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Biology subjects

Kharel, P.

Publications and source records attributed to Kharel, P..

6 recordsLinked to original sources

tRNA-derived fragments elevated in Alzheimer's disease facilitate Tau aggregation

Tauopathies, including Alzheimers disease (AD), are driven by pathological Tau aggregation, a process that requires co-factors. Small RNAs (sRNA) have been proposed as such co-factors, yet little is known about endogenous transcripts that promote Tau pathology. We identify stress-induced tRNA-derived RNAs or fragments (tDRs/tRFs) as the most dysregulated sRNA class in human AD brains, PS19 mice overexpressing mutant human Tau, and human neuronal tauopathy models. Notably, the highly accumulating 5GluCTC and 5GlyGCC tRFs directly bind Tau and induce its phosphorylation, oligomerization, fibril formation, and impact neurite growth. 5GluCTC is enriched in pathological Tau precipitates and co-localizes with oligomeric Tau in PS19 mouse brains. Inhibiting 5GluCTC mitigates Tau pathology. Furthermore, these tRFs are highly secreted by neurons and can be taken up by recipient cells, contributing to Tau pathology. Our findings establish 5GluCTC as a key regulator of Tau aggregation and suggest its inhibition as a promising therapeutic strategy for tauopathies. HighlightsO_LISpecific stress-induced 5tRFs strongly accumulate in Alzheimers disease brains C_LIO_LI5GluCTC binds and co-localizes with pathologic Tau in neurons and in the brain C_LIO_LI5GluCTC promotes pathologic Tau species while its inhibition reverses these effects C_LIO_LISpecific 5tRFs are horizontally transferred between neurons C_LI

neuroscience↗

G-quadruplex topologies determine the functional outcome of guanine-rich bioactive oligonucleotides

Guanine-rich nucleic acid sequences can exert sequence and/or structure specific activities to influence biological and pathobiological cellular processes. As such, it has been reported that different G-rich oligonucleotides (both DNA and RNA) can have cytotoxic as well as cytoprotective effects to the cells. However, the mechanisms of such a biological outcome are unclear. In this report, we report that G-rich DNA oligonucleotides (ODNs) that can form four stranded secondary structures called G-quadruplexes (G4s) can have topology-dependent biological outcome. Using different biochemical, biophysical, and cellular approaches, we demonstrate that only the parallel topology G4-forming ODNs can repress eukaryotic translation by directly interacting with eukaryotic translation initiation protein 1 (EIF4G1), while the antiparallel topology G4s do not have inhibitory effect on mRNA translation To the best of our knowledge, this is the first report to directly connect the G4 topological differences with differential functional biological impacts. Our study provides the foundation for the rational design of G-rich oligonucleotides for a desired therapeutic outcome.

biochemistry↗

HOXDeRNA activates a cancerous transcription program and super-enhancers genome-wide

BackgroundThe origin and genesis of highly malignant and heterogenous glioblastoma brain tumors remain unknown. We previously identified an enhancer-associated long non-coding RNA, LINC01116 (named HOXDeRNA here), that is absent in the normal brain but is commonly expressed in malignant glioma. HOXDeRNA has a unique capacity to transform human astrocytes into glioma-like cells. This work aimed to investigate molecular events underlying the genome-wide function of this lncRNA in glial cell fate and transformation. ResultsUsing a combination of RNA-Seq, ChIRP-Seq, and ChIP-Seq, we now demonstrate that HOXDeRNA binds in trans to the promoters of genes encoding 44 glioma-specific transcription factors distributed throughout the genome and derepresses them by removing the Polycomb repressive complex 2 (PRC2). Among the activated transcription factors are the core neurodevelopmental regulators SOX2, OLIG2, POU3F2, and SALL2. This process requires an RNA quadruplex structure of HOXDeRNA that interacts with EZH2. Moreover, HOXDeRNA-induced astrocyte transformation is accompanied by the activation of multiple oncogenes such as EGFR, PDGFR, BRAF, and miR-21, and glioma-specific super-enhancers enriched for binding sites of glioma master transcription factors SOX2 and OLIG2. ConclusionsOur results demonstrate that HOXDeRNA overrides PRC2 repression of glioma core regulatory circuitry with RNA quadruplex structure. These findings help reconstruct the sequence of events underlying the process of astrocyte transformation and suggest a driving role for HOXDeRNA and a unifying RNA-dependent mechanism of gliomagenesis.

molecular biology↗

Stress promotes RNA G-quadruplex folding in human cells

Guanine-rich nucleic acids can fold into G-quadruplex (G4) structures. Although endogenous RNAs contain sequences that can fold into RNA G4s (rG4s) in vitro, their folding and functions in vivo are not well understood. We show that the folding of putative rG4s in human cells into bona fide rG4 structures is dynamically regulated by stress. By using a high-throughput approach based on differential reactivity of dimethyl sulfate (DMS) towards Gs within folded vs unfolded rG4s, we identified hundreds of endogenous rG4s whose folding is promoted by cellular stress and validated them using a newly developed rG4-specific ligand. Stress-dependent rG4s are enriched in mRNA 3'-untranslated regions, suggesting their role in regulating mRNA stability under stress. Lastly, rG4 folding is reversible upon stress removal or adaptation. Our study show that rG4s function as regulatory elements in regulating mRNA stability and cellular stress response. One-Sentence SummaryRNA G-quadruplexes assemble under stress in human cells

molecular biology↗

Lysosomal Exocytosis Releases Pathogenic α-Synuclein Species from Neurons

Considerable evidence supports the release of pathogenic aggregates of the neuronal protein -Synuclein (Syn) into the extracellular space. While this release is proposed to instigate the neuron-to-neuron transmission and spread of Syn pathology in synucleinopathies including Parkinsons disease, the molecular-cellular mechanism(s) remain unclear. Here we show that pathogenic species of Syn accumulate within neuronal lysosomes in mouse brains and primary neurons. We then find that neurons release these pathogenic Syn species via SNARE-dependent lysosomal exocytosis; proposing a central mechanism for exocytosis of aggregated and degradation-resistant proteins from neurons.

cell biology↗

NAT8L mRNA oxidation is linked to neurodegeneration in multiple sclerosis

RNA oxidation has been implicated in neurodegeneration, but the underlying mechanism for such effects is unclear. Recently, we demonstrated extensive RNA oxidation within the neurons in multiple sclerosis (MS) brain. In this report we identified selectively oxidized mRNAs in neuronal cells that pertained to neuropathological pathways. N-acetyl aspartate transferase 8 like (NAT8L) mRNA is one such transcript, whose translated product enzymatically synthesizes N-acetyl aspartic acid (NAA), a neuronal metabolite important for myelin synthesis. We reasoned that impediment of translation of an oxidized NAT8L mRNA will result in reduction in its cognate protein, thus lowering NAA level. This assertion is directly supported by our studies on a model cellular system, an MS animal model and postmortem human MS brain. Reduced NAA level in the brain hampers myelin integrity making neuronal axons more susceptible to damage, which contributes in MS neurodegeneration. Overall, this work provides a framework for mechanistic understanding of the link between RNA oxidation and neurodegenerative diseases.

molecular biology↗