Biology subjects

Sardiello, M.

Publications and source records attributed to Sardiello, M..

7 recordsLinked to original sources

bioRxiv2025

Identifying and treating CLN3 disease outside the central nervous system

Background and aimsSevere gastrointestinal (GI) symptoms occur in people with CLN3 disease, a neurodegenerative disorder. If left untreated these GI symptoms compromise life quality and may contribute to death. We hypothesized GI symptoms in CLN3 disease are at least partially due to neurodegeneration in the enteric nervous system (ENS), the master regulator of bowel function. MethodsWe examined the integrity of the ENS in human CLN3 autopsy small bowel and colon, and in CLN3 deficient (Cln3{Delta}ex7/8) mice. We performed detailed immunohistological analyses of enteric neurons and glia and assessed bowel transit times at multiple disease stages. We then tested the therapeutic potential of neonatal intravenous gene therapy (AAV9-hCLN3) to prevent bowel phenotypes in Cln3{Delta}ex7/8 mice. ResultsHuman CLN3 bowel displayed a profound loss of enteric neurons and their neurites, with pathological effects upon enteric glia. Cln3{Delta}ex7/8 mice had normal appearing ENS at 1 month of age, but then experienced progressive loss of both enteric neurons and glia accompanied by marked bowel distention, resembling the human CLN3 phenotype. Degenerative changes in Cln3{Delta}ex7/8 mouse enteric neurons and glia were largely prevented by systemic neonatal delivery of AAV9-hCLN3 gene therapy, preventing bowel distention at disease endstage. ConclusionsOur findings demonstrate that CLN3 deficiency profoundly damages enteric neurons and glia in both murine and human CLN3 disease, contributing to GI dysfunction. This study provides preclinical evidence that systemic gene therapy may effectively treat multiple aspects of bowel pathology, expanding the therapeutic landscape beyond the CNS. What you need to know: Background and ContextSignificant gastrointestinal (GI) symptoms are evident in many pediatric neurological conditions. We hypothesized that, in addition to central nervous system (CNS) effects, defects in the enteric nervous system (ENS) may underlie these GI symptoms in some neurodegenerative diseases. Revealing such defects would open up new opportunities for treating these life-limiting and debilitating symptoms. New FindingsThe enteric nervous system is significantly impacted in human CLN3 disease, a feature that is recapitulated in CLN3 mice. Progressive enteric neurodegeneration in these mice follows a similar time course to neuron loss in the brain, resulting in severe bowel distention. Nevertheless, bowel distention and the majority of the pathology within the enteric nervous system can be mitigated via neonatal gene therapy. LimitationsOur human data will need to be replicated in larger numbers of CLN3 cases, and methods will need to be developed to treat the human bowel, avoiding the risk of liver tumors. ImpactThese results reveal that a neurodegenerative disease previously thought to primarily affect the CNS, damages the bowels enteric nervous system and that ENS degeneration can be prevented in mice by gene therapy. These data provide a new perspective on this pediatric disorder and may have relevance to other pediatric neurologic diseases. Lay SummaryThe progressive loss of neurons in CLN3 disease is not confined to the brain but also occurs in the bowel enteric nervous system, contributing directly to GI dysfunction. Neurodegeneration in the enteric nervous system can be prevented by treating the bowel with gene therapy.

neuroscience↗

bioRxiv2024

BioMedGraphica: An All-in-One Platform for Biomedical Prior Knowledge and Omic Signaling Graph Generation

Multi-omic data analysis is essential for scientific discovery in precision medicine. However, translating statistical results of omic data analysis into novel scientific hypothesis remains a significant challenge. Human experts must manually review analysis results and generate new hypothesis based on extensive and inter-connected biomedical prior knowledge, which is subjective and not scalable. While large language models (LLMs) can accelerate the discovery, their reasoning improves when grounded in structured, auditable and comprehensive biomedical prior knowledge. Biomedical knowledge, however, is scattered across heterogeneous databases that use diverse and inconsistent nomenclature systems, making it difficult to integrate resources into a unified format for scalable analysis. This fragmentation limits the ability of AI systems to fully leverage biomedical data for scientific discovery. To address these challenges, we developed BioMedGraphica, an all-in-one platform that harmonizes fragmented biomedical resources by integrating 11 entity types and 30 relation types from 43 databases into a unified knowledge graph containing 2,306,921 entities and 27,232,091 relations. In addition, to the best of our knowledge, this is the first work to propose a novel Textual-Numeric Graph (TNG) data-structure for multi-omics data analysis. In TNG, textual information captures prior biological knowledge (e.g., transcription start sites, functions, mechanisms), while numeric values represent quantitative biomedical features, and the integrated relations can help uncover mechanisms. By bridging prior knowledge with user-specific data, TNG is a novel and ideal data-structure for the development of graph foundation models, with the potential to improve prediction performance and interpretability, while also augmenting LLMs by supplying graph-structured mechanistic context to strengthen reasoning. The details for BioMedGraphica code can be accessed by github link: https://github.com/FuhaiLiAiLab/BioMedGraphica and BioMedGraphica knowledge graph data can be downloaded from huggingface dataset: https://huggingface.co/datasets/FuhaiLiAiLab/BioMedGraphica

bioinformatics↗

bioRxiv2023

TFEB degradation is regulated by an IKK/β-TrCP2 phosphorylation-ubiquitination cascade

Transcription factor EB (TFEB) is a master regulator of lysosomal biogenesis and autophagy that plays a key role in the regulation of cellular clearance pathways. TFEB is regulated via a complex array of post-translational modifications (PTMs), but the exact molecular mechanism that regulates TFEB stability has remained elusive. Here, we show that TFEB levels are critically regulated by a defined phosphorylation-ubiquitination cascade. A human kinome screen identifies IKK (inhibitor of {kappa}B kinase) as a TFEB modifier, and a combination of phosphorylation assays, mass spectrometry analyses, and site-specific mutagenesis unveils a previously unrecognized TFEB phospho-degron (423SPFPSLS429) as the target of IKK. We show that IKK-mediated phosphorylation of TFEB triggers ubiquitination of adjacent lysine residues (K430 and K431) by the E3 ligase {beta}-TrCP2 ({beta}-Transducin repeat-containing protein 2), thereby tagging TFEB for degradation. Modified TFEB constructs that abolish these PTMs show much increased stability and expression levels but remain equally sensitive to autophagy- or stress- related stimuli while maintaining the capability to promote the expression of TFEB target genes and the clearance of Alzheimers associated tau in a cellular model of disease. Our results therefore uncover an IKK/{beta}-TrCP2 phosphorylation-ubiquitination cascade as a major mechanism that governs TFEB stability independently of other TFEB regulators.

cell biology↗

bioRxiv2023

Bowel dysmotility and enteric neuron degeneration in lysosomal storage disease mice is prevented by gene therapy

Background and aimsChildren with neurodegenerative disease often have debilitating gastrointestinal (GI) symptoms that may be due at least in part to underappreciated involvement of neurons in the enteric nervous system (ENS), the master regulator of bowel function. MethodsWe investigated bowel motility in mouse models of CLN1 and CLN2 disease, neurodegenerative lysosomal storage disorders caused by deficiencies in palmitoyl protein thioesterase-1 (PPT1) and tripeptidyl peptidase-1 (TPP1), respectively. We then explored the integrity of ENS anatomy in immunostained bowel wholemount preparations from these mice. Lastly, we administered adeno-associated viral gene therapy to neonatal mice and determined if this would prevent these newly identified bowel phenotypes. ResultsMouse models of CLN1 and CLN2 disease both displayed slow bowel transit in vivo that worsened with age. Although the ENS appeared to develop normally, there was a progressive and profound loss of myenteric plexus neurons accompanied by changes in enteric glia in adult mice. Neonatal administration of adeno-associated virus-mediated gene therapy prevented bowel transit defects and the loss of many ENS neurons. ConclusionsWe show that two neurodegenerative lysosomal storage diseases cause profound and progressive damage to the mouse enteric nervous system and impair bowel motility. We also provide proof-of-principle evidence that gene therapy can prevent enteric nervous system disease. This study may have general therapeutic implications for many inherited neurodegenerative disorders. What you need to knowO_ST_ABSBackground and ContextC_ST_ABSMany pediatric central nervous system disorders also have debilitating gastrointestinal symptoms. For most of these diseases, it is not known if the enteric nervous system (ENS) is also affected and to what degree ENS defects contribute to GI symptoms. To date, no attempts have been made to directly treat or prevent enteric nervous system disease via gene therapy. New FindingsThe enteric nervous system is severely affected in mouse models of CLN1 and CLN2 disease, profoundly neurodegenerative lysosomal storage disorders. Bowel transit defects and most of the enteric nervous system pathology can be prevented by neonatal administration of gene therapy. LimitationsInformation about enteric nervous system disease in human children is still lacking, and methods will need to be developed to treat the human bowel. ImpactThese findings identify an underappreciated effect of neurodegenerative disease upon the bowel and demonstrate that enteric nervous system degeneration can be prevented in mice. This provides a new perspective on these childhood disorders that may be applicable to many other conditions that affect the bowel. Lay SummaryIn childrens diseases where the brain degenerates, nerve cells in the bowel also die causing gastrointestinal problems, but this can be prevented by gene therapy.

neuroscience↗

bioRxiv2023

TFEB-vacuolar ATPase signaling regulates lysosomal function and microglial activation in tauopathy

Transcription factor EB (TFEB) mediates gene expression through binding to the Coordinated Lysosome Expression And Regulation (CLEAR) sequence. TFEB targets include subunits of the vacuolar ATPase (v-ATPase) essential for lysosome acidification. Single nucleus RNA-sequencing (snRNA-seq) of wild-type and PS19 (Tau) transgenic mice identified three unique microglia subclusters in Tau mice that were associated with heightened lysosome and immune pathway genes. To explore the lysosome-immune relationship, we specifically disrupted the TFEB-v-ATPase signaling by creating a knock-in mouse line in which the CLEAR sequence of one of the v-ATPase subunits, Atp6v1h, was mutated. We show that the CLEAR mutant exhibited a muted response to TFEB, resulting in impaired lysosomal acidification and activity. Crossing the CLEAR mutant with Tau mice led to higher tau pathology but diminished microglia response. These microglia were enriched in a subcluster low in mTOR and HIF-1 pathways and was locked in a homeostatic state. Our studies demonstrate a physiological function of TFEB-v-ATPase signaling in maintaining lysosomal homoeostasis and a critical role of the lysosome in mounting a microglia and immune response in tauopathy and Alzheimers disease.

neuroscience↗

bioRxiv2019

A CLN6-CLN8 complex recruits lysosomal enzymes at the ER for Golgi transfer

Lysosomal enzymes are synthesized in the endoplasmic reticulum (ER) and transferred to the Golgi complex by interaction with the Batten disease protein CLN8. Here we investigated the relationship of this pathway with CLN6, an ER-associated protein of unknown function that is defective in a different Batten disease subtype. Experiments focused on protein interaction and trafficking identified CLN6 as an obligate component of a CLN6-CLN8 complex (herein referred to as EGRESS: ER-to-Golgi relaying of enzymes of the lysosomal system) which recruits lysosomal enzymes at the ER to promote their Golgi transfer. Simultaneous deficiency of CLN6 and CLN8 did not aggravate mouse pathology compared to the single deficiencies, indicating that the EGRESS complex works as a functional unit. Mutagenesis experiments showed that the second luminal loop of CLN6 is required for the interaction of CLN6 with the enzymes but dispensable for interaction with CLN8, and in vitro and in vivo studies showed that CLN6 deficiency results in inefficient ER export of lysosomal enzymes and diminished levels of the enzymes at the lysosome. These results identify CLN6 and the EGRESS complex as key players in lysosome biogenesis and shed light on the molecular etiology of Batten disease caused by defects in CLN6.

cell biology↗

bioRxiv2019

CELF1 is an EIF4E binding protein that promotes translation of epithelial-mesenchymal transition effector mRNAs

Mounting evidence is revealing a granularity within gene regulation that occurs at the level of mRNA translation. Within mammalian cells, canonical cap-dependent mRNA translation is dependent upon the interaction between the m7G cap-binding protein eukaryotic initiation factor 4E (eIF4E) and the scaffolding protein eukaryotic initiation factor 4G (eIF4G), the latter of which facilitates pre-translation initiation complex assembly, mRNA circularization, and ultimately ribosomal scanning. In breast epithelial cells, we previously demonstrated that the CELF1 RNA-binding protein promotes the translation of epithelial to mesenchymal transition (EMT) effector mRNAs containing GU-rich elements (GREs) within their 3 untranslated regions (UTRs). Here we show that within this context, CELF1 directly binds to both the eIF4E cap-binding protein and Poly(A) binding protein (PABP), promoting translation of GRE-containing mRNAs in mesenchymal cells. Disruption of this CELF1/eIF4E interaction inhibits both EMT induction and experimental metastasis. Our findings illustrate a novel way in which non-canonical mechanisms of translation initiation underlie transitional cellular states within the context of development or human disease.

cancer biology↗