Biology subjects

Khan, M.

Publications and source records attributed to Khan, M..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

Exploration of diuretic potential of different parts (flower, bark, leaf) of Butea Monosperma

Hypertension (HTN) or high blood pressure poses major global health concerns, and the conventional synthetic antihypertensive drugs are effective, though their long-term use is often limited due to adverse effects. Butea monosperma (B. monosperma), commonly known as the Flame of the Forest, the traditional use as medicinal plant for diuresis and other usage in rural areas in South Asia suggests a role for its antihypertensive potential. The study aimed, first to identify the diuretic constituents present from different parts (flower, bark, and leaf) of B. monosperma and to evaluate their diuretic activity through in vivo experimentation. The chemical profiling of the extracts of different parts were performed using Liquid Chromatography Mass Spectrometry (LC-MS/MS), while diuretic efficacy was assessed in Swiss Albino wistar rats. Urinary volume and electrolyte excretion (Na{square}, K{square}, and Cl{square}) were measured to elucidate the possible mechanism of action. Statistical analyses were conducted using one-way ANOVA followed by multiple comparison test, with significance set at p < 0.05. LC MS/MS analysis confirmed the presence of chlorthalidone, a thiazide-like diuretic compound, in all three plant parts under selective ionization mode. In vivo results demonstrated a significant, dose dependent increase in urine output and electrolyte excretion in treated rats compared to controls (p < 0.05). These findings provide both phytochemical and pharmacological evidence that B. monosperma possesses potent diuretic activity, supporting its traditional use and highlighting its potential as a natural source for the development of novel antihypertensive and diuretic therapeutics.

biochemistry↗

bioRxiv2025

Nanoplasmonic SERS reveals previously uncharacterised indole derivative in E. coli metabolism

Tryptophanase (TnaA) is a promiscuous enzyme which regulates the production of amino acid-derived metabolites, essential for bacterial communication. TnaA is known to convert tryptophan into indole, an important signalling molecule influencing a range of behaviours - from bacterial quorum sensing to urinary tract infections (UTI) - but other conversion routes remain obscure. Here, we show that nanoplasmonic surface-enhanced Raman spectroscopy (SERS) combined with targeted genetic subtraction enables the label-free, cellular characterisation and structural identification of TnaA-derived metabolites directly from Escherichia coli culture solutions, without isolation or purification. We systematically profile the SERS spectra of wild-type and tnaA gene knockout strains (E. coli BW25113 and the uropathogenic 536) supplemented with each of the twenty amino acids, uncovering a previously unreported TnaA-dependent metabolic signature, I*, whose Raman fingerprint does not match free indole or any common indole derivative characterised by mass spectrometry. Using isotopomer-labelled substrates together with structural reference compounds, we perform label-free structural deduction of I* directly from SERS spectra. We find I*s structure is consistent with an intact indole ring carrying a C3 substituent, likely produced indirectly from intracellular tryptophan. These findings introduce a novel indole metabolite, raise new hypotheses regarding the biological role of TnaA-mediated byproducts in bacterial signalling and virulence, and demonstrate that nanoplasmonic SERS provides a powerful framework for probing enzyme activity and bioactive metabolite production directly from living bacterial cultures with nanomolar sensitivity and structural specificity.

microbiology↗

bioRxiv2025

A De Novo Algorithm for Allele Reconstruction from Oxford Nanopore Amplicon Reads, with Application to CYP2D6

The Oxford Nanopore Technologies sequencing platform offers a path towards bedside genomics, producing long reads that can completely cover a gene of interest, and thus detect any known or novel variant the gene contains. However, the analysis of these long reads to identify actionable genotypes remains challenging and typically requires customization depending on the target gene. Here, we describe a generic algorithm to accurately reconstruct allele sequences derived from long-reads of genomic-amplicon origin. Rather than calling variants directly from these long-reads, our method takes a "sequence-first" approach, performing an unbiased reconstruction of the underlying amplicon sequences to generate high-confidence reconstructed allele sequences. This is done without user input of the expected target gene, allowing for any source amplicon to be reconstructed. These high-confidence reconstructed allele sequences are then compared to the genomic reference sequence of the gene to infer the specific diplotype present in the sample. This approach is agnostic towards the number of genes and alleles present and readily detects novel variants. We demonstrate our approach using three independent data sets for CYP2D6, a diverse and complex gene with over 175 known alleles of clinical significance affecting drug dosing. We show how our approach can accurately recover validated CYP2D6 diplotypes from 20 Coriell samples sequenced using different primer sets, on different Oxford Nanopore Technologies flow cell versions, and to different depths. This includes inferring occurrences of copy number variation from relative abundances of each allele, a critical factor for ascribing functional effects to a diplotype. Further, we demonstrate our approachs utility for other genomic regions, including HLA.

bioinformatics↗

bioRxiv2025

Central carbon metabolism switching in lytic versus temperate coral reef viral communities

Coral reefs are declining globally due in part to bacterial overgrowth, a process known as microbialization. However, the role of bacteriophages that may inhibit microbialization by infecting and killing these bacteria remains poorly understood, especially their metabolic impacts on bacterial proliferation. To address this, we analyzed central carbon metabolism gene frequencies in viral communities from healthy (lytic-dominated) and degraded (temperate-dominated) Central Pacific coral reefs. We found that viral metabolism shifted broadly from being dominated by metabolism that builds up pools of central intermediates on degraded reefs dominated by temperate viral infection ("anaplerotic" reactions) to metabolism that consumes these pools to prioritize production of metabolic precursors for virion construction on healthy reefs dominated by lytic infection ("cataplerotic" reactions). This switch was shown by the over-representation of Entner-Doudoroff (ED) glycolysis genes on degraded, temperate-dominated reefs and of pentose phosphate pathway (PPP) and reductive tricarboxylic acid cycle (TCA) genes on healthy, lytic-dominated reefs. As a result of this metabolic dichotomy, our qualitative compartment modeling revealed two distinct ecosystem states: (i) healthy reefs, where lytic viral metabolism enhances viral production and suppresses bacterial overgrowth, and (ii) degraded reefs, where temperate viral metabolism accelerates bacterial proliferation. Because viral switching between lytic and temperate lifestyles is a known function of host physiological state, these findings position viral metabolism as both a driver of reef decline and a conservation lever, with metabolically mediated "re-viralization" offering a novel strategy to restore reef resilience.

ecology↗

bioRxiv2025

Oral 4-fluorouridine completely suppresses epidemic Oropouche virus replication in mice and confers protection against virus-induced disease.

Oropouche virus (OROV) is an orthobunyavirus that causes increasingly frequent and severe outbreaks in Central and South America. We report that 4'-fluorouridine (4'-FlU) inhibits the in vitro replication of epidemic and pre-epidemic OROV strains in multiple cell lines. In vitro polymerase assays demonstrate that 4'-FlU (as its triphosphate) targets the Peribunyaviridae L protein, is incorporated during RNA synthesis and causes premature chain termination. Following 69 consecutive days of in vitro passages of OROV in the presence of suboptimal concentrations of 4'-FlU, no drug-resistant variants were identified in the viral polymerase. In stringent mouse (AG129) or Syrian hamster OROV-infection models, oral administration of 4'-FlU completely blocked viral replication and virus-induced disease, even when administration was delayed until 72 hours after infection. Our findings support exploring the potential of 4'-FlU for the management of OROV infections in humans.

microbiology↗

bioRxiv2025

Validation of a Microsampling-Compatible LC-MS/MS Method for Cannabinoid Quantitation in Whole Blood

Recently developed dried blood sampling methods for cannabinoid quantitation require small blood volumes, making them microsampling-compatible, but have notable limitations including hematocrit-related bias for dried blood spots (DBS) and higher consumable costs for volumetric absorptive microsampling (VAMS(R)). To address these issues, we developed a highly sensitive liquid chromatography-tandem mass spectrometry (LC-MS/MS) method capable of quantifying cannabinoids in 50 {micro}L of liquid whole blood, providing a practical microsampling alternative to dried blood approaches. Using liquid-liquid extraction (LLE) with sodium hydroxide alkalinization and acetonitrile precipitation, followed by quantitative analysis on an Agilent 6495 liquid chromatography-triple quadrupole (LC-TQ) mass spectrometer, we achieved lower limits of quantitation (LLOQs) of 0.10 ng/mL for {Delta}9-tetrahydrocannabinol (THC) and cannabinol (CBN), 0.20 ng/mL for cannabigerol (CBG), 0.30 ng/mL for cannabidiol (CBD), 0.50 ng/mL for 11-hydroxy-THC (11-OH-THC), and 5.0 ng/mL for 11-nor-9-carboxy-THC (THC-COOH). Calibration was linear from the LLOQ to 300 ng/mL for all analytes. To our knowledge, this is the first validated approach for cannabinoid quantitation in less than 100 {micro}L of liquid whole blood with an LLOQ for THC comparable to that with the most sensitive LC-MS/MS methods using standard blood volumes. The achieved LLOQs for other cannabinoids are also suitable for forensic toxicology applications. We anticipate particular utility for obtaining evidence from suspected impaired drivers at the roadside when paired with finger-prick sampling and liquid blood microcollection tubes.This approach enables measurement of THC levels at the time of driving and thereby overcoming current limitations, including the decrease in THC levels that occurs if blood sampling is delayed, the requirement for larger sample volumes ([≥]100 {micro}L), and dependence on trained phlebotomists for venipuncture.

pharmacology and toxicology↗

bioRxiv2025

Transitions in human gut viral communities from ancient to industrialized societies

The composition and function of the human gut microbial community (the microbiome) have changed substantially over millennia, with implications for human health. While microbiome research has focused primarily on bacterial dynamics, the long-term history of gut viral communities (the virome) remains largely unexplored, despite their crucial role in shaping bacterial populations. We analyzed gut viromes from 14 pre-modern human coprolites (1301 BCE-1400s CE), as well as 502 non-industrialized and 492 industrialized contemporary human fecal samples. We found that, from pre-modern to contemporary and industrialized populations, human gut viral communities have become more similar in gene content, increasingly dominated by temperate lifestyles, and more supportive of bacterial pathogenicity. These synergistic ecological shifts suggest that long-term changes, especially with industrialization, have fundamentally altered the gut virome, likely affecting human health. These insights into historical shifts in gut viral community and function open potential avenues for ecologically grounded therapeutics to enhance gut microbiome resilience.

microbiology↗

bioRxiv2025

Tool and hand adaptation and localization in immersive virtual reality

The human brain readily adapts movements to achieve motor goals. Most visuomotor adaptation studies use planar reaching with a cursor, where misaligned feedback leads to compensatory adjustments, reach aftereffects, and shifts in perceived hand location. Whether these effects extend to more natural settings and tool use remains unclear. In the Hand Experiment, we showed that in immersive virtual reality (VR), adaptation to 30{degrees} and 60{degrees} visuomotor rotations produced robust reach aftereffects and the expected shifts in hand localization. In the Pen Experiment, we extended this paradigm to a familiar hand-held tool, assessing localization of both the tool tip and the hand. Adaptation with the pen induced comparable or greater recalibration effects than with the hand-cursor, including shifts in both perceived tool and hand position. These findings demonstrate that visuomotor adaptation in immersive VR generalizes beyond cursor-based tasks, revealing how the sensorimotor system recalibrates internal representations of both the body and tools in realistic 3D environments. Author summary for PLOS ONEThis study shows that when people adapt their movements in virtual reality, the brain recalibrates not only the sensed position of the hand but also of familiar tools, highlighting how we update body and tool representations in everyday-like environments.

neuroscience↗

bioRxiv2025

Formic acid impairs α-synuclein seeding activity in human and mouse brains

-Synuclein (-syn) is an abundant monomeric protein that can aggregate into fibrils and form neuropathological inclusions in the brains of patients with synucleinopathies. New evidence suggests that the mouse-human transmission barrier of -syn is lower than previously reported, emphasizing the need for improved biosafety procedures when working with -syn aggregates. Histopathology of -syn-infected brain represents a significant potential source of occupational exposure, and current methods for tissue fixation do not inactivate the ability of pathologic -syn to seed the conversion of endogenous, monomeric -syn into fibrils. In this study, we tested whether 96% formic acid treatment could reduce the seeding activity of -syn aggregates in paraformaldehyde-fixed brain samples from dementia with Lewy bodies (DLB) patients and -syn pre-formed fibrils (PFF)-injected mouse brains. Using real-time quaking-induced conversion (RT-QuIC), we found that formic acid treatment reduced -syn seeding dose (picograms of -syn seeds per ml of brain homogenate) in DLB and mouse brain by 6 and 8 logarithms, respectively. RT-QuIC reactions seeded with formic acid-treated brain homogenates showed significantly longer lag phase, and decreased total thioflavin T fluorescence compared to untreated samples, indicating that formic acid treatment impairs the ability of pathological -syn to seed monomeric -syn. Importantly, the -syn pathologic features and the immunostaining quality were preserved in formic acid-treated tissues. Our results demonstrate that formic acid treatment is a quick and efficient procedure for reducing -syn seeding activity in fixed brain samples, thereby lowering the risk of accidental exposure in laboratories without compromising the quality of histopathological analysis. SummaryFormic acid treatment drastically reduces -synuclein seeding activity in fixed human and mouse brain samples while preserving histopathological quality.

neuroscience↗

bioRxiv2025

Tryptophan and IFN-γ Differentially Modulate Cellular Uptake, Intracellular Trafficking, and Gene Expression of Messenger RNA-Loaded Lipid Nanoparticles in Dendritic Cells

Lipid nanoparticle (LNP)-mediated mRNA delivery has emerged as a powerful platform for both immunostimulatory and immunomodulatory applications. However, the influence of local immunometabolic cues on the intracellular fate and translational efficiency of mRNA-LNPs remains poorly understood. In this study, we investigated how interferon-gamma (IFN-{gamma}), a potent inducer of indoleamine 2,3-dioxygenase 1 (IDO1), and tryptophan (Trp) deprivation independently and combinatorially affect mRNA-LNP function in DC2.4 dendritic cells. These two cues are canonical drivers of immunoregulatory microenvironments, particularly those that favor tolerogenic dendritic cell programming and the induction of regulatory T cells. Using dual-reporter mRNA constructs and high-resolution confocal imaging, we show that IFN-{gamma} stimulation reduces total cellular mRNA uptake and lysosomal accumulation without affecting translation efficiency and endosomal escape efficiency. Whereas Trp deprivation also reduces the overall cellular uptake of mRNA-LNPs, it also significantly impairs protein synthesis from mRNA-LNPs and modestly reduces endosomal escape, despite having minimal impact on lysosomal mRNA levels. Spatial compartmentalization analysis revealed that IFN-{gamma} and Trp limitation disrupt distinct steps in the delivery-translation cascade, acting independently but additively to suppress the ultimate protein translation from mRNA-LNPs in DC2.4 dendritic cells. These findings highlight the importance of considering local metabolic and cytokine contexts when deploying mRNA-LNPs for immunological applications. Our work provides mechanistic insights into how immunoregulatory environments impair the delivery and translation of mRNA-LNPs, suggesting strategies to tune delivery outcomes for tolerogenic purposes.

biochemistry↗

bioRxiv2025

Pathogenic fungus exploits the lateral root regulators to induce pluripotency in maize shoots

Biotrophic plant pathogens secrete effector molecules to redirect and exploit endogenous signaling and developmental pathways in their favor. The biotrophic fungus Ustilago maydis causes galls on all aerial parts of maize. However, identification and characterization of the responsible gall-inducing effectors and corresponding plant signaling pathway(s) are largely elusive. Here we reveal molecular components acting downstream of a group of plant TOPLESS (TPL)- corepressor interacting fungal effectors that are directly involved in gall formation. We classify these effectors into two classes based on distinct phenotypic responses when individually expressed in planta. While class I responses are characterized by leaf chlorosis, transgenic plants expressing class II TPL-interacting protein (Tip) effectors show a derepression of the AtARF7/AtARF19 branch of auxin signaling, resulting in pluripotent calli formation without the external addition of phytohormones. Subsequent comparative transcriptomics in maize also demonstrates a highly significant overlap of genes up-regulated during U. maydis-triggered leaf gall formation and during the developmental initiation of lateral root formation. This suggests that U. maydis can hijack the lateral root initiation pathway to induce galls in maize shoots. We demonstrate that underlying this is the transcriptional upregulation of downstream LATERAL ORGAN BOUNDARIES DOMAIN (LBD) transcription factors. Maize mutants in two LBD genes (ra2, rtcs) led to significantly reduced gall formation following U. maydis infection on homozygous mutants. This study reveals a set of dominantly acting cell proliferation-inducing fungal effectors and provides novel insight into plant developmental pathways that can be hijacked by biotrophic pathogens to induce gall formation.

plant biology↗

bioRxiv2025

Computational Modeling and Visualization of Ischemic Effects on an Advanced Purkinje Network

The cardiac Purkinje network plays a vital role in the hearts electrical conduction system, ensuring efficient and synchronized ventricular contraction. When impaired--particularly by ischemia--it can trigger life-threatening arrhythmias. In this study, we present an advanced computational model of the Purkinje network that integrates cell-level heterogeneity, spatial organization, and localized ischemic zones with customizable severity gradients. Developed in Python using open-source libraries (NumPy, matplotlib, pandas, seaborn), the model generates rich visualizations of network structure, conduction velocities, ischemia severity, and electrophysiological parameters. Simulations demonstrate how ischemia alters conduction and refractoriness in a spatially dependent manner, providing insights into arrhythmogenic risk. This modeling framework can advance understanding of cardiac conduction under pathological conditions and support therapeutic development.

bioinformatics↗

bioRxiv2025

Identification and characterization of a non-peptidic cyclophilin ligand with antiviral activity against feline and porcine α-coronaviruses.

Coronaviruses (CoVs) are emerging pathogens that have been extensively studied over the last 20 years and can cause acute respiratory diseases in humans, as exemplified by the SARS-CoV-2 pandemic. Coronaviruses are also known for their importance in veterinary medicine, being responsible for severe pathologies in pets and livestock. These include Feline Infectious Peritonitis Virus (FIPV), which causes a fatal disease in cats. In livestock, porcine coronaviruses such as Transmissible Gastroenteritis Virus (TGEV) and Porcine Epidemic Diarrhoea Virus (PEDV) are the causative agents of an acute enteric disease in piglets with a high mortality rate and a significant impact on the pork industry. In addition, animal coronaviruses may represent a zoonotic reservoir. Therefore, efficient antiviral strategies are required to inhibit the multiplication of coronaviruses infecting various animal species. Here, we synthesized 20 small-molecule ligands that target cyclophilins, a family of cellular chaperons hijacked by several viruses including CoVs. We screened their antiviral activity against feline and porcine alpha-CoVs, and identified a compound, F83233, as a potent inhibitor of FIPV, TGEV and PEDV replication at micromolar concentrations that was effective in feline, porcine and simian cells. As cyclophilins are highly conserved among mammals, F83233 could be a promising antiviral to treat different animal and zoonotic coronaviruses.

microbiology↗

bioRxiv2025

Interventionally targeting somatic CAG expansions can be a rapid disease-modifying therapeutic avenue: Preclinical evidence.

Huntington disease (HD) is caused by inherited CAG expansions, which continue expanding somatically in affected brain regions to hasten disease onset and progression. Therapeutically diminishing somatic expansions is expected to be clinically beneficial. However, it is not known if interventionally modifying somatic CAG expansions will actually modify in vivo clinically-relevant phenotypes, what the therapeutic window is, or which phenotypes will be altered. Here we show that acute (6-week) delivery of the contraction-inducing slipped-CAG DNA ligand naphthyridine-azaquinolone to young (4-week-old) (CAG)120 HD mice, induces contractions throughout brain regions, improves motor function (locomotion, balance, coordination, muscle strength), molecular disease landmarks (mHTT aggregates, nuclear envelope morphology, nucleocytoplasmic mRNA transport, transcriptomic dysregulation, neuroinflammation), and neurodegeneration. Beneficial effects of modifying somatic expansions were also evident in muscle and blood, where blood CAG instability correlated with brain instability and blood serum had diminished levels of neurofilament light (a biomarker for neurodegeneration) -- offering blood as having elements of target engagement and efficacy. These data support that targeting somatic repeat expansions can be a rapid disease-modifying therapeutic avenue for HD and possibly other repeat expansion diseases. Our findings support an etiologic pathway interconnected to somatic CAG expansions that will inform the design of clinical trials expecting clinical benefit by modulating somatic expansions.

genetics↗

bioRxiv2024

Age-dependent differential iron deficiency responses of rosette leaves during reproductive stages in Arabidopsis thaliana

Iron (Fe) is essential for plant development throughout the life cycle. Rosette leaves are responsive to Fe supply in Arabidopsis thaliana. Little is known about the dynamics of Fe deficiency (-Fe) responses of rosette leaves during the reproductive stages. We studied the dynamics of Fe-dependent responses at four consecutive reproductive stages (rosette, bolting, flowering, mature silique stages, hereby named RS, BS, FS, MS). We examined the growth of rosette leaves, elemental contents and gene expression patterns of Fe homeostasis genes belonging to differently regulated groups. We determined individual leaf sizes during seven days of +Fe and -Fe treatment at the RS. Young leaves responded to -Fe with growth inhibition and yellowing. Old and young leaves differed in gene expression patterns and elemental contents. Differences were noted between the early and late reproductive stages (primarily RS and BS versus MS) and correlations between ionomic contents and gene expression were detected. All leaves had induced Fe recycling genes at -Fe. Our findings highlight a developmental stage-dependent modulation of +Fe and -Fe responses in leaves. We discuss possible leaf signaling mechanisms accounting for the distinct responses between old and young leaves. This insight is informative to strengthen our understanding on plant iron management. Highlight/ One-sentence summaryThis study explores reproductive stage-dependent responses of rosette leaves to iron availability, revealing distinct growth, elemental contents, and gene expression patterns between young and old leaves and stages.

plant biology↗

bioRxiv2024

Pseudomonas aeruginosa-mediated cardiac dysfunction is driven by extracellular vesicles released during infection

Pseudomonas aeruginosa (P.a.) is a gram-negative, opportunistic bacterium abundantly present in the environment. Often P.a. infections cause severe pneumonia, if left untreated. Surprisingly, up to 30% of patients admitted to the hospital for community- acquired pneumonia develop adverse cardiovascular complications such as myocardial infarction, arrhythmia, left ventricular dysfunction, and heart failure. However, the underlying mechanism of infection-mediated cardiac dysfunction is not yet known. Recently, we demonstrated that P.a. infection of the lungs led to severe cardiac electrical abnormalities and left ventricular dysfunction with limited P.a. dissemination to the heart tissue. To understand the mechanism of cardiac dysfunction during P.a. infection, we utilized both in vitro and in vivo models. Our results revealed that inflammatory cytokines contribute but are not solely responsible for severe contractile dysfunction in human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs). Instead, exposure of hiPSC-CMs with conditioned media from P.a. infected human monocyte-derived macrophages (hMDMs) was sufficient to cause severe contractile dysfunction and arrhythmia in hiPSC-CMs. Specifically, exosomes released from infected hMDMs and bacterial outer membrane vesicles (OMVs) are the major drivers of cardiomyocyte contractile dysfunction. By using LC-MS/MS, we identified bacterial proteins, including toxins that are packaged in the exosomes and OMVs, which are responsible for contractile dysfunction. Furthermore, we demonstrated that systemic delivery of bacterial OMVs to mice caused severe cardiac dysfunction, mimicking the natural bacterial infection. In summary, we conclude that OMVs released during infection enter circulation and drive cardiac dysfunction.

immunology↗

bioRxiv2024

C9orf72 expansion creates the unstable folate-sensitive fragile site FRA9A

The hyper-unstable Chr9p21 locus, harbouring the interferon gene cluster, oncogenes and C9orf72, is linked to multiple diseases. C9orf72 (GGGGCC)n expansions (C9orf72Exp) are associated with incompletely penetrant amyotrophic lateral sclerosis, frontotemporal dementia and autoimmune disorders. C9orf72Exp patients display hyperactive cGAS-STING-linked interferon immune and DNA damage responses, but the source of immuno-stimulatory or damaged DNA is unknown. Here, we show C9orf72Exp in pre-symptomatic and ALS-FTD patient cells and brains cause the folate- sensitive chromosomal fragile site, FRA9A. FRA9A centers on >33kb of C9orf72 as highly-compacted chromatin embedded in an 8.2Mb fragility zone spanning 9p21, encompassing 46 genes, making FRA9A one of the largest fragile sites. C9orf72Exp cells show chromosomal instability, heightened global- and Chr9p-enriched sister-chromatid exchanges, truncated-Chr9s, acentric-Chr9s and Chr9-containing micronuclei, providing endogenous sources of damaged and immunostimulatory DNA. Cells from one C9orf72Exp patient contained highly-rearranged FRA9A-expressing Chr9 with Chr9-wide dysregulated gene expression. Somatic C9orf72Exp repeat instability and chromosomal fragility are sensitive to folate-deficiency. Age-dependent repeat instability, chromosomal fragility, and chromosomal instability can be transferred to CNS and peripheral tissues of transgenic C9orf72Exp mice, implicating C9orf72Exp as the source. Our results highlight unappreciated effects of C9orf72 expansions that trigger vitamin-sensitive chromosome fragility, adding structural variations to the disease-enriched 9p21 locus, and likely elsewhere. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=94 SRC="FIGDIR/small/620312v2_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@154b23borg.highwire.dtl.DTLVardef@1814a6dorg.highwire.dtl.DTLVardef@13d713eorg.highwire.dtl.DTLVardef@d5d994_HPS_FORMAT_FIGEXP M_FIG C_FIG

genetics↗

bioRxiv2024

What scRNA sequencing taught us about MGMT expression in glioblastoma

IntroductionThe promoter methylation status of O-6-methylguanine-DNA methyltransferase (MGMTp) is an established predictive and prognostic marker in GBM. Previous studies showed that the expression of MGMT based on immunohistochemistry was variable and lacked association with survival. This in part is because non-tumor cells including endothelial cells and macrophages express MGMT. Advanced technologies such as single-cell RNA (scRNA) sequencing have helped to elucidate the cellular composition of cancer and its microenvironment. scRNA sequencing allows to assess gene expression level in tumor cells specifically. MethodsWe used publicly available data from two recent GBM scRNA studies that included MGMTp methylation status data for patients to explore and uncover details about MGMT expression at the single-cell level: CPTAC (13 primary samples) and Neftel (20 primary samples). ResultsIn the CPTAC study, MGMT expression ranged from 0.19%-1.43% in the MGMTp methylated group (median 0.82%), and from 2.17%-28.36% in the MGMTp unmethylated group (median 5.7%). It therefore appears that 2% is a reasonable expression cutoff to predict the MGMTp methylation status based on scRNA data. In the Neftel study, MGMT expression ranged from 0-1.26% in the MGMTp methylated group (median 0.59%), and from 0.3-27.67% in the MGMTp unmethylated group (median 12.44%). Three unmethylated samples (out of 16) did not follow the 2% rule. It remains unclear if this is due to technical inaccuracies as the Neftel paper did not specify the method used to detect MGMTp methylation or even mere typos. Alternatively, could it be that truly MGMTp unmethylated samples can have low MGMT expression? Could this explain why some unmethylated MGMTp GBM patients surpass the expected survival? Interestingly, gene set enrichment analysis shows that MGMT expressing cells are enriched with mesenchymal genes, whereas MGMT negative cells are enriched with proneural genes. ConclusionFewer than 2% of GBM cells express MGMT when MGMTp is methylated.

cancer biology↗