Biology subjects

Winter, A.

Publications and source records attributed to Winter, A..

9 recordsLinked to original sources

bioRxiv2026

Longitudinal single-cell and spatial transcriptomics reveals intratumor heterogeneity, therapeutic response, and comparative value of canine marginal zone lymphoma

Diffuse B-cell lymphomas are the most prevalent canine hematologic malignancies, and their clinical presentation resembles that of human B-cell non-Hodgkin lymphomas (NHLs). However, a lack of a clear subtyping framework perpetuates imprecise treatment approaches that fail to address mechanisms of therapy resistance. Here, we employed deep phenotyping via serial sampling and longitudinal transcriptomics to evaluate intratumoral composition and therapy response in a 6-year-old neutered male goldendoodle with stage 5A marginal zone lymphoma (MZL). Following sequential treatment consisting of a single IV dose of oncolytic vesicular stomatitis virotherapy (VSV) and standard CHOP chemotherapy 30 days later, we performed scRNAseq on seven serial lymph node biopsies and spatial sequencing on a resection taken 10 days post-VSV treatment. B cells (>90%) comprised three transcriptionally distinct and temporally stable subpopulations, with specific copy number profiles and robust spatial organization despite disrupted lymph node architecture. Analysis across subpopulations revealed downregulation of the quiescence program including KLF2, suggesting similarity to KLF2-deficient human MZL. While VSV successfully reached target B cells, downstream transcriptional responses were predominantly localized to the T-cell compartment. T cells ([≤]6%) showed increased proliferation and upregulation of cytotoxicity markers post-VSV administration, enriching for leukocyte-mediated cytotoxicity pathways consistent with an anti-viral immune response. Ultimately, these results provide an in vivo proof-of-concept for the treatment paradigm in canine lymphoma, while emphasizing the need for improved subtyping frameworks and multidimensional treatment strategies targeting intratumoral heterogeneity.

cancer biology↗

bioRxiv2026

Projections from subfornical organ to infralimbic cortex modulate carbon dioxide associated fear

Most of our mechanistic understanding of threat responding and defensive fear behaviors is based on exposure to aversive stimuli in the environment. However, unpleasant, within-the body interoceptive signals can also regulate threat and emotion although underlying cell-circuit mechanisms are not well understood. Abnormal interoceptive sensitivity is associated with fear-associated psychiatric conditions such as panic disorder and PTSD. The ventromedial infralimbic (IL) subdivision of the prefrontal cortex plays a key role in threat appraisal and fear, however, IL engagement in interoceptive threat response and contributory afferent mechanisms are not known. Here, using an interoceptive clinical panicogen, carbon dioxide (CO2) inhalation, we report IL-mediated regulation of fear in mice via afferents from the subfornical organ (SFO), a key viscero-humoral circumventricular organ lacking a traditional blood brain barrier. Chemogenetic inhibition of SFO-to-IL (but not SFO-to-BNST) projections regulated defensive behaviors during CO2 inhalation and associative contextual fear. Notably, the SFO-IL circuit also modulated delayed CO2 effects on contextual fear conditioning-extinction, but not startle, neuroendocrine response or motivated behaviors. We also established more specifically that SFO angiotensin II receptor type-1 (AT-1R)+ve neuronal afferents to the IL regulate CO2-associated fear and long-term deficits in contextual fear extinction. CO2 inhalation reduced neuronal activation within the IL and optogenetic activation of SFO neurons activated inhibitory parvalbumin (PV) (but not somatostatin (SST)) interneurons in the IL. Collectively, these data reveal that aversive interoceptive signals can be directly conveyed to the IL via the SFO, a sensory hub for systemic perturbations, to regulate spontaneous and long-term fear. Our findings provide important mechanistic insights into fear-associated disorders with abnormal interoceptive threat sensitivity such as panic disorder and PTSD.

neuroscience↗

bioRxiv2026

Structural divergence in N-terminal domains of AAA proteases paraplegin (SPG7) and FtsH indicates a key structural function in complex formation

AAA proteases are hexameric ATP-dependent metallopeptidases that perform crucial proteolytic activities within prokaryotic and eukaryotic membranes. Structurally, protomers are comprised of catalytically active C-terminal domains that are anchored to the membrane by an N-terminal autonomous folding unit. In this study, we determined the fold, stability, and oligomeric state of the N-terminal intermembrane domains of human spastic paraplegia type 7 (SPG7)/ paraplegin protein and its bacterial orthologue FtsH using circular dichroism (CD), small-angle X-ray scattering (SAXS), small-angle neutron scattering (SANS) and X-ray crystallography. Solution-state analysis revealed that the N-terminal domain of paraplegin is a monomer in solution whereas FtsH forms a dimer. Unexpectedly, the N-terminal domain of paraplegin presents as a domain-swapped homodimer in our crystal structure that involves the first helix and first two beta-strands from one monomer and beta-strand 3, helix 2 and beta-strand 4 from another symmetry-related molecule. However, together they form an assembly which is similar to protomers observed for the N-terminal regions of FtsH and AfG3L2. Drawing from our structural data, we postulate that domain-swapping interactions of the N-terminal regions contribute to stability of the AAA protease hexamer containing paraplegin, demonstrating the extensive flexibility of the N-terminal portion of this protein and its role in achieving the appropriate molecular architecture required for function. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=87 SRC="FIGDIR/small/720153v1_ufig1.gif" ALT="Figure 1"> View larger version (26K): org.highwire.dtl.DTLVardef@1f4b9b5org.highwire.dtl.DTLVardef@1cc2242org.highwire.dtl.DTLVardef@dd211borg.highwire.dtl.DTLVardef@1a87722_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIFtsH-IMS forms a homo-dimer in solution, whereas paraplegin-IMS presents as a well-folded monomer in solution C_LIO_LIparaplegin-IMS crystallises as a domain-swapped homo-dimer but its domain-swapped monomers are structurally similar to other IMS-regions C_LIO_LIAfG3L2/paraplegin hexamer formation may be supported by domain swapping in paraplegin-IMS C_LIO_LIdomain-swapping in paraplegin could be a Bonafide feature under certain cellular conditions and may be related to disease in spastic paraplegia C_LI

biochemistry↗

bioRxiv2025

A novel interoceptive subfornical organ to infralimbic cortex circuit relays airway inflammation effects on fear extinction

There is growing interest in the impact of internal body states on the brain and behavior. The detrimental effects of chronic lung inflammation on mental health are well recognized, however, underlying mechanisms are not known. Here, using a murine model of allergic asthma we report compromised fear extinction in mice with severe but not mild airway inflammation (AI); an effect abolished by anti-interleukin-17A (IL-17A) antibodies. Investigation of innate immune cells, microglia as-well-as transcriptomic signatures in the subfornical organ (SFO), a brain interoceptive node lacking a traditional blood-brain-barrier, revealed significant alterations in severe AI mice. IL-17 Receptor A (IL-17RA) was expressed in SFO microglia and upregulated in severe AI mice. Notably, ablation of microglial IL-17RA improved fear extinction in severe AI mice. Furthermore, we identified direct SFO projections to the infralimbic (IL) cortex, a key area regulating extinction. Importantly, chemogenetic inhibition of the SFO-IL circuit led to improved fear extinction in severe AI mice. Collectively, we report a unique body-to-brain interoceptive mechanism engaging the SFO and an SFO-to-IL circuit, through which airway inflammatory mediators compromise fear extinction. Beyond asthma, our findings are relevant to other pulmonary pathologies (e.g. bacterial pneumonia, ARDS, COVID-19) highlighting a risk for cortical dysfunction and fear pathologies such as PTSD.

neuroscience↗

bioRxiv2024

Mitochondrial cardiolipin metabolism controlled by tafazzin enables ferroptosis

Mitochondria are important producers of reactive oxygen species, which are involved in triggering ferroptosis, a lipid peroxidation driven form of cell death. Paradoxically, in the rare inherited metabolic disease Barth Syndrome, we discovered a protection from erastin-induced ferroptosis, despite intrinsically elevated mitochondrial ROS levels. The affected transacylase tafazzin, which is mutated in Barth Syndrome, is pivotal for remodeling of the dimeric phospholipid cardiolipin. They unique to mitochondria and essential for shaping their membrane functionalities. We investigated which downstream effects of the pathogenic membrane alterations are responsible for the protective effect against ferroptosis. We found that while iron metabolism, the unsaturation of membrane lipids, and the metabolic activity of the cells were modifying factors, they were not causal. However, we observed that cardiolipin abnormalities are not limited to impair only inner, but also outer mitochondrial membrane protein complexes. Specifically, they impact abundance and oligomerization of voltage-dependent anion channels (VDAC) in response to oxidative stress. We found that tafazzin deficiency via alteration of cardiolipins affects VDAC functionality, thereby modulating small molecule transport and signaling between mitochondria and the remaining cell. This is in line with a reduction of mitochondria-associated membranes (MAM) sites that are formed through VDACs and trapping ROS in mitochondria where they are unable to contribute to ferroptosis. These findings demonstrate that the mitochondrial membrane architecture impacting on subcellular small molecule distribution crucially impact on the manifestation of cell fate decisions, including ferroptosis.

molecular biology↗

bioRxiv2024

Brain Structural Correlates of an Impending Initial Major Depressive Episode

BackgroundNeuroimaging research has yet to elucidate, whether reported gray matter volume (GMV) alterations in major depressive disorder (MDD) exist already before the onset of the first episode. Recruitment of presently healthy individuals with a known future transition to MDD (converters) is extremely challenging but crucial to gain insights into neurobiological vulnerability. Hence, we compared converters to patients with MDD and sustained healthy controls (HC) to distinguish pre-existing neurobiological markers from those emerging later in the course of depression. MethodsCombining two clinical cohorts (n=1709), voxel-wise GMV of n=45 converters, n=748 patients with MDD, and n=916 HC were analyzed in regions-of-interest approaches. By contrasting the subgroups and considering both remission state and reported recurrence at a 2-year clinical follow-up, we stepwise disentangled effects of 1) vulnerability, 2) the acute depressive state, and 3) an initial vs. a recurrent episode. ResultsAnalyses revealed higher amygdala GMV in converters relative to HC (pTFCE-FWE=.037, d=0.447) and patients (pTFCE-FWE=.005, d=0.508), remaining significant when compared to remitted patients with imminent recurrence. Lower GMV in the dorsolateral prefrontal cortex (pTFCE-FWE<.001, d=0.188) and insula (pTFCE-FWE=.010, d=0.186) emerged in patients relative to HC but not to converters, driven by patients with acute MDD. ConclusionBy examining one of the largest available converter samples in psychiatric neuroimaging, this study allowed a first determination of neural markers for an impending initial depressive episode. Our findings suggest a temporary vulnerability, which in combination with other common risk factors might facilitate prediction and in turn improve prevention of depression.

neuroscience↗

bioRxiv2023

Oncolytic vesicular stomatitis virus is safe and provides a survival benefit for dogs with naturally occurring osteosarcoma

Osteosarcoma is a devastating bone cancer that disproportionally afflicts children, adolescents, and young adults. Standard therapy includes surgical tumor resection combined with multiagent chemotherapy, but many patients still suffer from metastatic disease progression. Neoadjuvant systemic oncolytic virus (OV) therapy has the potential to improve clinical outcomes by targeting primary and metastatic tumor sites and inducing durable antitumor immune responses. Here we described the first evaluation of neoadjuvant systemic therapy with a clinical-stage recombinant oncolytic Vesicular stomatitis virus (VSV), VSV-IFN{beta}-NIS, in naturally occurring cancer, specifically appendicular osteosarcoma in companion dogs. Canine osteosarcoma has a similar natural disease history as its human counterpart. VSV-IFN{beta}-NIS was administered prior to standard of care surgical resection, permitting microscopic and genomic analysis of tumors. Treatment was well-tolerated and a "tail" of long-term survivors ([~]35%) was apparent in the VSV-treated group, a greater proportion than observed in two contemporary control cohorts. An increase in tumor inflammation was observed in VSV-treated tumors and RNAseq analysis showed that all the long-term responders had increased expression of a T-cell anchored immune gene cluster. We conclude that neoadjuvant VSV-IFN{beta}-NIS is safe and may increase long-term survivorship in dogs with naturally occurring osteosarcoma, particularly those that exhibit pre-existing antitumor immunity.

cancer biology↗

bioRxiv2023

Cross-validation for the estimation of effect size generalizability in mass-univariate brain-wide association studies

IntroductionStatistical effect sizes are systematically overestimated in small samples, leading to poor generalizability and replicability of findings in all areas of research. Due to the large number of variables, this is particularly problematic in neuroimaging research. While cross-validation is frequently used in multivariate machine learning approaches to assess model generalizability and replicability, the benefits for mass-univariate brain analysis are yet unclear. We investigated the impact of cross-validation on effect size estimation in univariate voxel-based brain-wide associations, using body mass index (BMI) as an exemplary predictor. MethodsA total of n=3401 adults were pooled from three independent cohorts. Brain-wide associations between BMI and gray matter structure were tested using a standard linear mass-univariate voxel-based approach. First, a traditional non-cross-validated analysis was conducted to identify brain-wide effect sizes in the total sample (as an estimate of a realistic reference effect size). The impact of sample size (bootstrapped samples ranging from n=25 to n=3401) and cross-validation on effect size estimates was investigated across selected voxels with differing underlying effect sizes (including the brain-wide lowest effect size). Linear effects were estimated within training sets and then applied to unseen test set data, using 5-fold cross-validation. Resulting effect sizes (explained variance) were investigated. ResultsAnalysis in the total sample (n=3401) without cross-validation yielded mainly negative correlations between BMI and gray matter density with a maximum effect size of R2p=.036 (peak voxel in the cerebellum). Effects were overestimated exponentially with decreasing sample size, with effect sizes up to R2p=.535 in samples of n=25 for the voxel with the brain-wide largest effect and up to R2p=.429 for the voxel with the brain-wide smallest effect. When applying cross-validation, linear effects estimated in small samples did not generalize to an independent test set. For the largest brain-wide effect a minimum sample size of n=100 was required to start generalizing (explained variance >0 in unseen data), while n=400 were needed for smaller effects of R2p =.005 to generalize. For a voxel with an underlying null effect, linear effects found in non-cross-validated samples did not generalize to test sets even with the maximum sample size of n=3401. Effect size estimates obtained with and without cross-validation approached convergence in large samples. DiscussionCross-validation is a useful method to counteract the overestimation of effect size particularly in small samples and to assess the generalizability of effects. Train and test set effect sizes converge in large samples which likely reflects a good generalizability for models in such samples. While linear effects start generalizing to unseen data in samples of n>100 for large effect sizes, the generalization of smaller effects requires larger samples (n>400). Cross-validation should be applied in voxel-based mass-univariate analysis to foster accurate effect size estimation and improve replicability of neuroimaging findings. We provide open-source python code for this purpose (https://osf.io/cy7fp/?view_only=a10fd0ee7b914f50820b5265f65f0cdb).

neuroscience↗

bioRxiv2018

Bone marrow-on-a-chip: Emulating the human bone marrow

Multipotent hematopoietic stem and progenitor cells HSPC reside in specialized stem cell niches within the bone marrow, that provide a suitable microenvironment for lifelong maintenance of the stem cells. Meaningful in vitro models recapitulating the in vivo stem cell niche biology can be employed for both basic research as well as for applied sciences and represent a powerful tool to reduce animal tests in preclinical studies. Recently we published the generation of an in vitro bone marrow niche model, capable of long-term cultivation of HSC based on an organ-on-a-chip platform. This study provides a detailed analysis of the 3D culture system including matrix environment analysis by SEM, transcriptome analysis and system intrinsic differentiation induction. Furthermore, the bone marrow on a chip model can serve to multiply and harvest HSPC, since repeated cell removal not compromised the functionality of the culture system. The prolongation of the culture time to 8 weeks demonstrate the capacity to apply the model in repeated drug testing experiments. The quality of the presented system is emphasized by the differentiation capacity of long-term cultivated HSPC in vitro and in vivo. Transplanted human HSPC migrated actively into the bone marrow of irradiated mice and contributed to the long-term reconstitution of the hematopoietic system after four and eight weeks of in vitro cultivation.\n\nThe introduced system offers a multitude of possible applications to address a broad spectrum of questions regarding HSPC, the corresponding bone marrow niche biology, and pathological aberrations.

bioengineering↗