Biology subjects

Goldberg, M.

Publications and source records attributed to Goldberg, M..

8 recordsLinked to original sources

bioRxiv2026

Human cerebral assembloids as a model to study the interaction of glioblastoma with resident glial cells

Glioblastoma (GB) is a highly invasive brain cancer characterized by extensive peritumoral glial reactivity. Although GB infiltration and recurrence remain major therapeutic challenges, the contribution of GB-induced gliosis to tumor progression is poorly understood. To investigate glia-GB interactions, we developed human iPSC-derived cerebral forebrain assembloids containing innate microglia and macroglia and transplanted them with GB cells. The model recapitulates key tumor features observed in patients, including distinct tumor regions, reactive gliosis, and altered tissue stiffness. Single-cell RNA sequencing revealed an unexpected enrichment of extracellular vesicles (EVs) in peritumoral reactive glia, which we validated in patient samples. EV inhibition impaired formation of the peritumoral niche, whereas EVs from GB-containing assembloids induced glial reactivity in GB-free assembloids. Furthermore, the modularity of our system enables incorporation of additional niche components, such as monocytes, allowing investigation of the monocyte-glia-tumor axis and providing a powerful platform to dissect mechanisms regulating the GB microenvironment.

neuroscience↗

bioRxiv2026

PLCγ2 deficiency compromises systemic immune tolerance and erodes myelin homeostasis while enhancing oxidative metabolism in the mouse brain

BackgroundPhospholipase C gamma-2 (PLC{gamma}2) catalyzes the hydrolysis of the membrane phosphatidylinositol-4,5-bisphosphate (PIP2) to form diacylglycerol (DAG) and inositol trisphosphate (IP3), feeding into diverse downstream signaling pathways. PLCG2 polymorphisms have been associated with reduced and/or increased risk of Alzheimers disease (AD) and related dementias, longevity, autoinflammation, and immune disorders. In the brain, PLC{gamma}2 is expressed in microglia, and other neuroimmune and vascular interface populations, yet its role in brain homeostasis remains incompletely defined. MethodsWe analyzed the brains of three-month-old Plcg2 wild-type (WT), heterozygous (Het KO) and homozygous knockout (Homo KO) littermate mice modeling human PLCG2 loss-of-function risk alleles linked to AD risk using a multiomic approach that included lipidomics, metabolomics, proteomics, and transcriptomics, together with immunofluorescence, as well as flow-cytometric profiling of peripheral and brain-draining immune compartments. ResultsPlcg2 deficiency substantially impaired early survival and produced splenomegaly without increasing total spleen cellularity, instead shifting spleen composition toward myeloid/innate-enriched cells and away from B cells, with expansion of age-associated B-cell (ABC-like) subsets and parallel reductions in CD4 and CD8 regulatory T cells in spleen and cervical lymph nodes. Brain lipidomics revealed selective depletion of PIP2, despite very low bulk PLC{gamma}2 protein abundance relative to other PLC family members. PLC{gamma}2 loss led to significant reductions in myelin-enriched lipid classes and myelin/paranode-associated proteins, accompanied by compensatory upregulation of oligodendrocyte/myelin genes, and modest shifts in microglial, lysosomal, complement, and oxidative metabolism pathways by NanoString and DIA-MS. Targeted acylcarnitine profiling demonstrated reprogramming of brain oxidative metabolism, with increased short-, medium-, and long-chain acylcarnitines and enrichment of mitochondrial matrix fatty-acid and amino-acid catabolic enzymes in Homo KO brains. ConclusionsLoss of PLC{gamma}2 installs a coordinated program that compromises systemic immune tolerance and subtly erodes central myelin and phosphoinositide homeostasis while enhancing brain oxidative metabolism, effects that extend beyond microglial phagocytic signaling and may underlie increased vulnerability to AD pathology and aging, providing a mechanistic framework for how PLCG2 variation may link systemic immune regulation, white-matter integrity, and neurodegenerative risk. LimitationsBecause constitutive Plcg2 Homo KO mice display high early mortality and intestinal vascular abnormalities, observed phenotypes may reflect developmental compensation and may not fully recapitulate protective human PLCG2 variants.

neuroscience↗

bioRxiv2025

Formic acid impairs α-synuclein seeding activity in human and mouse brains

-Synuclein (-syn) is an abundant monomeric protein that can aggregate into fibrils and form neuropathological inclusions in the brains of patients with synucleinopathies. New evidence suggests that the mouse-human transmission barrier of -syn is lower than previously reported, emphasizing the need for improved biosafety procedures when working with -syn aggregates. Histopathology of -syn-infected brain represents a significant potential source of occupational exposure, and current methods for tissue fixation do not inactivate the ability of pathologic -syn to seed the conversion of endogenous, monomeric -syn into fibrils. In this study, we tested whether 96% formic acid treatment could reduce the seeding activity of -syn aggregates in paraformaldehyde-fixed brain samples from dementia with Lewy bodies (DLB) patients and -syn pre-formed fibrils (PFF)-injected mouse brains. Using real-time quaking-induced conversion (RT-QuIC), we found that formic acid treatment reduced -syn seeding dose (picograms of -syn seeds per ml of brain homogenate) in DLB and mouse brain by 6 and 8 logarithms, respectively. RT-QuIC reactions seeded with formic acid-treated brain homogenates showed significantly longer lag phase, and decreased total thioflavin T fluorescence compared to untreated samples, indicating that formic acid treatment impairs the ability of pathological -syn to seed monomeric -syn. Importantly, the -syn pathologic features and the immunostaining quality were preserved in formic acid-treated tissues. Our results demonstrate that formic acid treatment is a quick and efficient procedure for reducing -syn seeding activity in fixed brain samples, thereby lowering the risk of accidental exposure in laboratories without compromising the quality of histopathological analysis. SummaryFormic acid treatment drastically reduces -synuclein seeding activity in fixed human and mouse brain samples while preserving histopathological quality.

neuroscience↗

bioRxiv2025

Manipulating PARK7/DJ-1 Levels by Genotoxic Stress Alters Noncoding RNAs and Cellular Homeostasis

DJ-1/PARK7 is a multifunctional protein that plays a vital role in sensing oxidative stress and maintaining redox homeostasis. As an oncogene, DJ-1 influences p53-mediated stress responses and contributes to cancer progression. This study investigates the impact of X-ray-induced DNA breaks on cellular responses post-irradiation under varying DJ-1 expression levels. Using siRNA knockdown and overexpression to modulate DJ-1 levels, transcriptional changes were analyzed through RNA-seq. Naive cells exhibited only a moderate transcriptional response to X-ray exposure, including suppression of the cell cycle and activation of stress pathways. Overexpression of DJ-1 led to pronounced gene expression suppression, particularly suppression of most ribosomal and mitochondrial genes. Conversely, DJ-1 knockdown caused extensive, non-specific transcriptional changes, indicating disrupted cellular homeostasis. Notably, around 25% of non-coding RNAs were differentially expressed under these conditions. DJ-1 overexpression suppressed lncRNA of the host genes for snoRNAs, thus altering the miRNA sponging capacity after X-ray exposure. These findings underscore DJ-1s critical role in modulating cellular responses to genotoxic stress, reshaping transcriptional landscapes, and regulating non-coding RNA profiles. DJ-1 emerges as essential for maintaining genomic stability.

molecular biology↗

bioRxiv2024

Drosophila Trus, the orthologue of mammalian PDCD2L, is required for proper cell proliferation, larval developmental timing, and oogenesis

Toys are us (Trus) is the Drosophila melanogaster ortholog of mammalian Programmed Cell Death 2-Like (PDCD2L), a protein that has been implicated in ribosome biogenesis, cell cycle regulation, and oncogenesis. In this study, we examined the function of Trus during Drosophila development. CRISPR/Cas9 generated null mutations in trus lead to partial embryonic lethality, significant larval developmental delay, and complete pre-pupal lethality. In mutant larvae, we found decreased cell proliferation and growth defects in the brain and imaginal discs. Mapping relevant tissues for Trus function using trus RNAi and trus mutant rescue experiments revealed that imaginal disc defects are primarily responsible for the developmental delay, while the pre-pupal lethality is likely associated with faulty central nervous system (CNS) development. Examination of the molecular mechanism behind the developmental delay phenotype revealed that trus mutations induce the Xrp1-Dilp8 ribosomal stress-response in growth-impaired imaginal discs, and this signaling pathway attenuates production of the hormone ecdysone in the prothoracic gland. Additional Tap-tagging and mass spectrometry of components in Trus complexes isolated from Drosophila Kc cells identified Ribosomal protein subunit 2 (RpS2), which is coded by string of pearls (sop) in Drosophila, and Eukaryotic translation elongation factor 1 alpha 1 (eEF11) as interacting factors. We discuss the implication of these findings with respect to the similarity and differences in trus genetic null mutant phenotypes compared to the haplo-insufficiency phenotypes produced by heterozygosity for mutants in Minute genes and other genes involved in ribosome biogenesis. Authors SummaryRibosomes are essential macromolecular machines required for decoding mRNA to make proteins, the major biomolecules that carry out all central cellular functions. As such, their structural and operational integrity is critical to organismal survival, and mutations that disrupt proper stoichiometry or assembly of ribosomes produce serious pathological consequences during an organisms development and/or adult life. The ribosome assembly factor PDCD2L is highly conserved from yeast to man, yet its overall function and requirement during development is poorly understood. By examining the developmental consequences of null mutations in trus, which encodes the Drosophila PDCD2L homolog, we demonstrate an essential role for this factor in cell-cycle regulation. Furthermore, disruption of Trus function in mitotically dividing imaginal tissue activates the Xrp1-dilp8 stress response pathway which limits production of ecdysone, the major arthropod molting hormone, leading to severe developmental delay during larval stages. These studies provide new insights on the requirements of this highly conserved ribosome assemble factor during development.

developmental biology↗

bioRxiv2024

Effects of systemic oxytocin and beta-3 receptor agonist (CL 316243) treatment on body weight and adiposity in male diet-induced obese rats

Previous studies have implicated hindbrain oxytocin (OT) receptors in the control of food intake and brown adipose tissue (BAT) thermogenesis. We recently demonstrated that hindbrain [fourth ventricle (4V)] administration of oxytocin (OT) could be used as an adjunct to drugs that directly target beta-3 adrenergic receptors ({beta}3-AR) to elicit weight loss in diet-induced obese (DIO) rodents. What remains unclear is whether systemic OT can be used as an adjunct with the {beta}3-AR agonist, CL 316243, to increase BAT thermogenesis and elicit weight loss in DIO rats. We hypothesized that systemic OT and {beta}3-AR agonist (CL 316243) treatment would produce an additive effect to reduce body weight and adiposity in DIO rats by decreasing food intake and stimulating BAT thermogenesis. To test this hypothesis, we determined the effects of systemic (subcutaneous) infusions of OT (50 nmol/day) or vehicle (VEH) when combined with daily systemic (intraperitoneal) injections of CL 316243 (0.5 mg/kg) or VEH on body weight, adiposity, food intake and brown adipose tissue temperature (TIBAT). OT and CL 316243 monotherapy decreased body weight by 8.0{+/-}0.9% (P<0.05) and 8.6{+/-}0.6% (P<0.05), respectively, but OT in combination with CL 316243 produced more substantial weight loss (14.9{+/-}1.0%; P<0.05) compared to either treatment alone. These effects were associated with decreased adiposity, energy intake and elevated TIBAT during the treatment period. The findings from the current study suggest that the effects of systemic OT and CL 316243 to elicit weight loss are additive and appear to be driven primarily by OT-elicited changes in food intake and CL 316243-elicited increases in BAT thermogenesis.

neuroscience↗

bioRxiv2022

Enhanced competitive protein exchange at the nano-bio interface enables ultra-deep coverage of the human plasma proteome

We have developed a scalable system that leverages protein-nano interactions to overcome current limitations of deep plasma proteomics in large cohorts. Introducing proprietary engineered nanoparticles (NPs) into a biofluid such as blood plasma leads to the formation of a selective and reproducible protein corona at the particle-protein interface, driven by the relationship between protein-NP affinity and protein abundance. Here we demonstrate the importance of tuning the protein to NP-surface ratio (P/NP), which determines the competition between proteins for binding. We demonstrate how optimized P/NP ratio affects protein corona composition, ultimately enhancing performance of a fully automated NP-based deep proteomic workflow (Proteograph). By limiting the available binding surface of NPs and increasing the binding competition, we identify 1.2 - 1.7x more proteins with only 1% false discovery rate on the surface of each NP, and up to 3x compared to a standard neat plasma proteomics workflow. Moreover, increased competition means proteins are more consistently identified and quantified across replicates, yielding precise quantification and improved coverage of the plasma proteome when using multiple physicochemically distinct NPs. In summary, by optimizing NPs and assay conditions, we capture a larger and more diverse set of proteins, enabling deep proteomic studies at scale.

biophysics↗

bioRxiv2020

Evaluation of saliva as a source of accurate whole-genome and microbiome sequencing data

This study sets out to establish the suitability of saliva-based whole-genome sequencing (WGS) through a comparison against blood-based WGS. To fully appraise the observed differences, we developed a novel technique of pseudo-replicates. We also investigated the potential of characterising individual salivary microbiomes from non-human DNA fragments found in saliva. We observed the majority of discordant genotype calls between blood and saliva calls fell into known regions of the human genome that are typically sequenced with low confidence; and could be identified by quality control measures. Pseudo-replication demonstrated that the levels of discordance between blood- and saliva-derived WGS data were entirely similar to what one would expect between technical replicates if an individuals blood or saliva had been sequenced twice. Finally, we successfully sequenced salivary microbiomes in parallel to human genomes as demonstrated by a comparison against the Human Microbiome Project. Author SummaryDNA is usually collected from blood for the analysis of human genomes. In France, a new and very large genetic dataset will be created where selected participants will be sent saliva-collection kits in the post as this data collection method presents numerous logistical benefits. It has been previously shown that good quality genetic data can be created from saliva, though existing studies have often not considered the latest technologies or have only analysed a very small number of individuals. In this study, we have analysed genetic data derived from saliva for 39 individuals to give a firm conclusion that the proposed genome sequencing approach of the new French dataset will be capable of provided high quality data by making a comparison to pre-existing genetic data derived from blood for these 39 individuals. In order to do so, we developed a novel method (presented here) to establish the similarity between two sets of genetic data for the same individual that are generated from separate DNA samples. Finally, we have also demonstrated an added bonus of colleting saliva samples: that it is possible to gather both human genetic data and potentially interesting salivary microbiome data at the same time by separating and analysing in parallel human and non-human DNA fragments.

genetics↗