Biology subjects

Ritter, A.

Publications and source records attributed to Ritter, A..

At least 19 recordsLinked to original sources

bioRxiv2026

Comparison of multiple video tracking-based behavioral summary approaches for compound discrimination

The rapidly increasing number of video tracking-based behavioral summary tools and methods raises the question as to the most suitable approaches for pharmacological fingerprinting in pre-clinical research. We have recently shown that social context has a strong effect on behavioral syntax in mice, further suggesting that treatment effects can be context dependent. Here, we aim to answer the question whether there is an optimal combination of context and behavioral summary method for effect detection and discrimination of different psychoactive substances in a controlled environment. To this end, we applied eight different treatment-dosage pairs (amphetamine 1.5,3,6 mg/kg; modafinil 5,10,50 mg/kg; seltorexant 3,10 mg/kg) and evaluated five different approaches to behavioral summary: parametric aggregation, unsupervised segmentation in Keypoint-MoSeq (KPMS) & Variational Animal Motion Encoding (VAME), and supervised segmentation in Simple Behavioral Analysis (SimBA) & A-SOiD, across two different contexts (Solitary & Social) in 314 recordings of freely moving mice in an open-field arena. Surprisingly, our results show no significant differences in performance across models and context. Across treatment effect detection to treatment-dose discrimination, all models showed performance significantly above chance that was insensitive to various data limitations and extensions. Overall, our study shows that under the tested conditions and treatments, the choice of a behavioral summary model does not meaningfully affect the description of treatment effects. Simple aggregate measures from tracking data and machine learning based behavioral summary approaches that are expensive, in terms of training data and computational resources, performed equally well. Our findings taken together with literature suggest that the fuller decomposition of complex behavior through unsupervised machine learning might be necessary for the description of large-scale datasets but does not necessarily align with the goals present in smaller-scale treatment discrimination tasks common in pre-clinical research.

animal behavior and cognition↗

bioRxiv2026

How tree diversity and ectomycorrhizal dominance affect biomass allocation of mixed deciduous forests

Biomass and surface area allocation affect resource uptake and carbon (C) residence time in forests, but the influence of tree diversity on allocation remains poorly understood. Moreover, mycorrhizal associations can alter this relationship, which has been rarely tested in mature forests. We investigated the role of both the proportion of ectomycorrhizal (ECM) trees and tree diversity on tree biomass and surface area allocation across a dual gradient of tree diversity (0 - 1.68 Shannon diversity) and ECM dominance (0 - 100 %) in a mixed deciduous forest area in Central Germany. We found that the two gradients affected tree biomass and surface area differently and mostly independently. Tree diversity had no significant effect on biomass or surface area in the investigated forest area, but increased the spatial variability of the leaf area index (LAI) from 21 % to 40 %. In contrast, a higher proportion of ECM trees was associated with an increase in fruit biomass (from 10 to 141 g m-2) and LAI (from 4 to 7 m2 m-2). Although tree diversity and the portion of ECM produced similar parsimonious models for explaining belowground biomass and surface area, neither showed a significant direct effect. Notably, their interaction enhanced the spatial variability of fine root biomass and root surface area; that is, forests with high diversity and a greater proportion of ECM trees exhibited a more heterogeneous distribution of fine roots. Allocation to fine root biomass appeared independent of tree diversity and the proportion of ECM trees, being influenced primarily by stand structure, with higher allocations observed in stands with lower stem basal area. We conclude that biomass allocation in this Central European Forest, where resource availability is relatively uniform, is primarily productivity-driven. A comparison of the biotic influences shows that ECM trees have a stronger control on aboveground surface area and fruit biomass than tree diversity, which may contribute to the ability of dominant ECM trees, such as European beech, to outcompete light competitors, but also puts temperate ECM forests at risk of physiological failures in increasingly drier future conditions.

ecology↗

bioRxiv2025

Targeting CXADR-mediated AKT signaling suppresses tumorigenesis and enhances chemotherapy efficacy in Ewing sarcoma

Distant metastasis is the leading cause of mortality in Ewing sarcoma (EwS) - a malignant bone or soft-tissue cancer mainly affecting children, adolescents, and young adults. Despite continuous efforts in understanding its pathogenesis, the molecular mechanisms driving EwS metastasis remain poorly understood, thus limiting the potential for therapeutic progress. Here, we identify the tight junction component Coxsackievirus and Adenovirus receptor (CXADR) as a critical regulator of cancer progression and metastasis in EwS. Differential gene expression analysis of patient tumors from two independent cohorts revealed that elevated CXADR levels are associated with metastatic disease and poor overall survival. In functional experiments, conditional CXADR knockdown reduced the growth of EwS cell line models in vitro, and suppressed local tumorigenesis. Notably, CXADR knockdown completely abrogated metastasis formation in vivo. Integration of transcriptome profiling and mechanistic studies uncovered that CXADR promotes the activation of AKT signaling, likely through complex formation with PTEN. Consequently, pharmacological targeting of AKT using the FDA-approved pan-AKT inhibitor Capivasertib showed CXADR-dependent cytotoxicity, with enhanced efficacy if combined with the EwS standard-of-care chemotherapeutic agent Vincristine. Collectively, our findings establish CXADR as a prognostic and predictive biomarker in EwS, highlighting AKT inhibition combined with chemotherapy as a promising strategy for patients with high CXADR expression. Together, these findings support a precision medicine approach combining molecular stratification and targeted therapies to improve patient outcomes in metastatic EwS.

cancer biology↗

bioRxiv2025

Exploration of oncogenic cooperation between germline variation and somatic mutation in prostate cancer progression

Prostate carcinoma (PCa) is the most common cancer of men, associated with a still unresolved issue of accurate risk-stratification. While recent advances in omics technologies have provided clues as to how molecular changes shape the onset and progression of PCa, it remains largely unclear whether germline variants and somatic mutations cooperate to contribute to PCa progression and outcome. Thus, we explored whether oncogenic cooperation between regulatory germline variants and somatic driver mutations can help explain why some PCa patients develop a more aggressive phenotype, which may have implications for risk-adapted medical treatment. Here, by employing an integrative functional genomics approach, we identified receptor-type protein-tyrosine phosphatase kappa (PTPRK) as a TMPRSS2::ERG (TE)-modulated gene associated with PCa progression whose expression is controlled by cooperation of the TE-fusion with a regulatory single nucleotide polymorphism (SNP). Analysis of available clinically annotated patient cohorts demonstrated that PTPRK is overexpressed in TE-positive PCa tumors and associated with higher Gleason scores and metastatic disease. TE knockdown in PCa cell lines reduced PTPRK expression, while ectopic overexpression of the fusion in TE-negative PCa cell lines and prostatic epithelium cells induced its expression. Functionally, PTPRK silencing inhibited cellular proliferation, cell cycle progression, and clonogenic growth of PCa cells, which was mirrored by dysregulation of corresponding gene and protein signatures in global transcriptomic and phospho-proteomic analyses after PTPRK knockdown. Analysis of TE ChIP-Seq and Hi-C data from PCa cells highlighted a proximal TE-bound DNA element whose TE-dependent enhancer activity was validated in reporter assays and which could be abrogated by a regulatory SNP. Collectively, our results provide evidence of how exploration of oncogenic cooperation may help to identify novel biomarkers and potentially druggable pathways and highlight the role of the regulatory genome in PCa progression.

cancer biology↗

bioRxiv2025

cIAP1 inhibitor of apoptosis is a tumor suppressor in Ewing sarcoma

Ewing sarcoma (EwS) is a highly aggressive pediatric malignancy driven by EWSR1::ETS fusion oncoproteins -primarily EWSR1::FLI1- which deregulate genes essential for differentiation, proliferation, and cell survival. To uncover key downstream targets of this fusion involved in cell differentiation, we combined transcriptomic profiling of EwS cell lines following EWSR1::FLI1 inhibition with gene ontology analysis, a clinically annotated gene expression dataset derived from EwS patient material and network analyses. This integrative approach identified inhibitor of apoptosis protein 1 (cIAP1, alias BIRC2) as an EWSR1::FLI1-suppresed gene. Despite its known oncogenic role in many cancers, cIAP1 showed minimal expression in EwS. Using inducible cIAP1 re-expression models in EwS cells, we demonstrated that cIAP1 re-expression suppresses proliferation, clonogenic growth, and 3D spheroid formation in vitro. Transcriptomic and proteomic analyses revealed that low cIAP1 expression enhances proliferation-related gene signatures, which are inhibited upon cIAP1 re-expression. In vivo xenograft models revealed that cIAP1 re-expression significantly reduces tumor growth, mitotic activity, and Ki-67 positivity, while increasing tumor necrosis and apoptosis. These findings highlight an unexpected tumor-suppressive role for cIAP1 in fusion-driven sarcomas, contrasting with its pro-survival function in other cancers. Collectively, our results identify cIAP1 as a prognostically relevant, EWSR1::FLI1-regulated hub whose re-expression disrupts tumor progression, offering a potential therapeutic strategy to restore tumor-suppressive pathways in EwS.

cancer biology↗

bioRxiv2025

EWSR1::ETS-low cells promote metabolic reprogramming of the tryptophan-kynurenine-AHR axis, immunosuppression, and poor outcome in Ewing sarcoma

The extent to which dynamic changes in oncogene activity shape cancer cell metabolism and drive disease progression remains poorly understood. Ewing sarcoma (EwS), driven by EWSR1::ETS fusion transcription factors, constitutes an ideal model to interrogate this question, as fluctuations in fusion activity direct divergent transcriptional programs. While EWSR1::ETS-high cells display a rather sessile but proliferative phenotype, EWSR1::ETS-low cells are more invasive. Yet, the mechanisms underlying these different phenotypes remain poorly characterized. Here, by employing an integrative functional metabolomics approach, we link reduced EWSR1::ETS activity in primary EwS tumors to adverse clinical outcome and pronounced activation of the aryl hydrocarbon receptor (AHR) pathway. Low EWSR1::ETS states foster tryptophan catabolism and accumulation of the AHR agonist kynurenine, which in turn promotes an immunosuppressive tumor microenvironment characterized by impaired natural killer (NK) cell cytotoxicity and enrichment of immunoregulatory infiltrates. Functionally, AHR silencing restores NK cell-mediated tumor recognition, while also directly suppressing EwS cell proliferation, clonogenicity, and spheroid growth in plasma-like media. Genetic inhibition of AHR reduces tumor burden and metastatic competence in xenograft models. These findings reveal a mechanistic link between oncogene fluctuation, amino acid metabolism, and immune evasion, positioning AHR as a central mediator of EwS progression and a tractable therapeutic vulnerability.

cancer biology↗

bioRxiv2024

Acid excretion is impaired in calcium oxalate stone formers

BackgroundUrine pH is a key factor in kidney stone formation. We aimed to identify whether acid excretion capacity is disturbed in calcium oxalate (CaOx) or calcium phosphate (CaP) stone formers. MethodUrinary, serum, clinical, and anthropomorphic baseline data were obtained from the Swiss Kidney Stone Cohort, a prospective, longitudinal, and multi-centric observational study. We included in this study 193 non-stone formers (NSF, confirmed by negative CT scan), and 309 CaOx and 28 CaP stone formers. Titratable acids, net acid excretion (NAE), NAE capacity (NAEC) and acid-base (AB) score were calculated. Logistic regression analyses were used to estimate the potential associations of various acid-base variables with the occurrence of CaOx kidney stones. ResultsCaOx stone formers showed a disturbed capacity to excrete acids in comparison to NSF (NAEC NSF = 3.49{+/-}12.6 mmol/24h; CaOx = -1.06{+/-}13.10; CaP = 0.97{+/-}14.70 and AB score NSF = 20.5{+/-}6.36 mmol/24h; CaOx = 17.9{+/-} 6.53; CaP = 18.8{+/-}6.10). The correlation between urine calcium and urine pH was altered in CaOx stone formers and between urine calcium and NAE was stronger in CaP stone formers. Logistic models showed that urinary ammonium was negatively associated with CaOx stone formation (unadjusted model, odds ratio 0.43[0.32-0.58], p< 0.001 for CaOx). Urine calcium was positively associated with CaOx kidney stones (2.85 [2.11-3.92], p<0.001). Similar results were obtained after adjusting for age, sex, and BMI. Replacing urine ammonium, pH, and phosphate with NAEC or ammonium and pH with AB score in our logistic regression models showed that NAEC and AB score are strongly associated with CaOx kidney stone formation. ConclusionAmmonium excretion, NAEC and AB score are associated with the occurrence of CaOx kidney stones suggesting a potential role of proximal tubule dysfunction in their formation. CaP stone formers exhibit a disproportionately higher calcium excretion when acid excretion increases. Key learning pointsO_ST_ABSWhat was knownC_ST_ABSUrine pH is a strong determinant in the formation of various urologically relevant crystals. Impaired urine acidification capacity has been observed in individuals who form calcium phosphate and uric acid stones. This study addsWhen compared to non-stone formers, calcium oxalate stone formers are marked by a reduced capacity of excreting acids when urine pH becomes more acidic. Potential impactThe calculation of net acid excretion capacity and acid-base score are novel tools to identify those under potential higher risk of developing calcium oxalate stones.

physiology↗

bioRxiv2024

Targeting the untargeted: Uncovering the chemical complexity of root exudates

The chemical complexity of root exudates has garnered significant attention in recent years, yet critical gaps remain in understanding the full scope of root exudate chemical variation across the plant kingdom. To address this, we conducted a systematic review of 57 studies, comprising 124 experiments, aimed at evaluating current methodologies and findings in untargeted root exudate chemical analysis. Our review revealed that hydroponic (44%) and soil-hydroponic hybrid (32%) sampling approaches, primarily utilising water as the collection medium, were the most common experimental setups. Liquid chromatography-mass spectrometry (LC-MS) was the predominant analytical technique used in 54% of the studies, followed by gas chromatography-mass spectrometry (GC-MS) in 31%. The average number of metabolites identified per analysis was 960, though the number of annotated metabolites varied considerably. Shikimates, phenylpropanoids, and carbohydrates were the most frequently identified classes, with their relative abundances varying widely. Several methodological challenges were highlighted, including inconsistencies in sampling techniques, underrepresentation of non-crop plants, and incomplete chemical annotation. To address these limitations, we propose a framework emphasising the need for representative exudate sampling, the use of multiple analytical approaches, the development of advanced bioinformatics tools, and the integration of these findings to enhance our understanding of root exudates and their ecological functions.

ecology↗

bioRxiv2024

Super-enhancer-driven CACNA2D2 is an EWSR1::WT1 signature gene encoding a diagnostic marker for desmoplastic small round cell tumor (DSRCT)

Desmoplastic small round cell tumor (DSRCT) is a highly aggressive cancer predominantly occurring in male adolescents and young adults. The lack of a comprehensive understanding on the biology of the disease is paralleled by its dismal survival rates (5-20%). To overcome this challenge, we first identified and prioritized urgently needed resources for clinicians and researchers. Thus, we established genome-wide single-cell RNA-sequencing and bulk proteomic data of in vitro and in vivo-generated knockdown models of the pathognomonic DSRCT fusion oncoprotein (EWSR1::WT1) and combined them with an original systems-biology-based pipeline including patient data and the largest histology collection of DSRCTs and morphological mimics available to date. These novel tools were enriched with curated public datasets including patient- and cell line-derived ChIP-seq, bulk and single-cell RNA-seq studies resulting in a multi-model and multi-omic toolbox for discovery analyses. As a proof of concept, our approach revealed the alpha-2/delta subunit of the voltage-dependent calcium channel complex, CACNA2D2, as a highly overexpressed, super-enhancer driven, direct target of EWSR1::WT1. Single-cell and bulk-level analyses of patient samples and xenografted cell lines highlighted CACNA2D2 as a critical component of our newly established EWSR1::WT1 oncogenic signature, that can be employed to robustly identify DSRCT in reference sets. Finally, we show that CACNA2D2 is a highly sensitive and specific single biomarker for fast, simple, and cost-efficient diagnosis of DSRCT. Collectively, we establish a large-scale multi-omics dataset for this devastating disease and provide a blueprint of how such toolbox can be used to identify new and clinically relevant diagnostic markers, which may significantly reduce misdiagnoses, and thus improve patient care.

cancer biology↗

bioRxiv2024

Serum Proteome Profiling Identifies N-Cadherin and C-Met as Early Marker Candidates of Therapeutic Response to Neoadjuvant Chemotherapy in Breast Cancer

Breast cancer remains the most common cancer in women worldwide. Neoadjuvant chemotherapy (NACT) is often preferred to adjuvant chemotherapy to achieve tumour shrinkage, monitor response to therapy and facilitate surgical removal in the absence of metastases. In addition, there is strong evidence that pathological complete remission (pCR) is associated with prolonged survival. In this study, we sought to identify candidate markers that signal response or resistance to therapy. We present a retrospective longitudinal serum proteomic study of 22 breast cancer patients (11 with pCR and 11 with non-pCR) matched with 21 healthy controls. Serum was analysed by LC-MS/MS after depletion of abundant proteins by immunoaffinity, trypsinisation, isobaric labelling and fractionation by reversed-phase HPLC. We observed an inverse behaviour of the serum proteins c-Met and N-cadherin after the second cycle of chemotherapy with a high predictive value (AUC 0.93). More pronounced changes were observed after the 6th cycle of NACT, with significant changes in the intensity of the proteins contactin-1, centrosomal protein, sex hormone-binding globuline and cholinesterase. Our study highlights the possibility of monitoring response to NACT using serum as a liquid biopsy.

cancer biology↗

bioRxiv2024

Glutaredoxin 3 (GLRX3) confers a fusion oncogene-dependent vulnerability to Ewing sarcoma

Ewing sarcoma (EwS) is a highly aggressive bone and soft-tissue associated cancer for which there are no effective targeted therapeutics available. Genetically, EwS is driven by aberrantly active EWSR1::ETS fusion transcription factors, most commonly EWSR1::FLI1. Despite their unique expression in EwS, all attempts to effectively target these fusion oncoproteins clinically were not yet successful, wherefore alternative targets are required. Here, we functionally characterize the evolutionarily conserved oxidative stress regulator glutaredoxin 3 (GLRX3) as a EwS-specific and EWSR1::FLI1-dependent vulnerability. Through integration of transcriptome-profiling, conditional drug screens in 3D cultures, and functional experiments, we discover that GLRX3 promotes EwS growth in vitro and in vivo, and that it has a key role in mitigation of oxidative stress and maintenance of iron homeostasis. These GLRX3 functions can be exploited in both GLRX3-high and -low expressing EwS cells by targeted therapeutics including CDK4/6 inhibitors and inducers of apoptotic and ferroptotic cell death. Collectively, our results exemplify how the interplay of an evolutionarily conserved oxidative stress regulator with a dominant oncogene can promote malignancy but provide opportunities for predictive diagnostics and personalized therapy.

cancer biology↗

bioRxiv2024

Long read subcellular fractionation and sequencing reveals the translational fate of full length mRNA isoforms during neuronal differentiation

Alternative splicing (AS) alters the cis-regulatory landscape of mRNA isoforms leading to transcripts with distinct localization, stability and translational efficiency. To rigorously investigate mRNA isoform-specific ribosome association, we generated subcellular fractionation and sequencing (Frac-seq) libraries using both conventional short reads and long reads from human embryonic stem cells (ESC) and neural progenitor cells (NPC) derived from the same ESC. We performed de novo transcriptome assembly from high-confidence long reads from cytosolic, monosomal, light and heavy polyribosomal fractions and quantified their abundance using short reads from their respective subcellular fractions. Almost half of all transcripts exhibited association with particular subcellular fractions relative to the cytosol. Of the multi-isoform genes, 27% and 18% exhibited significant differential isoform sedimentation in ESC and NPC, respectively. Alternative promoter usage and internal exon skipping accounted for the majority of differences between isoforms from the same gene. Random forest classifiers implicated 3 and 5 untranslated region (UTR) GC-content and coding sequence (CDS) and UTR lengths as important determinants of isoform-specific sedimentation profiles. Taken together our data demonstrate that alternative mRNA processing within the CDS and UTRs impacts the translational control of mRNA isoforms during stem cell differentiation, and highlights the utility of using a novel long read sequencing-based method to study translational control.

molecular biology↗

bioRxiv2024

The evolutionary dynamics of alternative splicing during primate neuronal differentiation

Alternative splicing (AS) is emerging as an important regulatory process for complex biological processes such as neuronal differentiation. To uncover the functional consequences of AS during neuronal differentiation we performed a comparative transcriptomic analysis using human, rhesus, chimpanzee and orangutan pluripotent stem cells. Transcriptomic studies commonly involve the identification and quantification of alternative processing events, but the need for predicting the functional consequences of changes to the relative inclusion of alternative events remains largely unaddressed. Many tools exist for the former task, albeit often limited to rudimentary event types. Few tools exist for the latter task; each with significant limitations. To address these issues we developed junctionCounts, which captures both simple and complex pairwise AS events and quantifies them with straightforward exon-exon and exon-intron junction reads in RNA-seq data, performing competently among similar tools in terms of sensitivity, false discovery and quantification accuracy. Its partner utility, cdsInsertion identifies transcript coding sequence information, including the presence of premature termination codons, gathered via in silico translation from annotated start codons. It then couples transcript-level information to AS events to predict functional effects, i.e. nonsense-mediated decay (NMD). We used junctionCounts and related tools to discover both conserved and species-specific splicing dynamics as well as regulation of NMD during differentiation. Our work demonstrates this tools capacity to robustly characterize AS and bridge the gap of predicting its potential effect on mRNA isoform fate. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=150 SRC="FIGDIR/small/581203v1_ufig1.gif" ALT="Figure 1"> View larger version (41K): org.highwire.dtl.DTLVardef@17b2be4org.highwire.dtl.DTLVardef@17e8992org.highwire.dtl.DTLVardef@79e47forg.highwire.dtl.DTLVardef@888161_HPS_FORMAT_FIGEXP M_FIG C_FIG junctionCounts is an alternative splicing analysis tool that identifies both simple and complex splicing events from a gene annotation and then measures their percent spliced-in from mapped RNA-seq junction reads.

molecular biology↗

bioRxiv2023

Accurate long-read transcript discovery and quantification at single-cell resolution with Isosceles

Accurate detection and quantification of mRNA isoforms from nanopore long-read sequencing remains challenged by technical noise, particularly in single cells. To address this, we introduce Isosceles, a computational toolkit that outperforms other methods in isoform detection sensitivity and quantification accuracy across single-cell, pseudo-bulk and bulk resolution levels, as demonstrated using synthetic and biologically-derived datasets. Isosceles improves the fidelity of single-cell transcriptome quantification at the isoform-level, and enables flexible downstream analysis. As a case study, we apply Isosceles, uncovering coordinated splicing within and between neuronal differentiation lineages. Isosceles is suitable to be applied in diverse biological systems, facilitating studies of cellular heterogeneity across biomedical research applications.

bioinformatics↗

bioRxiv2022

Prefrontal Control of Innate Escape Behavior - A Neural Mechanism of Enhanced Posttraumatic Threat Detection

Innate defensive responses, while primarily instinctive, must also be flexible and highly adaptive to changes in risk assessment. As such, efficient innate escape behavior requires intricate processing to minimize reaction time while maximizing the success and adaptivity of the action. The superior colliculus (SC) is a subcortical sensorimotor integration center linking sensory threat information and escape. Adaptive changes in innate escape after learning could take a maladaptive turn after severe stress. Posttraumatic stress disorder (PTSD) is associated with long-term maladaptive changes after exposure to traumatic events, related to enhanced threat detection and reaction. Such long-term modifications are thought to involve the medial prefrontal cortex (mPFC), which is implicated in integrating learned emotional values into decisions that drive actions and behaviors. Here, in a series of experiments, we establish the crucial physiological role of specific mPFC neurons, exerting influence on the SC both directly and indirectly through the basal ganglia, in threat detection and reaction after adversity.

neuroscience↗

bioRxiv2021

Towards Understanding Comprehensive Morphometric Changes and Its Correlation with Cognition and Exposure to Fighting in Active Professional Boxers

Professional athletes exposed to repetitive head impacts are at increased risk for developing a progressive neurological syndrome known as traumatic encephalopathy syndrome and neuropathology seen on autopsy called chronic traumatic encephalopathy (CTE). The early identification of individuals at increased risk for CTE is important and the search for biomarkers is underway. In this study, we utilized data from a large cohort study to compare differences in regional brain volumes, cortical thickness, voxel-based morphometric (VBM)-derived measures, and graph-theoretical measures derived from large-scale topographical maps in active professional boxers. We compared the above morphometric measures between active professional boxers with low cognitive scores (impaired boxers) and active professional boxers with intact cognitive scores (nonimpaired boxers). The cognitive scores were evaluated through neuropsychological evaluation. As an exploratory analysis, we also examined the power of various machine-learning algorithms to identify impaired and nonimpaired boxers using both group-level regression-driven analysis and previously identified hypothesis-driven cortical thickness and volumetric measures. We found significant group-level differences between impaired and nonimpaired boxers in cortical thickness in a single brain region (right precuneus), differences in VBM-derived gray matter density encompassing the caudate, putamen, and thalamus; and white matter density encompassing the right paracentral lobule, but no differences in any graph-theoretical network properties. Additionally, we found that a priori hypothesis-driven T1-derived cortical thickness and volumetric analysis performed better than traditional regression-based analysis. Overall, this study suggests that neuroanatomical differences exist between impaired and nonimpaired active professional boxers, and that hypothesis-driven techniques are likely necessary to become reliable biomarkers.

neuroscience↗

bioRxiv2021

Surveillance of in situ tumor arrays reveals early environmental control of cancer immunity

The immune phenotype of a tumor is a key predictor of its response to immunotherapy1-4. Patients who respond to immune checkpoint blockade generally present with tumors that are infiltrated by activated T cells, a tumor-immune phenotype referred to as immune inflamed5-7. However, not all immune inflamed tumors respond to therapy, and in addition the majority of patients presents with tumors that lack T cells ( immune desert) or that exclude T cells in the periphery of the tumor islet ( immune excluded)8. Despite the importance of these tumor-immune phenotypes in patients, little is known about their development, heterogeneity or dynamics due to an inability to model these features pre-clinically. Here, we describe an approach designated STAMP (skin tumor array by micro-poration), which combines in vivo noninvasive, high-throughput time-lapse imaging with excisional biopsies and next generation sequencing to characterize the establishment of the immunological niche and follow its evolution during immunotherapy. STAMP involves the seeding of dozens to hundreds clonal tumors in the superficial dermis of a single mouse ear that can be visualized in situ over weeks to months. Using this approach, we found that genetically identical tumors could display surprisingly different immune phenotypes. Although individual tumors of the same array were populated by the same T cell clonotypes, regression or progression of individual tumors were associated with distinct patterns of spatial organization of the T cells. In situ imaging of 14K tumors revealed that immune phenotypes were not static over-time but could rather evolve with tumor growth and response to treatment. Therapy-induced or spontaneous early conversion to the immune inflamed phenotype correlated with tumor regression and enhanced cytotoxic T cell activity. Therefore, STAMP provides a flexible approach to study the relationship between tumor evolution, immune cell dynamics, and tumor microenvironment with therapeutic response.

cancer biology↗

bioRxiv2020

CBX1 mutations cause a neurodevelopmental syndrome due to heterochromatin organizational alterations

PurposeThis study aimed to establish variants in CBX1, encoding heterochromatin protein 1{beta} (HP1{beta}), as a cause of a novel syndromic neurodevelopmental disorder. MethodsPatients with CBX1 variants were identified, and clinician researchers were connected using GeneMatcher and physician referrals. Clinical histories were collected from each patient. To investigate the pathogenicity of identified variants, we performed in vitro cellular assays, neurobehavioral and cytological analyses of neuronal cells obtained from newly generated Cbx1 mutant mouse lines. ResultsIn three unrelated individuals with developmental delay, hypotonia, and autistic features, we identified heterozygous de novo variants in CBX1. The identified variants were in the chromodomain, the functional domain of HP1 {beta}, which mediates interactions with chromatin. Cbx1 chromodomain mutant mice displayed increased latency-to-peak response, suggesting the possibility of synaptic delay or myelination deficits. Cytological and chromatin immunoprecipitation experiments confirmed the reduction of mutant HP1{beta} binding to heterochromatin, while HP1{beta} interactome analysis demonstrated that the majority of HP1{beta}-interacting proteins remained unchanged between the wild-type and mutant HP1{beta}. ConclusionThese collective findings confirm the role of CBX1 in developmental disabilities through the disruption of HP1{beta} chromatin binding during neurocognitive development. As HP1{beta} forms homodimers and heterodimers, mutant HP1{beta} likely sequesters wild-type HP1{beta} and other HP1 proteins, exerting dominant-negative effects.

genetics↗