in controlling pancreatic juice secretion through the regulation of water transport. Interestingly, patients affected by ALS also exhibit exocrine insufficiency. Thus the two major characteristics of LXRbeta-/- mice may be part of a single syndrome whose common etiology stems from defective LXRbeta signaling.
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