Biology subjects

Bryant, A.

Publications and source records attributed to Bryant, A..

10 recordsLinked to original sources

bioRxiv2026

Human cytomegalovirus UL2 is not required for lytic replication or viral latency and reactivation

Human cytomegalovirus (HCMV) remains a significant cause of morbidity and mortality in transplant patients and is a major cause of congenital disease. Understanding the role of viral genes during infection, viral replication, and viral latency establishment and reactivation is key to the development of new antivirals, which are currently limited. The viral RL11 is a conserved, but understudied viral locus, with previously described roles in specific phases of the viral lifecycle. Antisense to and within the RL11 region are two unrelated genes, including UL2. In this study, we investigate the role of UL2 during viral infection and find that UL2 is not required for lytic replication nor required for viral infection, latency establishment (or persistence) and reactivation in either THP-1 monocytes or primary human hematopoietic progenitor cells (HPCs). As viral genes are evolutionarily optimized for viral fitness, this study suggests that HCMV UL2 has a role outside of viral fitness and may be a unique target or contributor to HCMV-mediated processes including immune response or other viral co-factor regulation.

microbiology↗

bioRxiv2026

A complete human pancreatic cancer genome

Cancer genome sequencing is essential for understanding tumor evolution and advancing precision medicine.1 However, reference gaps and germline variants obscure detection of small and large somatic variants and methylation in repetitive regions.1-3 It is common for tumor cells to gain or lose chromosome arms due to somatic structural changes that occur inside highly repetitive satellite DNA sequences in the centromeres.4 To identify the full spectrum of somatic variants, including complex rearrangements, we construct and curate near-complete, haplotype-resolved assemblies of the most recent common ancestor of an early-passage broadly-consented hypodiploid pancreatic cancer cell line and matched normal tissues. The tumor assembly completely recapitulates all 35 tumor chromosomes observed with karyotyping, with multiple translocation-induced hybrid chromosomes. The hybrid chromosomes contain putative functional dicentric and fused centromeres, nested foldback inversions causing 14 breakpoints with a haplotype switch in a single event, and centromeric satellite tandem duplications up to 136 kbp. Direct comparison of tumor and normal assembly haplotypes uncovers >7,000 variants altering >1 Mbp of sequence in repetitive regions that have been hidden by reference gaps and germline variants. 44 % of somatic small variants change representation because they alter germline variants on GRCh38, impacting mutational signatures and kataegis/omikli clusters. Most somatic LINE insertions originate from two hypomethylated non-reference germline LINE insertions, highlighting their impact on insertion mutation burden. These assemblies demonstrate that centromeric, acrocentric, and telomeric regions conventionally excluded from analysis harbor extensive somatic and epigenetic changes. Resolving complete tumor genomes enables a deeper understanding of cancer structural plasticity and the endpoints of breakage-fusion-bridge cycles. These assembled, curated paired normal-tumor benchmarks will serve as a critical foundation for developing future algorithms to characterize the most intractable regions of cancer genomes.

genomics↗

bioRxiv2024

Engineering Human ARMMs as Therapeutic Non-Viral Vehicles for in vivo Delivery of Genome Editing Payloads

The ability to edit the human genome to treat previously incurable diseases or to modify previously undruggable targets has the potential to transform the lives of patients. However, delivery of genome editing machineries in vivo, and in a transient manner, continues to be a major challenge. We engineered human cell-derived ARRDC1-mediated microvesicles (ARMMs) as non-viral vehicles that mediate intracellular delivery of proteins, including DNA-modifying enzymes such as Cre recombinase and Cas9/guide RNA ribonucleoproteins (RNPs). ARMMs packaged multiple payloads per vesicle in our production system, yielding dose-dependent functional delivery of Cre or Cas9/gRNA RNP to a variety of cell types, including primary mouse and human cells. Oropharyngeal aspiration of ARMMs loaded with Cre led to biodistribution to alveolar macrophages (AMs), whereas intravenous administration predominantly to Kupffer cells (KCs), liver sinusoidal endothelial cells (LSECs), and splenocytes. Suprisingly, one administration of ARMMs loaded with Cas9 RNPs by oropharyngeal aspiration or intravenously resulted in efficient knockout of multiple genes in AMs or KCs, suggesting potential therapeutic utility. Through intravenous administration of ARMMs loaded with Cas9/NLRP3 gRNA we showed amelioration of drug-induced liver injury in a mouse model, supporting the use of ARMMs as human cell-derived therapeutic vehicles for genome editor delivery in vivo.

bioengineering↗

bioRxiv2024

DeepSomatic: Accurate somatic small variant discovery for multiple sequencing technologies

Somatic variant detection is an integral part of cancer genomics analysis. While most methods have focused on short-read sequencing, long-read technologies now offer potential advantages in terms of repeat mapping and variant phasing. We present DeepSomatic, a deep learning method for detecting somatic SNVs and insertions and deletions (indels) from both short-read and long-read data, with modes for whole-genome and exome sequencing, and able to run on tumor-normal, tumor-only, and with FFPE-prepared samples. To help address the dearth of publicly available training and benchmarking data for somatic variant detection, we generated and make openly available a dataset of five matched tumor-normal cell line pairs sequenced with Illumina, PacBio HiFi, and Oxford Nanopore Technologies, along with benchmark variant sets. Across samples and technologies (short-read and long-read), DeepSomatic consistently outperforms existing callers, particularly for indels.

bioinformatics↗

bioRxiv2024

Ionizing radiation has negligible effects on the age, telomere length, and corticosterone levels of Chornobyl tree frogs

Pollutants, such as ionizing radiation, released at high levels by human activities can shape ecological and evolutionary processes. The accident occurred at Chornobyl nuclear power plant (Ukraine, April 1986) contaminated a large extension of territory after the deposition of radioactive material. Beyond the immediate negative impact caused by the accident, it is still under debate whether the chronic exposure to the radiation levels currently present in the area signifies a serious threat for organisms. One hypothesis suggests that current levels of radiation may cause unobservable damage in the short-term, but have long-term effects such as decreases in longevity. Here, we investigate through a field-based approach, whether current levels of radiation in Chornobyl negatively impact the age of a semi-aquatic vertebrate, the Eastern tree frog Hyla orientalis. We also explore whether radiation induces changes in an ageing marker, telomere length, or in the stress hormone corticosterone. We found no effect of total individual absorbed radiation (including both external and internal exposure) on frog age (n = 197 individuals sampled in three consecutive years). We also did not find any relationship between individual absorbed radiation and telomere length, but a negative relationship between individual absorbed radiation and corticosterone levels. Our results suggest that radiation levels currently experienced by tree frogs in Chornobyl may not be high enough to cause severe chronic damage to semi-aquatic vertebrates such as this species. This is the first study addressing age and stress hormones in Chornobyl wildlife, and thus future research will confirm if these results can be extended to other taxa.

ecology↗

bioRxiv2023

Emergent spatiotemporal patterning of synthetic Notch signal transduction in vivo

Cell-cell communication through direct contact, or juxtacrine signaling, is important in development, disease, and many areas of physiology. Synthetic forms of juxtacrine signaling can be precisely controlled and operate orthogonally to native processes, making them a powerful reductionist tool with which to address fundamental questions in cell-cell communication in vivo. Here we investigate how cell-cell contact length and tissue growth dynamics affect juxtacrine signal responses through implementing a custom synthetic gene circuit in Drosophila wing imaginal discs alongside mathematical modeling to determine synthetic Notch (synNotch) activation patterns. We find that the area of contact between cells largely determines the extent of syn-Notch activation, leading to the prediction that the shape of the interface between signal-sending and signal-receiving cells will impact the magnitude of the synNotch response. Notably, synNotch outputs form a graded spatial profile that extends several cell diameters from the signal source, providing evidence that the response to juxtacrine signals can persist in cells as they proliferate away from source cells, or that cells remain able to communicate directly over several cell diameters. Our model suggests the former mechanism may be sufficient, since it predicts graded outputs without diffusion or long-range cell-cell communication. Overall, we identify that cell-cell contact area together with output synthesis and decay rates likely govern the pattern of synNotch outputs in both space and time during tissue growth, insights that may have broader implications for juxtacrine signaling in general.

biophysics↗

bioRxiv2022

FBXO11 deficiency in mice impairs lung development and aggravates cigarette smoke-induced airway fibrosis

Small airway fibrosis is a common pathology of chronic obstructive pulmonary disease (COPD) and contributes to airflow obstruction. However, the underlying fibrogenic mechanism is poorly understood. Epithelial-mesenchymal transition (EMT) has been proposed as a driver of fibrosis. EMT occurs in the airways of COPD patients and smokers, but it remains elusive whether EMT may contribute to airway fibrosis. We previously reported that FBXO11 is a critical suppressor of EMT and Fbxo11 deficiency in mice causes neonatal lethality and EMT in epidermis. Here, we found that Fbxo11-deficient mouse embryonic lungs showed impaired epithelial differentiation, excess fibroblast cells surrounding the airways, and thickened interstitial mesenchyme. We further generated conditional mutant mice to ablate Fbxo11 selectively in the club airway epithelial cells in adult mice, which induced partial EMT in the airways. To determine the effect of EMT on airway fibrosis, Fbxo11 conditional mutant mice were exposed to cigarette smoke. Airway-specific loss of Fbxo11 markedly enhanced smoking-induced airway fibrotic remodeling and collagen deposition. Taken together, our study suggests that EMT in the airway epithelium exacerbates cigarette smoke-induced airway fibrosis.

cell biology↗

bioRxiv2020

Heme Impairs Alveolar Epithelial Sodium Channels Post Toxic Gas Inhalation

We previously reported that cell-free heme (CFH) is increased in the plasma of patients with acute and chronic lung injury and causes pulmonary edema in animal model of acute respiratory distress syndrome (ARDS) post inhalation of halogen gas. However, the mechanisms by which CFH causes pulmonary edema are unclear. Herein we report for the first time the presence of CFH and chlorinated lipids (formed by the interaction of halogen gas, Cl2, with plasmalogens) in the plasma of patients and mice exposed to Cl2 gas. Ex vivo incubation of red blood cells (RBC) with halogenated lipids caused oxidative damage to RBC cytoskeletal protein spectrin, resulting in hemolysis and release of CFH. A single intramuscular injection of the heme-scavenging protein hemopexin (4 {micro}g/kg body weight) in mice, one hour post halogen exposure, reversed RBC fragility and decreased CFH levels to those of air controls. Patch clamp and short circuit current measurements revealed that CFH inhibited the activity of amiloride-sensitive (ENaC) and cation sodium (Na+) channels in mouse alveolar cells and trans-epithelial Na+ transport across human airway cells with EC50 of 125 nM and 500 nM, respectively. Molecular modeling identified 22 putative heme-docking sites on ENaC (energy of binding range: 86-1563 kJ/mol) with at least 2 sites within its narrow transmembrane pore, potentially capable of blocking Na+ transport across the channel. In conclusion, results suggested that CFH mediated inhibition of ENaC activity may be responsible for pulmonary edema post inhalation injury.

physiology↗

bioRxiv2018

Genomic and transcriptomic determinants of therapy resistance and immune landscape evolution during anti-EGFR treatment in colorectal cancer

Anti-epidermal growth factor receptor (EGFR) antibodies (anti-EGFR-Ab) are effective in a subgroup of patients with metastatic colorectal cancer (CRC). We applied genomic and transcriptomic analyses to biopsies from 35 RAS wild-type CRCs treated with the anti-EGFR-Ab cetuximab in a prospective trial to interrogate the molecular resistance landscape. This validated transcriptomic CRC-subtypes as predictors of cetuximab benefit; identified novel associations of NF1-inactivation and non-canonical RAS/RAF-aberrations with primary progression; and of FGF10- and non-canonical BRAF-aberrations with AR. No genetic resistance drivers were detected in 64% of AR biopsies. The majority of these had switched from the cetuximab-sensitive CMS2-subtype pretreatment to the fibroblast- and growth factor-rich CMS4-subtype at progression. Fibroblast supernatant conferred cetuximab resistance in vitro, together supporting subtype-switching as a novel mechanism of AR. Cytotoxic immune infiltrates and immune-checkpoint expression increased following cetuximab responses, potentially providing opportunities to treat CRCs with molecularly heterogeneous AR with immunotherapy.

cancer biology↗

bioRxiv2018

A transdiagnostic study of children with problems of attention, learning and memory (CALM)

BackgroundA substantial proportion of the school-age population experience cognitive-related learning difficulties. Not all children who struggle at school receive a diagnosis, yet their problems are sufficient to warrant additional support. Understanding the causes of learning difficulties is the key to developing effective prevention and intervention strategies for struggling learners. The aim of this project is to apply a transdiagnostic approach to children with cognitive developmental difficulties related to learning to discover the underpinning mechanisms of learning problems.\n\nMethods / DesignA cohort of 1000 children aged 5 to 18 years is being recruited. The sample consists of 800 children with problems in attention, learning and / memory, as identified by a health or educational professional, and 200 typically-developing children recruited from the same schools as those with difficulties. All children are completing assessments of cognition, including tests of phonological processing, short-term and working memory, attention, executive function and processing speed. Their parents/ carers are completing questionnaires about the childs family history, communication skills, mental health and behaviour. Children are invited for an optional MRI brain scan and are asked to provide an optional DNA sample (saliva).\n\nHypothesis-free data-driven methods will be used to identify the cognitive, behavioural and neural dimensions of learning difficulties. Machine-learning approaches will be used to map the multi-dimensional space of the cognitive, neural and behavioural measures to identify clusters of children with shared profiles. Finally, group comparisons will be used to test theories of development and disorder.\n\nDiscussionOur multi-systems approach to identifying the causes of learning difficulties in a heterogeneous sample of struggling learners provides a novel way to enhance our understanding of the common and complex needs of the majority of children who struggle at school. Our broad recruitment criteria targeting all children with cognitive learning problems, irrespective of diagnoses and comorbidities, are novel and make our sample unique. Our dataset will also provide a valuable resource of genetic, imaging and cognitive developmental data for the scientific community.

neuroscience↗