Biology subjects

Griffin, S.

Publications and source records attributed to Griffin, S..

14 recordsLinked to original sources

bioRxiv2026

A platform for deep topographic multiomic mapping of the bone marrow environment in multiple myeloma

Multiple myeloma is a genetically complex plasma cell malignancy in which profound intratumoral heterogeneity shapes disease progression and therapeutic resistance. Genomic subclones dynamically emerge and evolve under treatment pressure, yet their spatial organization within intact bone marrow remains poorly defined. We hypothesized that genetically distinct myeloma subclones occupy spatially discrete ecological niches associated with unique molecular and microenvironmental states. To test this, we here demonstrate a proof-of-concept spatial tri-omics workflow combining laser capture microdissection-based genomics and deep LC-MS/MS proteomics with single-cell spatial transcriptomics, integrated by digital co-registration of adjacent tissue sections. Applied to a myeloma bone marrow trephine, this approach enabled coordinated profiling of matched anatomical regions demonstrating that genomic, transcriptomic and proteomic profiles converged to define clone-specific microenvironmental programmes. We show that genetically distinct myeloma subclones occupy mutually exclusive regions of the same bone marrow biopsy. Remarkably, an aggressive del(17p) clone and a gain(12q) clone occupied defined anatomical territories within the same trephine-biopsied section, each clone exhibiting distinct genomic, transcriptomic, proteomic and cellular ecosystems. The del(17p) clone localized to a fibrotic, osteolytic and angiogenic niche enriched for activated stromal cells, osteoblasts, osteoclasts and immunoregulatory myeloid populations, whereas the gain(12q) clone occupied a comparatively quiescent marrow niche with limited stromal remodelling. Together, these findings demonstrate that genetically distinct myeloma subclones establish spatially and biologically discrete ecological niches through coordinated remodelling of stromal, immune and bone compartments, providing a framework for understanding clonal evolution within the bone marrow microenvironment.

cancer biology↗

bioRxiv2025

Oncolytic Reovirus mediates innate-driven SARS-CoV-2 elimination in the absence of cell toxicity

Interplay between type I interferon (IFN) driven innate responses and viral antagonism strongly influences SARS-CoV-2 transmission and the COVID-19 disease course. Hence, variant adaptation includes diminished induction of IFN stimulated genes (ISG) and/or evasion of their effector functions. Exogenous IFN treatment "rewires" innate responses to drive virus elimination, yet therapeutic trials to date have been unremarkable. Resolving this paradox could translate to variant-agnostic innate immunotherapy. By contrast, oncolytic viruses (OV) exhibit profoundly attenuated innate antagonism, resulting in potent IFN responses despite the inherently immunosuppressive nature of tumour microenvironments. Moreover, OV only undergo lytic replication within innate-deficient malignant cells, and not in cells where sufficient innate responses exist. This, combined with previous studies showing that OV suppressed replication of underlying oncogenic viruses in tumours, we explored whether clinical grade oncolytic Orthoreovirus (Reo) superinfection could eliminate SARS-CoV-2 from immune-competent lung epithelial cell lines in the absence of toxicity. Reo exerted profound activation of innate responses, including when SARS-CoV-2 infection was already established, rewiring cells towards an antiviral state emulating that of Reo infection alone. Both intracellular and paracrine mechanisms induced ISG repertoires including multiple known anti-SARS-CoV-2 effectors, as well as others that remain unvalidated. Amongst these, we demonstrate the first direct evidence that MX2 and XAF1 restrict SARS-CoV-2 replication. Thus, with an excellent safety record, self-amplification, and respiratory tract tropism, we propose that Reo superinfection may provide a tractable alternative to recombinant cytokines for innate antiviral immunotherapy.

immunology↗

bioRxiv2025

Separable global and local beta burst dynamics in motor cortex of primates

Sensorimotor beta band oscillations are known to modulate during normal movement control and abnormal beta modulation is linked to pathological bradykinesia. However, the functional differences between beta localized to one brain area versus beta synchronized across brain areas remains unclear. We monitored beta bursts in non-human primates, both neurotypical and stroke- impaired, during the performance of complex motor tasks. Across both groups of animals, we identified two distinct beta burst types: global bursts that tend to be synchronized across cortical and subcortical areas, and local bursts that tend to be confined to cortex. These two types exhibited distinct neural dynamics, with global bursts linked to reduced firing variability and overall slowed movements. In contrast, local bursts often occurred during the execution of complex behaviors, particularly during prehension. We found evidence for changes in the distribution of global and local bursts during recovery after stroke. In impaired animals early after stroke, global bursts predominated and were associated with reduced speed and impaired grasping. Notably, recovery of grasping was associated with a reduction in global bursts and an increase in local bursts, suggesting that local bursts may play an important role during prehension. Our findings reveal distinct roles of global and local beta bursts and indicate that the normalization of global and local burst timing tracks recovery of dexterity.

neuroscience↗

bioRxiv2024

TKI-conditioned immunotherapy using uv-inactivated reovirus promotes survival in hepatocellular carcinoma, mediated by cytotoxic CD4+ T-cells

Hepatocellular carcinoma (HCC) is the third most common cause of cancer deaths worldwide. Combination immunotherapy is now standard of care for advanced HCC, improving patient outcomes. However, a considerable number of patients remain unresponsive, or are unable to tolerate therapy. Tyrosine kinase inhibitors (TKIs), such as the former first-line agent sorafenib, remain an option for such patients, yet provide only marginal efficacy. We hypothesised that a clinically advanced immunogenic "oncolytic" virus, namely, human Orthoreovirus, might improve TKI mediated therapy. Surprisingly, uv-inactivated, replication-deficient reovirus, but not live virus, significantly extended survival when combined with sorafenib in preclinical immunocompetent HCC models. Favourable responses were dependent upon adaptive immunity, mediated by IFNB-induced skewing of the infiltrating T-cell ratio in favour of cytotoxic CD4+ T-cells expressing granzyme B and perforin. Interestingly, this subset effectively killed tumours via both contact juxtacrine and paracrine processes, the former being MHCII independent. Moreover, efficacy correlated with more rapid and robust IFN production by inactivated virus due to the absence of innate viral antagonists. Thus, we reveal a means to improve TKI-HCC outcomes through an alternative virus-driven immunotherapy, underpinned by non-classical immunological mechanisms. IMPACT AND IMPLICATIONSImmune checkpoint immunotherapy is revolutionising cancer treatment, yet considerable numbers of patients still fail to respond and must resort to older, more toxic and less effective therapies, including Sorafenib for the management of HCC. We demonstrate that burgeoning virus-driven immunotherapy can be successfully combined with Sorafenib to extend preclinical HCC survival, but only when the virus is uv-inactivated to prevent already attenuated innate immune antagonism, specifically increasing the magnitude of tumour IFNB responses. IFNB was essential to promote tumour infiltration of cytotoxic CD4+ cells during therapy, which was a hallmark of long-term survival mediated by ensuing adaptive responses. We anticipate this work will be of interest to clinicians and cancer immunology researchers, promoting closer inspection of the immune microenvironment and cancer-specific responses to OV therapy, specifically those driven by non-canonical anti-cancer mechanisms involving IFNB and cytotoxic CD4+ T-cells.

immunology↗

bioRxiv2022

Lung Tumor Microphysiological System with 3D Endothelium to Evaluate Modulators of T-Cell Infiltration

Lung cancer is a leading cause of death worldwide, with only a fraction of patients responding to immunotherapy. The correlation between increased T-cell infiltration and positive patient outcomes has motivated the search for therapeutics promoting T-cell infiltration. While transwell and spheroid platforms have been employed, these models lack flow and endothelial barriers, and cannot faithfully model T-cell adhesion, extravasation and migration through 3D tissue. Presented here is a 3D chemotaxis assay, in a lung tumor on chip model with 3D endothelium (LToC-Endo), to address this need. The described assay consists of a vascular tubule cultured under rocking flow, through which T-cells are added; a collagenous stromal barrier, through which T-cells infiltrate; and a chemoattractant/tumor compartment. Here, activated T-cells extravasate and infiltrate in response to gradients of rhCXCL11 and rhCXCL12. Adopting a T-cell activation protocol with a rest period enables proliferative burst prior to introducing T-cells into chips, increases T-cell expression of CXCR3 and CXCR4 receptors, and enhances assay sensitivity. In addition, incorporating this rest recovers endothelial activation in response to rhCXCL12. As a final control, we show that blocking ICAM-1 interferes with T-cell adhesion and chemotaxis. This microphysiological system, which mimics in vivo stromal and vascular barriers, can be used to evaluate potentiation of immune chemotaxis into tumors while probing for vascular responses to potential therapeutics. Finally, we propose a translational strategy by which this assay could be linked to preclinical and clinical models to support human dose prediction, personalized medicine, and the reduction, refinement, and replacement of animal models.

bioengineering↗

bioRxiv2022

CRISPR-LRS for mapping transgenes in the mouse genome

Microinjected transgenes, including bacterial artificial chromosomes (BACs), insert randomly in the mouse genome. Traditional methods of mapping a transgene are challenging, thus complicating breeding strategies and the accurate interpretation of phenotypes, particularly when a transgene disrupts critical coding or noncoding sequences. Here, we introduce CRISPR-Cas9 long-read sequencing (CRISPR-LRS) to ascertain transgene integration locus and estimated copy number. This method revealed integration loci for both a BAC and Cre-driver line, and estimated the copy numbers for two other BAC mouse lines. CRISPR-LRS offers an easy approach to establish robust breeding practices and accurate phenotyping of most any transgenic mouse line.

genetics↗

bioRxiv2021

Mosquito saliva sialokinin-dependent enhancement of arbovirus infection through endothelial barrier leakage

Viruses transmitted by Aedes mosquitoes constitute an increasingly important global health burden. Defining common determinants of host susceptibility to this large group of heterogenous pathogens are key for informing the rational design of new pan-viral medicines. Infection of the vertebrate host with these viruses is enhanced by the presence of mosquito saliva, a complex mixture of salivary gland-derived factors and microbiota. We show that enhancement of infection by saliva was dependent on vascular function and was independent of most anti-saliva immune responses, including to salivary microbiota. Instead, the Aedes gene product sialokinin mediated enhancement of virus infection through a rapid reduction in endothelial barrier integrity. Sialokinin is unique within the insect world as having vertebrate-like tachykinin sequence and is absent from non-vector competent Anopheles mosquitoes, whose saliva was not pro-viral and did not induce similar vascular permeability. Therapeutic strategies targeting sialokinin have potential to limit disease severity following infection with Aedes mosquito-borne viruses.

microbiology↗

bioRxiv2021

The CXCR6/CXCL16 axis links inflamm-aging to disease severity in COVID-19 patients

Advancing age and chronic health conditions, significant risk factors for severe COVID-19, are associated with a pro-inflammatory state, termed inflamm-aging. CXCR6+ T cells are known to traffic to the lung and have been reported to increase with age. The ligand of CXCR6, CXCL16, is constitutively expressed in the lung and upregulated during inflammatory responses and the CXCR6/CXCL16 axis is associated with severe lung disease and pneumonia. Genome-wide association studies have also recently identified 3p21.31, encompassing the CXCR6 gene, as a susceptibility locus for severe COVID-19. We assessed numbers T cells expressing the chemokine receptor CXCR6 and plasma levels of CXCL16, in control and COVID-19 patients. Results demonstrated that circulating CD8+CXCR6+ T cells were significantly elevated with advancing age, yet virtually absent in patients with severe COVID-19. Peripheral levels of CXCL16 were significantly upregulated in severe COVID-19 patients compared to either mild COVID-19 patients or SARS-CoV-2 negative controls. This study supports a significant role of the CXCR6/CXCL16 axis in the immunopathogenesis of severe COVID-19.

immunology↗

bioRxiv2020

Spatial integration during active tactile sensation drives elementary shape perception

Active haptic sensation is critical for object identification and manipulation, such as for tool use in humans, or prey capture in rodents. The neural circuit basis for recognizing objects through active touch alone is poorly understood. To address this gap, we combined optogenetics, two photon imaging, and high-speed behavioral tracking in mice solving a novel surface orientation discrimination task with their whiskers. We found that orientation discrimination required animals to summate input from multiple whiskers specifically along the whisker arc. Many animals discriminated the orientation of the stimulus per se, as their performance was invariant to the specific location of the presented stimulus. Two photon imaging showed that populations of neurons in the barrel cortex encoded each of the discriminated orientations, and this coding depended on integration over the whisker array. Finally, acute optogenetic inactivation of the barrel cortex strongly impaired surface orientation discrimination, and even cell-type specific optogenetic suppression of layer 4 excitatory neurons degraded performance, implying a role for superficial layers in this computation. These data suggest a model in which spatial summation over an active haptic array generates representations of an objects surface orientations. These computations may facilitate the encoding of complex three-dimensional objects during active exploration.

neuroscience↗

bioRxiv2020

STAGdb: a 30K SNP genotyping array and Science Gateway for Acropora corals and their dinoflagellate symbionts

Standardized identification of genotypes is necessary in animals that reproduce asexually and form large clonal populations such as coral. We developed a high-resolution hybridization-based genotype array coupled with an analysis workflow and database for the most speciose genus of coral, Acropora, and their symbionts. We designed the array to co-analyze host and symbionts based on bi-allelic single nucleotide polymorphisms (SNP) markers identified from genomic data of the two Caribbean Acropora species as well as their dominant dinoflagellate symbiont, Symbiodinium fitti. SNPs were selected to resolve multi-locus genotypes of host (called genets) and symbionts (called strains), distinguish host populations and determine ancestry of the coral hybrids in Caribbean acroporids. Pacific acroporids can also be genotyped using a subset of the SNP loci and additional markers enable the detection of symbionts belonging to the genera Breviolum, Cladocopium, and Durusdinium. Analytic tools to produce multi-locus genotypes of hosts based on these SNP markers were combined in a workflow called the Standard Tools for Acroporid Genotyping (STAG). In the workflow the users data is compared to the database of previously genotyped samples and generates a report of genet identification. The STAG workflow and database are contained within a customized Galaxy environment (https://coralsnp.science.psu.edu/galaxy/), which allows for consistent identification of host genet and symbiont strains and serves as a template for the development of arrays for additional coral genera. STAG data can be used to track temporal and spatial changes of sampled genets necessary for restoration planning as well as be applied to downstream genomic analyses.

genetics↗

bioRxiv2019

Site-directed M2 proton channel inhibitors enable synergistic combination therapy for rimantadine-resistant pandemic influenza

Pandemic influenza A virus (IAV) remains a significant threat to global health. Preparedness relies primarily upon a single class of neuraminidase (NA) targeted antivirals, against which resistance is steadily growing. The M2 proton channel is an alternative clinically proven antiviral target, yet a near-ubiquitous S31N polymorphism in M2 evokes resistance to licensed adamantane drugs. Hence, inhibitors capable of targeting N31 containing M2 (M2-N31) are highly desirable.\n\nRational in silico design and in vitro screens delineated compounds favouring either lumenal or peripheral M2 binding, yielding effective M2-N31 inhibitors in both cases. Hits included adamantanes as well as novel compounds, with some showing low micromolar potency versus pandemic \"swine\" H1N1 influenza (Eng195) in culture. Interestingly, a published adamantane-based M2-N31 inhibitor rapidly selected a resistant V27A polymorphism (M2-A27/N31), whereas this was not the case for non-adamantane compounds. Nevertheless, combinations of adamantanes and novel compounds achieved synergistic antiviral effects, and the latter synergised with the neuraminidase inhibitor (NAi), Zanamivir. Thus, site-directed drug combinations show potential to rejuvenate M2 as an antiviral target whilst reducing the risk of drug resistance.

microbiology↗

bioRxiv2018

Targeting hepatitis C virus p7 channel activity reveals prospect for bimodal antiviral prophylaxis

Since the 1960s, a single class of agent has been licensed targeting virus-encoded ion channels, or \"viroporins\", contrasting the success of channel blocking drugs in other areas of medicine. Although resistance arose to these prototypic adamantane inhibitors of the influenza A virus (IAV) M2 proton channel, a growing number of clinically and economically important viruses are now recognised to encode essential viroporins providing potential targets for modern drug discovery.\n\nWe describe the first rationally designed viroporin inhibitor with a comprehensive structure-activity relationship (SAR). This step-change in understanding not only revealed a second biological function for the p7 viroporin from hepatitis C virus (HCV) during virus entry, but also enabled the synthesis of a labelled tool compound that retained biological activity. Hence, p7 inhibitors (p7i) represent a unique class of HCV antiviral targeting both the spread and establishment of infection, as well as a precedent for future viroporin-targeted drug discovery.

microbiology↗

bioRxiv2018

Orbitofrontal cortex, dorsolateral prefrontal cortex, and hippocampus represent the magnitude of event saliency

Two primary functions attributed to the hippocampus and prefrontal cortex network are retaining the temporal and spatial associations of events and detecting deviant events. It is, however, unclear how these two functions converge onto one mechanism. Here, we tested whether increased activity with perceiving salient events is a deviant detection signal or contains information about the event associations by reflecting the magnitude of deviance (i.e., event saliency). We also tested how the deviant detection signal is affected by the degree of anticipation. We studied regional neural activity when people watched a movie that had varying saliency of a novel or an anticipated flow of salient events. Using intracranial electroencephalography from ten patients, we observed that high-frequency activity (50-150 Hz) in the hippocampus, dorsolateral prefrontal cortex (dorsolateral PFC), and medial orbitofrontal cortex (OFC) tracked event saliency. We also observed that medial OFC activity was stronger when the salient events were anticipated than when they were novel. These results suggest that dorsolateral PFC and medial OFC, as well as the hippocampus, signify the saliency magnitude of events, reflecting the hierarchical structure of event associations.

neuroscience↗

bioRxiv2017

Integrated analysis of anatomical and electrophysiological human intracranial data

The exquisite spatiotemporal precision of human intracranial EEG recordings (iEEG) permits characterizing neural processing with a level of detail that is inaccessible to scalp-EEG, MEG, or fMRI. However, the same qualities that make iEEG an exceptionally powerful tool also present unique challenges. Until now, the fusion of anatomical data (MRI and CT images) with the electrophysiological data and its subsequent analysis has relied on technologically and conceptually challenging combinations of software. Here, we describe a comprehensive protocol that addresses the complexities associated with human iEEG, providing complete transparency and flexibility in the evolution of raw data into illustrative representations. The protocol is directly integrated with an open source toolbox for electrophysiological data analysis (FieldTrip). This allows iEEG researchers to build on a continuously growing body of scriptable and reproducible analysis methods that, over the past decade, have been developed and employed by a large research community. We demonstrate the protocol for an example complex iEEG data set to provide an intuitive and rapid approach to dealing with both neuroanatomical information and large electrophysiological data sets. We explain how the protocol can be largely automated, taking under an hour to complete, and readily adjusted to iEEG data sets with other characteristics.

neuroscience↗