Biology subjects

Schneider, B.

Publications and source records attributed to Schneider, B..

At least 19 recordsLinked to original sources

bioRxiv2026

mRNA deep sequencing profiling and integrative miRNA-mRNA network analysis in pediatric Burkitt leukemia and lymphoma

Background: Although the genomic alterations in Burkitt leukemia and lymphoma (BL) have been extensively studied, data on genome-wide dysregulation of messenger RNA (mRNA) and microRNA (miRNA) in Burkitt leukemia (BuAL) and Burkitt lymphoma (BuLY) are scarce. The aim of this study was to analyze mRNA and miRNA expression profiles in pediatric BuAL/BuLY to identify dysregulated mRNA-miRNA networks. Methods: Total RNA from fresh tumor samples of 13 pediatric BL patients (BuAL n=7, BuLY n=6) and 4 pediatric normal control lymphoid tissue (NCLT) samples was included for mRNA-deep sequencing and miRNA-microarrays studies. Differential expression (DE) analysis of mRNAs and miRNAs as well as gene set and functional enrichment analysis were performed. The multiMiR R package was used to identify the validated target genes for the dysregulated miRNAs. miRNA-mRNA target interaction analysis was performed combining DE, validated targets observed among the inverse-significant miRNA-mRNA correlations, with evidence statistics retained (p[≤]-0.5 and Benjamini-Hochberg (BH) -adjusted correlation p-value< 0.05). Results: BL showed 1965 DE genes (DEG) compared to NCLT (1214 upregulated, 751 downregulated) (p-adj<0.05, log2FC>0.5) and 11 DE miRNAs (three upregulated and eight downregulated) (FC>1.5, p-adj<0.05). The transcriptional differences observed between BL and normal lymphoid tissue inferred by functional enrichment analysis identified along a MYC-driven proliferative backbone with strong E2F4 and MYB pathway activity, activation of the MAPK, PI3K and the G2/M checkpoint signaling pathways and repression of the JAK-STAT, NFkB, TP53, TRAIL and hypoxia pathways (p-adj<0.05). Functional enrichment analysis highlighted an upregulation of proliferative and metabolic pathways accompanied by an attenuated inflammatory and immunosurveillance signaling in BL compared to NCLT. Correlated miRNA-mRNA expression analysis identified DE dysregulated miRNAs and their validated target genes. DE downregulated miRNAs (hsa-miR-150-5p, hsa-miR-342-3p and hsa-miR-450-5p, among others) inversely correlated with upregulated mRNA targets showing pathway enrichment related to transcriptional activity and nuclear organization modules. mRNA targets of DE upregulated miRNAs (hsa-miR-106a-5p, hsa-miR-17-5p and hsa-miR-7-5p) were enriched in downregulated pathways related to immune response processes. Conclusions: Overall, this pilot study provides new insights on key proliferative, metabolic and cytokine-mediated immune signaling pathways in BL and highlights miRNA-mRNA networks influencing transcriptional activity and immune surveillance, paving the way for experimental validation models.

cancer biology↗

bioRxiv2026

Neurobiological alterations and autism-like phenotype in mice following regulatory-limit exposure to fungicides in drinking water

Neurodevelopmental conditions, including attention deficit hyperactivity disorder (ADHD) and autism spectrum disorders (ASD), have increased markedly over recent decades. This rise parallels the widespread use of agrochemicals, suggesting a contribution of environmental exposures. We hypothesize that pesticide residues may disrupt brain development and promote neurodevelopmental disorders. Here, we test whether concentrations permitted in drinking water affect brain development using a maternal exposure model in wild-type mice. Exposure to a fungicide mixture at 0.3 g/L, below the current European regulatory limit of 0.5 g/L, impairs corticogenesis and is associated with alterations in synaptic function and glutamatergic signaling. Offspring exhibit delays in sensory development, reduced social interactions, and increased stereotyped behaviors. We identify the adenosine A2A receptor as a molecular target of anilinopyrimidine fungicides. Together, these findings indicate that low-dose exposure to this fungicide mixture can induce an autism spectrum-like phenotype in the offspring.

neuroscience↗

bioRxiv2026

Scanning DIA on the ZenoTOF 8600 system enables ultra-sensitive and quantitative proteomics from single cells to post-translational modifications in a compact platform

Mass spectrometry-based proteomics increasingly demands platforms that combine quantitative rigor with the discovery capabilities of accurate mass systems. Here we present the ZenoTOF 8600 system, a compact mass spectrometry system that integrates enhanced ion capture and transmission optics with an optical detection system, Zeno trap-enhanced MS/MS, electron-activated dissociation, and scanning quadrupole data-independent acquisition (ZT Scan DIA). We show that ZT Scan DIA outperforms conventional variable-window DIA (Zeno SWATH DIA) in both identifications and quantitative reproducibility, and demonstrate the platforms versatility across proteomics applications: thousands of protein groups from bulk samples at up to 500 samples per day, single-cell proteomics yielding up to 4,700 proteins, accurate ratio recovery in mixed-species quantitative benchmarks, low-attomole targeted quantitation, and detection of disease-relevant phosphorylation in a Parkinsons disease cellular model using complementary CID and EAD fragmentation. The instruments compact footprint makes it attractive for settings where both analytical breadth and operational robustness are required.

biophysics↗

bioRxiv2025

Age-Related Differences in the Lexical Priming Effect Can Be Predominantly Attributed to Differences in Response Bias

Age-related declines in visual perception challenge older adults ability to locate and identify objects in noisy (e.g., fog, glare, inadequate lighting) or cluttered visual environments. To compensate, older adults often increase reliance on contextual information, which could be helpful, but may also lead to increased risk for "false seeing" - reporting expected objects based on contextual information rather than those actually presented - a phenomenon that Jacoby et al., (2012) observed in older adults under challenging viewing conditions. However, it remains unaddressed whether such false seeing is driven by older adults elevated tendency to rely on context, or by age-related declines in visual perceptual processes. The current study addressed this issue by examining the lexical priming effects in 18 younger and 18 older adults (M = 21.4 years; M = 76.2 years) in Experiment 1, and 13 younger and 13 older adults (M = 21.2 years; M = 74.8 years) in Experiment 2 using a two-alternative, forced-choice (2AFC) paradigm, while controlling for age-related perceptual differences. On each trial, participants identified a visually degraded target word preceded by an identical, semantically related, or unrelated prime. We applied Signal Detection Theory to isolate perceptual sensitivity (d) and response bias (c). Results revealed that once stimulus parameters were adjusted to eliminate age-differences in performance when the prime was unrelated to the target, age-related differences in target identification in the related priming conditions were predominantly driven by age-related differences in response bias rather than in any residual age-differences in perceptual sensitivity. Public Significance StatementTo compensate for age-related losses in visual processes, older adults tend to rely more on the overall context provided by the visual scene to identify individual objects than do younger adults. Using a word priming task, our study found that older adults use of supporting context to correctly identify target words masked by visual noise persisted even when overall word identification performance (correctly identifying words independent of whether the context was supporting or misleading) was equated for both age groups. Understanding such age-relate differences in visual perception can inform interventions that would support older adults visual processing in daily perceptually challenging environments.

neuroscience↗

bioRxiv2025

A broken power-law model of heart rate variability spectra in sleep

AimsThe aim of the study was to introduce a parametric description of RR-interval spectra using a broken power-law model, in addition to the parametrization of oscillatory peaks. Furthermore, to use this model to evaluate effects of age, sex and sleep architecture on overnight heart rate variability (HRV) in healthy subjects. Methods & ResultsFrom a polysomnography database, 215 whole-night, high quality electrocardiograms (ECGs) were extracted. The fractal and oscillatory power-spectral densities (PSDs) were calculated from evenly resampled RR-interval time-series, then a broken power-law model was fitted using piecewise linear regression to the double-logarithmic PSD, determining a custom breaking point in the fractal component, and allowing for two independent spectral slopes in the lower and higher frequency domains. The two-slope model provided a more optimal description compared to linear regression in all cases, even when penalizing increased model complexity. Peak detection was applied to the oscillatory component in the LF (0.04-0.15 Hz) and HF (0.15-0.4 Hz) bands, extracting the frequency and prominence of the dominant peak from each. The high frequency domain intercept, the breaking point frequency and the LF peak frequency decreased significantly with age. Both slopes were flatter in females, while the high domain intercept and the HF peak prominence was significantly increased. Waking after sleep onset and lightest sleep (N1) were associated with lower intercept values, while REM sleep had an opposite effect. ConclusionsThe broken power-law model proved to be more appropriate for the description of RR-interval spectra than the single-slope model, and also captured effects of age, sex and sleep structure that were corroborated by the literature. We would like to highlight that while HRV changes are often assumed to be of oscillatory origin, the fractal component has a major contribution to the total PSD, and thus to all measures derived from it.

physiology↗

bioRxiv2025

Spectral features of heart rate variability in Williams syndrome during sleep

AimsThe study aims to reveal the spectral alterations of heart rate variability (HRV) in Williams syndrome (WS) during sleep, using a two-slope, broken power-law model, taking into account the multi-fractal properties of the RR-interval spectra, including effects of aging and associations with sleep structure indicators. Methods & ResultsExtracting ECG recordings from a polysomnography database of 20 subjects with WS and 20 age and sex matched typically developing (TD) controls, RR-interval time series were constructed, then the fractal and oscillatory power-spectral densities computed using the Irregular-Resampling Auto-Spectral Analysis (IRASA) method. The fractal component was parametrized with a piecewise-linear function, that allowed for a custom breaking point in the power spectral density (PSD), and separate slope and intercept values in the lower and higher frequency domains. The frequency and prominence of the dominant peak was extracted from the LF (0.04-0.15 Hz) and HF (0.15-0.4 Hz) bands. Strong WS vs TD group differences were found in the frequency of the breaking point, high domain slope, intercept and HF peak prominence. Analysis of the LF peak frequency revealed age-dependent decrease in the TD, but not in the WS group, while generally decreased values in WS independent of age, potentially reflected accelerated aging, characteristic of the syndrome. As fractal parameters were correlated, a main component was identified using principal component analysis that described the typical alterations in the fractal spectrum in WS, and was correlated with sleep structure indices as well. ConclusionsThe broken power-law model proved to be successful in characterizing the fractal component of HRV spectra, furthermore it captured alterations in cardiac regulation in WS. A main spectral feature of WS was identified in the fractal component, being associated with sleep quality indicators, a possible biomarker of the degree of general autonomic deregulation inherent to the syndrome.

physiology↗

bioRxiv2025

Gene therapy-mediated overexpression of wild-type MFN2 improves Charcot-Marie-Tooth disease type 2A

Charcot-Marie-Tooth disease type 2A (CMT2A) is the most common axonal CMT and is associated with an early onset and severe motor-dominant phenotype. CMT2A is mainly caused by dominant mutations in the MFN2 gene, encoding Mitofusin-2, a GTPase located in the outer membrane of the mitochondria and endoplasmic reticulum (ER). Mutations in MFN2 are known to affect mitochondrial dynamics. We previously demonstrated that the mutated MFN2Arg94Gln further disrupts contacts between the ER and the mitochondria, leading to progressive axonal degeneration. There is no effective therapeutic approach to slow or reverse the progression of CMT2A, and treatments currently under development primarily focus on restoring mitochondrial function. Here, we provide proof-of-concept that neuronal overexpression of wild-type MFN2 (MFN2WT) provides therapeutic benefit in transgenic CMT2A mice carrying the mutated MFN2Arg94Gln. Intrathecal delivery of an AAV9 vector expressing MFN2WT effectively targets motor and sensory neurons, restoring ER-mitochondria contacts and mitochondrial morphology, thereby preserving both neuromuscular junction integrity and motor function. Strikingly, therapeutic efficacy is also achieved following vector injection after the onset of symptoms, rescuing the molecular hallmarks of CMT2A pathology and reversing locomotor. Notably, AAV administration was well tolerated, with no evidence neither of hepatotoxicity nor dorsal root ganglion inflammation. These results establish that boosting MFN2s levels using gene therapy is a promising therapeutic avenue for CMT2A.

neuroscience↗

bioRxiv2024

Light-dependent flavin redox and adduct states control the conformation and DNA binding activity of the transcription factor EL222

The activity of the transcription factor EL222 is regulated through protein-chromophore adduct formation, interdomain dynamics, oligomerization and protein-DNA interactions, all triggered by photo-excitation of its flavin mononucleotide (FMN) cofactor. To gain molecular-level insight into the photocycle of EL222, we applied complementary methods: macromolecular X-ray crystallography (MX), nuclear magnetic resonance (NMR) spectroscopy, optical spectroscopies (infrared and UV/visible), molecular dynamics/metadynamics (MD/metaD) simulations, and protein engineering using non-canonical amino acids. The observation of only subtle atomic displacements between crystal structures of EL222 with and without blue-light back-illumination, was confirmed by NMR data indicating no major changes in secondary structure and fold compactness. Kinetic experiments in solution provided evidence for two distinct EL222 conformations (lit1 and lit2) that become sequentially populated under illumination. These two lit states were assigned to covalently-bound N5 protonated, and non-covalently-bound hydroquinone forms of FMN, respectively. Molecular modeling revealed differential dynamics and domain separation times arising from the three FMN states (oxidized, adduct, and reduced). Furthermore, while the dark state is largely monomeric, both lit states undergo slow monomer-dimer exchange. The photoinduced loss of -helicity, seen by infrared difference spectroscopy, was ascribed to dimeric EL222 species. Unexpectedly, NMR revealed that all three EL222 species (dark, lit1, lit2) can associate with DNA to some extent, but only under illumination a high population of stable complexes is obtained. Overall, we propose a refined model of EL222 photo-activation where photoinduced changes in the oxidation state of FMN and thioadduct formation shift the population equilibrium towards an open conformation that favors self-association and DNA-binding. Significance StatementFlavin-binding light-oxygen-voltage (LOV) proteins constitute a prominent example of highly evolved chromophore-containing proteins that convert light into biochemical changes in the cell. However, it is not well understood how blue-light orchestrates changes in LOV structure and function. Here we show that the dynamics, oligomerization and DNA-binding properties of the photocontrolled transcription factor EL222 are dependent on both the flavin redox state and thioadduct formation. In the dark, monomeric EL222 forms transient encounter complexes with DNA. Under illumination, two distinct lit states are sequentially generated, termed lit1 and lit2, that are both able to assemble into EL222:DNA (2:1) complexes. Our results reveal the coupling between flavin photochemistry (protonation and covalent linkage) and fold stability in EL222 and potentially other flavoproteins.

biochemistry↗

bioRxiv2024

A Differential Ion Mobility Acoustic Ejection Mass Spectrometer System for Screening Isomerization-Mediating Enzyme Drug Targets

We report the first implementation of ion mobility mass spectrometry combined with an ultra-high throughput sample introduction technology for high throughput screening (HTS). The system integrates differential ion mobility (DMS) with acoustic ejection mass spectrometry (AEMS), termed DAEMS, enabling the simultaneous quantitation of structural isomers that are the sub-strates and products of isomerase mediated reactions in intermediary metabolism. We demonstrate this potential by comparing DAEMS to a luminescence assay for the isoform of phosphoglycerate mutase (iPGM) distinctively present in pathogens offering an opportunity as a drug target for a variety of microbial and parasite borne diseases. The metabolome consists of many structural isomers that require for separation a mobility resolving power of more than 300. Resolving powers measured in collision cross section space of 1588 and 1948 for 2- and 3-phosphoglycerate and the citrate/isocitrate isomeric pairs respectively are shown. These are the highest reported ion mobility resolving powers for molecules from the metabolome reported to date. The potential for DAEMS as a generalized screening tool is demonstrated with the separation of the substrates and products of two additional isomerases that present as potential therapeutic targets, chorismate mutase and triosephosphate isomerase. The separations are achieved at speeds compatible with the sample introduction rates of AEMS providing sufficient data points to integrate the peaks for quantitation without the use of internal standards. DMS hyphenated with acoustic sample ejection MS provides a unique solution to high throughput mass spectrom-etry applications where isomer and other types of separations are required.

biochemistry↗

bioRxiv2023

Fractal cycles of sleep: a new aperiodic activity-based definition of sleep cycles

Nocturnal human sleep consists of 4 - 6 ninety-minute cycles defined as episodes of non-rapid eye movement (non-REM) sleep followed by an episode of REM sleep. While sleep cycles are considered fundamental components of sleep, their functional significance largely remains unclear. One of the reasons for a lack of research progress in this field is the absence of a data-driven definition of sleep cycles. Here, we proposed to base such a definition on fractal (aperiodic) neural activity, a well-established marker of arousal and sleep stages. We explored temporal dynamics of fractal activity during nocturnal sleep using electroencephalography. Based on the observed pattern of fractal fluctuations, we introduced a new concept of fractal activity-based cycles of sleep or "fractal cycles" for short, defined as a time interval during which fractal activity descends from its local maximum to its local minimum and then leads back to the next local maximum. Next, we assessed correlations between fractal and classical (i.e., non-REM - REM) sleep cycle durations. We also studied cycles with skipped REM sleep, i.e., the cycles where the REM phase is expected to appear except that it does not, being replaced by lightening of sleep. Regarding the sample, we examined fractal cycles in healthy adults (age range: 18 - 75 years, n = 205) as well as in children and adolescents (range: 8 - 17 years, n = 21), the group characterized by deeper sleep and a higher frequency of cycles with skipped REM sleep. Further, we studied fractal cycles in major depressive disorder (n = 111), the condition characterized by altered REM sleep (in addition to its clinical symptoms). We found that fractal and classical cycle durations (89 {+/-} 34 min vs 90 {+/-} 25 min) correlated positively (r = 0.5, p < 0.001). Cycle-to-cycle overnight dynamics showed an inverted U-shape of both fractal and classical cycle durations and a gradual decrease in absolute amplitudes of the fractal descents and ascents from early to late cycles. In adults, the fractal cycle duration and participants age correlated negatively (r = -0.2, p = 0.006). Children and adolescents had shorter fractal cycles compared to young adults (76 {+/-} 34 vs 94 {+/-} 32 min, p < 0.001). The fractal cycle algorithm detected cycles with skipped REM sleep in 91 - 98% of cases. Medicated patients with depression showed longer fractal cycles compared to their own unmedicated state (107 {+/-} 51 min vs 92 {+/-} 38 min, p < 0.001) and age-matched controls (104 {+/-} 49 vs 88 {+/-} 31 min, p < 0.001). In conclusion, fractal cycles are an objective, quantifiable, continuous and biologically plausible way to display sleep neural activity and its cycles. They are useful in healthy adult and pediatric populations as well as in patients with major depressive disorder. Fractal cycles should be extensively studied to advance theoretical research on sleep structure. Highlights- Fractal activity-based cycles of sleep or "fractal cycles" for short is a new concept based on cyclic changes in fractal (aperiodic) neural activity during sleep. - Durations of fractal and classical cycles correlate, and both show an inverted U-shape when seen from early to late cycles. - The fractal cycle algorithm is effective in detecting cycles with skipped REM sleep. - Older healthy adults shower shorter fractal - but not classical - cycle durations. - Fractal cycle duration is shorter in children and adolescents compared to young adults. - In major depressive disorder, antidepressant medication is associated with longer fractal cycles.

neuroscience↗

bioRxiv2023

The Tabulae Paralytica: Multimodal single-cell and spatial atlases of spinal cord injury

Here, we introduce the Tabulae Paralytica--a compilation of four atlases of spinal cord injury (SCI) comprising a single-nucleus transcriptome atlas of half a million cells; a multiome atlas pairing transcriptomic and epigenomic measurements within the same nuclei; and two spatial transcriptomic atlases of the injured spinal cord spanning four spatial and temporal dimensions. We integrated these atlases into a common framework to dissect the molecular logic that governs the responses to injury within the spinal cord. The Tabulae Paralytica exposed new biological principles that dictate the consequences of SCI, including conserved and divergent neuronal responses to injury; the priming of specific neuronal subpopulations to become circuit-reorganizing neurons after injury; an inherent trade-off between neuronal stress responses and the activation of circuit reorganization programs; the necessity of reestablishing a tripartite neuroprotective barrier between immune-privileged and extra-neural environments after SCI; and a catastrophic failure to form this barrier in old mice. We leveraged the Tabulae Paralytica to develop a rejuvenative gene therapy that reestablished this tripartite barrier, and restored the natural recovery of walking after paralysis in old mice. The Tabulae Paralytica provides an unprecedented window into the pathobiology of SCI, while establishing a framework for integrating multimodal, genome-scale measurements in four dimensions to study biology and medicine.

genomics↗

bioRxiv2023

A 30-Color Full-Spectrum Flow Cytometry Panel to Characterize the Immune Cell Landscape in Spleen and Tumors within a Syngeneic MC-38 Murine Colon Carcinoma Model

Purpose and Appropriate Sample TypesThis panel was designed to characterize the immune cell landscape in the mouse tumor micro-environment as well as mouse lymphoid tissues (e.g., spleen). Previous Optimized Multicolor Immunofluorescence Panels (OMIP) with conventional cytometry were examples of high-quality fluorescent-based flow cytometry panels to characterize either the T-cell compartment or the myeloid compartment [1, 2]. The advent of spectral cytometry has enabled sufficient markers to be included in a panel to comprehensively characterize the immune cell landscape including both the T-cell and the myeloid cell compartments. In this body of work, we demonstrated that we could measure the frequency and characterize the functional status of CD4 T cells, CD8 T cells, regulatory T cells, NK cells, B cells, macrophages, granulocytes, monocytes, & dendritic cells. This panel is especially useful for understanding the immune landscape in "cold" preclinical tumor models with very low immune cell infiltration, and for investigating how therapeutic treatments may modulate the immune landscape.

cancer biology↗

bioRxiv2022

Genetically encoded non-canonical amino acids reveal asynchronous dark reversion of chromophore, backbone and side-chains in EL222

Photoreceptors containing the light-oxygen-voltage (LOV) domain elicit biological responses upon excitation of their flavin mononucleotide (FMN) chromophore by blue light. The mechanism and kinetics of dark-state recovery are not well understood. Here we incorporated the non-canonical amino acid p-cyanophenylalanine (CNF) by genetic code expansion technology at forty-five positions of the bacterial transcription factor EL222. Screening of light-induced changes in infrared (IR) absorption frequency, electric field and hydration of the nitrile groups identified residues CNF31 and CNF35 as reporters of monomer/oligomer and caged/decaged equilibria, respectively. Time-resolved multi-probe UV/Visible and IR spectroscopy experiments of the lit-to-dark transition revealed four dynamical events. Predominantly, rearrangements around the A helix interface (CNF31 and CNF35) precede FMN-cysteinyl adduct scission, folding of -helices (amide bands), and relaxation of residue CNF151. This study illustrates the importance of characterizing all parts of a protein and suggests a key role for the N-terminal A extension of the LOV domain in controlling EL222 photocycle length. SignificanceThe kinetics of fold switching between non-illuminated and blue-light-irradiated states in the transcription factor EL222 is important for understanding the signal transduction mechanism of LOV photoreceptors. Here we combine two native probes, the FMN chromophore (absorption bands in the UV/Visible region) and the protein backbone (amide bands in the infrared region), with genetically encoded cyano (C{equiv}N)-containing phenylalanine residues as infrared reporters of protein microenvironments. EL222 structural dynamics is more complex than expected if using a single type of probe. Local changes around residues 31 and 35 precede FMN-protein adduct rupture, which in turn precedes the global protein conformational relaxation. Our findings point the way forward to obtaining comprehensive descriptions of kinetic transitions in LOV and other photosensors.

biophysics↗

bioRxiv2022

Scale-free and oscillatory spectral measures of sleep stages in humans

Power spectra of sleep electroencephalograms (EEG) comprise two main components: a decaying power-law corresponding to the aperiodic neural background activity, and spectral peaks present due to neural oscillations.Traditional band-based spectral methods ignore this fundamental structure of the EEG spectra and thus are susceptible to misrepresenting the underlying phenomena. A fitting method that attempts to separate and parameterize the aperiodic and periodic spectral components called fitting oscillations & one over f (FOOOF) was applied to a set of annotated whole-night sleep EEG recordings of 251 subjects from a wide age range (4-69 years). Most of the extracted parameters exhibited sleep stage sensitivity; significant main effects and interactions of sleep stage, age, sex, and brain region were found. The spectral slope (describing the steepness of the aperiodic component) showed especially large and consistent variability between sleep stages (and low variability between subjects), making it a candidate indicator of sleep states. The limitations and arisen problems of the FOOOF method are also discussed, possible solutions for some of them are suggested.

bioinformatics↗

bioRxiv2021

Targeting the chemokine receptor CXCR4 with histamine analogue to reduce inflammation in juvenile arthritis: a proof of concept for COVID-19 therapeutic approach

Among immune cells, activated monocytes play a detrimental role in chronic and viral-induced inflammatory pathologies. The uncontrolled activation of monocytes and the subsequent excessive production of inflammatory factors damage bone-cartilage joints in Juvenile Idiopathic Arthritis (JIA), a childhood rheumatoid arthritis (RA) disease. Inflammatory monocytes also exert a critical role in the cytokine storm induced by SARS-CoV2 infection in severe COVID-19 patients. The moderate beneficial effect of current therapies and clinical trials highlights the need of alternative strategies targeting monocytes to treat RA and COVID-19 pathologies. Here, we show that targeting CXCR4 with small amino compound such as the histamine analogue clobenpropit (CB) inhibits spontaneous and induced-production of a set of key inflammatory cytokines by monocytes isolated from blood and synovial fluids of JIA patients. Moreover, daily intraperitoneal CB treatment of arthritic mice results in significant decrease in circulating inflammatory cytokine levels, immune cell infiltrates, joints erosion, and bone resorption leading to reduction of disease progression. Finally, we provide the prime evidence that the exposure of whole blood from hospitalized COVID-19 patients to CB significantly reduces levels of key cytokine-storm-associated factors including TNF-, IL-6 and IL-1{beta}. These overall data show that targeting CXCR4 with CB-like molecules may represent a promising therapeutic option for chronic and viral-induced inflammatory diseases.

immunology↗

bioRxiv2021

CULTURE AND MAINTENANCE OF URINE-DERIVED, 3-DIMENSIONAL CANINE TRANSITIONAL CELL CARCINOMA ORGANOIDS

Bladder cancer is the ninth most common malignancy in the world. Transitional cell carcinoma (TCC), also referred to as urothelial carcinoma (UC) is the most common form of bladder cancer, occurring in 90% of cases. In this study, we explore urine-derived, 3-dimensional, canine TCC organoids as a possible model to study bladder TCC ex vivo. After establishing the cell lines, we subjected the 3D cells to RNA in situ hybridization (RNA-ISH) and cell viability assays. Overall, 3D cell culture from urine samples of TCC diagnosed canines expressed RNA biomarkers in a similar manner to parent tumors via RNA-ISH and showed more sensitivity to cisplatin treatment when compared to 2D human TCC cells. With further experimentation, canine TCC organoids could become an ideal model to study TCC ex vivo.

cancer biology↗

bioRxiv2020

Specific decorations of 17-hydroxygeranyllinalool diterpene glycosides solve the autotoxicity problem of chemical defense in Nicotiana attenuata

17-hydroxygeranyllinalool diterpene glycosides (HGL-DTGs) are abundant and potent anti-herbivore defense metabolites in Nicotiana attenuata whose glycosylation and malonylation biosynthetic steps are regulated by jasmonate signaling. To characterize the biosynthetic pathway of HGL-DTGs, we conducted a genome-wide analysis of uridine diphosphate glycosyltransferases (UGTs) and identified 107 members of family-1 UGTs. Tissue-specific time-course transcriptional profiling revealed that the transcripts of three UGTs were highly correlated with two HGL-DTG key biosynthetic genes: geranylgeranyl diphosphate synthase (NaGGPPS) and geranyllinalool synthase (NaGLS). NaGLSs role in HGL-DTG biosynthesis was confirmed by virus-induced gene-silencing. Silencing the UDP-rhamnosyltransferase, UGT91T1, indicated its role in the rhamnosylation of HGL-DTGs. In vitro enzyme assays revealed that UGT74P3 and UGT74P4 use UDP-glucose for the glucosylation of 17-hydroxygeranyllinalool (17-HGL) to lyciumoside I. UGT74P3 and UGT74P5 stably silenced plants were severely developmentally deformed, suggesting a phytotoxic effect of 17-HGL. Applications of synthetic 17-HGL and silencing of these UGTs in HGL-DTG-free plants confirmed the phytotoxic effect of 17-HGL. Feeding assays with Manduca sexta larvae revealed the defensive functions of the glucosylation and rhamnosylation steps in HGL-DTG biosynthesis. Glucosylation is a critical step that contributes to the metabolites defensive function and solves the autotoxicity problem of this potent chemical defense.

plant biology↗

bioRxiv2020

CSPα reduces aggregates and rescues striatal dopamine release in αsynuclein transgenic mice

Synuclein aggregation at the synapse is an early event in Parkinsons disease and is associated with impaired striatal synaptic function and dopaminergic neuronal death. The cysteine string protein (CSP) and synuclein have partially overlapping roles in maintaining synaptic function and mutations in each cause neurodegenerative diseases. CSP is a member of the DNAJ/HSP40 family of co-chaperones and like synuclein, chaperones the SNARE complex assembly and neurotransmitter release. Synuclein can rescue neurodegeneration in CSPKO mice. However, whether synuclein aggregation alters CSP expression and function is unknown. Here we show that synuclein aggregation at the synapse induces a decrease in synaptic CSP and a reduction in the complexes that CSP forms with HSC70 and STGa. We further show that viral delivery of CSP rescues in vitro the impaired vesicle recycling in PC12 cells with synuclein aggregates and in vivo reduces synaptic synuclein aggregates restoring normal dopamine release in 1-120hsyn mice. These novel findings reveal a mechanism by which synuclein aggregation alters CSP at the synapse, and show that CSP rescues synuclein aggregation-related phenotype in 1-120hsyn mice similar to the effect of synuclein in CSPKO mice. These results implicate CSP as a potential therapeutic target for the treatment of early-stage PD.

neuroscience↗