Custom scripts related to Graziano, M. et al. (2025) “A molecular atlas of cell-type specific signatures in the parkinsonian striatum”
By onScripts by Graziano and Masarapu aid in analyzing single-nucleus RNA sequencing data from Parkinson's Disease striatum, mapping vulnerabilities, and inferring cell trajectories. Giacomello Lab scripts are available on GitHub.
Code used in “Lrrk2 G2019S mutation incites increased cell-intrinsic neutrophil effector functions and intestinal inflammation in a model of infectious colitis”
By onUsing scRNAseq and flow cytometry, we demonstrated that the Lrrk2-G2019S mutation is associated with an increased neutrophil presence in the colonic lamina propria, Th17 skewing, upregulated Il17a, and greater colonic pathology during infection.
Transcriptomic analysis of colonic lamina propria cells in LRRK2 G2019S mice compared to wild type following intestinal microbial infection
By onUsing scRNAseq and flow cytometry, we demonstrated that the Lrrk2 G2019S mutation is associated with an increased neutrophil presence in the colonic lamina propria during infection and a Th17 skewing, upregulated Il17a, and greater colonic pathology
Re-activation of neurogenic 2 niches in aging brain
By onWe developed a multimodal MERFISH platform to map cell fate in the brain, revealing quiescent neural stem cells in aged mice and humans. PTBP1 suppression reactivates them, driving neurogenesis and neuron integration with therapeutic potential.
Rapid LRRK2 Activation Induced by α-synuclein Preformed Fibrils Triggers Rab5 Phosphorylation and Dysregulates Endolysosomal Function, Gene Expression and Synaptic Activity in Neurons
By onα-Synuclein fibrils activate LRRK2 on early endosomes, disrupting Rab5 function and endolysosomal homeostasis in neurons, triggering chromatin changes and transcriptional reprogramming.
Single-nucleus multiomic profiling of the aging mouse substantia nigra reveals conserved gene alterations linked to Parkinson’s disease
By onSingle-nucleus analysis of mouse substantia nigra reveals cell-type-specific aging changes, highlighting PD-linked genes. Aging alters protein folding, myelination, and stress-response pathways, offering insights into PD risk.
Activation of transposable elements is linked to a region- and cell-type-specific interferon response in Parkinson’s disease
By onStudy explores transposable elements role in Parkinson's disease neuroinflammation. TE activation in specific brain regions correlates with innate immune responses, indicating potential involvement in chronic neuroinflammation and PD progression.
Tailored workflows for the analysis of transposable elements (Garza et al, 2025)
By onGarza et al. (2025) created customized workflows for transposable element analysis across various data types. Workflows are in Snakemake, Jupyter notebooks, R markdowns, and scripts. Details are in the GitHub README.
Reconstitution of BNIP3/NIX-mitophagy initiation reveals hierarchical flexibility of the autophagy machinery
By onThis Zenodo deposit is a collection of Microscopy data, KRT, Read me Files associated with the publication "Reconstitution of BNIP3/NIX-mitophagy initiation reveals hierarchical flexibility of the autophagy machinery" by Adriaenssens et al.
Elevated brain α-synuclein, phosphorylated-tau, and oxidative stress in mice that survived influenza A pneumonitis
By onInfluenza virus infection does not alter acute lung infection course in mice with Lrrk2 mutations. Surviving mice showed elevated neurodegeneration markers post-infection, suggesting a link between influenza and neurodegenerative diseases in humans.
Structure and activation of the human autophagy-initiating ULK1C:PI3KC3-C1 supercomplex
By onOriginal gels with their repeats, associated with pre-print
Source data for Motor Cortical Neuronal Hyperexcitability Associated with α-Synuclein Aggregation
By onChen et al (2024) study links α-synuclein aggregation to hyperexcitability in motor cortical neurons.
Source data for the article “α-Synuclein aggregation decreases cortico-amygdala connectivity and impairs social behavior in mice”
By onα-Synuclein aggregation in mice reduces cortico-amygdala connectivity, leading to impaired social behavior.
DNA and Expression Following Nucleosome Depletion (DEFND) Sequencing on Cryopreserved Colon Tissue
By onThis protocol details DNA and Expression Following Nucleosome Depletion (DEFND) sequencing optimized for cryopreserved colon tissue.
Faecalibacterium prausnitzii, depleted in the Parkinson’s disease microbiome, improves motor deficits in α-synuclein overexpressing mice
By onTreatment with an 8-member consortium of bacteria depleted in PD patients, or the single member F. prausnitzii, improves motor and GI function and reduces αSyn aggregates in the brain of a mouse model of PD.
Motor behavior, GI behavior, protein, and volatile fatty acid assay data and analysis code associated with Moiseyenko et al. 2025
By onCode and data used for the statistical analysis of motor behavior and gut physiology tests, and downstream protein assays from Moiseyenko et al. (2025)
RNAseq data associated with Moiseyenko et al. 2025
By onBAM files for RNA sequencing of large intestine of wild-type, Thy1-ASO, and Faecalibacterium prausnitzii-treated Thy1-ASO mice from Moiseyenko et al. (2025)
Data and code for shotgun metagenomics associated with Moiseyenko et al. 2025
By onData and scripts to retrieve and analyze shotgun metagenomic data of wild-type, Thy1-ASO, and Faecalibacterium prausnitzii-treated Thy1-ASO mice from Moiseyenko et al. (2025)
Adult-specific Reelin expression alters striatal neuronal organization: implications for neuropsychiatric disorders
By onReelin levels might modulate the numbers of striatal interneurons and the density of the nigrostriatal dopaminergic projections, suggesting that these changes may be involved in the protection of Reelin against neuropsychiatric disorders.
A RAB7A Phosphoswitch Coordinates Rubicon Homology Protein Regulation of PINK1/Parkin-Dependent Mitophagy
By onPublished: Structural and functional data support a model in which the TBK1-dependent phosphorylation of RAB7A serves as a switch, promoting mitophagy by relieving Rubicon inhibition and favoring Pacer activation. View original preprint.
