Biology subjects

Higgins, C.

Publications and source records attributed to Higgins, C..

12 recordsLinked to original sources

bioRxiv2026

FLIP is essential for oncogenic KRAS-driven lung cancer

Mutations in KRAS represent the most common oncogenic event in human cancer and occur in approximately 30% of lung adenocarcinomas. The mechanisms by which lung tumours evade apoptosis induced by oncogenic KRAS-driven stress remain incompletely understood. Here, we identify the anti-apoptotic regulator FLIP (CFLAR) as a critical dependency in KRAS-mutant lung cancers. We demonstrate that KRAS-mutant human lung cancer cell lines exhibit elevated FLIP expression and enhanced dependence on FLIP for survival compared to KRAS wild-type counterparts. Subsequently, using genetically engineered mouse models (GEMMs), we show that FLIP is essential for Kras-driven lung tumour development in vivo. In vitro, FLIP-deficient lung cancer cells display spontaneous, caspase-8- dependent apoptosis and hyper-sensitivity to the immune/inflammatory cytokines TNF and TRAIL. Strikingly, FLIP-null lung cancer cells fail to engraft even in highly immunodeficient orthotopic models that lack TRAIL-expressing immune cells but retain TNF-expressing monocytes. Moreover, silencing of TNFR1 or TNF but not TRAIL-R2 rescued constitutive caspase-8-dependent apoptosis in FLIP null lung cancer cells, implicating TNF/TNFR1 in mediating this apoptotic response. Mechanistically, we find that mutant KRAS sustains FLIP expression via ERK1/2 signalling, thereby protecting cells from caspase-8 activation. Notably, KRAS inhibition downregulates FLIP, sensitising cells to TNF- and TRAIL-induced apoptosis. These findings uncover a novel KRAS-ERK-FLIP axis that protects tumour cells from caspase-8-mediated apoptosis and reveal FLIP as a key survival factor co-opted by KRAS-mutant lung cancers. Beyond identifying FLIP as a promising therapeutic target in KRAS mutant lung cancer, our work also provides mechanistic insight into the pro-apoptotic effects of KRAS inhibitors and suggests that FLIP expression may serve as a predictive biomarker to enhance patient stratification and the therapeutic efficacy of these agents in lung cancer.

cancer biology↗

bioRxiv2026

Anterior default mode brain state dynamics predict depressive symptom severity before and during TMS treatment

Transcranial magnetic stimulation (TMS) targeting the left dorsolateral prefrontal cortex is known to progressively reduce symptoms of depression. However, the neural mechanisms supporting this effect are poorly understood. To address this gap, we analysed longitudinal EEG recordings from 70 people undergoing TMS therapy and fitted an established dynamic network model of resting-state activity. Greater baseline symptom severity was associated with reduced occupancy of and fewer transitions into an anterior default mode brain state, alongside increased activity in a posterior default mode state. During treatment, decreases in anterior default mode state engagement following TMS predicted symptom improvement in the latter half of the intervention. Brain state activity exhibited structured, cyclical dynamics, with slower cycles linked to greater baseline severity. These findings suggest that symptoms of depression are characterised by gradual alterations in brain state dynamics, highlighting a central and dissociable role of default mode brain states in the persistence and remission of symptoms.

neuroscience↗

bioRxiv2025

Canonical Hidden Markov Model Networks for Studying M/EEG

Dynamic brain networks identified in magneto/encephalography (M/EEG) recordings provide new insights into human brain activity. One established method uses Hidden Markov Models (HMMs) and has been shown to infer reproducible, fast-switching brain networks in a variety of cognitive and disease conditions. Often these studies are done on small bespoke (boutique) datasets (N < 100) and analysed in isolation of other M/EEG datasets. Instead of training a new model for each boutique study, which is computationally expensive, we propose the use of a canonical HMM. This provides a common reference through which different studies can be described using the same set of networks. We provide HMMs for a range of model orders (4-16 states) in parcellated source space and sensor space. These HMMs were trained on 1849 MEG recordings (N = 621, 18-88 years old, 194 hours), capturing population variability in both rest and task data. We illustrate applications of this canonical HMM approach in parcellated source space using boutique MEG and EEG datasets. Applying the canonical HMM in parcel space requires the boutique dataset to be preprocessed and source reconstructed in the same way as the canonical HMM training data. Applying the canonical HMM in the sensor space requires the same sensor layout and preprocessing as the canonical HMM training data. The canonical HMMs have been made publicly available as an open-access resource, providing sets of canonical brain networks that can be used to compare individuals within and across a range of datasets. HighlightsO_LIInstead of training a new HMM for every study, which is computationally expensive and can lead to less reliable results, we propose a canonical HMM instead. C_LIO_LIThe canonical HMM provides a common reference through which different studies can be described using the same set of networks. C_LIO_LIThe canonical HMM was learnt from 1849 MEG recordings (194 hours of data; resting state and task) in participants aged 18-88 years. C_LIO_LIWe demonstrate applications of the canonical HMM on three parcellated source space boutique studies: an Alzheimers resting-state MEG dataset, a working memory task MEG dataset, and a resting-state EEG dataset. C_LIO_LIWe transfer the parcel-level canonical HMM to sensor space, avoiding the need for source reconstruction. C_LIO_LIWe release the canonical HMM (for varying model orders) as an open-access resource for M/EEG research. C_LI

neuroscience↗

bioRxiv2025

Whole-genome sequence of Potamopyrgus antipodarum: a model system for the maintenance of sexual reproduction reveals a recent whole-genome duplication

Key unanswered questions in biology center on the causes, consequences, and maintenance of sexual reproduction ("sex"). Genome-driven processes are central to the evolutionary and genetic mechanisms inherent to sex, making genomic resources a fundamental part of answering these questions. We present the first genome assembly for a species that is uniquely well-suited for the study of (a)sex in nature, Potamopyrgus antipodarum. This New Zealand snail is unusual in featuring multiple separate transitions from obligately sexual to obligately asexual reproduction, leading to the coexistence of phenotypically similar sexual and asexual forms, a feature that is required to directly study the maintenance of sex. These separately derived asexual lineages constitute separate evolutionary experiments, providing a powerful means of characterizing how the absence of sex affects genome evolution. Our genome assembly provides critical steps towards understanding causes and consequences of sex in this system and important resources for the rapidly growing P. antipodarum and molluscan genomics research community. In characterizing this genome, we uncovered unexpected evidence for a recent whole-genome duplication (WGD) in P. antipodarum. This discovery sets the stage for using P. antipodarum to evaluate processes of rediploidization following WGD and assess whether WGD might drive transitions to asexuality.

genomics↗

bioRxiv2023

Genome evolution and introgression in the New Zealand mud snails Potamopyrgus estuarinus and Potamopyrgus kaitunuparaoa

We have sequenced, assembled, and analyzed the nuclear and mitochondrial genomes and transcriptomes of Potamopyrgus estuarinus and Potamopyrgus kaitunuparaoa, two prosobranch snail species native to New Zealand that together span the continuum from estuary to freshwater. These two species are the closest known relatives of the freshwater species P. antipodarum--a model for studying the evolution of sex, host-parasite coevolution, and biological invasiveness--and thus provide key evolutionary context for understanding its unusual biology. The P. estuarinus and P. kaitunuparaoa genomes are very similar in size and overall gene content. Comparative analyses of genome content indicate that these two species harbor a near-identical set of genes involved in meiosis and sperm functions, including seven genes with meiosis-specific functions. These results are consistent with obligate sexual reproduction in these two species and provide a framework for future analyses of P. antipodarum--a species comprising both obligately sexual and obligately asexual lineages, each separately derived from a sexual ancestor. Genome-wide multigene phylogenetic analyses indicate that P. kaitunuparaoa is likely the closest relative to P. antipodarum. We nevertheless show that there has been considerable introgression between P. estuarinus and P. kaitunuparaoa. That introgression does not extend to the mitochondrial genome, which appears to serve as a barrier to hybridization between P. estuarinus and P. kaitunuparaoa. Nuclear-encoded genes whose products function in joint mitochondrial-nuclear enzyme complexes exhibit similar patterns of non-introgression, indicating that incompatibilities between the mitochondrial and the nuclear genome may have prevented more extensive gene flow between these two species. Significance StatementNo whole-nuclear genome sequences are currently available for snails of the genus Potamopyrgus, best known for Potamopyrgus antipodarum, an invasive species of rivers and lakes worldwide, and a famous model for the study of the evolution of sex. We have sequenced and analyzed the genome of sexual P. estuarinus and P. kaitunuparaoa, the closest known relatives of P. antipodarum. We show that 1) the genomes are very similar in gene content and size, 2) P. kaitunuparaoa is the closest relative to P. antipodarum, 3) significant introgression has occurred between P. estuarinus and P. kaitunuparaoa; these genomes set the stage for powerful direct analyses of the genomic features, e.g., sex to asexual transitions and invasive success, that make P. antipodarum unique.

evolutionary biology↗

bioRxiv2023

Second Harmonic Generation Imaging Reveals Entanglement of Collagen Fibers in the Elephant Trunk Skin Dermis

Form-function relationships often have tradeoffs: if a material is tough, it is often inflexible, and vice versa. This is particularly relevant for the elephant trunk, where the skin should be protective yet elastic. To investigate how this is achieved, we used classical histochemical staining and second harmonic generation microscopy to describe the morphology and composition of elephant trunk skin. We report structure at the macro and micro scales, from the thickness of the dermis to the interaction of 10 m thick collagen fibers. We analyzed several sites along the length of the trunk, to compare and contrast the dorsal-ventral and proximal-distal skin morphologies and compositions. We find the dorsal skin of the elephant trunk can have keratin armor layers over 2mm thick, which is nearly 100 times the thickness of the equivalent layer in human skin. We also found that the structural support layer (the dermis) of elephant trunk contains a distribution of collagen-I (COL1) fibers in both perpendicular and parallel arrangement. The bimodal distribution of collagen is seen across all portions of the trunk, and is dissimilar from that of human skin where one orientation dominates within a body site. We hypothesize that this distribution of COL1 in the elephant trunk allows both flexibility and load-bearing capabilities. Additionally, when viewing individual fiber interaction of 10 m thick collagen, we find the fiber crossings per unit volume are five times more common than in human skin, suggesting that the fibers are entangled. We surmise that these intriguing structures permit both flexibility and strength in the elephant trunk. The complex nature of the elephant skin may inspire the design of materials that can combine strength and flexibility.

bioengineering↗

bioRxiv2023

Large-scale cortical networks are organized in structured cycles

The brain needs to perform a diverse set of cognitive functions essential for survival, but it is unknown how it is organized to ensure that each of these functions is fulfilled within a reasonable period. One way in which this requirement can be met is if each of these cognitive functions occur as part of a repeated cycle. Here, we studied the temporal evolution of canonical large-scale cortical networks, and show that while network dynamics are stochastic, the overall ordering of their activity forms a robust cyclical pattern. This cyclical structure groups states with similar function and spectral content at specific phases of the cycle and occurs at timescales of (300-1000 ms). These results are reproduced in five large magnetoencephalography (MEG) datasets. Moreover, we show that metrics that characterize the cycle strength and speed are heritable, and relate to age, cognition, and behavioural performance. These results reveal for the first time that the activations of a canonical set of large-scale cortical networks are organised in an inherently cyclical manner, ensuring periodic activation of essential cognitive functions.

neuroscience↗

bioRxiv2023

Hydraulic Conductivity of The Hemp Stems Under Water Stress

The hydraulic conductivity of hemp stems under water-stress conditions was investigated to assess the impact on water transport from the root to the leaves. Water-stress conditions induce embolism (cavitation) in xylem channels, thereby affecting water flow. The percentage loss of water transfer ability within the xylem channels can be represented by a vulnerability curve (VC). This study utilized an air injection technique to induce embolisms in the stem and measured the subsequent changes in hydraulic conductivity using a specialized measurement apparatus. The results revealed that the shape of the vulnerability curve for hemp was influenced by the xylem area, which is an atypical finding with no prior evidence in other plant species. The statistical analysis confirmed the significance of this effect (p-value=0.003 at 95% confidence intervals). Consequently, a non-traditional mathematical equation (simple power law) was developed to describe the relationship between pressure and xylem area. Furthermore, our findings demonstrated that hemp stems are more responsive to water stress compared to other plant species documented in previous literature. The minimum pressure (0.15 MPa) at which initial cavitation is observed and the maximum pressure ([~]2.4 MPa) at which all stem conductance is lost were among the lowest reported values, indicating that hemp growth may be significantly affected by deficit irrigation strategies. Thus, careful monitoring of the irrigation schedule is crucial, particularly for younger stems with smaller xylem cross-sectional areas. These insights into the hydraulic behavior of hemp can contribute to the development of improved irrigation strategies in agriculture, ultimately enhancing water-use efficiency and optimizing crop production. HighlightO_LIThe hydraulic conductivity of hemp stems under water-stress conditions was investigated to assess the impact on water transport from the root to the leaves. C_LIO_LIThe results revealed that the shape of the vulnerability curve for hemp was influenced by the xylem area, which is an atypical finding with no prior evidence in other plant species. C_LIO_LIOur findings demonstrated that hemp stems are more responsive to water stress compared to other plant species documented in previous literature. C_LIO_LIThe minimum pressure (0.15 MPa) at which initial cavitation is observed and the maximum pressure ([~]2.4 MPa) at which all stem conductance is lost were among the lowest reported values, indicating that hemp growth may be significantly affected by deficit irrigation strategies. C_LIO_LIThus, careful monitoring of the irrigation schedule is crucial, particularly for younger stems with smaller xylem cross-sectional areas. These insights into the hydraulic behavior of hemp can contribute to the development of improved irrigation strategies in agriculture, ultimately enhancing water-use efficiency and optimizing crop production. C_LI

cell biology↗

bioRxiv2022

Mixtures of large-scale dynamic functional brain network modes

Accurate temporal modelling of functional brain networks is essential in the quest for understanding how such networks facilitate cognition. Researchers are beginning to adopt time-varying analyses for electrophysiological data that capture highly dynamic processes on the order of milliseconds. Typically, these approaches, such as clustering of functional connectivity profiles and Hidden Markov Modelling (HMM), assume mutual exclusivity of networks over time. Whilst a powerful constraint, this assumption may be compromising the ability of these approaches to describe the data effectively. Here, we propose a new generative model for functional connectivity as a time-varying linear mixture of spatially distributed statistical "modes". The temporal evolution of this mixture is governed by a recurrent neural network, which enables the model to generate data with a rich temporal structure. We use a Bayesian framework known as amortised variational inference to learn model parameters from observed data. We call the approach DyNeMo (for Dynamic Network Modes), and show using simulations it outperforms the HMM when the assumption of mutual exclusivity is violated. In resting-state MEG, DyNeMo reveals a mixture of modes that activate on fast time scales of 100-150 ms, which is similar to state lifetimes found using an HMM. In task MEG data, DyNeMo finds modes with plausible, task-dependent evoked responses without any knowledge of the task timings. Overall, DyNeMo provides decompositions that are an approximate remapping of the HMMs while showing improvements in overall explanatory power. However, the magnitude of the improvements suggests that the HMMs assumption of mutual exclusivity can be reasonable in practice. Nonetheless, DyNeMo provides a flexible framework for implementing and assessing future modelling developments.

neuroscience↗

bioRxiv2021

Brain stimulation boosts perceptual learning by altering sensory GABAergic plasticity and functional connectivity

Interpreting cluttered scenes --a key skill for successfully interacting with our environment-- relies on our ability to select relevant sensory signals while filtering out noise. Training is known to improve our ability to make these perceptual judgements by altering local processing in sensory brain areas. Yet, the brain-wide network mechanisms that mediate our ability for perceptual learning remain largely unknown. Here, we combine transcranial direct current stimulation (tDCS) with multi-modal brain measures to modulate cortical excitability during training on a signal-in-noise task (i.e. detection of visual patterns in noise) and test directly the link between processing in visual cortex and its interactions with decision-related areas (i.e. posterior parietal cortex). We test whether brain stimulation alters inhibitory processing in visual cortex, as measured by magnetic resonance spectroscopy (MRS) of GABA and functional connectivity between visual and posterior parietal cortex, as measured by resting state functional magnetic resonance imaging (rs-fMRI). We show that anodal tDCS during training results in faster learning and decreased GABA+ during training, before these changes occur for training without stimulation (i.e. sham). Further, anodal tDCS decreases occipito-parietal interactions and time-varying connectivity across the visual cortex. Our findings demonstrate that tDCS boosts learning by accelerating visual GABAergic plasticity and altering interactions between visual and decision-related areas, suggesting that training optimises gain control mechanisms (i.e. GABAergic inhibition) and functional inter-areal interactions to support perceptual learning.

neuroscience↗

bioRxiv2019

Regulation of FLIP(L) and TRAIL-R2 signalling by the SCFSkp2 Ubiquitin Ligase Complex

Depending on its expression levels, the long splice form of the pseudo-caspase FLIP (FLIP(L)) can act as an inhibitor (high expression) or activator (low expression) of apoptosis induction by the TRAIL-R2 death-inducing signalling complex (DISC); its expression levels are therefore tightly regulated. Here, we demonstrate that the Skp1-Cullin-1-F-box (SCF) Cullin-Ring E3 Ubiquitin Ligase complex containing Skp2 (SCFSkp2) regulates the stability of FLIP(L) (but not the short splice form FLIP(S)), and, unusually, this is mediated by direct binding of FLIP(L) to Cullin-1 rather than via Skp2. By fine mapping the interaction of FLIP(L) with Cullin-1 to the large subunit of its pseudo-caspase domain, we found that the interaction is significantly stronger with FLIP(L)s DISC-processed p43-form. Importantly, this interaction disrupts the ability of p43-FLIP to interact with FADD, caspase-8 and another DISC component, TRAF2. Moreover, we find that SCFSkp2 associates with TRAIL-R2 constitutively and does so independently of FLIP(L) and other canonical DISC components. Inhibition of Cullin-1 expression (using siRNA) or activity (using a NEDDylation inhibitor, MLN4924) enhanced FLIP(L) and TRAF2 levels at the TRAIL-R2 DISC and enhanced caspase-8 processing. This suggests that processing of FLIP(L) to p43-FLIP at the TRAIL-R2 DISC enhances its interaction with co-localised SCFSkp2, leading to disruption of p43-FLIPs association with the DISC thereby altering caspase-8 processing. These findings provide important new insights into how FLIP(L) expression and TRAIL-R2 signaling is controlled.

molecular biology↗

bioRxiv2018

Analysis of head and neck carcinoma progression reveals novel and relevant stage-specific genetic changes associated with immortalisation and malignancy.

Head and neck squamous cell carcinoma (HNSCC) is a widely prevalent cancer globally with high mortality and morbidity. We report here changes in the genomic landscape in the development of HNSCC from potentially premalignant lesions (PPOLS) to malignancy and lymph node metastases. Frequent likely pathological mutations are restricted to a relatively small set of genes including TP53, CDKN2A, FBXW7, FAT1, NOTCH1 and KMT2D; these arise early in tumour progression and are present in PPOLs with NOTCH1 mutations restricted to cell lines from lesions that subsequently progressed to HNSCC. The most frequent genetic changes are of consistent somatic copy number alterations (SCNA). The earliest SCNAs involved deletions of CSMD1 (8p23.2), FHIT (3p14.2) and CDKN2A (9p21.3) together with gains of chromosome 20. CSMD1 deletions or promoter hypermethylation were present in all of the immortal PPOLs and occurred at high frequency in the immortal HNSCC cell lines (promoter hypermethylation ~63%, hemizygous deletions ~75%, homozygous deletions ~18%). Forced expression of CSMD1 in the HNSCC cell line H103 showed significant suppression of proliferation (p=0.0053) and invasion in vitro (p=5.98X10-5) supporting a role for CSMD1 inactivation in early head and neck carcinogenesis. In addition, knockdown of CSMD1 in the CSMD1-expressing BICR16 cell line showed significant stimulation of invasion in vitro (p=1.82 x 10-5) but not cell proliferation (p=0.239). HNSCC with and without nodal metastases showed some clear differences including high copy number gains of CCND1, hsa-miR-548k and TP63 in the metastases group. GISTIC peak SCNA regions showed significant enrichment (adj P<0.01) of genes in multiple KEGG cancer pathways at all stages with disruption of an increasing number of these involved in the progression to lymph node metastases. Sixty-seven genes from regions with statistically significant differences in SCNA/LOH frequency between immortal PPOL and HNSCC cell lines showed correlation with expression including 5 known cancer drivers.\n\nLay SummaryCancers affecting the head and neck region are relatively common. A large percentage of these are of one particular type; these are generally detected late and are associated with poor prognosis. Early detection and treatment dramatically improve survival and reduces the damage associated with the cancer and its treatment. Cancers arise and progress because of changes in the genetic material of the cells. This study focused on identifying such changes in these cancers particularly in the early stages of development, which are not fully known. Identification of these changes is important in developing new treatments as well as markers of behaviour of cancers and also the early or premalignant lesions. We used a well-characterised panel of cell lines generated from premalignant lesions as well as cancers, to identify mutations in genes, and an increase or decrease in number of copies of genes. We mapped new and previously identified changes in these cancers to specific stages in the development of these cancers and their spread. We additionally report here for the first time, alterations in CSMD1 gene in early premalignant lesions; we further show that this is likely to result in increased ability of the cells to spread and possibly, multiply faster as well.

cancer biology↗