Biology subjects

Ismail, A.

Publications and source records attributed to Ismail, A..

At least 19 recordsLinked to original sources

bioRxiv2026

pH-dependent anti-TfR1 NANOBODY(R) molecules deliver efficacious oligonucleotide payloads to muscle and CNS tissues

The blood-brain barrier (BBB) is a highly selective, semi-permeable border of endothelial cells that prevents solutes and therapeutic agents in systemic circulation from passively crossing into the central nervous system (CNS) parenchyma. The Transferrin receptor 1 (TfR1) endocytosis pathway for iron homeostasis is one of the most well-characterized strategies for therapeutic delivery across the BBB. The work presented here showcases the discovery of novel anti-TfR1 NANOBODY(R) shuttles. The identified anti-TfR1 NANOBODY(R) molecules display cross-reactivity and pH-dependent binding to human, cynomolgus (cyno), and mouse TfR1. Structural data further explain and support the underlying mechanism of this pH-dependent binding. These anti-TfR1 NANOBODY(R) molecules were successfully conjugated to both short-interfering RNA (siRNA) and antisense oligonucleotide (ASO) tool payloads. anti-TfR1 NANOBODY(R)-siRNA conjugates can induce up to 60% knockdown of the target mRNA transcript in skeletal muscle up to two weeks post a single IV dose in mice and up to 35-40% at four weeks post dose. Furthermore, extending the half-life of the anti-TfR1 NANOBODY(R)-ASO shuttles enhances heart, sciatic nerve, and brain exposure and enables up to 30-60% target knockdown in different CNS cell types. Altogether, these results highlight important features for the development of anti-TfR1 shuttles for the purpose of downregulating target mRNA transcripts in muscle and CNS for a variety of neurologic and neuromuscular indications.

neuroscience↗

bioRxiv2026

Targeting DNA Methylation Reactivates Type I Interferon Signalling in Bone-Metastatic Breast Cancer

Bone metastasis remains a major clinical challenge in advanced breast cancer. Downregulation of type I interferon signalling, a critical immunomodulatory pathway in anti-cancer immunity and disease progression, is a defining feature of this process. Here, we utilised an IFN-reporter system to perform unbiased epigenetic compound screens to identify agents that could restore type I IFN signalling. This screen identified Decitabine, a DNA hypomethylating agent, that enhanced tumor immunogenicity across a broad range of mouse and human breast cancer cell lines, including bone-derived lines. Mechanistically, suppression of interferon-stimulated genes is highly correlated with elevated DNMT1 expression in bone metastasis compared with primary tumor, in both mouse models and matched human samples. Decitabine treatment was sufficient to reactivate interferon stimulated genes in bone-derived 4T1.2 cell lines via hypomethylation of type I interferon pathway gene promoter regions. Correspondingly, in the syngeneic 4T1.2 metastasis mouse model, Decitabine treatment conferred a survival benefit and reduced metastatic potential, particularly in bone. Our findings reveal DNA methylation as a key regulator of the transcriptional programs underlying bone metastasis, providing mechanistic insight into how Decitabine reactivates type I interferon signalling and reduces metastatic potential, highlighting epigenetic reprogramming as a promising approach for targeting metastatic breast cancer. STATEMENT OF SIGNIFICANCEBone metastasis remains a major clinical challenge and a key mechanism of progression to bone is the suppression of tumor-inherent type I interferon signalling. We identified Decitabine, a DNA hypomethylating agent, as a promising therapeutic agent to enhance tumor immunogenicity across a broad range of breast cancer cell lines, including bone metastasis-derived lines. Our findings support DNA methylation as a key regulator of transcriptional programs associated with bone metastatic progression, and provide mechanistic insight into how Decitabine reactivates type I interferon signalling and reduces metastatic potential in vivo. These results highlight epigenetic reprogramming as a promising approach for targeting metastatic breast cancer.

Cancer Biology↗

bioRxiv2026

Soluble Urokinase Plasminogen Activator Receptor Primes Macrophages and Worsens Heart Failure with Preserved Ejection Fraction

BackgroundHeart failure with preserved ejection fraction (HFpEF) is a systemic inflammatory syndrome with few effective therapies. Soluble urokinase plasminogen activator receptor (suPAR), a circulating immune-derived glycoprotein, independently predicts adverse outcomes in HFpEF beyond natriuretic peptides, but whether it is a causal driver or a passive marker of inflammatory burden has remained unresolved. MethodsWe tested the hypothesis that elevated circulating suPAR is sufficient to amplify HFpEF by acting on the innate immune system. suPAR-transgenic (suPAR-Tg) and wild-type mice were subjected to a cardiometabolic two-hit model (high-fat diet plus L-NAME) for 15 weeks. Cardiac structure and diastolic function were assessed by serial echocardiography alongside blood pressure, glucose tolerance, and gravimetric endpoints, and left ventricular tissue was profiled by bulk RNA sequencing with in silico cellular deconvolution. Myeloid populations in the heart, spleen, and peripheral blood were quantified by spectral flow cytometry and corroborated by galectin-3 immunofluorescence, and the direct effect of suPAR on macrophages was tested by priming bone marrow-derived macrophages with recombinant suPAR before LPS and IFN-{gamma} stimulation. ResultsSustained suPAR elevation worsened the established HFpEF phenotype, producing greater diastolic dysfunction (higher E/e' and E/A ratios) and pulmonary congestion without altering blood pressure or ejection fraction, indicating a mechanism downstream of the canonical hemodynamic stimulus. Bulk RNA sequencing of left ventricular tissue revealed a coordinated transcriptional shift, with suppression of mitochondrial oxidative phosphorylation and amplification of innate and adaptive immune programs, including interleukin-1{beta} production, leukocyte chemotaxis, and antigen presentation. Spectral flow cytometry demonstrated stepwise expansion of CCR2 inflammatory monocytes and macrophages across cardiac, splenic, and peripheral compartments, corroborated in situ by increased galectin-3 macrophage density. In vitro, recombinant suPAR was not a stand-alone inflammatory ligand but instead primed bone marrow-derived macrophages to markedly amplify TNF-, IL-1{beta}, IL-6, and NLRP3 responses to LPS and IFN-{gamma}. ConclusionsTogether, these findings establish that elevated suPAR is sufficient to act as an upstream amplifier of HFpEF, identify the CCR2 inflammatory monocyte-macrophage axis as its proximate effector, and convert two decades of epidemiologic association into a mechanistically grounded, therapeutically tractable hypothesis with immediate relevance to clinical-stage anti-suPAR antibodies.

immunology↗

bioRxiv2025

Epitranscriptomic landscape of vascular smooth muscle cell phenotypic transitions highlights uridine RNA modifications associated with post-transcriptional regulation

BackgroundVascular smooth muscle cells (VSMCs) phenotypic plasticity can modulate atherosclerosis progression. Although several gene regulatory steps towards pro-inflammatory phenotypes have been well-studied, epitranscriptomic changes during this transition and their regulatory roles remain unexplored. Methods and ResultsPrimary human VSMCs stimulated with TGF-{beta}1 to induce atheroprotective, contractile, and matrix-producing state and with IL1-{beta} plus PDGF-BB to induce a highly energetic, pro-inflammatory state, confirmed by Illumina bulk RNA sequencing and proteomics. Untargeted screening of mRNA base modifications using Oxford Nanopore Technologies direct RNA sequencing and xPore analysis revealed enhanced uridine modification within a GUUUU motif in pro-inflammatory VSMCs. Modified uridines were enriched in 3-UTR and accessible RNA structures, with implications on Poly(A) tail dynamics and miRNA binding. ConclusionsAtheroprotective and pro-atherogenic treatments induce distinct epitranscriptomic landscapes composed of different modification types, often co-localized in the transcript. Modified uridines in mRNAs are abundant in a high-energy, pro-inflammatory VSMC state and associated with post-transcriptional regulation. n summary, epitranscriptomics adds a novel regulatory layer to VSMC phenotypic transitions critical for atherosclerosis development and progression. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=74 SRC="FIGDIR/small/694735v2_ufig1.gif" ALT="Figure 1"> View larger version (19K): org.highwire.dtl.DTLVardef@933071org.highwire.dtl.DTLVardef@151564borg.highwire.dtl.DTLVardef@f862e9org.highwire.dtl.DTLVardef@125c509_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphic AbstractC_FLOATNO C_FIG

molecular biology↗

bioRxiv2025

Multi-omics integration and batch correction using a modality-agnostic deep learning framework

State-of-the-art biotechnologies allow the detection of different molecular species on the same biological sample, generating complex highly-dimensional multi-modal datasets. Gaining a holistic understanding of biological phenomena, such as oncogenesis or aging, requires integrating these diverse modalities into low-dimensional data representations while correcting for technical artifacts. Here we present MIMA, a modular, unsupervised AI framework for multi-omics data integration and batch correction. Applied to complex spatial and single-cell datasets, MIMA effectively removes batch effects, while preserving biologically relevant information, and learns representations predictive of expert pathologist annotations. Additionally, it enables cross-modal translation, uncovers molecular patterns not captured by manual annotations, and despite being modality-agnostic performs on par with specialized state-of-the-art tools. MIMAs flexibility and scalability make it a powerful tool for multimodal data analysis. MIMA provides a foundation for AI-based, multi-omics augmented digital pathology frameworks, offering new opportunities for improved patient stratification and precision medicine through the comprehensive integration of high-dimensional molecular data and histopathological imaging.

bioinformatics↗

bioRxiv2025

Spatial profiling of longitudinal glioblastoma reveals consistent changes in cellular architecture, post-treatment

Glioblastoma (GBM), the most aggressive adult brain cancer, comprises a complex tumour microenvironment (TME) with diverse cellular interactions driving progression and pathobiology. How these spatial patterns and interactions evolve with treatment remains unclear. Here, we apply imaging mass cytometry to analyse protein-level changes in paired pre- and post-treatment GBM samples from five patients. We find a significant post-treatment increase in normal brain cells alongside a reduction in vascular cells. Moreover, despite minimal overall change in cellular diversity, interactions among astrocytes, oligodendrocytes, and vascular cells increase post-treatment, suggesting reorganisation of the TME. The GBM TME cells form spatially organized layers driven by hypoxia pre-treatment, but this influence diminishes post-treatment, giving way to less organised layers with organisation driven by reactive astrocytes and lymphocytes. These findings provide insight into treatment-induced shifts in GBMs cellular landscape, highlighting aspects of the evolving TME that appear to facilitate recurrence and are, therefore, potential therapeutic targets. Key pointsO_LISpatial organisation in primary GBM consist of layers driven by the presence of hypoxia C_LIO_LIThe layers in recurrent GBM appear are driven more by the presence of reactive astrocytes C_LIO_LIIncreased cellular cross-talk in recurrent GBM presents novel therapeutic targets C_LI

cancer biology↗

bioRxiv2025

South African brown locusts, Locustana pardalina, hosts fluconazole resistant Candidozyma (Candida) auris (Clade III)

The environmental niche and mode of transmission from the environment to humans of the emerging pathogenic yeast, Candidozyma (Candida) auris is a subject of speculation, with hypotheses including avian species and marine environments. Interestingly, yeasts related to C. auris have been repeatedly observed associated with various insects. This lprompted us to investigate a thermophilic insect, Locustana pardalina as possible host for C. auris. Here we report the isolation and identification of three C auris strains from the gut of L. pardalina as well as the phenotypic characterisation of one of these isolates. Interestingly, the isolate was able to survive at 50oC and grew at 15% NaCl. In addition, it was susceptible to the tested disinfectants and antifungals, except fluconazole. Genome sequencing and SNP analyses placed the isolate in Clade III, which is common is South Africa. This highlights the role of insects in the evolution and dissemination of emerging pathogenic yeasts.

microbiology↗

bioRxiv2024

Preliminary report on the molecular epidemiology of mpox, South Africa 2024

Mpox is an emerging viral infection and has since May 2022 been reported in a multi-country outbreak involving predominantly previously non-endemic countries. In addition, the number of cases of mpox is also rising in some endemic countries in Western and Central Africa. The disease is a notifiable medical condition in South Africa, with no cases reported before 2022. However, in 2022, coinciding with the peak of a multi-country mpox outbreak, five mpox cases were diagnosed in the country. Genomic sequencing and analysis revealed the presence of a monkeypox virus variant, which was circulating during the multi-country outbreak, namely Clade IIb sub-lineage B.1.7 (hMPXV). After the fifth case was reported in 2022, there were no cases detected for the following 20 months. In May 2024, mpox cases were again detected in South Africa leading to concerns that the virus may have been silently transmitting in the country since 2022. Genomic sequencing and analysis for 22 mpox cases reported during May to September 2024, were compared with sequences obtained from mpox cases reported in South Africa in 2022, and cases that have been reported globally. It was found that the sequences of the 2024 cases analysed in this study, clustered with Clade IIb hMPXV and sub-lineage B.1.20 and B.1.6 sequences. The results indicate that the detection of mpox cases in South Africa was an extension of the ongoing multi-country outbreak. Detection of different sub-lineages of hMPXV indicates reintroductions of the virus in the country since 2022, with local transmission of Clade IIb B1.20 hMPXV.

microbiology↗

bioRxiv2024

Experimental evolution of gene essentiality in bacteria

Essential gene products carry out fundamental cellular activities in interaction with other components. However, the lack of essential gene mutants and appropriate methodologies to link essential gene functions with their partners poses significant challenges. Here, we have generated deletion mutants in 32 genes previously identified as essential, with 23 mutants showing extremely slow growth in the SK36 strain of Streptococcus sanguinis. The 23 genes corresponding to these mutants encode components of diverse pathways, are widely conserved among bacteria, and are essential in many other bacterial species. Whole-genome sequencing of 243 independently evolved populations of these mutants has identified >1000 spontaneous suppressor mutations in experimental evolution. Many of these mutations define new gene and pathway relationships, such as F1Fo-ATPase/V1Vo-ATPase/TrkA1-H1 that were demonstrated across multiple Streptococcus species. Patterns of spontaneous mutations occurring in essential gene mutants differed from those found in wildtype. While gene duplications occurred rarely and appeared most often at later stages of evolution, substitutions, deletions, and insertions were prevalent in evolved populations. These essential gene deletion mutants and spontaneous mutations fixed in the mutant populations during evolution establish a foundation for understanding gene essentiality and the interaction of essential genes in networks.

evolutionary biology↗

bioRxiv2024

node2vec2rank: Large Scale and Stable Graph Differential Analysis via Multi-Layer Node Embeddings and Ranking

1Advances in computational biology now enable the inference of increasingly accurate, genome-wide molecular interaction networks from multi-omic data collected across large cohorts. Comparing such networks across distinct biological states can identify biologically informative and potentially actionable higher-order interactions that differentiate these states. However, developing methods for effective graph differential analysis remains challenging as it requires capturing subtle structural changes within the context of complex, high-dimensional networks shaped by heterogeneous biological processes. We introduce node2vec2rank (n2v2r), a multi-layer spectral embedding algorithm that, in contrast to conventional feature-based approaches, compares graphs by inferring node representations that summarize network structure in a data-driven manner. Node2vec2rank is computationally efficient, stable, and provably recovers the correct ranking of differences between weighted graphs. We used n2v2r to compare networks from breast cancer subtypes, to analyze networks capturing single-cell dynamics, and to investigate sex differences in lung adenocarcinoma. The results of these analyses show that n2v2r is a versatile and powerful tool that can uncover biologically relevant insights from complex biological networks, distinguishing between states of health and disease.

bioinformatics↗

bioRxiv2024

Cramming Protein Language Model Training in 24 GPU Hours

Protein language models (pLMs) are ubiquitous across biological machine learning research, but state-of-the-art models like ESM2 take hundreds of thousands of GPU hours to pre-train on the vast protein universe. Resource requirements for scaling up pLMs prevent fundamental investigations into how optimal modeling choices might differ from those used in natural language. Here, we define a "cramming" challenge for pLMs and train performant models in 24 hours on a single GPU. By re-examining many aspects of pLM training, we are able to train a 67 million parameter model in a single day that achieves comparable performance on downstream protein fitness landscape inference tasks to ESM-3B, a model trained for over 15, 000x more GPU hours than ours. We open source our library1 for training and inference, LBSTER: Language models for Biological Sequence Transformation and Evolutionary Representation.

bioengineering↗

bioRxiv2024

Investigating the effects of protons versus x-rays on radiation-induced lymphopenia after brain irradiation

BackgroundConventional x-ray-based radiotherapy is a standard treatment for patients with brain tumors. However, is associated with systemic effects like lymphopenia that correlates with poor prognosis. Proton therapy has emerged as a new radiation strategy, given that the lower entry dose and absence of exit dose can be exploited to spare healthy brain tissues and reduce side-effects caused by systemic inflammation. We evaluated if brain irradiation with protons could spare circulating leukocytes along with other variables in rodent models. MethodsTumor-free C57BL/6 mice were irradiated with a total dose of 20Gy in 2.5Gy twice-daily sessions over four consecutive days with either x-rays or protons. Groups of mice were defined according to irradiation volume (whole-brain or hemisphere) and dose rate (1 or 2Gy/min). Blood was withdrawn at various time points and circulating lymphoid, with myeloid subpopulations analyzed using flow cytometry. Brain tissue histochemical analyses were performed late after irradiation. ResultsBlood sampling showed severe and acute radiation-induced lymphopenia after x-rays, with marked depletion of 50% CD4+ and CD8+, as well as B and NK cells. With protons, the decrease was 20% on average for whole-brain irradiations, suggesting a conservative effect on circulating lymphocytes. The data showed no effect in CD11b+ myeloid cells for both x-rays and protons. Histological analyses revealed a more intense expression level of CD68 and Iba1 immunostaining after x-ray irradiation. GFAP staining was well detected after both beams. ConclusionProton therapy for brain tumors differs from photon therapy in terms of its effects on circulating cells and tissues. Key pointsO_LIX-ray brain irradiation induced an acute severe lymphopenia, with a reduction of at least 50% lymphocytes. The whole-brain irradiation caused a more pronounced decrease in lymphocytes than hemisphere irradiation. Proton brain irradiation exhibited a conservative effect on circulating leukocytes. C_LIO_LIX-ray irradiation-induced lymphopenia is followed by a recovery of all lymphocyte subpopulations to control levels. However, this recovery is longer for CD3+ lymphocytes, and B and NK cells, depending on irradiation modalities. C_LIO_LILong-term brain tissue histochemical analyses demonstrated differences between the two beams, consisting of a macrophage/microglial activation seen mostly after x-rays while an astrocyte reaction was seen after brain exposure to the two beams. These differences may explain the disparities observed in leukocytes, thereby favoring a specific biological reaction between the brain and blood. C_LI Importance of the StudyOur study demonstrated that while whole-brain or hemispheric irradiation with x-rays resulted in lymphopenia, proton brain irradiation exhibited a conservative effect on circulating lymphocytes, which was paralleled by a less intense brain tissue reaction.

cell biology↗

bioRxiv2023

Analysis of nasopharyngeal microbiome patterns in Zambian infants with fatal acute febrile illness

IntroductionAssociative connections have previously been identified between nasopharyngeal infections and infant mortality. The nasopharyngeal microbiome may potentially influence the severity of these infections. MethodsWe conducted an analysis of a longitudinal prospective cohort study of 1,981 infants who underwent nasopharyngeal sampling from 1 week through 14 weeks of age at 2-3-week intervals. In all, 27 microbiome samples from 9 of the infants in the cohort who developed fatal acute febrile illness (fAFI) were analyzed in pooled comparisons with 69 samples from 10 healthy comparator infants. We completed 16S rRNA amplicon gene sequencing all infant NP samples and characterized the maturation of the infant NP microbiome among the fAFI(+) and fAFI(-) infant cohorts. ResultsBeta diversity measures of fAFI(-) infants were markedly higher than those of fAFI(+) infants. The fAFI(+) infant NP microbiome was marked by higher abundances of Escherichia, Pseudomonas, Leuconostoc, and Weissella, with low relative presence of Alkalibacterium, Dolosigranulum, Moraxella, and Streptococcus. ConclusionsOur results suggest that nasopharyngeal microbiome dysbiosis precedes fAFI in young infants. Early dysbiosis, involving microbes such as Escherichia, may play a role in the causal pathway leading to fAFI or could be a marker of other pathogenic forces that directly lead to fAFI.

microbiology↗

bioRxiv2023

Potent GST ketosteroid isomerase activity relevant to ecdysteroidogenesis in the malaria vector Anopheles gambiae

Nobo is a glutathione transferase (GST) crucially contributing to ecdysteroid biosynthesis in insects of the orders Diptera and Lepidoptera. Ecdysone is a vital steroid hormone in insects, which governs larval molting and metamorphosis, and suppression of its synthesis has potential as a novel approach to insect growth regulation and combatting vectors of disease. In general, GSTs catalyze detoxication, whereas the specific function of Nobo in ecdysteroidogenesis is unknown. We report that Nobo from the malaria-spreading mosquito Anopheles gambiae is a highly efficient ketosteroid isomerase catalyzing double-bond isomerization in the steroids 5-androsten-3,17-dione and 5-pregnen-3,20-dione. These mammalian ketosteroids are unknown in mosquitoes, but the discovered prominent catalytic activity with these compounds suggests that the unknown Nobo substrate in insects has a ketosteroid functionality. Nobo Asp111 is essential for activity with the steroids, but not for conventional GST substrates. Further characterization of Nobo may guide the development of new insecticides to prevent malaria.

biochemistry↗

bioRxiv2023

IDHwt glioblastomas can be stratified by their transcriptional response to standard treatment, with implications for targeted therapy

Glioblastoma (GBM) brain tumours lacking IDH1 mutations (IDHwt) have the worst prognosis of all brain neoplasms. Patients receive surgery and chemoradiotherapy but tumours almost always fatally recur. Using RNAseq data from 107 pairs of pre- and post-standard treatment locally recurrent IDHwt GBM tumours, we identified two responder subtypes based on therapy-driven changes in gene expression. In two thirds of patients a specific subset of genes is up-regulated from primary to recurrence (Up responders) and in one third the same genes are down-regulated (Down responders). Characterisation of the responder subtypes indicates subtype-specific adaptive treatment resistance mechanisms. In Up responders treatment enriches for quiescent proneural GBM stem cells and differentiated neoplastic cells with increased neurotransmitter signalling, whereas Down responders commonly undergo therapy-driven mesenchymal transition. Stratifying GBM tumours by response subtype may lead to more effective treatment. In support of this, modulators of gamma aminobutyric acid (GABA) neurotransmitter signalling differentially sensitise Up and Down responder GBM models to standard treatment in vitro.

cancer biology↗

bioRxiv2022

Illuminating protein space with a programmable generative model

Three billion years of evolution have produced a tremendous diversity of protein molecules, and yet the full potential of this molecular class is likely far greater. Accessing this potential has been challenging for computation and experiments because the space of possible protein molecules is much larger than the space of those likely to host function. Here we introduce Chroma, a generative model for proteins and protein complexes that can directly sample novel protein structures and sequences and that can be conditioned to steer the generative process towards desired properties and functions. To enable this, we introduce a diffusion process that respects the conformational statistics of polymer ensembles, an efficient neural architecture for molecular systems based on random graph neural networks that enables long-range reasoning with sub-quadratic scaling, equivariant layers for efficiently synthesizing 3D structures of proteins from predicted inter-residue geometries, and a general low-temperature sampling algorithm for diffusion models. We suggest that Chroma can effectively realize protein design as Bayesian inference under external constraints, which can involve symmetries, substructure, shape, semantics, and even natural language prompts. With this unified approach, we hope to accelerate the prospect of programming protein matter for human health, materials science, and synthetic biology.

bioinformatics↗

bioRxiv2022

GBMdeconvoluteR accurately infers proportions of neoplastic and immune cell populations from bulk glioblastoma transcriptomics data

The biological and clinical impact of neoplastic and immune cell type ratios in the glioblastoma (GBM) tumour microenvironment is being realised. Characterising and quantifying cell types within GBMs at scale will facilitate a better understanding of the association between the cellular landscape and tumour phenotypes or clinical correlates. This study aimed to develop a tool that can deconvolute immune and neoplastic cells within the GBM tumour microenvironment from bulk RNA sequencing data. We developed an IDH wild-type (IDHwt) GBM specific single immune cell reference dataset, from four independent studies, consisting of B cells, T cells, NK cells, microglia, tumour associated macrophages, monocytes, mast and DC cells. We used this alongside an existing neoplastic single cell-type dataset consisting of astrocyte-like, oligodendrocyte- and neuronal-progenitor like and mesenchymal GBM cancer cells to create both marker and gene signature matrix-based deconvolution tools. We then applied single-cell resolution imaging mass cytometry (IMC) to ten IDHwt GBM samples, five paired primary and recurrent tumours, in parallel with these tools to determine which performed best. Marker based gene expression deconvolution using GBM tissue specific markers, which we have packaged as GBMdeconvoluteR, gave the most accurate results. The correlation between immune cell quantification by IMC and by GBMdeconvoluteR for primary IDHwt GBM samples was 0.52 (Pearsons P=7.8x10-3) and between neoplastic cell quantification by IMC and by GBMdeconvoluteR was 0.75 (Pearsons P=1.2x10-3). We applied GBMdeconvoluteR to bulk GBM RNAseq data from The Cancer Genome Atlas (TCGA) and were able to recapitulate recent findings from multi-omics single cell studies with regards associations between mesenchymal GBM cancer cells and both lymphoid and myeloid cells. Furthermore, we were able to expand upon this to show that these associations are stronger in patients with worse prognosis. GBMdeconvoluteR is accessible online at https://gbmdeconvoluter.leeds.ac.uk. Key pointsGBMdeconvoluteR is a glioblastoma-specific cellular deconvolution tool. When applied to bulk GBM RNAseq data, it accurately quantifies the neoplastic and immune cells in that tumour. It is available online at https://gbmdeconvoluter.leeds.ac.uk

cancer biology↗

bioRxiv2020

Naa12 rescues embryonic lethality in Naa10-Deficient Mice in the amino-terminal acetylation pathway

Amino-terminal acetylation is catalyzed by a set of N-terminal acetyltransferases (NATs). The NatA complex (including X-linked Naa10 and Naa15) is the major acetyltransferase, with 40-50% of all mammalian proteins being potential substrates. However, the overall role of amino-terminal acetylation on a whole-organism level is poorly understood, particularly in mammals. Male mice lacking Naa10 show no globally apparent in vivo amino-terminal acetylation impairment and do not exhibit complete embryonic lethality. Rather Naa10 nulls display increased neonatal lethality, and the majority of surviving undersized mutants exhibit a combination of hydrocephaly, cardiac defects, homeotic anterior transformation, piebaldism and urogenital anomalies. Naa12 is a previously unannotated Naa10-like paralogue with NAT activity that genetically compensates for Naa10. Mice deficient for Naa12 have no apparent phenotype, whereas mice deficient for Naa10 and Naa12 display embryonic lethality. The discovery of Naa12 adds to the currently known machinery involved in amino-terminal acetylation in mice.

developmental biology↗