Biology subjects

Freund, Y.

Publications and source records attributed to Freund, Y..

5 recordsLinked to original sources

bioRxiv2026

An atlas of the aging glycoproteome reveals how glycosylation modulates autoantibody binding in the brain

N-glycosylation generates substantial molecular diversity, yet how glycan composition varies throughout aging remains poorly understood. We mapped the N-glycoproteome of brain, liver, spleen, kidney, and plasma across nine ages spanning the mouse lifespan, identifying 80,618 unique N-glycopeptides at 9,211 glycosites on 4,391 glycoproteins, together with matched proteomic trajectories (glycoproteinatlas.org). Organ identity was the dominant determinant of glycan composition, but numerous glycosites nevertheless underwent remodeling with age. The brain showed a prominent age-associated increase in short paucimannose glycans, driven in part by the age-associated increase in the glycan-processing enzyme HEXB. In white matter, a hotspot for this change, aging increased the paucimannosylation of Myelin oligodendrocyte glycoprotein (MOG), a major target of central nervous system autoimmunity. We identified MOG-reactive autoantibodies in aged individuals and patients with MOG antibody-associated disease (MOGAD) and showed that the glycan at MOG N60 modulates autoantibody binding. Experimental autoimmune encephalomyelitis (EAE) recapitulated a subset of the age-associated glycosite changes, revealing shared glycosylation signatures between aging and autoimmune targeting of MOG. Together, these findings reveal site-specific N-glycosylation as both a marker of age and a regulator of molecular interactions.

neuroscience↗

bioRxiv2026

Inference and validation of causal genetic interactions in aging human fibroblasts

In the past hundred years, the fraction of fatalities due to age-related disease has risen from an envied minority of cases to the leading cause of death and economic morbidity in the developed world. Despite notable advances in understanding aging, its intrinsic complexity has prevented major therapeutic breakthroughs. This complexity extends across all systems and scales in an organism, leaving a "fingerprint of aging" across every aspect of cell and tissue behavior whose interrelationships are difficult to untangle. Compounding this problem, human aging is observed largely through cross-sectional rather than longitudinal data. Whether such data retain sufficient dynamical information to reveal causal interactions is unclear. Here we show that they can. Using convergent cross mapping (CCM), a method for identifying causal interactions in nonlinear dynamical systems, we reconstruct directed genetic interactions from age-ordered, cross-sectional transcriptomic data - recovering dynamics from populations rather than individuals. Applied to dermal fibroblasts from 490 GTEx donors, CCM identifies a genome-scale causal network whose topology, together with age-dependent changes in gene expression, predicts candidate drivers of aging. We tested these predictions experimentally by single-gene overexpression in fibroblasts from 55-year-old donors. Single-cell RNA sequencing confirmed 53.8% of testable CCM-predicted causal interactions, showing that dynamics reconstructed from cross-sectional populations contain experimentally recoverable information about gene-gene interactions. This 53.8% additionally exceeded that produced by multiple comparanda methods and a random null. We then asked whether this information could identify interventions that reverse cellular aging. Independent transcriptomic and high-dimensional morphological assays show that CCM-selected perturbations shift old fibroblasts toward states characteristic of young cells. These two measures of rejuvenation are strongly correlated, and the strongest interventions cause a majority of 55-year-old cells to resemble cells from 25-year-old donors. Thus, causal dynamics can be recovered from cross-sectional population data and used to identify interventions in aging. More generally, the results suggest a way to distinguish genes that change with age from genes that drive those changes, providing experimentally testable targets for altering the aging phenotype.

systems biology↗

bioRxiv2026

Domain-specific proteome remodeling defines mouse myelin aging

Myelin, once regarded as a static insulating structure, is now recognized as a dynamic component of the nervous system, capable of remodeling in response to experience. Its breakdown is linked to cognitive decline and neurodegenerative diseases, often preceding neuronal dysfunction. While the myelin proteome has been studied, the age- and sex-related changes it undergoes remain poorly understood. In this study, we purified myelin proteins from young, middle-aged, and aged male and female mice. Using mass spectrometry-based proteomics, we identified 4,095 unique proteins in males and 3,931 in females, with roughly 30% showing significant age-related changes in both sexes. We find an age-related increase in compact myelin structural proteins, such as MBP, MOBP, and CLDN11, and a selective vulnerability in non-compact myelin cytoskeletal proteins, such as SEPTIN2, SEPTIN8, and OPALIN. Notably, disease-associated proteins previously characterized in single-cell transcriptomics appear at the protein level in aged myelin. To firmly distinguish between proteins derived from oligodendrocytes and other cell types in vivo we labeled nascent oligodendrocyte proteins with bio-orthogonal non-canonical amino acid tagging (BONCAT). We discovered a dramatic age-related increase in lysosomal and vesicle-associated proteins, while translation and synaptic proteins decrease in myelin with age in both sexes. This dataset highlights molecular mechanisms underlying the loss of myelin integrity and function with age and provides a novel tool for studying oligodendrocyte-derived nascent proteins in vivo.

neuroscience↗

bioRxiv2023

Machine assisted annotation in neuroanatomy

One of the important yet labor intensive tasks in neuroanatomy is the identification of select populations of cells. Current high-throughput techniques enable marking cells with histochemical fluorescent molecules as well as through the genetic expression of fluorescent proteins. Modern scanning microscopes allow high resolution multi-channel imaging of the mechanically or optically sectioned brain with thousands of marked cells per square millimeter. Manual identification of all marked cells is prohibitively time consuming. At the same time, simple segmentation algorithms suffer from high error rates and sensitivity to variation in fluorescent intensity and spatial distribution. We present a methodology that combines human judgement and machine learning that serves to significantly reduce the labor of the anatomist while improving the consistency of the annotation. As a demonstration, we analyzed murine brains with marked premotor neurons in the brainstem. We compared the error rate of our method to the disagreement rate among human anatomists. This comparison shows that our method can reduce the time to annotate by as much as ten-fold without significantly increasing the rate of errors. We show that our method achieves significant reduction in labor while achieving an accuracy that is similar to the level of agreement between different anatomists.

neuroscience↗

bioRxiv2018

The trypanocidal benzoxaborole AN7973 inhibits trypanosome mRNA processing

Kinetoplastid parasites - trypanosomes and leishmanias - infect millions of humans and cause economically devastating diseases of livestock, and the few existing drugs have serious deficiencies. Benzoxaborole-based compounds are very promising potential novel anti-trypanosomal therapies, with candidates already in human and animal clinical trials. Their targets in trypanosomes were hitherto unknown. We investigated the mechanism of action of several benzoxaboroles, including AN7973, an early candidate for veterinary trypanosomosis.\n\nIn all kinetoplastids, transcription is polycistronic. Individual mRNA 5-ends are created by trans splicing of a short leader sequence, with coupled polyadenylation of the preceding mRNA. Treatment of Trypanosoma brucei with AN7973 inhibited trans splicing within 1h, as judged by loss of the Y-structure splicing intermediate and reduced levels of mRNA, and accumulation of peri-nuclear granules which are typical for splicing inhibition. Methylation of the spliced leader precursor RNA was not affected, but more prolonged AN7973 treatment caused an increase in S-adenosyl methionine and methylated lysine. Together, these results indicate that mRNA processing is the primary target of AN7973. Polyadenylation is required for kinetoplastid trans splicing. The EC50 for AN7973 in T. brucei was increased three-fold by over-expression of the T. brucei cleavage and polyadenylation factor CPSF3, identifying CPSF3 as a potential molecular target. Our results thus chemically validate mRNA processing as a viable drug target in trypanosomes.\n\nSeveral other benzoxaboroles showed metabolomic and splicing effects that were similar to those of AN7973, identifying splicing inhibition as a common mode of action, and suggesting that it might be linked to subsequent changes in methylated metabolites. Granule formation, splicing inhibition, and resistance after CPSF3 expression did not, however, always correlate, and prolonged selection of trypanosomes in AN7973 resulted in only 1.5-fold resistance. This suggests that the modes of action of oxaboroles that target trypanosome mRNA processing may extend beyond CPSF3 inhibition.\n\nAuthor summaryTrypanosomes and leishmanias infect millions of humans and cause economically devastating diseases of livestock; the few existing drugs have serious deficiencies. Trypanosomosis of cattle, caused mainly by Trypanosoma congolense and Trypanosoma vivax, is a serious problem in Africa, because bovids are used not only for meat and milk, but also for traction. Only two drugs are in routine use for chemotherapy and chemoprophylaxis of bovine trypanosomosis. A single injection of the benzoxaborole compound AN7973 was sufficient to cure T. congolense infection in cattle and goats, but AN7973 was less effective against T. vivax. This precluded development of AN7973 as a commercially viable treatment against cattle trypanosomosis, but it could still have potential for diseases caused by other salivarian trypanosomes.\n\nWe used a large range of methods to find out how AN7973 kills trypanosomes, and compared it with several other benzoxaboroles. AN7973 and some of the other compounds had effects on parasite metabolism that resembled those previously seen for a benzoxaborole that is being tested for human sleeping sickness. The most rapid effect of AN7973, however, was on processing of trypanosome mRNA. As a consequence, amounts of mRNA decreased and synthesis of proteins stopped. We conclude that AN7973 and some other benzoxaboroles kill trypanosomes by stopping gene expression.

microbiology↗