Biology subjects

Kramer, M.

Publications and source records attributed to Kramer, M..

At least 19 recordsLinked to original sources

bioRxiv2026

Comprehensive Molecular Characterization of High-Grade Endometrial Cancer in an Ancestrally-Diverse Cohort

Endometrial cancer (EC) exhibits one of the most striking racial disparities in oncology with black women disproportionately affected by aggressive high-grade subtypes that have poorer outcomes. While social and environmental factors undoubtedly contribute, the molecular underpinnings of these disparities remain critically understudied. To bridge this knowledge gap, we performed matched tumor-normal whole-genome sequencing and tumor transcriptome sequencing on 71 predominantly high-grade EC patient samples from an ancestrally diverse cohort of women recruited at a large hospital system in the New York metropolitan area. Our analysis characterized the germline and somatic mutation landscape, identifying ancestry-associated molecular differences. Notably, focal amplification of the EVI1 transcription factor (encoded at the MECOM locus) was significantly more frequent in African ancestry patients and associated with poorer clinical outcomes in an external validation cohort. Additionally transcriptome analysis revealed decreased CD8+ T cell infiltration with increasing African ancestry, suggesting tumor immune microenvironment differences with potential therapeutic implications. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=163 SRC="FIGDIR/small/721962v1_ufig1.gif" ALT="Figure 1"> View larger version (63K): org.highwire.dtl.DTLVardef@12125b9org.highwire.dtl.DTLVardef@133c787org.highwire.dtl.DTLVardef@707af0org.highwire.dtl.DTLVardef@97615c_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIThis study represents the most ancestrally diverse whole-genome sequencing characterization of high-grade endometrial cancer, with 62% of patients of African ancestry. C_LIO_LIMECOM focal amplification preferentially targets the oncogenic short isoform (EVI1) and is more frequent in patients of African ancestry. C_LIO_LIAfrican ancestry is associated with reduced CD8+ T cell infiltration and differential activation of immune and metabolic pathways in copy-number high endometrial tumors. C_LI

cancer biology↗

bioRxiv2026

A Patient-derived Organoid Platform for Uterine Carcinosarcoma that Emulates Disease Characteristics

Uterine carcinosarcoma (UCS) is a rare but extremely lethal endometrial cancer that metastasizes early and resists current treatment modalities. It is biphasic, built from malignant epithelial and mesenchymal cells. Genomic studies indicate that these tumors are clonal, and that the mesenchymal cells arise from the epithelial cells through cancer cell plasticity. This biology has been hard to study, because faithful patient-derived models are scarce. The gap is widened by inequity. Women of African ancestry carry the greatest burden of UCS, yet are underrepresented in existing models. To address this, we established patient-derived organoids (PDOs) from an ancestrally inclusive UCS cohort, alongside matched normal endometrial PDOs. The organoids reproduced the biphasic histology of the original tumors. Across four sequencing platforms, they retained the tumor mutation and copy-number landscape, remained stable across passages, and expanded for up to 28 months. At single-cell resolution, UCS PDOs captured both malignant compartments and traced continuous transcriptional trajectories along the epithelial-to-mesenchymal axis, capturing patient-specific cancer cell plasticity. The models also nominated candidate vulnerabilities in proof-of-concept therapeutic testing. UCS PDOs were enriched for CREB-family transcriptional programs, and CREB inhibition reduced their viability. Combined FGFR and YAP inhibition outperformed either agent alone. Together, this work delivers a histologically, genomically, and transcriptionally faithful, ancestrally inclusive, and lineage-resolved UCS organoid platform for studying cancer cell plasticity and its vulnerabilities in an aggressive and inequitably burdened cancer.

cancer biology↗

bioRxiv2026

Invisible shield: Sprayable supramolecular antimicrobial microscale films for preventing wound and medical device infections

Wound and device-associated infections remain difficult to eradicate because biofilms block host immunity and antibiotics, accelerating chronicity and resistance. Here, we present a portable, low-cost dual-syringe spray that deposits an ultra-thin, self-assembling antimicrobial film directly on wounds and implant surfaces. The device co-delivers oppositely charged hyaluronic acid (HA) and a cationic antimicrobial peptide (polyarginine, PAR30), which rapidly form a conformal nanometric polyelectrolyte complex at the tissue-material interface. Molecular dynamics simulation revealed pronounced positional heterogeneity within the PAR30/HA complex and identified an N-terminal arginine as a dominant interaction hotspot. The resulting coating adheres to diverse substrates, kills bacteria on contact, prevents biofilm formation, and sustains antimicrobial efficacy. Across vitro assays and murine wound infection models, treatment produced 4 to 5 log reductions in bacterial burden against methicillin-resistant Staphylococcus aureus and Gram-negative pathogens, including Pseudomonas aeruginosa and Escherichia coli. The formulation is biocompatible, did not increase cutaneous inflammation or IL-6 levels in vivo, and reduced post-surgical pain and motor deficits in a mouse incision model. To our knowledge, this is the first antimicrobial treatment system applicable to both tissues and medical devices. Developed under a safe-and-sustainable-by-design approach, this technology combines biocompatible components, nanometric coating for minimal material use, and a simple syringe-based delivery device, offering a scalable, antibiotic-free strategy for wound care and medical device infection prevention. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=173 HEIGHT=200 SRC="FIGDIR/small/717441v1_ufig1.gif" ALT="Figure 1"> View larger version (68K): org.highwire.dtl.DTLVardef@49381aorg.highwire.dtl.DTLVardef@1023e64org.highwire.dtl.DTLVardef@4e282aorg.highwire.dtl.DTLVardef@12eeae4_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2026

Patient-derived organoid xenografts reveal the multifaceted role of the lncRNA MALAT1 in breast cancer progression

Long non-coding RNAs (lncRNAs) have emerged as key regulators of tumor biology, however, thus far none have translated to cancer therapies. The lncRNA MALAT1 is overexpressed in more than 20 cancers, including breast cancer and has been shown to function via various mechanisms in a context-dependent manner, in 2D cell lines and mouse models. However, its functional role and therapeutic potential have not been evaluated in clinically relevant patient-derived models. We investigated the therapeutic potential of MALAT1-targeting antisense oligonucleotides (ASOs) for breast cancer, using clinically relevant 3D human patient-derived organoids (PDOs) and PDO-xenograft (PDO-X) models. We systematically evaluated the efficiency of MALAT1-targeting ASOs using a biobank of 28 PDO models. Across three independent PDO-X models of triple negative breast cancer (TNBC), MALAT1 depletion reproducibly drove widespread alternative splicing changes across all event types, with an enrichment of intron retention. Differentially spliced transcripts were enriched for targets of shared cancer-associated transcription factors, and MALAT1 knockdown specifically altered the relative abundance of previously unannotated splicing isoforms. Beyond tumor-intrinsic effects, tumor-specific MALAT1 depletion induced a consistent reduction in macrophage-associated gene signatures and reduced lung metastatic burden. Our data defines MALAT1s multifaceted role in TNBC, coordinating alternative splicing, tumor-stroma crosstalk, and metastatic progression. Our study provides strong preclinical evidence supporting MALAT1-targeted ASO therapy and establishes PDO-X models as a clinically relevant platform for functional interrogation of TNBC therapies. SignificanceUsing clinically relevant human PDO-X models, we show that MALAT1 influences alternative splicing, metastatic potential and the tumor microenvironment. These data support the potential of oncogenic lncRNA MALAT1 as a therapeutic target.

cancer biology↗

bioRxiv2026

Entomoscope 2.0 and ENIMAS 2.0: An Open-Source, AI-Integrated Platform for Rapid and Affordable Insect Digitization

The rapid decline of global biodiversity necessitates scalable and accessible tools for monitoring insect populations, yet the high cost and slow pace of specimen digitization remain significant bottlenecks. To address this challenge, we present the Entomoscope 2.0, an open-source platform that integrates a low-cost photomicroscope with an AI-integrated software suite, ENIMAS 2.0. The system combines optimized hardware with an end-to-end software module for digital specimen curation. This module comprises automated specimen cropping, background standardization, morphometric analysis using an Oriented Bounding Box (OBB) with a human-in-the-loop (HITL) supervision, and a flexible interface for rapid taxonomic screening using custom AI identification models. With a material cost of only 400 {euro}, the system offers a cost-effective alternative to expensive commercial solutions. We compare results from the Entomoscope 2.0 with a high-end commercial system (Keyence) using 54 insect specimens and demonstrate the efficiency of the proposed AI workflow. Entomoscope 2.0 completed the whole digitization process in an average of 54.6 seconds per specimen, representing a 2.28-fold increase in speed over the Keyence systems multi-step workflow (124.3 seconds). Crucially, all hardware specifications and construction manuals are freely available to support widespread adoption. By lowering financial barriers and accelerating research workflows, the Entomoscope 2.0 platform offers a practical solution to enable high-throughput digitization for researchers, educators, and citizen scientists.

bioengineering↗

bioRxiv2025

A human missense variant in BSX decouples circadian behaviour from metabolic rhythmicity while preserving lifespan in mice

Mammalian circadian organisation is orchestrated by a light-entrained master pacemaker in the suprachiasmatic nucleus (SCN) and SCN-independent, food- and metabolism-responsive oscillators in the brain and periphery; feeding can entrain these systems, enabling anticipation of feeding time. Here, we show that a human missense variant (Q159K) in the homeodomain of the brain-specific transcription factor BSX causes profound loss of circadian behavioural rhythms and food anticipatory activity (FAA) in mice. Whole-brain imaging reveals failure of the compact dorsomedial hypothalamus (DMHc) to form and the absence of histaminergic neurons in the tuberomammillary nucleus (TMN) in BsxQ159K/Q159K mice. Consequently, under light-dark (LD) and constant darkness (DD), sleep-wake cycles and circadian locomotor rhythmicity are profoundly lost, whereas total wake time and spontaneous locomotor activity are preserved, with daily caloric intake substantially shifted from the dark to the light cycle. Therefore, in DD, metabolic recordings reveal a rhythmic respiratory exchange ratio (RER) pattern that differs substantially from that of wild-type mice and is markedly attenuated under LD conditions. In addition, BsxQ159K/Q159K mice lack FAA during restricted feeding and fail to increase locomotor activity upon food deprivation. Despite the loss of circadian behavioural rhythms and altered daily feeding behaviour, BsxQ159K/Q159Kmice maintain metabolic homeostasis, a lean body composition into advanced age, and a normal lifespan under ad libitum feeding and controlled LD. These findings provide genetic evidence that circadian organization is not universally required for metabolic homeostasis, suggesting instead that circadian rhythmicity is an adaptive feature advantageous primarily under diurnal conditions.

genetics↗

bioRxiv2025

Complete post-transcriptional modification profiles in individual Staphylococcus aureus tRNA species

Transfer RNAs play a critical role in protein synthesis by matching mRNA codons to their corresponding amino acids. Their post-transcriptional modifications, shaping structure, stability, and codon decoding, are now recognized as key regulators of translation and cellular adaptation, including in bacterial pathogens. Here, we provide a comprehensive analysis of tRNA modifications in Staphylococcus aureus using extensive oligonucleotide mass spectrometry and deep-sequencing methods, generating a high-confidence modification map for each individual tRNA species, including the non-proteogenic tRNAGly. While the overall tRNA modification landscape is conserved among Gram-positive bacteria, our data uncovered unexpected S. aureus-specific features. These include the absence of [m2A]37 in tRNAs despite the presence of the methyltransferase RlmN, a single multi-site DusB2 enzyme catalyzing all tRNA dihydrouridylation, and a dedicated pseudouridine synthase responsible for [{Psi}]32 formation. Besides, heterogenous modification patterns were observed in tRNALeu(UAA) and tRNALys(CAA), highlighting a complex interplay in anticodon hypermodification. Integration of ribosome profiling and Nanopore tRNA sequencing offered a global view of the decoding properties of the reduced S. aureus tRNA set, revealing efficient four-way wobble recognition, slower translation of rare codons by low abundant tRNAs, and distinctive decoding dynamics of Gly codons potentially influenced by the unusual modification status of tRNAGly(UCC). This work establishes a framework for future research aimed at dissecting the role of specific tRNA modifications in S. aureus physiology and pathogenesis.

molecular biology↗

bioRxiv2025

A potential role of altered SIgA-targeting of gut microbiota in long-term dysbiosis in pediatric solid organ transplant recipients

BackgroundComposition of gut microbiota (GM) is altered in solid organ transplantation (SOT) patients, where the degree of dysbiosis is associated with long-term survival. Factors governing dysbiosis are poorly understood with immunosuppression therapy believed to be involved in altering GM composition in those patients, either directly or via the immune system. At the interface stands secretory (S)IgA, however, little is known on its role governing dysbiosis in the context of SOT. In this study, we performed quantitative metagenomic analyses of GM accompanied by SIgA sequencing in 48 pediatric SOT recipients (age = 10.6 {+/-} 4.7 years) receiving either a heart (HTR, n=10), a kidney (KTR, n=11) or a liver (LTR, n=27) and compared results to healthy controls (HC, n=16). ResultsWe confirmed compositional and functional dysbiosis in SOT patients that broadly clustered into two groups, where cluster 1 (n=23) comprised most LTR patients and was closer to HC compared with cluster 2 (n=24) that exhibited stronger dysbiosis and included most HTR and KTR patients. The degree of dysbiosis was associated with Tacrolimus (TAC) levels. Overall, patients exhibited higher SIgA levels than HC, along with an increased percentage of bacteria targeted and altered target spectra. Furthermore, altered SIgA responses were associated with the degree of dysbiosis and were especially increased in cluster 2, in particular in HTR patients. A mechanistic model connecting immunosuppression, GM composition and SIgA targeting is proposed. ConclusionOur study suggests that altered SIgA responses play an important role for GM alterations observed in SOT patients. It opens new therapeutic angles to combat GM dysbiosis and associated long-erm complications.

microbiology↗

bioRxiv2025

Accounting for Edge Uncertainty in Stochastic Actor-Oriented Models for Dynamic Network Analysis

Stochastic Actor-Oriented Models (SAOMs) were designed in the social network setting to capture network dynamics representing a variety of influences on network change. The standard framework assumes the observed networks are free of false positive and false negative edges, which may be an unrealistic assumption. We propose a hidden Markov model (HMM) extension to these models, consisting of two components: 1) a latent model, which assumes that the unobserved, true networks evolve according to a Markov process as they do in the SAOM framework; and 2) a measurement model, which describes the conditional distribution of the observed networks given the true networks. An expectation-maximization algorithm is developed for parameter estimation. We address the computational challenge posed by a massive discrete state space, of a size exponentially increasing in the number of vertices, through the use of the missing information principle and particle filtering. We present results from a simulation study, demonstrating our approach offers improvement in accuracy of estimation, in contrast to the standard SAOM, when the underlying networks are observed with noise. We apply our method to functional brain networks inferred from electroencephalogram data, revealing larger effect sizes when compared to the naive approach of fitting the standard SAOM.

neuroscience↗

bioRxiv2024

Chromosome-level Genome Assembly and Annotation of Petunia hybrida

Petunia hybrida is the worlds most popular garden plant and is regarded as a supermodel for studying the biology associated with the Asterid clade, the largest of the two major groups of flowering plants. Unlike other Solanaceae, petunia has a base chromosome number of seven, not 12. This along with recombination suppression has previously hindered efforts to assemble its genome to chromosome level. Here we achieve a chromosome-level assembly for P. hybrida using a combination of short-read and long-read sequencing, optical mapping (Bionano) and Hi-C technologies. The resulting assembly spans 1253.6 Mb with a BUSCO score of 99.8%. A total of 35,089 genes were predicted and of those 29,655 were functionally annotated. Syntenic regions between petunia, tomato and pepper were identified, highlighting rearrangements that have occurred since their divergence indicating that the 12 chromosomes of Solanaceae did not originate from whole genome duplication of an ancestral species with seven chromosomes like petunia. This chromosome-level assembly will significantly enhance trait mapping efficiency in petunia and serve as a valuable resource for functional genomic studies in this key plant model.

genomics↗

bioRxiv2024

Exploring the genetic and epigenetic underpinnings of early-onset cancers: Variant prioritization for long read whole genome sequencing from family cancer pedigrees

Despite significant advances in our understanding of genetic cancer susceptibility, known inherited cancer predisposition syndromes explain at most 20% of early-onset cancers. As early-onset cancer prevalence continues to increase, the need to assess previously inaccessible areas of the human genome, harnessing a trio or quad family-based architecture for variant filtration, may reveal further insights into cancer susceptibility. To assess a broader spectrum of variation than can be ascertained by multi-gene panel sequencing, or even whole genome sequencing with short reads, we employed long read whole genome sequencing using an Oxford Nanopore Technology (ONT) PromethION of 3 families containing an early-onset cancer proband using a trio or quad family architecture. Analysis included 2 early-onset colorectal cancer family trios and one quad consisting of two siblings with testicular cancer, all with unaffected parents. Structural variants (SVs), epigenetic profiles and single nucleotide variants (SNVs) were determined for each individual, and a filtering strategy was employed to refine and prioritize candidate variants based on the family architecture. The family architecture enabled us to focus on inapposite variants while filtering variants shared with the unaffected parents, significantly decreasing background variation that can hamper identification of potentially disease causing differences. Candidate de novo and compound heterozygous variants were identified in this way. Gene expression, in matched neoplastic and pre-neoplastic lesions, was assessed for one trio. Our study demonstrates the feasibility of a streamlined analysis of genomic variants from long read ONT whole genome sequencing and a way to prioritize key variants for further evaluation of pathogenicity, while revealing what may be missing from panel based analyses.

genomics↗

bioRxiv2024

MaizeCODE reveals bi-directionally expressed enhancers that harbor molecular signatures of maize domestication.

Modern maize was domesticated from Teosinte parviglumis, with subsequent introgressions from Teosinte mexicana, yielding increased kernel row number, loss of the hard fruit case and dissociation from the cob upon maturity, as well as fewer tillers. Molecular approaches have identified several transcription factors involved in the development of these traits, yet revealed that a complex regulatory network is at play. MaizeCODE deploys ENCODE strategies to catalog regulatory regions in the maize genome, generating histone modification and transcription factor ChIP-seq in parallel with transcriptomics datasets in 5 tissues of 3 inbred lines which span the phenotypic diversity of maize, as well as the teosinte inbred TIL11. Integrated analysis of these datasets resulted in the identification of a comprehensive set of regulatory regions in each inbred, and notably of distal enhancers which were differentiated from gene bodies by their lack of H3K4me1. Many of these distal enhancers expressed non- coding enhancer RNAs bi-directionally, reminiscent of "super enhancers" in animal genomes. We show that pollen grains are the most differentiated tissue at the transcriptomic level, and share features with endosperm that may be related to McClintocks chromosome breakage- fusion-bridge cycle. Conversely, ears have the least conservation between maize and teosinte, both in gene expression and within regulatory regions, reflecting conspicuous morphological differences selected during domestication. The identification of molecular signatures of domestication in transcriptional regulatory regions provides a framework for directed breeding strategies in maize.

plant biology↗

bioRxiv2023

Functional analysis of chromatin-associated proteins in Sordaria macrospora reveals similar roles for RTT109 and ASF1 in development and DNA damage response

We performed a functional analysis of two potential partners of ASF1, a highly conserved histone chaperone that plays a crucial role in the sexual development and DNA damage resistance in the ascomycete Sordaria macrospora. ASF1 is known to be involved in nucleosome assembly and disassembly, binding histones H3 and H4 during transcription, replication and DNA repair and has direct and indirect roles in histone recycling and modification as well as DNA methylation, acting as a chromatin modifier hub for a large network of chromatin-associated proteins. Here, we functionally characterized two of these proteins, RTT109 and CHK2. RTT109 is a fungal-specific histone acetyltransferase, while CHK2 is an ortholog to PRD-4, a checkpoint kinase of Neurospora crassa that performs similar cell cycle checkpoint functions as yeast RAD53. Through the generation and characterization of deletion mutants, we discovered striking similarities between RTT109 and ASF1 in terms of their contributions to sexual development, histone acetylation and protection against DNA damage. Phenotypic observations revealed a developmental arrest at the same stage in {Delta}rtt109 and {Delta}asf1 strains, accompanied by a loss of H3K56 acetylation, as detected by western blot analysis. Deletion mutants of rtt109 and asf1 are sensitive to the DNA damaging agent MMS (methylmethane sulfonate), but not HU (hydroxyurea). In contrast, chk2 mutants are fertile and resistant to MMS, but not HU. Our findings suggest a close functional association between ASF1 and RTT109 in the context of development, histone modification and DNA damage response, while indicating a role for CHK2 in separate pathways of the DNA damage response. Article summaryIn the filamentous fungus Sordaria macrospora, the conserved histone chaperone ASF1, which interacts with histones H3 and H4, was previously shown to be required for multicellular development and DNA damage response. Here, we have analyzed two additional chromatin-associated proteins. rtt109 encodes a histone acetyltransferase, and deletion of the gene in S. macrospora results in a phenotype similar to that of a {Delta}asf1 mutant, whereas chk2 is involved in different aspects of the DNA damage response, but not in development.

molecular biology↗

bioRxiv2023

The genome of the Wollemi pine, a critically endangered living fossil unchanged since the Cretaceous, reveals extensive ancient transposon activity.

We present the genome of the living fossil, Wollemia nobilis, a southern hemisphere conifer morphologically unchanged since the Cretaceous. Presumed extinct until rediscovery in 1994, the Wollemi pine is critically endangered with less than 60 wild adults threatened by intensifying bushfires in the Blue Mountains of Australia. The 12 Gb genome is among the most contiguous large plant genomes assembled, with extremely low heterozygosity and unusual abundance of DNA transposons. Reduced representation and genome re-sequencing of individuals confirms a relictual population since the last major glacial/drying period in Australia, 120 ky BP. Small RNA and methylome sequencing reveal conservation of ancient silencing mechanisms despite the presence of thousands of active and abundant transposons, including some transferred horizontally to conifers from arthropods in the Jurassic. A retrotransposon burst 8-6 my BP coincided with population decline, possibly as an adaptation enhancing epigenetic diversity. Wollemia, like other conifers, is susceptible to Phytophthora, and a suite of defense genes, similar to those in loblolly pine, are targeted for silencing by sRNAs in leaves. The genome provides insight into the earliest seed plants, while enabling conservation efforts.

genomics↗

bioRxiv2023

Three-dimensional chromatin organization promotes genome evolution in a fungal plant pathogen

The spatial organization of eukaryotic genomes is linked to their biological functions, although it is not clear how this impacts the overall evolution of a genome. Here, we uncover the three-dimensional (3D) genome organization of the phytopathogen Verticillium dahliae, known to possess distinct genomic regions, designated adaptive genomic regions (AGRs), enriched in transposable elements and genes that mediate host infection. Short-range DNA interactions form clear topologically associating domains (TADs) with gene-rich boundaries that show reduced levels of gene expression and reduced genomic variation. Intriguingly, TADs are less clearly structured in AGRs than in the core genome. At a global scale, the genome contains bipartite long-range interactions, particularly enriched for AGRs and more generally containing segmental duplications. Notably, the patterns observed for V. dahliae are also present in other Verticillium species. Thus, our analysis links 3D genome organization to evolutionary features conserved throughout the Verticillium genus.

microbiology↗

bioRxiv2023

Bioinformatics-Guided Discovery of Biaryl-Tailored Lasso Peptides

Lasso peptides are a class of ribosomally synthesized and post-translationally modified peptides (RiPPs) that feature an isopeptide bond and a distinct lariat fold. A growing number of secondary modifications have been described that further decorate lasso peptide scaffolds. Using genome mining, we have discovered a pair of lasso peptide biosynthetic gene clusters (BGCs) that include cytochrome P450 genes. Here, we report the structural characterization of two unique examples of (C-N) biaryl-containing lasso peptides. Nocapeptin A, from Nocardia terpenica, is tailored with Trp-Tyr crosslink while longipepetin A, from Longimycelium tulufanense, features Trp-Trp linkage. Besides the unusual bicyclic frame, longipepetin A receives an S-methylation by a new Met methyltransferase resulting in unprecedented sulfonium-bearing RiPP. Our bioinformatic survey revealed P450(s) and further maturating enzyme(s)-containing lasso BGCs awaiting future characterization.

biochemistry↗

bioRxiv2022

Neuroinflammation in neuronopathic Gaucher disease: Role of microglia and NK cells

BackgroundNeuronopathic Gaucher Disease (nGD) is a rare neurodegenerative disorder caused by biallelic mutations in Gba, and buildup of glycosphingolipids in lysosomes. Neuronal injury and cell death are prominent pathological features, however the role of Gba in individual cell types and involvement of microglia, blood derived macrophages and immune infiltrates in nGD pathology remains enigmatic. MethodsHere, using single cell resolution of mouse nGD brains, we found induction of neuroinflammation pathways involving microglia, NK cells, astrocytes, and neurons. ResultsTargeted rescue of Gba in microglia and in neurons, respectively in Gba deficient, nGD mice reversed the buildup of glucosylceramide (GlcCer) and glucosylsphingosine (GlcSph), concomitant with amelioration of neuroinflammation, reduced level of serum neurofilament light chain (Nf-L) and improved survival. The levels of bioactive lipid, GlcSph was strongly correlated with serum Nf-L and ApoE in nGD mouse models as well as GD patients. Gba rescue in microglia/macrophage compartment prolonged survival, that was further enhanced upon treatment with brain permeant inhibitor of glucosylceramide synthase, effects mediated via improved glycosphingolipid homeostasis and reversal of neuroinflammation involving activation of microglia, brain macrophages and NK cells. ConclusionsTogether, our study delineates individual cellular effects of Gba deficiency in nGD brains, highlighting the central role of neuroinflammation driven by microglia activation and the role of brain permeant small molecule glucosylceramide inhibitor in reversing complex multidimensional pathophysiology of nGD. Our findings advance disease biology whilst identifying compelling biomarkers of nGD to improve patient management, enrich clinical trials and illuminate therapeutic targets. FundingResearch grant from Sanofi Genzyme; other support includes R01NS110354.Yale Liver Center P30DK034989, pilot project grant.

immunology↗

bioRxiv2022

Deep Phenotyping and Lifetime Trajectories Reveal Limited Effects of Longevity Regulators on the Aging Process in C57BL/6J Mice

Current concepts regarding the biology of aging are based on studies aimed at identifying factors regulating natural lifespan. However, lifespan as a sole proxy measure for aging can be of limited value because it may be restricted by specific sets of pathologies, rather than by general physiological decline. Here, we employed large-scale phenotyping to analyze hundreds of phenotypes and thousands of molecular markers across tissues and organ systems in a single study of aging male C57BL/6J mice. For each phenotype, we established lifetime profiles to determine when age-dependent phenotypic change is first detectable relative to the young adult baseline. We examined central genetic and environmental lifespan regulators (putative anti-aging interventions, PAAIs; the following PAAIs were examined: mTOR loss-of-function, loss-of-function in growth hormone signaling, dietary restriction) for a possible countering of the signs and symptoms of aging. Importantly, in our study design, we included young treated groups of animals, subjected to PAAIs prior to the onset of detectable age-dependent phenotypic change. In parallel to our studies in mice, we assessed genetic variants for their effects on age-sensitive phenotypes in humans. We observed that, surprisingly, many PAAI effects influenced phenotypes long before the onset of detectable age-dependent changes, rather than altering the rate at which these phenotypes developed with age. Accordingly, this subset of PAAI effects does not reflect a targeting of age-dependent phenotypic change. Overall, our findings suggest that comprehensive phenotyping, including the controls built in our study, is critical for the investigation of PAAIs as it facilitates the proper interpretation of the mechanistic mode by which PAAIs influence biological aging. HighlightsO_LIPhenotyping at scale defines lifetime trajectories of age-dependent changes in C57BL/6J mice C_LIO_LICentral genetic and environmental lifespan regulators (putative anti-aging interventions; PAAIs) influence age-sensitive phenotypes (ASPs) often long before the appearance of age-dependent changes in these ASPs C_LIO_LICorresponding genetic variants in humans also have age-independent effects C_LIO_LIMany PAAI effects shift the baseline of ASPs rather than slowing their rate of change C_LI

physiology↗