Biology subjects

Ye, T.

Publications and source records attributed to Ye, T..

At least 55 records · Page 3Linked to original sources

bioRxiv2024

Lipid nanoparticle composition for adjuvant formulation modulates disease after influenza virus infection in QIV vaccinated mice.

Adjuvants can enhance vaccine effectiveness of currently licensed influenza vaccines. We tested influenza vaccination in a mouse model with two adjuvants: Sendai virus derived defective interfering (SDI) RNA, a RIG-I agonist, and an amphiphilic imidazoquinoline (IMDQ-PEG-Chol), TLR7/8 adjuvant. The negatively charged SDI RNA was formulated into lipid nanoparticles (LNPs) facilitating the direct delivery of a RIG-I agonist to the cytosol. We have previously tested SDI and IMDQ-PEG-Chol as standalone and combination adjuvants for influenza and SARS-CoV-2 vaccines. Here we tested two different ionizable lipids, K-Ac7-Dsa and S-Ac7-Dog, for LNP formulations. The adjuvanticity of IMDQ-PEG-Chol with and without empty or SDI-loaded LNPs was validated in a licensed vaccine setting (quadrivalent influenza vaccine or QIV) against H1N1 influenza virus, showing robust induction of antibody titres and T cell responses. Depending on the adjuvant combination and LNP lipid composition (K-Ac7-Dsa or S-Ac7-Dog lipids), humoral and cellular vaccine responses could be tailored towards type 1 or type 2 host responses with specific cytokine profiles that correlated with protection during viral infection. The extent of protection conferred by different vaccine/LNP/adjuvant combinations was examined against challenge with the vaccine-matching strain of H1N1 influenza A virus. Groups that received either LNP formulated with SDI, IMDQ-PEG-Chol or both showed very low levels of viral replication in their lungs at five days post virus infection. LNP ionizable lipid composition as well as loading (empty versus SDI) also skewed host responses to infection, as reflected in the cytokine and chemokine levels in lungs of vaccinated animals upon infection. These studies show the potential of LNPs as adjuvant delivery vehicles for licensed vaccines and illustrate the importance of LNP composition for subsequent host responses to infection, an important point of consideration for vaccine safety.

microbiology↗

bioRxiv2024

Unraveling the oscillatory dynamics of mRNA metabolism and chromatin accessibility during the cell cycle through integration of single-cell multiomic data

The cell cycle is a tightly regulated process that requires precise temporal expression of hundreds of cell cycledependent genes. However, the genome-wide dynamics of mRNA metabolism throughout the cell cycle remain uncharacterized. Here, we combined single-cell multiome sequencing, biophysical modeling, and deep learning to quantify rates of mRNA transcription, splicing, nuclear export, and degradation. Our approach revealed that both transcriptional and post-transcriptional processes exhibit distinct oscillatory waves at specific cell cycle phases, with post-transcriptional regulation playing a prominent role in shaping mRNA accumulation. We also observed dynamic changes in chromatin accessibility and transcription factor binding footprints, identifying key regulators underlying the oscillatory dynamics of mRNA. Taken together, our approach uncovered a high-resolution map of RNA metabolism dynamics and chromatin accessibility, offering new insights into the temporal control of gene expression in proliferating cells. HighlightsO_LIFourierCycle combines single-cell multiome sequencing, deep learning, and biophysical modeling to quantify gene-specific rates of mRNA metabolism during the cell cycle C_LIO_LIRates of mRNA transcription, nuclear export, and degradation show gene-specific oscillatory waves at distinct cell cycle phases. C_LIO_LIPost-transcriptional regulation, including mRNA degradation and nuclear export, plays a prominent role in shaping mRNA accumulation during the cell cycle C_LIO_LIDynamics of chromatin accessibility and transcription factor binding footprints uncover key regulators underlying the transcriptional control of gene expression C_LI Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=195 HEIGHT=200 SRC="FIGDIR/small/575159v2_ufig1.gif" ALT="Figure 1"> View larger version (34K): org.highwire.dtl.DTLVardef@1d2d315org.highwire.dtl.DTLVardef@2031aaorg.highwire.dtl.DTLVardef@19cc54eorg.highwire.dtl.DTLVardef@15d9105_HPS_FORMAT_FIGEXP M_FIG C_FIG

systems biology↗

bioRxiv2023

Inhibiting the GPI Transamidase Subunit GPAA1 Abolishes CD24 Surface Localization and Enhances Macrophage-Mediated Phagocytosis of Ovarian Cancer Cells

The CD24-Siglec10 signaling axis is an immune checkpoint pathway that shields ovarian cancer cells from phagocytosis by tumor-associated macrophages (TAMs), making it an appealing immunotherapeutic target. Here, we investigate factors influencing CD24 cell surface expression and assess their suitability as drug targets. Using a CRISPR-based knockout screen, we identify GPAA1 (glycosylphosphatidylinositol anchor attachment-1) as a positive regulator of CD24 cell surface expression. GPAA1 is a crucial component of the multi-subunit GPI transamidase complex, which facilitates the attachment of GPI lipid anchor to the C-terminus of CD24, enabling its surface localization. Reducing the activity of GPAA1 in ovarian cancer cells, either by genetic ablation or targeting with an aminopeptidase inhibitor bestatin, disrupts GPI attachment to CD24. This disruption impairs CD24 cell surface localization, enhances phagocytosis by TAMs, and suppresses tumor growth in mice. Our study highlights the potential of GPAA1 targeting as a therapeutic approach for CD24-positive ovarian cancers.

cancer biology↗

bioRxiv2023

The impact of multiband and in-plane acceleration on white matter microstructure analysis

Accelerated imaging has been broadly adopted in diffusion MRI studies, yet little is known about its impacts. Acceleration can achieve higher spatial and q-space resolution in shorter time, reduce motion artifacts, and reduce patient burden. However, it leads to noise amplification, and its impacts in clinical cohorts are poorly understood. This study examined the impact of multiband (also called simultaneous multislice, or SMS) and in-plane acceleration (IPA, also called phase acceleration) in diffusion imaging in forty older adults differing in cognitive status. We evaluated a total of 400 scans from five acquisitions: no acceleration (S1P1); SMS=3 with no in-plane acceleration (S3P1); SMS=3 with IPA=2 (S3P2); S6P1; and S6P2. The number of diffusion directions and b-values was kept constant such that acquisition times varied from 21:28 to 3:56. We found that diffusion metrics were highly sensitive to acceleration factor, with a trend towards higher fractional anisotropy (FA) and lower orientation dispersion (OD) with acceleration. The differences between accelerated and unaccelerated acquisitions could be partly explained by the noise amplification (g-factor) and reduced motion. Intraclass correlations (ICCs) of FA and OD in white matter were excellent in both S1P1 and S3P1 (median >0.8), good but lower in S3P2 and S6P1 (medians around 0.70), and poor to fair in S6P2 (medians 0.46 and 0.57). In-plane acceleration decreased ICC, including areas of high susceptibility distortion. In a comparison of mild cognitive impairment versus healthy controls, acceleration tended to reduce group differences, particularly in the fornix, with greater costs in OD than FA. Our results provide guidance regarding the costs of acceleration (possible biases and reduced effect sizes) while also characterizing the benefits (reduced motion, good reliability at higher multiband with no in-plane).

bioengineering↗

bioRxiv2023

Dynamics and quantitative contribution of the aminoglycoside 6'-N-acetyltransferase type Ib to amikacin resistance

Aminoglycosides are essential components in the available armamentarium to treat bacterial infections. The surge and rapid dissemination of resistance genes strongly reduce their efficiency, compromising public health. Among the multitude of modifying enzymes that confer resistance to aminoglycosides, the aminoglycoside acetyltransferase AAC(6')-Ib is the most prevalent and relevant in the clinical setting as it can inactivate numerous aminoglycosides, such as amikacin. Although the mechanism of action, structure, and biochemical properties of the AAC(6')-Ib protein have been extensively studied, the contribution of the intracellular milieu to its activity remains unclear. In this work, we used a fluorescent-based system to quantify the number of AAC(6')-Ib per cell in Escherichia coli, and we modulated this copy number with the CRISPR interference method. These tools were then used to correlate enzyme concentrations with amikacin resistance levels. Our results show that resistance to amikacin increases linearly with a higher concentration of AAC(6')-Ib until it reaches a plateau at a specific protein concentration. In vivo imaging of this protein shows that it diffuses freely within the cytoplasm of the cell, but it tends to form inclusion bodies at higher concentrations in rich culture media. Addition of a chelating agent completely dissolves these aggregates and partially prevents the plateau in the resistance level, suggesting that AAC(6')-Ib aggregation lowers resistance to amikacin. These results provide the first step in understanding the cellular impact of each AAC(6')-Ib molecule on aminoglycoside resistance. They also highlight the importance of studying its dynamic behavior within the cell. ImportanceAntibiotic resistance is a growing threat to human health. Understanding antibiotic resistance mechanisms can serve as foundation for developing innovative treatment strategies to counter this threat. While numerous studies clarified the genetics and dissemination of resistance genes and explored biochemical and structural features of resistance enzymes, their molecular dynamics and individual contribution to resistance within the cellular context remain unknown. Here, we examined this relationship modulating expression levels of AAC(6')-Ib, an enzyme of clinical relevance. We show a linear correlation between copy number of the enzyme per cell and amikacin resistance levels up to a threshold where resistance plateaus. We propose that at concentrations below the threshold, the enzyme diffuses freely in the cytoplasm but aggregates at the cell poles at concentrations over the threshold. This research opens promising avenues for studying enzyme solubilitys impact on resistance, creating opportunities for future approaches to counter resistance.

microbiology↗

bioRxiv2023

Inhibition of Topoisomerase 2 catalytic activity impacts the integrity of heterochromatin and repetitive DNA and leads to interlinks between clustered repeats

DNA replication and transcription generate DNA supercoiling, which can cause topological stress and intertwining of daughter chromatin fibers, posing challenges to the completion of DNA replication and chromosome segregation. Type II topoisomerases (Top2s) are enzymes that relieve DNA supercoiling and decatenate braided sister chromatids. How Top2 complexes deal with the topological challenges in different chromatin contexts, and whether all chromosomal contexts are subjected equally to torsional stress and require Top2 activity is unknown. Here we show that catalytic inhibition of the Top2 complex in interphase has a profound effect on the stability of heterochromatin and repetitive DNA elements. Mechanistically, we find that catalytically inactive Top2 is trapped around heterochromatin leading to DNA breaks and unresolved catenates, which necessitate the recruitment of the structure specific endonuclease, Ercc1-XPF, in an Slx4- and SUMO-dependent manner. Our data are consistent with a model in which Top2 complex resolves not only catenates between sister chromatids but also inter-chromosomal catenates between clustered repetitive elements.

cell biology↗

bioRxiv2023

High red/far-red ratio promotes root colonization of Serratia plymuthica A21-4 in tomato by root exudates-stimulated chemotaxis and biofilm formation

Effective colonization on plant roots is a prerequisite for plant growth promoting rhizobacterias (PGPR) to exert beneficial activities. Light is essential for plant growth, development and stress response. However, how light modulates root colonization of PGPR remains unclear. Here, we found that high red/far red(R/FR) light promoted and low R/FR light inhibited the colonization and growth enhancement of Serratia plymuthica A21-4 on tomato. Non-targeted metabolomic analysis of root exudates collected from different R/FR ratio treated tomato seedlings with A21-4 inoculation by ultra performance liquid chromatography-tandem mass spectrometry showed that 64 primary metabolites including amino acids, sugars and organic acids in high R/FR light-grown plants significantly increased compared with those determined for low R/FR light-grown plants. Among them, 7 amino acids, 1 organic acid and 1 sugar obviously induced the chemotaxis and biofilm formation of A21-4 compared to the control. Furthermore, exogenous addition of five artificial root exudate compontents (leucine, methionine, glutamine, 6-aminocaproic acid and melezitose) regained and further increased the colonization and growth promoting ability of A21-4 in tomato under low R/FR light and high R/FR light, respectively, indicating their involvement in high R/FR light-regulated the interaction of tomato root and A21-4. Taken together, our results, for the first time, clearly demonstrate that high R/FR light-induced root exudates play a key role in chemotaxis, biofilm formation and root colonization of A21-4. This study provides new insights into the interactions of plant-PGPR under different light conditions and can help promote the combined application of light supplementation and PGPR to facilitate crop growth and health in green agricultural production.

microbiology↗

bioRxiv2023

Mechanism of DNA origami folding elucidated by mesoscopic simulations

DNA nanotechnology leverages the canonical base-pairing rules and geometry of DNA to create highly precise nanoscale structures with many potential applications. While the design and fabrication of DNA nanostructures is well-established, the self-assembly process that produces these structures is still poorly understood, especially for DNA origami that involve the assembly of hundreds of strands. Many experimental and computational efforts have sought to better understand DNA origami folding, but the small length and time scales of individual binding events and the long timescale over which folding occurs have posed significant challenges. Here, we present a new mesoscopic model that uses a switchable force field to capture the mechanical behavior of single- and double-stranded DNA motifs and transition between them at a coarseness level of up to 8 nucleotides per particle, allowing access to the long assembly timescales of DNA origami up to several kilobases in size. Brownian dynamics simulations of 4-helix bundle (4HB) structures using this model reveal a hierarchical folding process involving the zipping of structural domains into a partially folded precursor structure followed by gradual crystallization into the final structure. We elucidate the role of hybridization strength, scaffold routing, and staple design in the folding order and kinetics. Simulation of larger 32HB structures reveals heterogeneous staple incorporation kinetics and frequent trapping in metastable states, as opposed to smaller, more accessible structures like the 4HB, which exhibit first-order kinetics and virtually defect-free folding. The development of this model opens an avenue to better understand and design DNA nanostructures for improved yield and folding performance.

biophysics↗

bioRxiv2023

Sex-dependent contributions of ventrolateral orbitofrontal cortex and basolateral amygdala to learning under uncertainty

Reversal learning measures the ability to form flexible associations between choice outcomes with stimuli and actions that precede them. This type of learning is thought to rely on several cortical and subcortical areas, including highly interconnected orbitofrontal cortex (OFC) and basolateral amygdala (BLA), and is often impaired in various neuropsychiatric and substance use disorders. However, unique contributions of these regions to stimulus- and action-based reversal learning have not been systematically compared using a chemogenetic approach and particularly before and after the first reversal that introduces new uncertainty. Here, we examined the roles of ventrolateral OFC (vlOFC) and BLA during reversal learning. Male and female rats were prepared with inhibitory DREADDs targeting projection neurons in these regions and tested on a series of deterministic and probabilistic reversals during which they learned about stimulus identity or side (left or right) associated with different reward probabilities. Using a counterbalanced within-subject design, we inhibited these regions prior to reversal sessions. We assessed initial and pre-post reversal changes in performance to measure learning and adjustments to reversals, respectively. We found that inhibition of vlOFC, but not BLA, eliminated adjustments to stimulus-based reversals. Inhibition of BLA, but not vlOFC, selectively impaired action-based probabilistic reversal learning, leaving deterministic reversal learning intact. vlOFC exhibited a sex-dependent role in early adjustment to action-based reversals, but not in overall learning. These results reveal dissociable roles for BLA and vlOFC in flexible learning and highlight a more crucial role for BLA in learning meaningful changes in the reward environment. Significance StatementInflexible learning is a feature of several neuropsychiatric disorders. We investigated how the ventrolateral orbitofrontal cortex (vlOFC) and basolateral amygdala (BLA) are involved in learning of stimuli or actions under reinforcement uncertainty. Following chemogenetic inhibition of these regions in both male and females, we measured learning and adjustments to deterministic and probabilistic reversals. For action learning, BLA, but not vlOFC, is needed for probabilistic reversal learning. However, BLA is not necessary for initial probabilistic learning or retention, indicating a critical role for learning of unexpected changes. For stimulus learning, vlOFC, but not BLA, is required for adjustments to reversals, particularly in females. These findings provide insight into the complementary cortico-amygdalar substrates of learning under different forms of uncertainty.

neuroscience↗

bioRxiv2023

KCNN4 links PIEZO-dependent mechanotransduction to NLRP3 inflammasome activation

Immune cells sense the microenvironment to fine-tune their inflammatory responses. Patients with cryopyrin associated periodic syndrome (CAPS), caused by mutations in the NLRP3 gene, develop auto-inflammation triggered by non-antigenic, e.g. environmental cues. However, the underlying mechanisms are poorly understood. Here, we uncover that KCNN4, a calcium-activated potassium channel, links PIEZO-mediated mechanotransduction to NLRP3 inflammasome activation. Yoda1, a PIEZO1 agonist, lowers the threshold for NLRP3 inflammasome activation. PIEZO-mediated sensing of stiffness and shear stress increases NLRP3-dependent inflammation. Myeloid-specific deletion of PIEZO1/2 protects mice from gouty arthritis. Activation of PIEZO1 triggers calcium influx, which activates KCNN4 to evoke potassium efflux promoting NLRP3 inflammasome activation. Activation of PIEZO signaling is sufficient to activate the inflammasome in cells expressing CAPS-causing NLRP3 mutants via KCNN4. Finally, pharmacologic inhibition of KCNN4 alleviates auto-inflammation in CAPS patient cells and in CAPS-mimicking mice. Thus, PIEZO-dependent mechanical inputs augment inflammation in NLRP3-dependent diseases including CAPS. One Sentence SummaryPIEZO-mediated mechanotransduction stimulates KCNN4-dependent potassium efflux to potentiate NLRP3 inflammasome activation.

immunology↗

bioRxiv2023

Parasitism and locomotory capacity calibrate the mitogenomic evolutionary rates in Bilateria

The evidence that parasitic lineages exhibit elevated evolutionary rates is limited to Arthropoda and inconsistent. Similarly, the evidence that mitogenomic evolution is faster in species with low locomotory capacity (LC) is limited to a handful of animal lineages. We hypothesised that these two variables are associated and that LC is a major underlying factor driving the elevated evolutionary rates in parasites. We tested this hypothesis by studying mitogenomic evolutionary patterns in 10,911 bilaterian species classified according to their locomotory capacity and parasitic/free-living life history (LH). Evolutionary rates were significantly elevated in endoparasites, ectoparasites with reduced LC, and free-living lineages with reduced LC, but not in ectoparasites and parasitoids with high LC. Nematoda and Arachnida were the only lineages where parasitism was not associated with faster evolution. We propose that LC may also explain these two major outliers. Overall, the LH categorisation explained 35-37%, LC categorisation 26-28%, and together they explained 41-44% of the variance in branch lengths across the Bilateria. Our findings suggest that these two variables play a major role in calibrating the molecular clock in bilaterian animals.

evolutionary biology↗

bioRxiv2023

Measuring chondrocyte viability of articular cartilage based on label-free two-photon microscopy and deep learning image analysis

ObjectiveChondrocyte viability (CV) is an important indicator of articular cartilage health. Two-photon excitation autofluorescence (TPAF) and second harmonic generation (SHG) microscopy provide a label-free method for imaging chondrocytes. In this study, we propose an automated assessment of CV using deep learning cell segmentation and counting based on acquired TPAF/SHG images. DesignLabel-free TPAF/SHG images of cartilage samples from rats and porcine were acquired using both commercial and home-built two-photon microscopes, respectively. TPAF/SHG images were merged to form RGB color images with red, green, and blue channels assigned to TPAF (two channels) and SHG signals, respectively. To make the training datasets for the deep learning networks, individual chondrocyte areas on the RGB color images were manually circled and live or dead chondrocytes were validated by using Calcein-AM and Ethidium homodimer-1 dye labeling. We first built a chondrocyte viability network (MCV-Net) using the Mask R-CNN architecture, which could provide individual segmented cellular areas with live or dead status. Wiener deconvolution preprocessing was added before the input of MCV-Net to improve the accuracy of the CV analysis, forming the Wiener deconvolution CV network (wMCV-Net). ResultsTraining (300 images) and test (120 images) datasets were built for rats and porcine cartilage respectively. Wiener deconvolution could improve the Peak Signal-to-Noise Ratio (PSNR) for 30-40%. We demonstrated that both MCV-Net and wMCV-Net significantly improved the accuracy of the CV measurement. ConclusionA custom desktop TPAF/SHG microscope was used in collaboration with deep learning algorithm wMCV-Net based label-free method to assess the CV and get 95% accuracy with both rats and porcine samples.

bioengineering↗

bioRxiv2023

Super-enhancer driven expression of BAHCC1 promotes melanomacell proliferation and genome stability

Super enhancers (SE) are stretches of active enhancers ensuring high expression levels of key genes associated with cell function and survival. The identification of cancer-specific SE-driven genes and their functional characterization may prove to be a powerful means for the development of innovative therapeutic strategies. By performing epigenomic profiling in patient-derived short-term melanoma cultures, we identify a SE promoting the specific expression of BAHCC1 in a broad panel of cutaneous and uveal melanoma cells. BAHCC1 is highly expressed in metastatic melanoma, correlates with decreased patient survival and is required for tumor growth. Integrative genomics analyses reveal that BAHCC1 is a transcriptional regulator controlling expression of a subset of E2F/KLF-dependent cell cycle and DNA repair genes. BAHCC1 associates with BRG1-containing remodeling complexes at the promoters of these genes. In agreement, BAHCC1 silencing leads to decreased cell proliferation and delay in DNA repair. Consequently, BAHCC1 deficiency cooperates with PARP inhibition to induce melanoma cell death. Our study identifies a novel SE-driven gene expressed in cutaneous and uveal melanoma and demonstrates how its inhibition can be exploited as a therapeutic target, alone or in combination with DNA damage-inducing agents.

cancer biology↗

bioRxiv2022

Simultaneous Noise Reduction and Layer Segmentation for Visible Light Optical Coherence Tomography in Human Retina

Visible light optical coherence tomography (VIS-OCT) of human retina is an emerging imaging modality that uses shorter wavelength in visible light range than conventional near infrared (NIR) light. It provides one-micron level axial resolution to better separate stratified retinal layers, as well as microvascular oximetry. However, due to the practical limitation of laser safety and comfort, the permissible illumination power is much lower than NIR OCT which can be challenging to obtain high quality VIS-OCT images and subsequent image analysis. Therefore, improving VIS-OCT image quality by denoising is an essential step in the overall workflow in VIS-OCT clinical applications. In this paper, we provide the first VIS-OCT retinal image dataset from normal eyes, including retinal layer annotation and "noisy-clean" image pairs. We propose an efficient co-learning deep learning framework for parallel self-denoising and segmentation simultaneously. Both tasks synergize within the same network and improve each others performance. The significant improvement of segmentation (2% higher Dice coefficient compared to segmentation-only process) for ganglion cell layer (GCL), inner plexiform layer (IPL) and inner nuclear layer (INL) is observed when available annotation drops to 25%, suggesting an annotation-efficient training. We also showed that the denoising model trained on our dataset generalizes well for a different scanning protocol.

bioengineering↗

bioRxiv2022

Drivers of interlineage variability in mitogenomic evolutionary rates in flatworms (Platyhelminthes) are multifactorial

The forces driving interlineage variability in the evolutionary rates (both sequence and architecture) of mitochondrial genomes are often inconsistent and unpredictable. Herein we studied the impacts of multiple variables using 223 flatworm (Platyhelminthes) species and phylogenetic multilevel regression models. We found that: 1. Mitogenomic sequence evolution is faster in parasites associated with the thermally stable environment of endothermic hosts, but the overall impact of thermic habitat is small; 2. Mitogenome sizes are smaller in parasites of endothermic hosts, but the effects are small and inconsistent; 3. Mitogenomic gene order rearrangements (GORR) are positively correlated with mitogenomic size; 4. The expected positive correlation between GORR and sequence evolution is lineage-specific, and non-parasitic species exhibited a strong negative correlation; 5. Longevity has negligible impacts on mitogenomic evolution; 6. Parasitic (Neodermata) flatworm lineages exhibit higher evolutionary rates than non-parasitic lineages; 7. The effective population size has negligible impacts on mitogenomic evolution; 8. Comparatively, parasitism had by far the greatest impact on the mitogenomic evolution, but due to the monophyletic origin of this life-history strategy, alternative hypotheses cannot be rejected. A large number of factors impact the mitogenomic evolution in flatworms, with lineage-specific relative contributions, which sometimes produces incongruent lineage-specific mitogenomic evolution patterns.

evolutionary biology↗

bioRxiv2022

High-dimensional and spatial analysis reveals immune landscape dependent progression in cutaneous squamous cell carcinoma

PurposeThe tumour immune microenvironment impacts the biological behaviour of the tumour but its effect on clinical outcomes in head and neck cutaneous squamous cell carcinomas (HNcSCC) is largely unknown. Experimental DesignWe compared the immune milieu of high-risk HNcSCC that never progressed to metastasis with those that metastasised using multi-parameter imaging mass cytometry. The cohort included both immunosuppressed patients (IS) and patients with an absence of clinical immune-suppression (ACIS). Spatial analyses were used to identify cellular interactions that were associated with tumour behaviour. ResultsNon-progressing primary HNcSCC were characterised by higher CD8+ and CD4+ T cell responses, including numerically increased Regulatory T cells. By contrast, primary lesions from HNcSCC patients who progressed were largely devoid of T cells with lower numbers of innate immune cells and increased expression of checkpoint receptors and in the metastatic lesions were characterised by an accumulation of B cells. Spatial analysis reveals multiple cellular interactions associated with non-progressing primary tumours that were distinct in primary tumours of disease progressing patients. Cellular regional analysis of the tumour microenvironment also shows squamous cell-enriched tumour regions associated with primary non-progressing tumours. ConclusionsEffective responses from both CD8+ and CD4+ T cells in the tumour microenvironment are essential for immune control of primary HNcSCC. Our findings indicate that the early events that shape the immune responses in primary tumours dictate progression and disease outcomes in HNcSCC. Translational RelevanceThe ability to predict metastatic tumour progression at the time of initial diagnosis of primary HNcSCC could tailor personalised medical care including disease surveillance strategies and identifying patients who will benefit most from adjuvant therapy. One Sentence SummaryThe immune landscape of high-risk cutaneous squamous cell carcinoma differs in tumours that never progress compared to those that progress to metastasis.

pathology↗

bioRxiv2022

Epigenomic mapping identifies a super-enhancer repertoire that regulates cell identity in bladder cancers through distinct transcription factor networks

Muscle-invasive bladder cancer (BLCA) is an aggressive disease. Consensus BLCA transcriptomic subtypes have been proposed, with two major Luminal and Basal subgroups, presenting distinct molecular and clinical characteristics. However, how these distinct subtypes are regulated remains unclear. We hypothesized that epigenetic activation of distinct super-enhancers could drive the transcriptional programs of BLCA subtypes. Through integrated RNA-sequencing and epigenomic profiling of histone marks in primary tumours, cancer cell lines, and normal human urothelia, we established the first integrated epigenetic map of BLCA and demonstrated the link between subtype and epigenetic control. We identified the repertoire of activated super-enhancers and highlighted Basal, Luminal and Normal-associated SEs. We revealed the super-enhancer-regulated networks of candidate master transcription factors for Luminal and Basal subgroups including FOXA1 and ZBED2 respectively. FOXA1 CRISPR-Cas9 mutation triggered a shift from Luminal to Basal phenotype, confirming its role in Luminal identity regulation and induced ZBED2 overexpression. In parallel, we showed that both FOXA1 and ZBED2 play concordant roles in preventing inflammatory response in cancer cells through STAT2 inhibition. Our study furthers the understanding of epigenetic regulation of muscle-invasive BLCA and identifies a co-regulated network of super-enhancers and associated transcription factors providing potential targets for the treatment of this aggressive disease.

cancer biology↗

bioRxiv2021

Extrasynaptic NMDA receptors bidirectionally modulate intrinsic excitability of inhibitory neurons

The NMDA subtype glutamate receptors (NMDARs) play important roles in both physiological and pathological processes in the brain. Comparing to their critical roles in synaptic modifications and excitotoxicity in the excitatory neurons, much less is understood about the functional contributions of NMDARs to the inhibitory/GABAergic neurons. By using selective NMDAR inhibitors and potentiators, we here show that NMDARs bi-directionally modulate the intrinsic excitability (defined as spontaneous/evoked spiking activity and EPSP-spike coupling) in the inhibitory/GABAergic neurons. This modulation depends on GluN2C/2D-but not GluN2A/2B-containing NMDARs. We further show that NMDAR modulator EU1794-4 mostly enhances extrasynaptic NMDAR activity, and by using it we demonstrate a significant contribution of extrasynaptic NMDARs to the modulation of intrinsic excitability in the inhibitory neurons. Altogether, this bidirectional modulation of intrinsic excitability reveals a previously less appreciated importance of NMDARs in the second-to-second functioning of inhibitory/GABAergic neurons.

neuroscience↗