Biology subjects

Norman, J.

Publications and source records attributed to Norman, J..

8 recordsLinked to original sources

bioRxiv2026

An adolescent neuroimaging database combining movie-watching, eye-tracking and cognitive tasks

Adolescence is a critical period of neurodevelopment, yet most neuroimaging datasets focus on adult populations, leaving a gap in our understanding of how the brain processes information during this formative stage. Here we present a multimodal neuroimaging dataset acquired from 41 adolescent participants aged 11-18 years, combining 3T fMRI data with concurrent eye-tracking and physiological monitoring during naturalistic movie-watching. Data are shared in BIDS-compliant format and technical validation demonstrates good data quality across participants, with low head motion and strong inter-subject neural synchronisation during movie-watching. In addition to the scanning session, participants completed remote assessments covering a broad range of self-reported developmental and mental health traits, alongside cognitive tasks targeting reward-based and social learning. This dataset offers a rich resource for studying the adolescent brain, with particular utility for research on individual differences in mental health and cognition. All data and processing code is openly available to facilitate reproducible science.

neuroscience↗

bioRxiv2025

Antibody Reveals Conformational Latch Controlling Herpesvirus Proteases

Human herpesviruses (HHVs) are widespread pathogens that cause severe disease. Their replication depends on the HHV protease (HHV Pr), an enzyme essential for capsid maturation. Because HHV Pr must dimerize to become catalytically active, disrupting dimer formation is a promising strategy for antiviral therapeutic development. We isolated a conformationally selective antibody inhibitor, Fab5, from a fully human naive Fab-phage library that recognizes monomeric human cytomegalovirus protease (HCMV Pr). A 2.6 [A] cryoelectron microscopy (cryo-EM) structure of the Fab5-HCMV Pr complex revealed that Fab5 binds a flexible loop distal from the active site and dimer interface which we call the latch loop. In HCMV Pr dimers, this loop secures the C-terminal tail to the protein core. Structure-guided mutagenesis confirmed that the latch loop is essential for HCMV Pr dimerization and activity. This loop is structurally conserved across all HHV Prs, and we show its functional role in Kaposis Sarcoma-associated herpesvirus (KSHV) Pr as well. The latch loop plays a mechanistic role in the conformational transition required for HHV Pr activity, and it forms a cryptic site that presents a new avenue for future allosteric inhibitor development.

biochemistry↗

bioRxiv2025

Tissue-wide, synchronous Erk oscillations time the segmentation of the zebrafish notochord

The generation of a segmented body plan is a hallmark of vertebrate development. Biological oscillators provide a mechanism for timing the formation of repeated structures, yet to date only a few examples of signaling oscillators have been identified in development. Here, we show that the periodic addition of mineralizing segments in the zebrafish notochord is timed by tissue-wide oscillations of Erk activity. We report delayed oscillations in the transcription of spry and dusp genes, suggesting that they act as negative feedback. Erk activity is regulated by EGFR signaling and increased egf expression marks the emergence of oscillations via an infinite-period bifurcation, revealing the mechanism controlling the onset of notochord segmentation and the tunability of the oscillator. Our results show a remarkable degree of synchronization across the notochord and reveal an instance of biological clocks timing a patterning process, crucial for the development of the vertebral column from the notochord.

developmental biology↗

bioRxiv2024

NoButter: An R package for reducing transcript dis-persion in CosMx Spatial Molecular Imaging Data

MotivationAdvances in spatial transcriptomics technologies at single-cell resolution have high-lighted the need for innovative quality assessment approaches and improved analytical tools. Imaging-based spatial transcriptomics technologies, such as the CosMx Spatial Molecular Imager (SMI), provide the location and abundance of transcripts through multifocal imaging. Optical sections (or Z-slices) form a Z-stack that represents the tissue depth. Transcript dispersion can be observed across these Z-slice and introduce considerable levels of technical noise to the data that can negatively impact downstream analysis. Package FunctionalityNoButter is an R package designed to evaluate transcript dispersion in CosMx SMI spatial transcriptomics data. Using the raw data, the transcript distribution is assessed for each Z-slice of a Z-stack across multiple fields of views (FOVs). To systematically identify transcript dispersion, the percentage of transcripts located outside cell boundaries is calculated. Z-slices exhibiting high levels of transcript dispersion can be excluded, while high-confidence transcripts are preserved. Usage ScenarioTo demonstrate the functionalities of NoButter, spatial transcriptomics data was generated using the CosMx SMI for lymph node tissue, a lung sample, and two triple-negative breast cancers (TNBCs). Use cases illustrate substantial transcript dispersion in optical planes closer to the glass slide. In these Z-slices, on average, an additional 10% of the transcripts were discarded using NoButter. Cleaning such Z-slices with high dispersion rates reduces technical noise and improves the overall quality of the spatial transcriptomics data. AvailabilityThe package can be accessed at https://github.com/cancerbioinformatics/NoButter.

bioinformatics↗

bioRxiv2023

eIF4A1 is essential for reprogramming the translational landscape of Wnt-driven colorectal cancers

Dysregulated translation is a hallmark of cancer. Targeting the translational machinery represents a therapeutic avenue which is being actively explored. eIF4A inhibitors target both eIF4A1, which promotes translation as part of the eIF4F complex, and eIF4A2, which can repress translation via the CCR4-NOT complex. While high eIF4A1 expression is associated with poor patient outcome, the role of eIF4A2 in cancer remains unclear. Furthermore, the on-target toxicity of targeting specific eIF4A paralogues in healthy tissue is under-explored. We show that while loss of either paralogue is tolerated in the wild-type intestine, eIF4A1 is specifically required to support the translational demands of oncogenic Wnt signalling. Intestinal tumourigenesis is suppressed in colorectal cancer models following loss of eIF4A1 but accelerated following loss of eIF4A2, while eIF4A inhibition with eFT226 mimics loss of eIF4A1 in these models.

cancer biology↗

bioRxiv2023

Axial segmentation by iterative mechanical signaling

In bony fishes, formation of the vertebral column, or spine, is guided by a metameric blueprint established in the epithelial sheath of the notochord. Generation of the notochord template begins days after somitogenesis and even occurs in the absence of somite segmentation. However, patterning defects in the somites lead to imprecise notochord segmentation, suggesting these processes are linked. Here, we reveal that spatial coordination between the notochord and the axial musculature is necessary to ensure segmentation of the zebrafish spine both in time and space. We find that the connective tissues that anchor the axial skeletal musculature, known as the myosepta in zebrafish, transmit spatial patterning cues necessary to initiate notochord segment formation, a critical pre-patterning step in spine morphogenesis. When an irregular pattern of muscle segments and myosepta interact with the notochord sheath, segments form non-sequentially, initiate at atypical locations, and eventually display altered morphology later in development. We determine that locations of myoseptum-notochord connections are hubs for mechanical signal transmission, which are characterized by localized sites of deformation of the extracellular matrix (ECM) layer encasing the notochord. The notochord sheath responds to the external mechanical changes by locally augmenting focal adhesion machinery to define the initiation site for segmentation. Using a coarse-grained mathematical model that captures the spatial patterns of myoseptum-notochord interactions, we find that a fixed-length scale of external cues is critical for driving sequential segment patterning in the notochord. Together, this work identifies a robust segmentation mechanism that hinges upon mechanical coupling of adjacent tissues to control patterning dynamics.

developmental biology↗

bioRxiv2021

Increased apoptotic priming of glioblastoma enables therapeutic targeting by BH3-mimetics

IDH wild-type glioblastoma (GBM) is the most prevalent malignant primary brain tumour in adults. GBM typically has a poor prognosis, mainly due to a lack of effective treatment options leading to tumour persistence or recurrence. Tackling this, we investigated the therapeutic potential of targeting anti-apoptotic BCL-2 proteins in GBM. Levels of anti- apoptotic BCL-xL and MCL-1 were consistently increased in GBM compared with non- malignant cells and tissue. Moreover, we found that relative to their differentiated counterparts, patient-derived GBM stem-like cells also displayed higher expression of anti- apoptotic BCL-2 family members. Surprisingly, high anti-apoptotic BCL-xL and MCL-1 expression correlated with heightened susceptibility of GBM to BCL-2 family protein- targeting BH3-mimetics. This is indicative of increased apoptotic priming. Indeed, GBM displayed an obligate requirement for MCL-1 expression in both tumour development and maintenance. Investigating this apoptotic sensitivity, we found that sequential inhibition of BCL-xL and MCL-1 led to robust anti-tumour responses in vivo, in the absence of overt toxicity. These data demonstrate that BCL-xL and MCL-1 pro-survival function is a fundamental prerequisite for GBM survival that can be therapeutically exploited by BH3- mimetics.

cancer biology↗

bioRxiv2019

Variants in the degron of AFF3 cause a multi-system disorder with mesomelic dysplasia, horseshoe kidney and developmental and epileptic encephalopathy

The ALF transcription factor paralogs, AFF1, AFF2, AFF3 and AFF4, are components of the transcriptional super elongation complex that regulates expression of genes involved in neurogenesis and development. We describe a new autosomal dominant disorder associated with de novo missense variants in the degron of AFF3, a nine amino acid sequence important for its degradation. Consistent with a causative role of AFF3 variants, the mutated AFF3 proteins show reduced clearance. Ten affected individuals were identified, and present with a recognizable pattern of anomalies, which we named KINSSHIP syndrome (KI for horseshoe KIdney, NS for Nievergelt/Savarirayan type of mesomelic dysplasia, S for Seizures, H for Hypertrichosis, I for Intellectual disability and P for Pulmonary involvement), partially overlapping the AFF4 associated CHOPS syndrome. An eleventh individual with a microdeletion encompassing only the transactivation domain and degron motif of AFF3 exhibited overlapping clinical features. A zebrafish overexpression model that shows body axis anomalies provides further support for the pathological effect of increased amount of AFF3 protein.\n\nWhereas homozygous Aff3 knockout mice display skeletal anomalies, kidney defects, brain malformation and neurological anomalies, knock-in animals modeling the microdeletion and the missense variants identified in affected individuals presented with lower mesomelic limb deformities and early lethality, respectively.\n\nTranscriptome analyses as well as the partial phenotypic overlap of syndromes associated with AFF3 and AFF4 variants suggest that ALF transcription factors are not redundant in contrast to what was previously suggested

genetics↗