Biology subjects

Richter, J.

Publications and source records attributed to Richter, J..

At least 19 recordsLinked to original sources

bioRxiv2026

TMEM55B promotes anterograde transport and distal axonal distribution of LAMP1-positive organelles

Lysosomal function throughout life is vital for the proper functioning and survival of post-mitotic neurons by mediating cellular signaling, degradation, and recycling processes. Their intracellular transport relies on microtubule-dependent mechanisms involving kinesin and dynein motors. While lysosomes were long thought absent from axons, recent studies have demonstrated the importance of LAMP1-positive endo-/lysosomal organelles in axonal compartments. This study investigates the physiological role of TMEM55B, a lysosomal membrane protein involved in lysosome positioning and motor coupling in neurons. TMEM55B is highly expressed in LAMP1-positive organelles in cortical neurons. We generated viable Tmem55b knockout mice that exhibited altered lysosomal positioning in neurons. Lysosomes clustered abnormally in the pre-axonal exclusion zone and the proximal axon, with many forming elongated tubular structures. Similarly, in primary rat neurons, TMEM55B depletion resulted in lysosomal tubulation and impaired bidirectional lysosomal transport, particularly in distal axon segments, without affecting lysosome velocity in the proximal and mid-axon. These transport defects were consistent with disrupted JIP4 function, a scaffold linking TMEM55B to both dynein and kinesin motors. TMEM55B deficiency did not result in neurodegeneration, behavioral deficits, or reduced lifespan in mice. As an orthogonal approach, we analyzed TMEM55B function in C. elegans. Worms lacking the TMEM55B homolog Y71H2AM.2 showed altered lysosomal dynamics in cholinergic neurons, supporting an evolutionarily conserved role. To test the involvement of TMEM55B's paralog, TMEM55A, in regulating neuronal lysosome positioning, we generated Tmem55a/b double-knockout mice, which exhibit impaired growth, premature death, and an overall aggravated phenotype. Collectively, our findings demonstrate that both TMEM55B and TMEM55A regulate lysosome distribution in neurons, particularly in axons, by influencing JIP4-dependent retro- and, notably, anterograde motor protein-mediated transport. This function is critical for spatial lysosomal homeostasis. Our study underscores the importance of TMEM55A/TMEM55B in regulating neuronal organelle dynamics and may be a factor considered in neurodegenerative diseases involving lysosomal trafficking defects.

cell biology↗

bioRxiv2026

A Scalable and Robust Workflow for Cost-Effective Post-Translational Modifications Profiling by Chemical Proteomics

Mass spectrometry-based chemical proteomics is a powerful method to analyze proteins labelled by small molecules to identify protein targets of active compounds and to profile protein post-translational modifications. The throughput and high protein input for chemical proteomics workflows has been often a limiting factor for application of the technology for specialized and difficult to culture cell lines. The high protein input was necessary to gain significant difference of noise to signal ratio in proteomics readout. Here, we describe a general chemical proteomics workflow, which is performed in 96-well plate and necessitate only 25 g of protein input to profile post-translationally modified proteins including abundant O-GlcNAcylated proteins as well as low abundant AMPylated proteins. The workflow integrates advances in Cu(I)-catalyzed azide-alkyne cycloaddition to minimize chemical side-reactivity of the click reaction and data-independent acquisition mode during LC-MS/MS measurement. An iterative optimization of protein clean-up on carboxylate-coated paramagnetic beads led to significant saving of the beads usage and lowers the unspecific protein background that resulted in sensitivity gain.

biochemistry↗

bioRxiv2026

Purinergic signaling promotes gliomagenesis through nuclear calcium transients

Intracellular Ca2+ transients drive key developmental and physiological processes, yet their role in oncogenesis remains incompletely understood. In glioblastoma (GBM), an aggressive brain malignancy, tumor cellular networks exhibit self-sustaining Ca2+ transients that promote tumor growth through unclear mechanisms. Using patient-derived GBM models, we show that these transients depend primarily on intracellular Ca2+ stores and extend to the nucleus to drive tumorigenesis. A neuromodulator screen identified extracellular purines ATP and ADP as potent inducers of both nuclear and cytosolic Ca2+ transients via activation of metabotropic purinergic P2RY1 receptors, whose knockdown attenuates tumorigenicity in vitro and in vivo. Mechanistically, Ca2+ transients promote tumorigenesis via the nuclear Ca2+/calmodulin-dependent kinase CAMK4, which regulates transcriptional and epigenetic programs, as well as ribosomal DNA transcription. From the therapeutic perspective, pharmacologic P2RY1 inhibition suppresses tumor growth in vitro and in vivo. Collectively, these findings reveal a pharmacologically targetable oncogenic mechanism in GBM and possibly other malignancies.

cancer biology↗

bioRxiv2025

Deep single-cell immune and signaling profiles predict long term therapy response in chronic myeloid leukemia within hours

Chronic myeloid leukemia (CML) is effectively treated with small molecule BCR::ABL1 tyrosine kinase inhibitors (TKIs) but like in all cancers, early identification of suboptimal- and non-responders is a challenge. Through mass cytometry analysis of peripheral blood leukocytes, we collected high-dimensional data from de novo chronic phase CML patients enrolled in two multicenter clinical trials (clinicaltrials.gov NCT01725204 and NCT01061177). In leukocytes, dasatinib and nilotinib inhibited intracellular signaling within one or three hours after first per oral dose, and each TKI had a unique signaling signature reflecting its kinase specificity profile beyond BCR::ABL1. An immune and signaling profile was constructed for each patient, predicting the treatment response (BCR::ABL1IS, %) the first 12 months of treatment. These results show that single cell immune and signaling profiles within hours of first dose can predict 12 months treatment response, anticipating future optimalization of kinase inhibitor treatment within days rather than months.

cancer biology↗

bioRxiv2025

A high-coverage genome from a 200,000-year-old Denisovan

Denisovans, an extinct sister group of Neandertals who lived in Eastern Eurasia during the Middle and Late Pleistocene, are known only from a handful of skeletal remains and limited genetic data, including the high-coverage genome of a woman who lived [~]65,000 years ago. Here, we present a second high-quality Denisovan genome, reconstructed from a molar found at Denisova Cave. It belonged to a man who lived [~]200,000 years ago in a small Denisovan group. This group mixed with early Neandertals and was then replaced by Denisovans who had mixed with later Neandertals. We show that in addition Denisovans received gene flow from hominins that diverged before the split of the ancestors of Denisovans and modern humans. The two Denisovan genomes allow us to disentangle Denisovan ancestry in present-day humans revealing contributions from at least three distinct Denisovan groups. In particular, Oceanians and South Asians independently inherited DNA from a deeply diverged Denisovan population which was likely isolated in South Asia. This supports an early migration of the ancestors of Oceanians through South Asia followed by the later arrival of the ancestors of present-day South Asians. East Asians do not share this Denisovan component in their genomes, suggesting that their ancestors arrived independently, perhaps by a northerly route. Finally, the two high-quality Denisovan genomes allow us to refine the catalogue of genetic changes that arose on the Denisovan lineage, some of which were contributed to present-day humans.

genomics↗

bioRxiv2025

Vibrational noise pollution in bee hives generated by railway traffic

Anthropogenic noise pollution has become a threat for the fauna with possible effects on animal physiology and behaviour. We explored the effects of anthropogenic vibrational noise on honey bees (Apis mellifera). The intensity of substrate borne vibrations generated by trains on the ground, on the front comb of a hive and on its base as well as the airborne sound pressure were recorded at different distances and sites. Vibrational noise of amplitudes that can be detected by honey bees is present on the ground surface, on the comb and on the base over distances up to 20 m from the railway track and the attenuation of the airborne sounds is higher than the attenuation of the substrate borne vibrations. Bees placed in an observational hive and exposed to simulated substrate borne vibrations caused by a cargo train show significant behavioural reactions. The same substrate borne vibration was presented to bee colonies every 5 minutes continuously for six months at realistic amplitudes. On the colony level no differences are found for capped and open worker brood, worker eggs, adult drone population, capped and open drone brood, brood development, varroa mites, collected pollen and honey production; while some significant differences are present for worker population and pollen collecting foragers. We conclude that honey bee colonies in the vicinity of railroads are exposed to substrate borne vibrational noise above their threshold of sensitivity up to 20 m. At the individual level bees show reactions to the vibrations; however, at the population level bees seem to cope with the disturbance. As higher amplitudes and additional stress factors might affect the colonies, it seems to be anyways advisable to generally avoid placing bee colonies close to anthropogenic vibrational noise sources.

animal behavior and cognition↗

bioRxiv2025

Spatiotemporal dynamics of cryptococcal infection reveal novel immune modulatory mechanisms and antifungal targets

The threat and incidence of fungal diseases are increasing, as is the severity and mortality rates associated with these infections. New strategies to combat fungal infections are urgently needed to overcome rising rates of resistance and the emergence of new pathogens. To promote invasion within a host, fungi use highly adapted and regulated virulence factors, and, in turn, the host adopts an active and dynamic immune response to suppress infection. Understanding the interplay between these processes is crucial to move fungal disease management and treatment forward and improve global health outcomes. Within the present study, we tackle these challenges using state-of-the-art mass spectrometry instrumentation to explore proteome remodeling during active infection of Cryptococcus neoformans at an unprecedented depth with spatiotemporal resolution. Our prioritization of three host organs (i.e., lungs, brain, spleen) critical to initiation, progression, and response of disease discovers tissue-specific remodeling across time. Within the lungs, we revealed early and sustained activation of the host immune response integrated with characterization of a promising new antifungal target, and we propose the discovery of a competitive inhibitor for functional target disruption. Within the brain, proteome remodeling aligns with disease progression, and we define a new mechanistic role for haptoglobin in fungal cell modulation, as well as showcasing an adaptive survival response of C. neoformans within an hypoxic environment. Within the spleen, we reveal new dynamics of immune system activation upon cryptococcal infection. Overall, we provide the deepest integrated view of cryptococcal disease dynamics across temporal and spatial scales, revealing unrecognized mechanisms of host immunity and fungal pathogenesis that offer new avenues for targeted therapeutic intervention and disease management.

microbiology↗

bioRxiv2025

Transcranial direct current stimulation over the frontal eye field has no effect on visual search performance

Top-down attention for the goal-directed (de-)prioritization of information is fundamental for successful everyday-life behavior and poses tremendous problems when negatively impacted by disease. Attention-targeting enhancement and rehabilitation attempts using non-invasive brain stimulation techniques like transcranial direct current stimulation (tDCS) are therefore of major importance. tDCS-driven excitation of the left frontal eye field (FEF; a key region within fronto-parietal attention networks) has recently been suggested to improve attention-guided visual search with stronger effects for lower baseline performers. Here, we report two preregistered tDCS experiments that tested 1) whether the previously observed visual search improvement could be boosted through stimulation over the allegedly more dominant right FEF and 2) whether tDCS-related visual search improvements might depend on search field size. To this end, in experiments one and two, N=29 and N=31 healthy participants performed a visual search task, in which they searched for an upside-down T amongst upright Ts and Ls within small or large search fields, before and during the application of anodal (excitatory) or sham (control) tDCS over the right or left FEF, respectively. In contrast to previous studies, in both experiments (i.e., independent of stimulation site and search field size) we found neither tDCS-specific (anodal > sham) visual search improvements, nor stimulation-specific baseline dependencies (larger improvements for lower baseline performers were observed in both tDCS conditions, suggesting rather stimulation-unspecific effects like regression to the mean). Together, our results provide evidence against reliable top-down attention-guided visual search improvements through FEF tDCS.

neuroscience↗

bioRxiv2025

Whole blood proteome dynamics defines predictive diagnostic and prognostic signatures of cryptococcal infection

Across the globe, fungi are impacting the lives of millions of people through the development of infections ranging from superficial to systemic with limited treatment options. To effectively combat fungal disease, rapid and reliable diagnostic methods are required, including current methodologies using antigen detection, culturing, microscopy, and molecular tools. However, the flexibility of these platforms to diagnose infection using non-invasive methods and predict the outcome of disease are limited. In this study, we apply state-of-the-art mass spectrometry-based proteomics to perform dual perspective (i.e., host and pathogen) profiling of cryptococcal infection. Whole blood collected over a temporal scale following murine model challenged with the human fungal pathogen, Cryptococcus neoformans, detected >3,000 host proteins and 160 fungal proteins. From the host perspective, temporal regulation of known immune-associated proteins, including eosinophil peroxidase and lipocalin-2, along with suppression of lipoproteins, demonstrated infection- and time-dependent host remodeling. Conversely, from the pathogen perspective, known and putative virulence-associated proteins were detected, including proteins associated with fungal extracellular vesicles and host immune modulation. We also observed and validated a new mechanism of immune system response to C. neoformans through modulation of haptoglobin. Further, we assessed the predictive power of dual perspective proteome profiling toward prognostics of cryptococcal infection and report a previously undisclosed integration among virulence factor production, immune system modulation, and individual model survival. Together, our findings pose novel biomarkers of cryptococcal infection from whole blood and highlight the potential of personal proteome profiles to determine the prognosis of cryptococcal infection, a new parameter in fungal disease management.

microbiology↗

bioRxiv2024

Amyloid Beta Precursor Protein contributes to brain aging and learning decline in short-lived turquoise killifish (Nothobranchius furzeri)

Brain aging is a key risk factor for many neurodegenerative diseases, yet its molecular and cellular mechanisms remain elusive. Amyloid-beta precursor protein (APP) is among the most studied proteins linked to brain pathology; however, its role in non-pathological brain aging remains poorly characterized. Here, we investigate the natural impact of APP on normal brain aging using the short-lived turquoise killifish (Nothobranchius furzeri), which exhibits rapid and spontaneous age-related decline. We found that a pyroglutamated APP derivative (APPpE11) accumulates intra-neuronally in an age-dependent manner, co-localizing with a marker of cell death. We found that intraneuronal APPpE11 is also present in brains from healthy elderly humans, suggesting deep evolutionary conservation. To determine APPs role in spontaneous brain aging, we knock-out "amyloid precursor protein a" (appa) in killifish via CRISPR/Cas9. The lack of appa mitigated brain aging from a proteome-wide perspective, reduced age-related cell death and inflammation, and improved neuronal activity and learning capacity in aged individuals. Our findings show an ancestral and previously unrecognized role of amyloid-beta precursor protein in non-pathological brain aging, making it an ideal target for anti-aging interventions.

neuroscience↗

bioRxiv2024

Refined Enterotyping Reveals Dysbiosis in Global Fecal Metagenomes

BackgroundEnterotypes describe human fecal microbiomes grouped by similarity into clusters of microbial community composition, often associated with disease, medications, diet, and lifestyle. Numbers and determinants of enterotypes have been derived by diverse frameworks and applied to cohorts that often lack diversity or inter-cohort comparability. ResultsTo overcome these limitations, we selected 16,772 fecal metagenomes collected from 38 countries to revisit the enterotypes using state-of-the-art fuzzy clustering and found robust clustering regardless of underlying taxonomy, consistent with previous findings. Quantifying the strength of enterotype classifications enriched the enterotype landscape, also reflecting some continuity of microbial compositions. As the classification strength was associated with the patients health status, we established an "Enterotype Dysbiosis Score" (EDS) as a latent covariate for various diseases. ConclusionThis global study confirms the enterotypes, reveals a dysbiosis signal within the enterotype landscape, and enables robust classification of metagenomes with an online "Enterotyper" tool, allowing reproducible analysis in future studies. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=79 SRC="FIGDIR/small/607711v3_ufig1.gif" ALT="Figure 1"> View larger version (30K): org.highwire.dtl.DTLVardef@1611a2org.highwire.dtl.DTLVardef@dfbb57org.highwire.dtl.DTLVardef@848ac0org.highwire.dtl.DTLVardef@1b15808_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2023

Single cell multi-omics analysis of chronic myeloid leukemia links cellular heterogeneity to therapy response

The advent of tyrosine kinase inhibitors (TKIs) as treatment of chronic myeloid leukemia (CML) is a paradigm in molecularly targeted cancer therapy. Nonetheless, TKI insensitive leukemia stem cells (LSCs) persist in most patients even after years of treatment. The sustained presence, heterogeneity and evolvability of LSCs are imperative for disease progression as well as recurrence during treatment-free remission (TFR). However, dynamic changes among LSC sub-populations upon TKI therapy impede their measurement and targeting. Here, we used cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq) to generate high-resolution single cell multiomics maps from CML patients at diagnosis, retrospectively stratified by BCR::ABL1IS (%) following 12 months of TKI therapy as per European LeukemiaNet (ELN) recommendations. Simultaneous measurement of global gene expression profiles together with >40 surface markers from the same cells revealed that each patient harbored a unique composition of stem and progenitor cells at diagnosis demonstrating that cellular heterogeneity is a hallmark of CML. The patients with treatment failure after 12 months of therapy had markedly higher abundance of molecularly defined primitive cells at diagnosis compared to the optimal responders. Furthermore, deconvolution of an independent dataset of CML patient-derived bulk transcriptomes (n=59) into constituent cell populations showed that the proportion of primitive cells versus lineage primed sub-populations significantly connected with the TKI-treatment outcome. The multiomic feature landscape enabled visualization of the primitive fraction as a heterogenous mixture of molecularly distinct Lin-CD34+CD38-/low BCR::ABL1+ LSCs and BCR::ABL1- hematopoietic stem cells (HSCs) in variable ratio across patients and guided their prospective isolation by a combination of CD26 and CD35 cell surface markers. We for the first time show that BCR::ABL1+ LSCs and BCR::ABL1- HSCs can be distinctly separated as CD26+CD35- and CD26-CD35+ respectively. In addition, we found the relative proportion of CD26-CD35+ HSCs to be higher in optimal responders when compared to treatment failures, at diagnosis as well as following 3 months of TKI therapy, and that the LSC/HSC ratio was increased in patients with prospective treatment failure. Collectively, the patient-specific cellular heterogeneity multiomics maps build a framework towards understanding therapy response and adapting treatment by devising strategies that either extinguish TKI-insensitive LSCs or engage the immune effectors to suppress the residual leukemogenic cells.

cancer biology↗

bioRxiv2021

Bacterial growth, communication and guided chemotaxis in 3D bioprinted hydrogel environments

Bioprinting of engineered bacteria is of great interest for applications of synthetic biology in the context of living biomaterials, but so far only few viable approaches are available for the printing of gels hosting live Escherichia coli bacteria. Here we develop a gentle bioprinting method based on an alginate/agarose bioink that enables precise printing of E.coli into three-dimensional hydrogel structures up to 10 mm in height. Addition of a calcium peroxide-based oxygen generation system enables maturation of fluorescent proteins deep within the printed structures. We utilize spatial patterning with the bioprinter to control different types of chemical interaction between bacteria. We first show quorum sensing-based chemical communication between engineered sender and receiver bacteria placed at different positions inside the bioprint, and then demonstrate the fabrication of barrier structures defined by non-motile bacteria that can guide the movement of chemotactic bacteria inside a gel.

bioengineering↗

bioRxiv2021

In depth analysis of Cyprus-specific mutations of SARS-CoV-2 strains using computational approaches

This study aims to characterize SARS-CoV-2 mutations which are primarily prevalent in the Cypriot population. Moreover, using computational approaches, we assess whether these mutations are associated with changes in viral virulence. We utilize genetic data from 144 sequences of SARS-CoV-2 strains from the Cypriot population obtained between March 2020 and January 2021, as well as all data available from GISAID. We combine this with countries regional information, such as deaths and cases per million, as well as COVID-19-related public health austerity measure response times. Initial indications of selective advantage of Cyprus-specific mutations are obtained by mutation tracking analysis. This entails calculating specific mutation frequencies within the Cypriot population and comparing these with their prevalence world-wide throughout the course of the pandemic. We further make use of linear regression models to extrapolate additional information that may be missed through standard statistical analysis. We report a single mutation found in the ORF1ab gene (S6059F) that appears to be significantly enriched within the Cypriot population. We further analyse this mutation using regression models to investigate possible associations with increased deaths and cases per million. Moreover, protein structure prediction tools show that the mutation infers a conformational change to the protein that significantly alters its structure when compared to the reference protein. Investigating Cyprus-specific mutations for SARS-CoV-2 can not only lead to important findings from which to battle the pandemic on a national level, but also provide insights into viral virulence worldwide.

bioinformatics↗

bioRxiv2020

Patient Similarity Network of Newly Diagnosed Multiple Myeloma Identifies Patient Sub-groups with Distinct Genetic Features and Clinical Implications

The remarkable genetic heterogeneity of Multiple Myeloma (MM) poses a significant challenge for proper prognostication and clinical management of patients. Accurate dissection of the genetic and molecular landscape of the disease and the robust identification of homogeneous classes of patients are essential steps to reliable risk stratification and the development of novel precision medicine strategies. Here we introduce MM-PSN, the first multi-omics Patient Similarity Network of newly diagnosed MM. MM-PSN has enabled the identification of three broad patient groups and twelve distinct sub-groups defined by five data types generated from genomic and transcriptomic patient profiling of 655 patients. The MM-PSN classification uncovered novel associations between distinct MM hallmarks with significant prognostic implications and allowed further refinement of risk stratification. Our analysis revealed that gain of 1q is the most important single lesion conferring high risk of relapse, and its association with an MMSET translocation is the most significant determinant of poor outcome. We developed a classifier and validated these results in an independent dataset of 559 pts. Our findings suggest that gain of 1q should be incorporated in routine staging systems and risk assessment tools. The MM-PSN classifier is available as a free resource to allow for an easy implementation in most clinical settings.

cancer biology↗

bioRxiv2020

Prophage exotoxins enhance colonization fitness in epidemic scarlet fever-causing Streptococcus pyogenes

The re-emergence of scarlet fever poses a new global public health threat. The capacity of North-East Asian serotype M12 (emm12) Streptococcus pyogenes (group A Streptococcus, GAS) to cause scarlet fever has been linked epidemiologically to the presence of novel prophages, including prophage {Phi}HKU.vir encoding the secreted superantigens SSA and SpeC and the DNase Spd1. Here we report the comprehensive molecular characterization of {Phi}HKU.vir-encoded exotoxins. We demonstrate that streptolysin O (SLO)-induced glutathione efflux from host cellular stores is a previously unappreciated GAS virulence mechanism that promotes SSA release and activity, representing the first description of a thiol-activated bacterial superantigen. Spd1 is required for optimal growth in human blood, confers resistance to neutrophil killing, and degrades neutrophil extracellular traps (NETs). Investigating single, double and triple isogenic knockout mutants of the {Phi}HKU.vir-encoded exotoxins, we find that SpeC and Spd1 act synergistically to facilitate nasopharyngeal colonization in a mouse model. These results offer insight into the etiology and pathogenesis of scarlet fever-causing GAS mediated by phage {Phi}HKU.vir exotoxins.

microbiology↗

bioRxiv2019

FMRP Control of Ribosome Translocation Promotes Chromatin Modifications and Alternative Splicing of Neuronal Genes Linked to Autism

Silencing of FMR1 and loss of its gene product FMRP results in Fragile X Syndrome. FMRP binds brain mRNAs and inhibits polypeptide elongation. Using ribosome profiling of the hippocampus, we find that ribosome footprint levels in Fmr1-deficient tissue mostly reflect changes in RNA abundance. Profiling over a time course of ribosome runoff in wildtype tissue reveals a wide range of ribosome translocation rates; on many mRNAs, the ribosomes are stalled. Sucrose gradient ultracentrifugation of hippocampal slices after ribosome runoff reveals that FMRP co-sediments with stalled ribosomes; and its loss results in decline of ribosome stalling on specific mRNAs. One such mRNA encodes SETD2, a lysine methyltransferase that catalyzes H3K36me3. ChIP-Seq demonstrates that loss of FMRP alters the deployment of this epigenetic mark on chromatin. H3K36me3 is associated with alternative pre-RNA processing, which we find occurs in an FMRP-dependent manner on transcripts linked to neural function and autism spectrum disorders. Highlights- Loss of FMRP results in decline of ribosome stalling on specific mRNAs (eg., SETD2) - Increased SETD2 protein levels alter H3K36me3 marks in FMRP deficient hippocampus - Genome-wide changes in mRNA alternative splicing occur in FMRP deficient hippocampus - H3K36me3 marks and alternative splicing changes occur on transcripts linked to autism

neuroscience↗

bioRxiv2019

Genetic Rescue of Fragile X Syndrome Links FMRP Deficiency to Codon Optimality-Dependent RNA Destabilization

Fragile X syndrome (FXS) is caused by inactivation of the FMR1 gene and loss of encoded FMRP, an RNA binding protein that represses translation of some of its target transcripts. Here we use ribosome profiling and RNA-seq to investigate the dysregulation of translation in the mouse brain cortex. We find that most changes in ribosome occupancy on hundreds of mRNAs are largely driven by dysregulation in transcript abundance. Many downregulated mRNAs, which are mostly responsible for neuronal and synaptic functions, are highly enriched for FMRP binding targets. RNA metabolic labeling demonstrates that in FMRP-deficient cortical neurons, mRNA downregulation is caused by elevated degradation, and is correlated with codon optimality. Moreover, FMRP preferentially binds mRNAs with optimal codons, suggesting that it stabilizes such transcripts through direct interactions via the translational machinery. Finally, we show that the paradigm of genetic rescue of FXS-like phenotypes in FMRP-deficient mice by deletion of the Cpeb1 gene is mediated by restoration of steady state RNA levels and consequent rebalancing of translational homeostasis. Our data establish an essential role of FMRP in codon optimality-dependent mRNA stability as an important factor in FXS.

molecular biology↗